From deaa1dd67284175e35fea33685fbdfe54123f8a4 Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Fri, 2 Feb 2018 21:42:12 +0100 Subject: [PATCH 001/127] Regrouper of GumTree results. --- .../uni/serval/FixPatternParser/Parser.java | 1 - .../violations/FixedViolationHunkParser.java | 405 +++--------------- .../violations/FixedViolationParser.java | 116 ----- .../FixedViolationSingleStatementParser.java | 3 +- .../violations/TestHunkParser.java | 1 - .../MultipleThreadsParser/AkkaParser.java | 65 +-- .../ParseFixPatternActor.java | 28 +- .../ParseFixPatternWorker.java | 87 +--- .../SingleThreadParser.java | 2 +- .../lu/uni/serval/config/Configuration.java | 10 +- .../uni/serval/diffentry/DiffEntryHunk.java | 10 + .../regroup/HierarchicalActionSet.java | 4 +- .../gumtree/regroup/HunkActionFilter.java | 237 ++-------- 13 files changed, 161 insertions(+), 808 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java index 132f305..e02a1a7 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java @@ -13,7 +13,6 @@ import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.ActionFilter; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; /** diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index e0045fa..72ad67d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -1,9 +1,6 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import java.io.BufferedReader; import java.io.File; -import java.io.IOException; -import java.io.StringReader; import java.util.ArrayList; import java.util.List; @@ -13,8 +10,6 @@ import edu.lu.uni.serval.FixPatternParser.Tokenizer; import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.diffentry.DiffEntryHunk; import edu.lu.uni.serval.diffentry.DiffEntryReader; -import edu.lu.uni.serval.gumtree.GumTreeGenerator; -import edu.lu.uni.serval.gumtree.GumTreeGenerator.GumTreeType; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter; import edu.lu.uni.serval.gumtree.regroup.SimpleTree; @@ -29,8 +24,6 @@ import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; */ public class FixedViolationHunkParser extends FixedViolationParser { - private static final int THRESHOLD_LINE = 3; - public String testingInfo = ""; public int nullMappingGumTreeResult = 0; @@ -39,47 +32,31 @@ public class FixedViolationHunkParser extends FixedViolationParser { public int nullSourceCode = 0; public int nullMatchedDiffEntry = 0; public int testInfos = 0; - - public FixedViolationHunkParser() { - } - public FixedViolationHunkParser(File positionFile) { - setPositionFile(positionFile); - } - public String unfixedViolations = ""; @Override public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { - List allViolations = readViolations(prevFile, revFile); -// if (allViolations.size() >= 0) return; // GumTree results List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); if (this.resultType != 0) { - String type = ""; - if (this.resultType == 1) { - type = "#NullGumTreeResult:"; - } else if (this.resultType == 2) { - type = "#NoSourceCodeChange:"; - } else if (this.resultType == 3) { - type = "#NoStatementChange:"; - } - for (Violation v : allViolations) { - this.unfixedViolations += type + revFile.getName() + ":" + v.getStartLineNum() + ":" + v.getEndLineNum() + ":" + v.getViolationType() + "\n"; - } +// String type = ""; +// if (this.resultType == 1) { +// type = "#NullGumTreeResult:"; +// } else if (this.resultType == 2) { +// type = "#NoSourceCodeChange:"; +// } else if (this.resultType == 3) { +// type = "#NoStatementChange:"; +// } } else { List diffentryHunks = new DiffEntryReader().readHunks2(diffentryFile); - // Identify DiffEntry hunks by positions of violations. - List violations = identifyFixRangeHeuristically(allViolations, diffentryHunks, revFile); //Filter out the modify actions, which are not in the DiffEntry hunks. HunkActionFilter hunkFilter = new HunkActionFilter(); - List selectedViolations = hunkFilter.filterActionsByModifiedRange2(violations, actionSets, revFile, prevFile); - this.unfixedViolations += hunkFilter.unfixedViolations; - this.nullMappingGumTreeResult += violations.size() - selectedViolations.size(); + List selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile); - for (Violation violation : selectedViolations) { - List hunkActionSets = violation.getActionSets(); + for (DiffEntryHunk patchHunk : selectedPatchHunks) { + List hunkActionSets = patchHunk.getActionSets(); // multiple UPD, and some UPD contain other UPD. removeOverlapperdUPD(hunkActionSets); @@ -117,43 +94,27 @@ public class FixedViolationHunkParser extends FixedViolationParser { } if (fixStartLine == 0 && bugStartLine == 0) { - this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + violation.getStartLineNum() + ":" + violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; + this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; this.nullMappingGumTreeResult ++; continue; } if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions. -// this.pureDeletions ++; -// this.unfixedViolations += "#PureDeletion:" + revFile.getName() + ":" + violation.getStartLineNum() + ":" + violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; // get the exact buggy code by violation's position. TODO later } // if (children.size() == 0) continue; boolean isPureInsert = false; - if (bugStartLine == 0 && violation.getBugStartLineNum() > 0) { - bugStartLine = violation.getStartLineNum(); - bugEndLine = violation.getEndLineNum(); + if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) { + bugStartLine = patchHunk.getBugLineStartNum(); + bugEndLine = bugStartLine + patchHunk.getBuggyHunkSize() - 1; isPureInsert = true; // continue; } if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE && !isPureInsert) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { -// this.largeHunk ++; -// this.unfixedViolations += "#LargeHunk:" + revFile.getName() + ":" + violation.getStartLineNum() -// + ":" + violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; // continue; } - // Obtain Source Code of patches from DiffEntries. - String patchSourceCode = this.readPatchSourceCode(violation, bugStartLine, bugEndLine, fixStartLine, fixEndLine); - if ("".equals(patchSourceCode)) { - patchSourceCode = getPatchSourceCode(prevFile, revFile, bugStartLine, bugEndLine, fixStartLine, fixEndLine, isPureInsert); - if ("".equals(patchSourceCode)) { - this.nullSourceCode ++; - this.unfixedViolations += "#NullSourceCode:" + revFile.getName() + ":" + violation.getStartLineNum() - + ":" + violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; - continue; - } - } /** * Select edit scripts for deep learning. @@ -162,8 +123,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { // 1. First level: AST node type. String astEditScripts = getASTEditScriptsDeepFirst(hunkActionSets, bugEndPosition, fixEndPosition); if (astEditScripts.contains("\n") || astEditScripts.split(" ").length % 3 != 0) { - System.err.println("===+++===: " + revFile.getName() + ":" +violation.getStartLineNum() + ":" + - violation.getEndLineNum() + ":" + violation.getViolationType()); + System.err.println("===+++===: " + revFile.getName() + ":" +patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize()); } // 2. source code: raw tokens // 3. abstract identifiers: @@ -171,141 +131,82 @@ public class FixedViolationHunkParser extends FixedViolationParser { String[] editScriptTokens = astEditScripts.split(" "); int size = editScriptTokens.length; if (size == 1) { -// if ("MOVMethodDeclaration".equals(astEditScripts)) { -// this.nullMappingGumTreeResult ++; -// this.unfixedViolations += "#NullMatchedGumTreeResult:" + revFile.getName() + ":" +violation.getStartLineNum() + ":" + -// violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; -// continue; -// } this.nullMappingGumTreeResult ++; - this.unfixedViolations += "#NullMatchedGumTreeResult1:" + revFile.getName() + ":" +violation.getStartLineNum() + ":" + - violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; + this.unfixedViolations += "#NullMatchedGumTreeResult1:" + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; continue; } - String alarmType = violation.getViolationType(); - String patchPosition = "\n" + revFile.getName() + "\nPosition: " + violation.getStartLineNum() + " --> " + violation.getEndLineNum() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; -// String patchPosition = "\n" + "Position: " + violation.getStartLineNum() + " --> " + violation.getEndLineNum() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; - String info = Configuration.PATCH_SIGNAL + "\nAlarm Type :" + alarmType + "\n" + patchPosition + patchSourceCode + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; -// String patchPosition = "\n" + "Position: " + violation.getStartLineNum() + " --> " + violation.getEndLineNum() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; -// String info = Configuration.PATCH_SIGNAL + "\nAlarm Type :" + alarmType + "\n" + patchSourceCode + "\n\n";// + patchPosition + revFile.getName() + "\n"; + String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; +// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; + String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; // if (noUpdate(editScriptTokens)) { -// -// if (!"SE_NO_SERIALVERSIONID".equals(alarmType)) { -// if (containsFiledDeclaration(hunkActionSets)) { -//// this.nullMappingGumTreeResult ++; -// this.testingInfo += info + revFile.getName() + "\n"; -// this.testingInfo += "#TestingInfo: " + revFile.getName() + ":" + violation.getStartLineNum() -// + ":" + violation.getEndLineNum() + ":" + violation.getViolationType(); -// this.unfixedViolations += "#TestingInfo:" + revFile.getName() + ":" + violation.getStartLineNum() -// + ":" + violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; -// this.testInfos ++; -// continue; -// } -// } -// -// if ("UL_UNRELEASED_LOCK".equals(alarmType) || -// "SF_SWITCH_NO_DEFAULT".equals(alarmType) || -// "SF_SWITCH_FALLTHROUGH".equals(alarmType) || -// "SE_NO_SERIALVERSIONID".equals(alarmType) || -// "REC_CATCH_EXCEPTION".equals(alarmType) || -// "OS_OPEN_STREAM".equals(alarmType) || -// "NP_ALWAYS_NULL".equals(alarmType) || -// "IS2_INCONSISTENT_SYNC".equals(alarmType) || -// "EI_EXPOSE_REP".equals(alarmType) ) { -// -// } else if (containSpecialStmt(hunkActionSets, bugEndPosition, fixEndPosition)) { -// -// } else { -//// this.nullMappingGumTreeResult ++; -// this.testingInfo += info + revFile.getName() + "\n"; -// this.testingInfo += "#TestingInfo: " + revFile.getName() + ":" + violation.getStartLineNum() -// + ":" + violation.getEndLineNum() + ":" + violation.getViolationType(); -// this.unfixedViolations += "#TestingInfo:" + revFile.getName() + ":" + violation.getStartLineNum() -// + ":" + violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; -// this.testInfos ++; -// continue; -// } // } this.patchesSourceCode += info; this.sizes += size + "\n"; this.astEditScripts += astEditScripts + "\n"; - this.violationTypes += alarmType + "\n"; -// this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + simpleTree.toString() + "\n"; - SimpleTree simpleTree = getBuggyCodeTree(violation, bugEndPosition, prevFile, bugStartLine, bugEndLine); + SimpleTree simpleTree = getBuggyCodeTree(patchHunk, bugEndPosition, prevFile, bugStartLine, bugEndLine); String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); - if ("Block Block".equals(tokens)) { - tokens = getContextTokens(patchSourceCode); - } this.tokensOfSourceCode += tokens + "\n"; -// this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" + readActionSet(actionSet, "") + "\n"; -// this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" + actionSet.getOriginalTree().toString() + "\n"; - } } } - private SimpleTree getBuggyCodeTree(Violation violation, int bugEndPosition, File prevFile, int bugStartLine, int bugEndLine) { - SimpleTree simpleTree = null; + private String getAstEditScripts(List hunkActionSets) { + String scripts = ""; + for (HierarchicalActionSet hunkActionSet : hunkActionSets) { + scripts += hunkActionSet.toString() + "\n"; + } + return scripts; + } + + private SimpleTree getBuggyCodeTree(DiffEntryHunk patchHunk, int bugEndPosition, File prevFile, int bugStartLine, int bugEndLine) { + SimpleTree simpleTree = new SimpleTree(); + simpleTree.setLabel("Block"); + simpleTree.setNodeType("Block"); + List children = new ArrayList<>(); - String type = violation.getViolationType(); - if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(type)|| "HE_EQUALS_USE_HASHCODE".equals(type) || "HE_INHERITS_EQUALS_USE_HASHCODE".equals(type)|| - "SE_NO_SUITABLE_CONSTRUCTOR".equals(type) || "RI_REDUNDANT_INTERFACES".equals(type) - ||"CN_IDIOM".equals(type)||"SE_NO_SERIALVERSIONID".equals(type) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(type)) { - // Class name level, tokens - // classStartP <= vS <= vE <= classEndP - ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, violation.getStartLineNum(), violation.getEndLineNum()); - ITree classNameTree = parser.getClassNameTokens(); - simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(classNameTree, null); - } else { - simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - - int vStartLine = violation.getStartLineNum(); - int vEndLine = violation.getEndLineNum(); - if (bugStartLine < vStartLine && vEndLine < bugEndLine) { - ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, violation.getStartLineNum(), violation.getEndLineNum()); - parser.extract(); - List matchedTrees = parser.getViolationSourceCodeTrees(); - if (matchedTrees.size() > 0) { - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, simpleTree); - children.add(simpleT); - } - } - } - if (children.size() == 0) { - List hunkActionSets = violation.getActionSets(); - /* - * Convert the ITree of buggy code to a simple tree. - * It will be used to compute the similarity. - */ - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - // TODO simplify buggy tree with buggy code. - /** - * Select edit scripts for deep learning. - * Edit scripts will be used to mine common fix patterns. - */ -// // 1. First level: AST node type. -// // 2. source code: raw tokens -// // 3. abstract identifiers: -// // 4. semi-source code: - SimplifyTree abstractIdentifier = new SimplifyTree(); - abstractIdentifier.abstractTree(hunkActionSet, bugEndPosition); - SimpleTree simpleT = hunkActionSet.getSimpleTree(); - if (simpleT == null) { // Failed to get the simple tree for INS actions. - continue; - } + int vStartLine = patchHunk.getBugLineStartNum(); + int vEndLine = vStartLine + patchHunk.getBuggyHunkSize() + 1; + if (bugStartLine < vStartLine && vEndLine < bugEndLine) { + ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, vStartLine, vEndLine); + parser.extract(); + List matchedTrees = parser.getViolationSourceCodeTrees(); + if (matchedTrees.size() > 0) { + for (ITree matchedTree : matchedTrees) { + SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, simpleTree); children.add(simpleT); } } - simpleTree.setChildren(children); - simpleTree.setParent(null); } + if (children.size() == 0) { + List hunkActionSets = patchHunk.getActionSets(); + /* + * Convert the ITree of buggy code to a simple tree. + * It will be used to compute the similarity. + */ + for (HierarchicalActionSet hunkActionSet : hunkActionSets) { + // TODO simplify buggy tree with buggy code. + /** + * Select edit scripts for deep learning. + * Edit scripts will be used to mine common fix patterns. + */ +// // 1. First level: AST node type. +// // 2. source code: raw tokens +// // 3. abstract identifiers: +// // 4. semi-source code: + SimplifyTree abstractIdentifier = new SimplifyTree(); + abstractIdentifier.abstractTree(hunkActionSet, bugEndPosition); + SimpleTree simpleT = hunkActionSet.getSimpleTree(); + if (simpleT == null) { // Failed to get the simple tree for INS actions. + continue; + } + children.add(simpleT); + } + } + simpleTree.setChildren(children); + simpleTree.setParent(null); return simpleTree; } @@ -344,170 +245,4 @@ public class FixedViolationHunkParser extends FixedViolationParser { actionSets.removeAll(overlappedUpdates); } - private List identifyFixRangeHeuristically(List violations, List diffentryHunks, File revFile) { - List selectedViolations = new ArrayList<>(); - for (Violation violation : violations) { - - int violationStartLineNum = violation.getBugStartLineNum(); - - if (violationStartLineNum > 0) { - int violationEndLineNum = violation.getEndLineNum(); - for (int index = 0, hunkListSize = diffentryHunks.size(); index < hunkListSize; index ++) { - DiffEntryHunk hunk = diffentryHunks.get(index); - int bugStartLine = hunk.getBugLineStartNum(); - int bugRange = hunk.getBugRange(); - if (violationStartLineNum > bugStartLine + bugRange - 1) continue; - if (violationEndLineNum < bugStartLine) break; - - int fixStartLine = hunk.getFixLineStartNum(); - String diffentry = hunk.getHunk(); - BufferedReader reader = new BufferedReader(new StringReader(diffentry)); - String line = null; - try { - int currentBugLine = bugStartLine - 1; - int currentFixLine = fixStartLine - 1; - int fixedLines = 0; - int bugS = 0; - int fixS = 0; - int fixE = 0; - int bugFixStartLine = 0; // the heuristic inferred fix start line of the corresponding bug - int bugFixEndLine = 0; // the heuristic inferred fix end line of the corresponding bug - boolean isFixRange= false; - while ((line = reader.readLine()) != null) { - if (line.startsWith("+")) { - currentFixLine ++; - fixedLines++; - if ((violationStartLineNum <= currentBugLine && currentBugLine <= violationEndLineNum) || - (violationStartLineNum <= bugS && bugS <= violationEndLineNum)) { - if (fixS == 0) fixS = currentFixLine; - if (bugFixStartLine == -1) bugFixStartLine = currentFixLine; - if (isFixRange) bugFixEndLine = currentFixLine; - fixE = currentFixLine; - } else { - fixedLines = 0; - bugS = 0; - } - } else if (line.startsWith("-")) { - currentBugLine ++; - if (bugS == 0 || fixS != 0) bugS = currentBugLine;// currentBugLine may be larger than the violation end line. - - // INS combined with DEL, UPD or MOV. - // Infer the fix range for a violation heuristically. - if (currentBugLine >= violation.getStartLineNum() && currentBugLine <= violation.getEndLineNum()) { - bugFixStartLine = -1; - } - if (currentBugLine <= violation.getEndLineNum() && bugFixStartLine != 0) { - isFixRange = true; - } - if (bugFixEndLine > 0) isFixRange = false; - if (bugFixStartLine <= 0) fixS = 0; - } else { - currentBugLine ++; - currentFixLine ++; - - // pure INS - // Infer the fix range for a violation heuristically. - if (currentBugLine == violation.getStartLineNum()) { - if (bugFixStartLine <= 0) { - if (fixedLines != 0) { - if (fixedLines > THRESHOLD_LINE) { - fixedLines = THRESHOLD_LINE;// insert 3 lines. - } - bugFixStartLine = currentFixLine - fixedLines; - if (bugFixStartLine < violationStartLineNum) { - bugFixStartLine = violationStartLineNum; - } - } - else bugFixStartLine = currentFixLine; - } - } - if (currentBugLine == violation.getEndLineNum()) { - if (bugFixStartLine != 0 && bugFixEndLine == 0) { - bugFixEndLine = currentFixLine + THRESHOLD_LINE; - if (bugFixEndLine > violationEndLineNum) { - bugFixEndLine = violationEndLineNum; - } - } - } - if (bugFixEndLine > 0) isFixRange = false; - } - - if ((violationStartLineNum <= currentBugLine && currentBugLine <= violationEndLineNum)) { - if (!violation.getHunks().contains(hunk)) - violation.getHunks().add(hunk); - } - } - if (violation.getFixStartLineNum() == 0) { - violation.setFixStartLineNum(fixS); - } - violation.setFixEndLineNum(fixE); - - if (violation.getBugFixStartLineNum() == 0 && bugFixStartLine > 0) { - violation.setBugFixStartLineNum(bugFixStartLine); - } - if (bugFixEndLine > 0) { - violation.setBugFixEndLineNum(bugFixEndLine); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - } - - - if (violation.getHunks().size() == 0) { - // This fixed violation cannot be matched with a DiffEntry, it is difficult to identify related source code change for it. - this.nullMatchedDiffEntry ++; - this.unfixedViolations += "#NullDiffEntry: " + revFile.getName() + " : " +violation.getStartLineNum() + " : " - + violation.getEndLineNum() + " : " + violation.getViolationType() + "\n"; - } else { - selectedViolations.add(violation); - } - } else { - selectedViolations.add(violation); - } - } - - return selectedViolations; - } - - private String getContextTokens(String patchSourceCode) { - BufferedReader reader = new BufferedReader(new StringReader(patchSourceCode)); - String line = null; - String context = ""; - try { - while ((line = reader.readLine()) != null) { - if (line.startsWith("+") || line.startsWith("-")) { - continue; - } - context += line + "\n"; - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - if ("".equals(context)) { - return "Block Block"; - } else { - ITree tree = new GumTreeGenerator().generateITreeForCodeBlock(context, GumTreeType.EXP_JDT); - if (tree == null) { - return "Block Block"; - } - SimpleTree simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(tree, null); - String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); - return tokens; - } - } - } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java index 4b68cdd..9d48ade 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java @@ -10,13 +10,11 @@ import java.util.List; import com.github.gumtreediff.actions.model.Action; import edu.lu.uni.serval.FixPatternParser.Parser; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; -import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; /** * Parse fix patterns with GumTree. @@ -36,13 +34,7 @@ public class FixedViolationParser extends Parser { */ public int resultType = 0; - private File positionFile = null; protected String violationTypes = ""; -// protected List uselessViolations; - - public void setPositionFile(File positionFile) { - this.positionFile = positionFile; - } @Override public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { @@ -90,60 +82,6 @@ public class FixedViolationParser extends Parser { } } - protected List readViolations(File prevFile, File revFile) { - String fileName = revFile.getName(); - List violations = new ArrayList<>(); - String fileContent = FileHelper.readFile(positionFile); - BufferedReader reader = null; - reader = new BufferedReader(new StringReader(fileContent)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - String[] positionStr = line.split(":"); - int startLine = Integer.parseInt(positionStr[1]); - int endLine = Integer.parseInt(positionStr[2]); - String violationType = positionStr[0]; - - Violation violation = new Violation(startLine, endLine, violationType); - violation.setFileName(fileName); - - if (startLine == -1) { - violation.setBugStartLineNum(0); - continue; - } - - /* - * Get the parent range of a violation. - * Read DiffEntries with this range to get the start line and end line of a violation. - */ - ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(prevFile, startLine, endLine); - alarmTree.locateParentNode(violationType); - int violationStartLine = alarmTree.getViolationFinalStartLine(); - violation.setBugStartLineNum(violationStartLine); - if (violationStartLine > 0) {// 0: no source code, -1: range is too large, which contains several inner classes, methods or fields. - violation.setBugEndLineNum(alarmTree.getViolationFinalEndLine()); -// if (violationType.equals("SE_NO_SERIALVERSIONID")){ -// FileHelper.outputToFile("OUTPUT/list1.txt", line + ":" + revFile.getName() + "\n", true); -// } - } else { -// if (!violationType.equals("SE_NO_SERIALVERSIONID")) { -// FileHelper.outputToFile("OUTPUT/list.txt", line + ":" + revFile.getName() + "\n", true); -// } - } - violations.add(violation); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return violations; - } - /** * Read patch source code from buggy and fixed files. * @param prevFile @@ -193,60 +131,6 @@ public class FixedViolationParser extends Parser { return sourceCode; } - /** - * Read patch source code from diffentries. - * @param violation - * @param bugStartLine - * @param bugEndLine - * @param fixStartLine - * @param fixEndLine - * @return - */ - protected String readPatchSourceCode(Violation violation, int bugStartLine, int bugEndLine, int fixStartLine, int fixEndLine) { - String patch = ""; - List diffentries = violation.getHunks(); - for (DiffEntryHunk diffentry : diffentries) { - int currentBugLine = diffentry.getBugLineStartNum() - 1; - int currentFixLine = diffentry.getFixLineStartNum() - 1; - String sourceCode = diffentry.getHunk(); - - BufferedReader reader = new BufferedReader(new StringReader(sourceCode)); - String line = null; - - try { - while ((line = reader.readLine()) != null) { - if (line.startsWith("+")) { - currentFixLine ++; - if (fixStartLine <= currentFixLine && currentFixLine <= fixEndLine) { - patch += line + "\n"; - } - } else if (line.startsWith("-")) { - currentBugLine ++; - if (bugStartLine <= currentBugLine && currentBugLine <= bugEndLine) { - patch += line + "\n"; - } - } else { - currentFixLine ++; - currentBugLine ++; - if ((bugStartLine <= currentBugLine && currentBugLine <= bugEndLine) || - (fixStartLine <= currentFixLine && currentFixLine <= fixEndLine)) { - patch += line + "\n"; - } - } - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - } - return patch; - } - public String getAlarmTypes() { return violationTypes; } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java index 390f597..6fe1e46 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java @@ -39,7 +39,6 @@ public class FixedViolationSingleStatementParser extends FixedViolationParser { } // Read the positions of checked violations - List violations = readViolations(prevFile, revFile); for (HierarchicalActionSet actionSet : actionSets) { // position of buggy statements int startPosition = 0; @@ -95,7 +94,7 @@ public class FixedViolationSingleStatementParser extends FixedViolationParser { int startLine2 = revUnit.getLineNumber(startPosition2); int endLine2 = revUnit.getLineNumber(endPosition2); - Violation violation = findViolation(startLine, endLine, violations); + Violation violation = null;//findViolation(startLine, endLine, violations); if (violation == null) continue; if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2 ) continue; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index a0aa1f8..a370e99 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -54,7 +54,6 @@ public class TestHunkParser { // int counter = 0; for (MessageFile msgFile : msgFiles) { FixedViolationHunkParser parser = new FixedViolationHunkParser(); - parser.setPositionFile(msgFile.getPositionFile()); final ExecutorService executor = Executors.newSingleThreadExecutor(); // schedule the work diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java index 4a9a5d4..e1fdeb2 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java @@ -22,11 +22,28 @@ public class AkkaParser { private static Logger log = LoggerFactory.getLogger(AkkaParser.class); + /** + * Two parameters: + * First one: the root path of input data. + * Second one: the number of threads. + * Third one: the threshold of selecting patch hunks. + * @param args + */ @SuppressWarnings("deprecation") public static void main(String[] args) { + String inputRootPath = args[0]; + int numberOfWorkers = Integer.parseInt(args[1]); + int hunkThreshold = 0; + try { + hunkThreshold = Integer.parseInt(args[2]); + } catch (NumberFormatException e1) { + hunkThreshold = 10; + } + + Configuration.ROOT_PATH = inputRootPath; + Configuration.HUNK_SIZE = hunkThreshold; // input data log.info("Get the input data..."); -// final List msgFiles = getMessageFiles(); final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); log.info("MessageFiles: " + msgFiles.size()); @@ -35,22 +52,19 @@ public class AkkaParser { final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH; final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH; final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH; - final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE_PATH; FileHelper.deleteDirectory(editScriptsFilePath); FileHelper.deleteDirectory(patchesSourceCodeFilePath); FileHelper.deleteDirectory(buggyTokensFilePath); FileHelper.deleteDirectory(editScriptSizesFilePath); - FileHelper.deleteDirectory(alarmTypesFilePath); ActorSystem system = null; ActorRef parsingActor = null; - int numberOfWorkers = 431; final WorkMessage msg = new WorkMessage(0, msgFiles); try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath, alarmTypesFilePath), "mine-fix-pattern-actor"); + patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { system.shutdown(); @@ -59,47 +73,6 @@ public class AkkaParser { } - - /** - * Get bug commit-related files. - * - * @return - */ - public static List getMessageFiles() { - String inputPath = Configuration.GUM_TREE_INPUT; //DiffEntries prevFiles revFiles - File inputFileDirector = new File(inputPath); - File[] files = inputFileDirector.listFiles(); // project folders - log.info("Projects: " + files.length); - List msgFiles = new ArrayList<>(); - - for (File file : files) { - if (!file.isDirectory()) continue; -// if (!(file.getName().startsWith("k") || file.getName().startsWith("l"))) continue; - if (file.getName().startsWith("a") || file.getName().startsWith("b") - || file.getName().startsWith("c") || file.getName().startsWith("d") - || file.getName().startsWith("e") || file.getName().startsWith("f") - || file.getName().startsWith("g") || file.getName().startsWith("h") - ||file.getName().startsWith("h") || file.getName().startsWith("i") - || file.getName().startsWith("k") || file.getName().startsWith("l") - || file.getName().startsWith("j") || file.getName().startsWith("t")) continue; -// if (!file.getName().startsWith("j")) continue; - log.info("Project name: " + file.getName()); - String projectFolder = file.getPath(); - File revFileFolder = new File(projectFolder + "/revFiles/");// revised file folder - File[] revFiles = revFileFolder.listFiles(); - for (File revFile : revFiles) { - if (revFile.getName().endsWith(".java")) { - File prevFile = new File(projectFolder + "/prevFiles/prev_" + revFile.getName());// previous file - File diffentryFile = new File(projectFolder + "/DiffEntries/" + revFile.getName().replace(".java", ".txt")); // DiffEntry file - MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); - msgFiles.add(msgFile); - } - } - } - - return msgFiles; - } - /** * Get violation-related files. * diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java index dc1b5af..746db72 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java @@ -1,6 +1,5 @@ package edu.lu.uni.serval.MultipleThreadsParser; -import java.util.ArrayList; import java.util.List; import org.slf4j.Logger; @@ -21,15 +20,15 @@ public class ParseFixPatternActor extends UntypedActor { private int counter = 0; public ParseFixPatternActor(int numberOfWorkers, String editScriptsFilePath, String patchesSourceCodeFilePath, - String buggyTokensFilePath, String editScriptSizesFilePath, String alarmTypesFilePath) { + String buggyTokensFilePath, String editScriptSizesFilePath) { mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) .props(ParseFixPatternWorker.props(editScriptsFilePath, patchesSourceCodeFilePath, - buggyTokensFilePath, editScriptSizesFilePath, alarmTypesFilePath)), "mine-fix-pattern-router"); + buggyTokensFilePath, editScriptSizesFilePath)), "mine-fix-pattern-router"); this.numberOfWorkers = numberOfWorkers; } public static Props props(final int numberOfWorkers, final String editScriptsFilePath, final String patchesSourceCodeFilePath, - final String buggyTokensFilePath, final String editScriptSizesFilePath, final String alarmTypesFilePath) { + final String buggyTokensFilePath, final String editScriptSizesFilePath) { return Props.create(new Creator() { @@ -38,7 +37,7 @@ public class ParseFixPatternActor extends UntypedActor { @Override public ParseFixPatternActor create() throws Exception { return new ParseFixPatternActor(numberOfWorkers, editScriptsFilePath, patchesSourceCodeFilePath, - buggyTokensFilePath, editScriptSizesFilePath, alarmTypesFilePath); + buggyTokensFilePath, editScriptSizesFilePath); } }); @@ -50,26 +49,25 @@ public class ParseFixPatternActor extends UntypedActor { if (message instanceof WorkMessage) { List files = ((WorkMessage) message).getMsgFiles(); int size = files.size(); - int average = (int) Math.round((double) size / numberOfWorkers); + int average = size / numberOfWorkers; + int reminder = size % numberOfWorkers; + int counter = 0; for (int i = 0; i < numberOfWorkers; i ++) { - int fromIndex = i * average; - int toIndex = (i + 1) * average; - if (i == numberOfWorkers - 1) { - toIndex = size; - } + int fromIndex = i * average + counter; + if (counter < reminder) counter ++; + int toIndex = (i + 1) * average + counter; - List filesOfWorkers = new ArrayList<>(); - filesOfWorkers.addAll(files.subList(fromIndex, toIndex)); + List filesOfWorkers = files.subList(fromIndex, toIndex); final WorkMessage workMsg = new WorkMessage(i + 1, filesOfWorkers); mineRouter.tell(workMsg, getSelf()); logger.info("Assign a task to worker #" + (i + 1) + "..."); } } else if ("STOP".equals(message.toString())) { counter ++; - logger.info(counter + " workers finished their work..."); + logger.info(counter + " workers finailized their work..."); if (counter >= numberOfWorkers) { - logger.info("All workers finished their work..."); + logger.info("All workers finailized their work..."); this.getContext().stop(mineRouter); this.getContext().stop(getSelf()); this.getContext().system().shutdown(); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index 2e2d5ae..f4982cf 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -31,19 +31,17 @@ public class ParseFixPatternWorker extends UntypedActor { private String patchesSourceCodeFilePath; private String editScriptSizesFilePath; private String buggyTokensFilePath; - private String alarmTypesFilePath; public ParseFixPatternWorker(String editScriptsFilePath, String patchesSourceCodeFilePath, - String buggyTokensFilePath, String editScriptSizesFilePath, String alarmTypesFilePath) { + String buggyTokensFilePath, String editScriptSizesFilePath) { this.editScriptsFilePath = editScriptsFilePath; this.patchesSourceCodeFilePath = patchesSourceCodeFilePath; this.editScriptSizesFilePath = editScriptSizesFilePath; this.buggyTokensFilePath = buggyTokensFilePath; - this.alarmTypesFilePath = alarmTypesFilePath; } public static Props props(final String editScriptsFile, final String patchesSourceCodeFile, final String buggyTokensFilePath, - final String editScriptSizesFilePath, final String alarmTypesFilePath) { + final String editScriptSizesFilePath) { return Props.create(new Creator() { private static final long serialVersionUID = -7615153844097275009L; @@ -51,7 +49,7 @@ public class ParseFixPatternWorker extends UntypedActor { @Override public ParseFixPatternWorker create() throws Exception { return new ParseFixPatternWorker(editScriptsFile, patchesSourceCodeFile, - buggyTokensFilePath, editScriptSizesFilePath, alarmTypesFilePath); + buggyTokensFilePath, editScriptSizesFilePath); } }); @@ -66,13 +64,11 @@ public class ParseFixPatternWorker extends UntypedActor { StringBuilder patchesSourceCode = new StringBuilder(); StringBuilder sizes = new StringBuilder(); StringBuilder tokens = new StringBuilder(); - StringBuilder alarmTypes = new StringBuilder(); StringBuilder testingInfo = new StringBuilder(); int id = msg.getId(); int counter = 0; - int testViolations = 0; int nullGumTreeResults = 0; int noSourceCodeChanges = 0; int noStatementChanges = 0; @@ -85,28 +81,15 @@ public class ParseFixPatternWorker extends UntypedActor { int timeouts = 0; StringBuilder builder = new StringBuilder(); - // Read violations with Null_Violation_Hunk or Illegal_Line_Position -// List uselessViolations = new ArrayList<>();// readUselessViolations("logs/FixedViolationCodeParseResults.log"); - for (MessageFile msgFile : files) { File revFile = msgFile.getRevFile(); File prevFile = msgFile.getPrevFile(); File diffentryFile = msgFile.getDiffEntryFile(); File positionFile = msgFile.getPositionFile(); - if (revFile.getName().toLowerCase().contains("test#") || revFile.getName().toLowerCase().contains("tests#")) { -// testViolations += countAlarms(positionFile, "#TestViolation:", uselessViolations); - testViolations += countAlarms(positionFile, "#TestViolation:"); + if (revFile.getName().toLowerCase().contains("test")) { continue; } -// Parser parser = null; -// if (containsAlarmTypes || positionFile != null) { -// parser = new FixedViolationHunkParser(positionFile); -// containsAlarmTypes = true; -// } else { -// parser = new CommitPatchSingleStatementParser(); -// } - FixedViolationHunkParser parser = new FixedViolationHunkParser(positionFile); -// parser.setUselessViolations(uselessViolations); + FixedViolationHunkParser parser = new FixedViolationHunkParser(); final ExecutorService executor = Executors.newSingleThreadExecutor(); // schedule the work @@ -128,20 +111,15 @@ public class ParseFixPatternWorker extends UntypedActor { if ("".equals(editScript)) { if (parser.resultType == 1) { nullGumTreeResults += countAlarms(positionFile, ""); -// System.err.println("#NullGumTreeResult:" + revFile.getName()); } else if (parser.resultType == 2) { noSourceCodeChanges += countAlarms(positionFile, ""); } else if (parser.resultType == 3) { noStatementChanges += countAlarms(positionFile, ""); -// } else if (parser.resultType == 4) { -// illegalV += countAlarms(positionFile, "", uselessViolations); } } else { editScripts.append(editScript); patchesSourceCode.append(parser.getPatchesSourceCode()); sizes.append(parser.getSizes()); -// tokens.append(parser.getTokensOfSourceCode()); - alarmTypes.append(parser.getAlarmTypes()); tokens.append(parser.getTokensOfSourceCode()); counter ++; @@ -154,26 +132,23 @@ public class ParseFixPatternWorker extends UntypedActor { patchesSourceCode.setLength(0); sizes.setLength(0); tokens.setLength(0); - FileHelper.outputToFile(alarmTypesFilePath + "alarmTypes_" + id + ".list", alarmTypes, true); - alarmTypes.setLength(0); - log.info("Worker #" + id +"Finish of parsing " + counter + " files..."); + log.info("Worker #" + id +" finialized parsing " + counter + " files..."); FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); testingInfo.setLength(0); } } } catch (TimeoutException e) { -// err.println("task timed out"); future.cancel(true); timeouts += countAlarms(positionFile, "#Timeout:"); -// System.err.println("#Timeout: " + revFile.getName()); + System.err.println("#Timeout: " + revFile.getName()); } catch (InterruptedException e) { timeouts += countAlarms(positionFile, "#TimeInterrupted:"); -// err.println("task interrupted"); -// System.err.println("#TimeInterrupted: " + revFile.getName()); + System.err.println("#TimeInterrupted: " + revFile.getName()); + e.printStackTrace(); } catch (ExecutionException e) { timeouts += countAlarms(positionFile, "#TimeAborted:"); -// err.println("task aborted"); -// System.err.println("#TimeAborted: " + revFile.getName()); + System.err.println("#TimeAborted: " + revFile.getName()); + e.printStackTrace(); } finally { executor.shutdownNow(); } @@ -189,58 +164,24 @@ public class ParseFixPatternWorker extends UntypedActor { sizes.setLength(0); tokens.setLength(0); - FileHelper.outputToFile(alarmTypesFilePath + "alarmTypes_" + id + ".list", alarmTypes, true); - alarmTypes.setLength(0); FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); testingInfo.setLength(0); } - String statistic = "TestViolations: " + testViolations + "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + + String statistic = "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + "\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults + "\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + "\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts; FileHelper.outputToFile("OUTPUT/statistic_" + id + ".list", statistic, false); FileHelper.outputToFile("OUTPUT/UnfixedV_" + id + ".list", builder, false); - log.info("Worker #" + id +"Finish of parsing " + counter + " files..."); - log.info("Worker #" + id + " finished the work..."); + log.info("Worker #" + id +"finialized parsing " + counter + " files..."); + log.info("Worker #" + id + " finialized the work..."); this.getSender().tell("STOP", getSelf()); } else { unhandled(message); } } -// private List readUselessViolations(String filePath) { -// List uselessViolations = new ArrayList<>(); -// -// String content = FileHelper.readFile(filePath); -// BufferedReader reader = new BufferedReader(new StringReader(content)); -// String line = null; -// try { -// while ((line = reader.readLine()) != null) { -// if (line.startsWith("#")) { -// String[] elements = line.split(":"); -// String fileName = elements[1]; -// int startLine = Integer.parseInt(elements[2]); -// int endLine = Integer.parseInt(elements[3]); -// String violationType = elements[4]; -// -// Violation violation = new Violation(startLine, endLine, violationType); -// violation.setFileName(fileName); -// uselessViolations.add(violation); -// } -// } -// } catch (IOException e) { -// e.printStackTrace(); -// } finally { -// try { -// reader.close(); -// } catch (IOException e) { -// e.printStackTrace(); -// } -// } -// return uselessViolations; -// } - private int countAlarms(File positionFile, String type) {//, List uselessViolations) { int counter = 0; String content = FileHelper.readFile(positionFile); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java index 015cd6b..80b03db 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java @@ -66,7 +66,7 @@ public class SingleThreadParser { testViolations += countAlarms(positionFile, "#TestViolation:"); continue; } - FixedViolationHunkParser parser = new FixedViolationHunkParser(positionFile); + FixedViolationHunkParser parser = new FixedViolationHunkParser(); // parser.setUselessViolations(uselessViolations); final ExecutorService executor = Executors.newSingleThreadExecutor(); diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 90eb62a..b86ac0e 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,11 +2,11 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 300000L; + public static final long SECONDS_TO_WAIT = 300L; - public static final String ROOT_PATH = "../FPM_Violations/"; // The root path of all output data. + public static String ROOT_PATH = "../FPM_Violations/"; // The root path of all output data. - public static final int HUNK_SIZE = 10; // The limitation of source code lines of each DiffEntry, which will be selected as training data. + public static int HUNK_SIZE = 10; // The limitation of source code lines of each DiffEntry, which will be selected as training data. public static final String BUGGY_TREE_SIGNAL = "BUGGY_TREE###"; // The starting signal of the tree of buggy source code . public static final String PATCH_SIGNAL = "PATCH###"; // The starting signal of each patch. @@ -86,9 +86,5 @@ public class Configuration { public static final String SUPERVISED_LEARNING_MODEL = ROOT_PATH + "TestingOutput/SupervisedLearningModel.zip"; public static final String FEATURES_OF_COMMON_CLUSTERS = ROOT_PATH + "FeaturesOfCommonClusters/"; - public static final String TESTING_DATA_BUGS90 = ROOT_PATH + "Bugs/bugs90.list"; - public static final String TESTING_DATA_BUGS80 = ROOT_PATH + "Bugs/bugs80.list"; - public static final String TESTING_DATA_BUGS70 = ROOT_PATH + "Bugs/bugs70.list"; - public static final String TESTING_DATA_BUGS60 = ROOT_PATH + "Bugs/bugs60.list"; } diff --git a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java b/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java index 8c3c62e..ece32e5 100644 --- a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java +++ b/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java @@ -1,5 +1,10 @@ package edu.lu.uni.serval.diffentry; +import java.util.ArrayList; +import java.util.List; + +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; + public class DiffEntryHunk { private int bugLineStartNum; @@ -10,6 +15,7 @@ public class DiffEntryHunk { private int buggyHunkSize; private int fixedHunkSize; private String file; + private List actionSets = new ArrayList<>(); public DiffEntryHunk(int bugLineStartNum, int fixLineStartNum, int bugRange, int fixRange) { super(); @@ -66,6 +72,10 @@ public class DiffEntryHunk { public void setFile(String file) { this.file = file; } + + public List getActionSets() { + return actionSets; + } @Override public String toString() { diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java index e304e87..7823826 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java @@ -214,7 +214,7 @@ public class HierarchicalActionSet implements Comparable actionSet.toString(); List strList1 = actionSet.strList; for (String str1 : strList1) { - strList.add("----" + str1); + strList.add("---" + str1); } } } else { @@ -224,7 +224,7 @@ public class HierarchicalActionSet implements Comparable actionSet.toString(); List strList1 = actionSet.strList; for (String str1 : strList1) { - strList.add("----" + str1); + strList.add("---" + str1); } } } diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java index 1b64b87..6dbe24f 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java @@ -361,237 +361,56 @@ public class HunkActionFilter { * @param prevFile * @return */ - public List filterActionsByModifiedRange2(List violations, + public List filterActionsByModifiedRange2(List diffentryHunks, List actionSets, File revFile, File prevFile) { - List selectedViolations = new ArrayList<>(); + List selectedViolations = new ArrayList<>(); CUCreator cuCreator = new CUCreator(); CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); if (prevUnit == null || revUnit == null) { - for (Violation violation : violations) { - this.unfixedViolations += "#NullMatchedGumTreeResult:" + revFile.getName() + ":" +violation.getStartLineNum() + ":" + - violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; - } return selectedViolations; } - for (Violation violation : violations) { - int violationStartLine = violation.getStartLineNum(); - int violationEndLine = violation.getEndLineNum(); - int bugHunkStartLine = violation.getBugStartLineNum(); + for (DiffEntryHunk diffentryHunk : diffentryHunks) { +// int violationEndLine = violationStartLine + diffentryHunk.getBugRange(); + int bugHunkStartLine = diffentryHunk.getBugLineStartNum(); + int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1; + int fixHunkStartLine = diffentryHunk.getFixLineStartNum(); + int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1; - if (!specialVioaltionTypes(violation, actionSets, prevUnit, revUnit)) { - if (bugHunkStartLine == 0) {// Null source code matched for this violation. -// String type = getType(violation); - } else if (bugHunkStartLine == -1) {// -// specialVioaltionTypes(violation, actionSets, prevUnit, revUnit); - } else { - int bugHunkEndLine = violation.getBugEndLineNum(); - int fixHunkStartLine = violation.getFixStartLineNum(); - int fixHunkEndLine = violation.getFixEndLineNum(); - int bugFixStartLineNum = violation.getBugFixStartLineNum(); - int bugFixEndLineNum = violation.getBugFixEndLineNum(); - - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - int actionBugEndLine = actionSet.getBugEndLineNum(); - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { - if (fixHunkStartLine <= actionFixStartLine && actionFixEndLine <= fixHunkEndLine) { - if (actionBugStartLine != 0) { - if (violationStartLine <= actionBugEndLine && violationEndLine >= actionBugStartLine) { - violation.getActionSets().add(actionSet); - continue; - } - } - - // INS with MOV actions that are not identified in previous IF predicate, and pure INS actions - if (bugFixStartLineNum >= actionFixEndLine && actionFixStartLine <= bugFixEndLineNum && Math.abs(bugFixStartLineNum - actionFixStartLine) <= 3 - && Math.abs(bugFixEndLineNum - actionFixEndLine) <= 3) { - violation.getActionSets().add(actionSet); - } - } - } else {//if (!actionStr.startsWith("MOV")){// ignore move actions. - if (bugHunkStartLine <= actionBugStartLine && violationEndLine <= bugHunkEndLine) { - if (violationStartLine <= actionBugEndLine && violationEndLine >= actionBugStartLine) { - violation.getActionSets().add(actionSet); - } - } + for (HierarchicalActionSet actionSet : actionSets) { + int actionBugStartLine = actionSet.getBugStartLineNum(); + if (actionBugStartLine == 0) { + actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); + } + int actionBugEndLine = actionSet.getBugEndLineNum(); + int actionFixStartLine = actionSet.getFixStartLineNum(); + int actionFixEndLine = actionSet.getFixEndLineNum(); + + String actionStr = actionSet.getActionString(); + if (actionStr.startsWith("INS")) { + if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) { + if (actionBugStartLine != 0) { + diffentryHunk.getActionSets().add(actionSet); } } + } else { + if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) { + diffentryHunk.getActionSets().add(actionSet); + } } } - if (violation.getActionSets().size() > 0) { - selectedViolations.add(violation); - } else { - this.unfixedViolations += "#NullMatchedGumTreeResult:" + revFile.getName() + ":" +violation.getStartLineNum() + ":" + - violation.getEndLineNum() + ":" + violation.getViolationType() + "\n"; + if (diffentryHunk.getActionSets().size() > 0) { + selectedViolations.add(diffentryHunk); } } return selectedViolations; } - public String unfixedViolations = ""; - private boolean specialVioaltionTypes(Violation violation, List actionSets, CompilationUnit prevUnit, CompilationUnit revUnit) { - String type = violation.getViolationType(); - - if ("NM_METHOD_NAMING_CONVENTION".equals(type) || "SE_NO_SUITABLE_CONSTRUCTOR_FOR_EXTERNALIZATION".equals(type)) { - int startLine = violation.getStartLineNum(); - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - if (actionSet.getActionString().startsWith("UPD MethodDeclaration@@")) { - if (Math.abs(startLine - actionBugStartLine) <= 2) { - violation.getActionSets().add(actionSet); - break; - } - } - } - } else if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(type)) { - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - if (actionSet.getActionString().startsWith("INS MethodDeclaration@@MethodName:equals")) { - violation.getActionSets().add(actionSet); - break; - } - } - } else if ("HE_EQUALS_USE_HASHCODE".equals(type) || "HE_INHERITS_EQUALS_USE_HASHCODE".equals(type)) { - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - if (actionSet.getActionString().startsWith("INS MethodDeclaration@@MethodName:hashCode")) { - violation.getActionSets().add(actionSet); - break; - } - } - } else if ("SE_NO_SUITABLE_CONSTRUCTOR".equals(type) || "RI_REDUNDANT_INTERFACES".equals(type)) { - int startLine = violation.getStartLineNum(); - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - if (actionSet.getActionString().startsWith("UPD TypeDeclaration@@")) { - if (Math.abs(startLine - actionBugStartLine) <= 2) { - violation.getActionSets().add(actionSet); - break; - } - } - } - } else if ("CN_IDIOM".equals(type)) { // 202 23 - //add clone method. or update clone method - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - if (actionSet.getActionString().startsWith("INS MethodDeclaration@@MethodName:clone")) { -// || actionSet.getActionString().startsWith("UPD MethodDeclaration@@clone")) { - violation.getActionSets().add(actionSet); - break; - } - } - } else if ("SE_NO_SERIALVERSIONID".equals(type) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(type)) {// 12 1960 - // change superclass or interface, add field or remove @SuppressWarnings("serial"), some are inner class - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - if (actionSet.getActionString().startsWith("INS FieldDeclaration@") && actionSet.getNode().getLabel().contains("serialVersionUID")) { - violation.getActionSets().add(actionSet); - break; - } - if (actionSet.getActionString().startsWith("UPD TypeDeclaration@")) { - int startLine = violation.getStartLineNum(); - if (Math.abs(startLine - actionBugStartLine) <= 2) { - violation.getActionSets().add(actionSet); - break; - } - } - } - } else { - return false; - } - return true; - } - - - private String getType(Violation violation) { - String type = violation.getViolationType(); - switch (type) { - case "CI_CONFUSED_INHERITANCE":// field - // update fieldDeclaration - break; - case "CO_ABSTRACT_SELF": - // java file is an interface, and delete compareTo(). - break; - case "EQ_ABSTRACT_SELF": - // java file is an interface, and delete equals(). - break; - case "SE_NO_SERIALVERSIONID": - // add a field: serialVersionUID - break; - case "EQ_COMPARETO_USE_OBJECT_EQUALS": - //Update or Delete compareTo(), Add equals() - break; - case "EQ_DOESNT_OVERRIDE_EQUALS": - //override equals() - break; - case "HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS": - //remove equals() - break; - case "ME_MUTABLE_ENUM_FIELD": - // under enum, field add final keyword - break; - case "MF_CLASS_MASKS_FIELD": - // change super class or delete the field with a same name in super class. - break; - case "MS_SHOULD_BE_FINAL": - // add final to field - break; - case "STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE": - //remove public static final DateFormat DATE_FORMAT.... or SimpleDateFormat - break; - case "UUF_UNUSED_FIELD": - //remove unused fields. not sure - break; - case "UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD": - //remove unused fields. not sure - case "UWF_NULL_FIELD": - //update field, remove field - break; - case "UWF_UNWRITTEN_FIELD": - //field - break; - case "UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD": - //remove field - break; - case "VO_VOLATILE_REFERENCE_TO_ARRAY": - //field - break; - default: - break; - } - return null; - } /** * Filter out the modify actions, which are not in the DiffEntry hunks, without considering DiffEntry hunks. From 5309b0cbe96d966da201c8c11c45560b34a5ed75 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 8 Feb 2018 14:38:26 +0100 Subject: [PATCH 002/127] commit for c parser --- FixPatternMiner.iml | 59 +++++ .../serval/FixPattern/utils/ASTNodeMap.java | 2 +- .../uni/serval/FixPattern/utils/CNodeMap.java | 71 ++++++ .../uni/serval/FixPatternParser/Parser.java | 2 +- .../violations/FixedViolationHunkParser.java | 11 +- .../violations/FixedViolationParser.java | 7 +- .../MultipleThreadsParser/AkkaParser.java | 88 ++++--- .../MultipleThreadsParser/AkkaParser2.java | 114 +++++++++ .../ParseFixPatternWorker.java | 26 +- .../lu/uni/serval/config/Configuration.java | 5 +- .../regroup/HierarchicalRegrouper.java | 4 +- .../regroup/HierarchicalRegrouperForC.java | 240 ++++++++++++++++++ 12 files changed, 568 insertions(+), 61 deletions(-) create mode 100644 FixPatternMiner.iml create mode 100644 src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java create mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java create mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml new file mode 100644 index 0000000..1f288a8 --- /dev/null +++ b/FixPatternMiner.iml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java index 18bfe4e..29d2699 100644 --- a/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java @@ -103,7 +103,7 @@ public class ASTNodeMap { map.put(88, "NameQualifiedType"); map.put(89, "CreationReference"); map.put(90, "ExpressionMethodReference"); - map.put(91, "SuperMethhodReference"); + map.put(91, "SuperMethodReference"); map.put(92, "TypeMethodReference"); } } diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java new file mode 100644 index 0000000..70db730 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java @@ -0,0 +1,71 @@ +package edu.lu.uni.serval.FixPattern.utils; + +import java.util.HashMap; +import java.util.Map; + +public class CNodeMap { + + public static Map map; + + static { + map = new HashMap(); + map.put(300100, "If"); + map.put(410100, "DefineFunc"); + map.put(340000, "Storage"); + map.put(240800, "Postfix"); + map.put(280100, "Goto"); + map.put(280003, "Return"); + map.put(300100, "If"); + map.put(270100, "Label"); + map.put(290001, "None"); + map.put(450200, "Definition"); + map.put(200000, "ParamList"); + map.put(310300, "For"); + map.put(241200, "ArrayAccess"); + map.put(240600, "Sequence"); + map.put(241600, "SizeOfType"); + map.put(240500, "CondExpr"); + map.put(240100, "Ident"); + map.put(290100, "Some"); + map.put(280002, "Break"); + map.put(360100, "InitExpr"); + map.put(241300, "RecordAccess"); + map.put(280001, "Continue"); + map.put(470000, "GenericList"); + map.put(241500, "SizeOfExpr"); + map.put(310100, "While"); + map.put(240900, "Infix"); + map.put(460000, "Program"); + map.put(360200, "InitList"); + map.put(450300, "CppTop"); + map.put(380000, "Definition"); + map.put(330000, "Compound"); + map.put(240700, "Assignment"); + map.put(241000, "Unary"); + map.put(280200, "ReturnExpr"); + map.put(270400, "Default"); + map.put(420100, "DefineExpr"); + map.put(241400, "RecordPtAccess"); + map.put(450800, "FinalDef"); + map.put(240400, "FunCall"); + map.put(241100, "Binary"); + map.put(20100, "Left"); + map.put(490100, "IfToken"); + map.put(300200, "Switch"); + map.put(400200, "Include"); + map.put(242000, "ParenExpr"); + map.put(410001, "DefineVar"); + map.put(310200, "DoWhile"); + map.put(420001, "DefineEmpty"); + map.put(241700, "Cast"); + map.put(270200, "Case"); + map.put(240200, "Constant"); + map.put(450100, "Declaration"); + map.put(480000, "GenericString"); + map.put(400100, "Define"); + map.put(450600, "EmptyDef"); + map.put(220100, "ParameterType"); + map.put(260300, "ExprStatement"); + map.put(350100, "DeclList"); + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java index e02a1a7..f5eb979 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java @@ -36,7 +36,7 @@ public abstract class Parser implements ParserInterface { protected List parseChangedSourceCodeWithGumTree(File prevFile, File revFile) { List actionSets = new ArrayList<>(); // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile); if (gumTreeResults != null && gumTreeResults.size() > 0) { // Regroup GumTre results. List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 72ad67d..1804185 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -137,8 +137,9 @@ public class FixedViolationHunkParser extends FixedViolationParser { } String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; -// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; - String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; + String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; + //TODO uncomment the line below for more detailed gumtree input +// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; // if (noUpdate(editScriptTokens)) { // } @@ -146,9 +147,9 @@ public class FixedViolationHunkParser extends FixedViolationParser { this.sizes += size + "\n"; this.astEditScripts += astEditScripts + "\n"; - SimpleTree simpleTree = getBuggyCodeTree(patchHunk, bugEndPosition, prevFile, bugStartLine, bugEndLine); - String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); - this.tokensOfSourceCode += tokens + "\n"; +// SimpleTree simpleTree = getBuggyCodeTree(patchHunk, bugEndPosition, prevFile, bugStartLine, bugEndLine); +// String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); +// this.tokensOfSourceCode += tokens + "\n"; } } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java index 9d48ade..272560a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java @@ -12,7 +12,8 @@ import com.github.gumtreediff.actions.model.Action; import edu.lu.uni.serval.FixPatternParser.Parser; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; + +import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouperForC; import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; @@ -50,7 +51,7 @@ public class FixedViolationParser extends Parser { protected List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { List actionSets = new ArrayList<>(); // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile); if (gumTreeResults == null) { this.resultType = 1; return null; @@ -59,7 +60,7 @@ public class FixedViolationParser extends Parser { return actionSets; } else { // Regroup GumTre results. - List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); + List allActionSets = new HierarchicalRegrouperForC().regroupGumTreeResults(gumTreeResults); // for (HierarchicalActionSet actionSet : allActionSets) { // String astNodeType = actionSet.getAstNodeType(); // if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java index e1fdeb2..d171fed 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java @@ -2,6 +2,7 @@ package edu.lu.uni.serval.MultipleThreadsParser; import java.io.File; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; import org.slf4j.Logger; @@ -31,44 +32,61 @@ public class AkkaParser { */ @SuppressWarnings("deprecation") public static void main(String[] args) { - String inputRootPath = args[0]; - int numberOfWorkers = Integer.parseInt(args[1]); - int hunkThreshold = 0; - try { - hunkThreshold = Integer.parseInt(args[2]); - } catch (NumberFormatException e1) { - hunkThreshold = 10; - } +// String inputRootPath = args[0]; + int numberOfWorkers = 5; //Integer.parseInt(args[1]); + int hunkThreshold = 10; +// try { +// hunkThreshold = Integer.parseInt(args[2]); +// } catch (NumberFormatException e1) { +// hunkThreshold = 10; +// } - Configuration.ROOT_PATH = inputRootPath; +// Configuration.ROOT_PATH = inputRootPath; Configuration.HUNK_SIZE = hunkThreshold; - // input data - log.info("Get the input data..."); - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); - log.info("MessageFiles: " + msgFiles.size()); - - // output path - final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH; - final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH; - final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH; - final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH; - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - ActorSystem system = null; - ActorRef parsingActor = null; - final WorkMessage msg = new WorkMessage(0, msgFiles); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); + List pjList = Arrays.asList("APACHE-CAMEL","APACHE-HBASE","APACHE-HIVE","COMMONS-CODEC","COMMONS-COLLECTIONS", + "COMMONS-COMPRESS","COMMONS-CONFIGURATION","COMMONS-CRYPTO","COMMONS-CSV","COMMONS-IO","COMMONS-LANG", + "COMMONS-MATH","COMMONS-WEAVER","JBOSS-ENTESB","JBOSS-JBMETA","SPRING-AMQP","SPRING-ANDROID","SPRING-BATCH", + "SPRING-BATCHADM","SPRING-DATACMNS","SPRING-DATAGRAPH","SPRING-DATAJPA","SPRING-DATAMONGO","SPRING-DATAREDIS", + "SPRING-DATAREST","SPRING-LDAP","SPRING-MOBILE","SPRING-ROO","SPRING-SEC","SPRING-SECOAUTH","SPRING-SGF","SPRING-SHDP", + "SPRING-SOCIAL","SPRING-SOCIALFB","SPRING-SOCIALLI","SPRING-SOCIALTW","SPRING-SPR","SPRING-SWF","SPRING-SWS","WILDFLY-ELY", + "WILDFLY-SWARM","WILDFLY-WFARQ","WILDFLY-WFCORE","WILDFLY-WFLY","WILDFLY-WFMP"); + for (String pj : pjList) { + String[] split = pj.split("-"); + String pjPath = split[0]; + String pjName = split[1]; +// String rootPath = "/Volumes/data/bugStudy/"; +// String DATASET_FILE_PATH = rootPath + "/dataset/GumTreeInput/" + pjName; +// String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; + log.info(pjName); + // input data + log.info("Get the input data..."); + final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"gitrepo/"); + log.info("MessageFiles: " + msgFiles.size()); + + // output path + final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH + pjName + "/"; + final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH+ pjName + "/"; + final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH+ pjName + "/"; + final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH+ pjName + "/"; + FileHelper.deleteDirectory(editScriptsFilePath); + FileHelper.deleteDirectory(patchesSourceCodeFilePath); + FileHelper.deleteDirectory(buggyTokensFilePath); + FileHelper.deleteDirectory(editScriptSizesFilePath); + + ActorSystem system = null; + ActorRef parsingActor = null; + final WorkMessage msg = new WorkMessage(0, msgFiles); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Mining-FixPattern-System"); + parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, + patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } } } diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java new file mode 100644 index 0000000..ab1b332 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -0,0 +1,114 @@ +package edu.lu.uni.serval.MultipleThreadsParser; + +import akka.actor.ActorRef; +import akka.actor.ActorSystem; +import edu.lu.uni.serval.config.Configuration; +import edu.lu.uni.serval.utils.FileHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +/** + * Multi-thread parser of parsing the difference between buggy code file and fixed code file. + * + * @author kui.liu + * + */ +public class AkkaParser2 { + + private static Logger log = LoggerFactory.getLogger(AkkaParser2.class); + + /** + * Two parameters: + * First one: the root path of input data. + * Second one: the number of threads. + * Third one: the threshold of selecting patch hunks. + * @param args + */ + @SuppressWarnings("deprecation") + public static void main(String[] args) { +// String inputRootPath = args[0]; + int numberOfWorkers = 10; //Integer.parseInt(args[1]); + int hunkThreshold = 5; +// try { +// hunkThreshold = Integer.parseInt(args[2]); +// } catch (NumberFormatException e1) { +// hunkThreshold = 10; +// } + +// Configuration.ROOT_PATH = inputRootPath; + Configuration.HUNK_SIZE = hunkThreshold; + + + + String pjName = "linux-stable"; +// String rootPath = "/Volumes/data/bugStudy/"; +// String DATASET_FILE_PATH = rootPath + "/dataset/GumTreeInput/" + pjName; +// String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; + log.info(pjName); + // input data + log.info("Get the input data..."); + final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"/"); + log.info("MessageFiles: " + msgFiles.size()); + + // output path + final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH + pjName + "/"; + final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH+ pjName + "/"; + final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH+ pjName + "/"; + final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH+ pjName + "/"; + FileHelper.deleteDirectory(editScriptsFilePath); + FileHelper.deleteDirectory(patchesSourceCodeFilePath); + FileHelper.deleteDirectory(buggyTokensFilePath); + FileHelper.deleteDirectory(editScriptSizesFilePath); + + ActorSystem system = null; + ActorRef parsingActor = null; + final WorkMessage msg = new WorkMessage(0, msgFiles); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Mining-FixPattern-System"); + parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, + patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } + + + } + + /** + * Get violation-related files. + * + * @param gumTreeInput + * @return + */ + public static List getMessageFiles(String gumTreeInput) { + String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile + File revFilesPath = new File(inputPath + "revFiles/"); + File[] revFiles = revFilesPath.listFiles(); // project folders + List msgFiles = new ArrayList<>(); + + for (File revFile : revFiles) { + if (revFile.getName().endsWith(".c") || revFile.getName().endsWith(".h")) { + String fileName = revFile.getName(); + File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file +// fileName = fileName.replace(".java", ".txt"); + File diffentryFile = new File(gumTreeInput + "diffentries/" + fileName); // DiffEntry file + File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); + msgFile.setPositionFile(positionFile); + msgFiles.add(msgFile); + + } +// } + } + + return msgFiles.subList(10,20); + } +} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index f4982cf..0d81521 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -85,10 +85,10 @@ public class ParseFixPatternWorker extends UntypedActor { File revFile = msgFile.getRevFile(); File prevFile = msgFile.getPrevFile(); File diffentryFile = msgFile.getDiffEntryFile(); - File positionFile = msgFile.getPositionFile(); - if (revFile.getName().toLowerCase().contains("test")) { +// File positionFile = msgFile.getPositionFile(); + /*if (revFile.getName().toLowerCase().contains("test")) { continue; - } + }*/ FixedViolationHunkParser parser = new FixedViolationHunkParser(); final ExecutorService executor = Executors.newSingleThreadExecutor(); @@ -109,13 +109,13 @@ public class ParseFixPatternWorker extends UntypedActor { String editScript = parser.getAstEditScripts(); if ("".equals(editScript)) { - if (parser.resultType == 1) { - nullGumTreeResults += countAlarms(positionFile, ""); - } else if (parser.resultType == 2) { - noSourceCodeChanges += countAlarms(positionFile, ""); - } else if (parser.resultType == 3) { - noStatementChanges += countAlarms(positionFile, ""); - } +// if (parser.resultType == 1) { +// nullGumTreeResults += countAlarms(positionFile, ""); +// } else if (parser.resultType == 2) { +// noSourceCodeChanges += countAlarms(positionFile, ""); +// } else if (parser.resultType == 3) { +// noStatementChanges += countAlarms(positionFile, ""); +// } } else { editScripts.append(editScript); patchesSourceCode.append(parser.getPatchesSourceCode()); @@ -139,14 +139,14 @@ public class ParseFixPatternWorker extends UntypedActor { } } catch (TimeoutException e) { future.cancel(true); - timeouts += countAlarms(positionFile, "#Timeout:"); +// timeouts += countAlarms(positionFile, "#Timeout:"); System.err.println("#Timeout: " + revFile.getName()); } catch (InterruptedException e) { - timeouts += countAlarms(positionFile, "#TimeInterrupted:"); +// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); System.err.println("#TimeInterrupted: " + revFile.getName()); e.printStackTrace(); } catch (ExecutionException e) { - timeouts += countAlarms(positionFile, "#TimeAborted:"); +// timeouts += countAlarms(positionFile, "#TimeAborted:"); System.err.println("#TimeAborted: " + revFile.getName()); e.printStackTrace(); } finally { diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index b86ac0e..4ff7b50 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,9 +2,10 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 300L; + public static final long SECONDS_TO_WAIT = 100L; - public static String ROOT_PATH = "../FPM_Violations/"; // The root path of all output data. +// public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. + public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. public static int HUNK_SIZE = 10; // The limitation of source code lines of each DiffEntry, which will be selected as training data. public static final String BUGGY_TREE_SIGNAL = "BUGGY_TREE###"; // The starting signal of the tree of buggy source code . diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java index 921e7b8..5590c48 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java @@ -1,5 +1,6 @@ package edu.lu.uni.serval.gumtree.regroup; +import java.io.File; import java.util.ArrayList; import java.util.List; @@ -13,6 +14,7 @@ import com.github.gumtreediff.tree.ITree; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; import edu.lu.uni.serval.FixPattern.utils.Checker; +import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.utils.ListSorter; /** @@ -22,7 +24,7 @@ import edu.lu.uni.serval.utils.ListSorter; * */ public class HierarchicalRegrouper { - + public List regroupGumTreeResults(List actions) { /* * First, sort actions by their positions. diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java new file mode 100644 index 0000000..9f7ef12 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -0,0 +1,240 @@ +package edu.lu.uni.serval.gumtree.regroup; + +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPattern.utils.CNodeMap; +import edu.lu.uni.serval.gumtree.GumTreeComparer; +import edu.lu.uni.serval.utils.ListSorter; + +import java.io.File; +import java.util.ArrayList; +import java.util.List; + +/** + * Regroup GumTree results to a hierarchical construction. + * + * @author kui.liu + * + */ +public class HierarchicalRegrouperForC { + + public static void main(String[] args) { + GumTreeComparer com = new GumTreeComparer(); + File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c"); + File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c"); + List action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2); + List actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action); + System.out.println(actionSet); + } + + public List regroupGumTreeResults(List actions) { + /* + * First, sort actions by their positions. + */ +// List actions = new ListSorter(actionsArgu).sortAscending(); +// if (actions == null) { +// actions = actionsArgu; +// } + + /* + * Second, group actions by their positions. + */ + List actionSets = new ArrayList<>(); + HierarchicalActionSet actionSet = null; + for(Action act : actions){ + Action parentAct = findParentAction(act, actions); + if (parentAct == null) { + actionSet = createActionSet(act, parentAct, null); + actionSets.add(actionSet); + } else { + if (!addToAactionSet(act, parentAct, actionSets)) { + // The index of the parent action in the actions' list is larger than the index of this action. + actionSet = createActionSet(act, parentAct, null); + actionSets.add(actionSet); + } + } + } + + /* + * Third, add the subActionSet to its parent ActionSet. + */ + List reActionSets = new ArrayList<>(); + for (HierarchicalActionSet actSet : actionSets) { + Action parentAct = actSet.getParentAction(); + if (parentAct != null) { + addToActionSets(actSet, parentAct, actionSets); + } else { + // TypeDeclaration, FieldDeclaration, MethodDeclaration, Statement. + // CatchClause, ConstructorInvocation, SuperConstructorInvocation, SwitchCase + String astNodeType = actSet.getAstNodeType(); +// if (astNodeType.endsWith("TypeDeclaration") || astNodeType.endsWith("FieldDeclaration") || astNodeType.endsWith("EnumDeclaration") || +// astNodeType.endsWith("MethodDeclaration") || astNodeType.endsWith("Statement") || +// astNodeType.endsWith("ConstructorInvocation") || astNodeType.endsWith("CatchClause") || astNodeType.endsWith("SwitchCase")) { + reActionSets.add(actSet); +// } + } + } + return reActionSets; + } + + private HierarchicalActionSet createActionSet(Action act, Action parentAct, HierarchicalActionSet parent) { + HierarchicalActionSet actionSet = new HierarchicalActionSet(); + actionSet.setAction(act); + actionSet.setActionString(parseAction(act.toString())); + actionSet.setParentAction(parentAct); + actionSet.setNode(act.getNode()); + actionSet.setParent(parent); + return actionSet; + } + + private String parseAction(String actStr1) { + // UPD 25@@!a from !a to isTrue(a) at 69 + String[] actStrArrays = actStr1.split("@@"); + String actStr = ""; + int length = actStrArrays.length; + for (int i =0; i < length - 1; i ++) { + String actStrFrag = actStrArrays[i]; + int index = actStrFrag.lastIndexOf(" ") + 1; + String nodeType = actStrFrag.substring(index); + if (!"".equals(nodeType)) { + if (Character.isDigit(nodeType.charAt(0)) || (nodeType.startsWith("-") && Character.isDigit(nodeType.charAt(1)))) { + try { + int typeInt = Integer.parseInt(nodeType); + if (CNodeMap.map.containsKey(typeInt)) { + String type = CNodeMap.map.get(Integer.parseInt(nodeType)); + nodeType = type; + } + } catch (NumberFormatException e) { + nodeType = actStrFrag.substring(index); + } + } + } + actStrFrag = actStrFrag.substring(0, index) + nodeType + "@@"; + actStr += actStrFrag; + } + actStr += actStrArrays[length - 1]; + return actStr; + } + + private void addToActionSets(HierarchicalActionSet actionSet, Action parentAct, List actionSets) { + Action act = actionSet.getAction(); + for (HierarchicalActionSet actSet : actionSets) { + if (actSet.equals(actionSet)) continue; + Action action = actSet.getAction(); + + if (!areRelatedActions(action, act)) continue; + if (action.equals(parentAct)) { // actSet is the parent of actionSet. + actionSet.setParent(actSet); + actSet.getSubActions().add(actionSet); + sortSubActions(actSet); + break; + } else { + if (isPossibileSubAction(action, act)) { + // SubAction range： startPosition2 <= startPosition && startPosition + length <= startPosition2 + length2 + addToActionSets(actionSet, parentAct, actSet.getSubActions()); + } + } + } + } + + private boolean isPossibileSubAction(Action parent, Action child) { + if ((parent instanceof Update && !(child instanceof Addition)) + || (parent instanceof Delete && child instanceof Delete) + || (parent instanceof Insert && (child instanceof Insert))) { + int startPosition = child.getPosition(); + int length = child.getLength(); + int startPosition2 = parent.getPosition(); + int length2 = parent.getLength(); + + if (!(startPosition2 <= startPosition && startPosition + length <= startPosition2 + length2)) { + // when act is not the sub-set of action. + return false; + } + } + return true; + } + + private void sortSubActions(HierarchicalActionSet actionSet) { + ListSorter sorter = new ListSorter(actionSet.getSubActions()); + List subActions = sorter.sortAscending(); + if (subActions != null) { + actionSet.setSubActions(subActions); + } + } + + private boolean addToAactionSet(Action act, Action parentAct, List actionSets) { + for(HierarchicalActionSet actionSet : actionSets) { + Action action = actionSet.getAction(); + + if (!areRelatedActions(action, act)) continue; + + if (action.equals(parentAct)) { // actionSet is the parent of actSet. + HierarchicalActionSet actSet = createActionSet(act, actionSet.getAction(), actionSet); + actionSet.getSubActions().add(actSet); + sortSubActions(actionSet); + return true; + } else { + if (isPossibileSubAction(action, act)) { + // SubAction range： startPosition2 <= startPosition && startPosition + length <= startP + length2 + List subActionSets = actionSet.getSubActions(); + if (subActionSets.size() > 0) { + boolean added = addToAactionSet(act, parentAct, subActionSets); + if (added) { + return true; + } else { + continue; + } + } + } + } + } + return false; + } + + private Action findParentAction(Action action, List actions) { + + ITree parent = action.getNode().getParent(); + if (action instanceof Addition) { + parent = ((Addition) action).getParent(); // parent in the fixed source code tree + } + + if (parent.getType() == 55) { + int type = action.getNode().getType(); + // Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation + if (type != 83 && type != 77 && type != 78 && type != 79 + && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 + && type != 76 && type != 84 && type != 87 && type != 88 && type != 42) { + // ArrayType, PrimitiveType, SimpleType, ParameterizedType, + // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName + return null; + } +// } else if (parent.getType() == 31) { // method declaration +// int type = action.getNode().getType(); +// if (Checker.isStatement(type)) {// statements +// return null; +// } + } + + for (Action act : actions) { + if (act.getNode().equals(parent)) { + if (areRelatedActions(act, action)) { + return act; + } + } + } + return null; + } + + private boolean areRelatedActions(Action parent, Action child) { + if (parent instanceof Move && !(child instanceof Move)) {// If action is MOV, its children must be MOV. + return false; + } + if (parent instanceof Delete && !(child instanceof Delete)) {// If action is INS, its children must be MOV or INS. + return false; + } + if (parent instanceof Insert && !(child instanceof Addition)) {// If action is DEL, its children must be DEL. + return false; + } + return true; + } +} From bab35c353fe7b5464e3d1890daae3045d6db0716 Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Thu, 8 Feb 2018 16:37:25 +0100 Subject: [PATCH 003/127] Update in regrouper. --- .../regroup/HierarchicalRegrouperForC.java | 30 +++++++++++-------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index 9f7ef12..f636ded 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -42,7 +42,11 @@ public class HierarchicalRegrouperForC { List actionSets = new ArrayList<>(); HierarchicalActionSet actionSet = null; for(Action act : actions){ + if (act.toString().startsWith("UPD")) { + System.out.println(); + } Action parentAct = findParentAction(act, actions); + if (parentAct == null) { actionSet = createActionSet(act, parentAct, null); actionSets.add(actionSet); @@ -66,7 +70,7 @@ public class HierarchicalRegrouperForC { } else { // TypeDeclaration, FieldDeclaration, MethodDeclaration, Statement. // CatchClause, ConstructorInvocation, SuperConstructorInvocation, SwitchCase - String astNodeType = actSet.getAstNodeType(); +// String astNodeType = actSet.getAstNodeType(); // if (astNodeType.endsWith("TypeDeclaration") || astNodeType.endsWith("FieldDeclaration") || astNodeType.endsWith("EnumDeclaration") || // astNodeType.endsWith("MethodDeclaration") || astNodeType.endsWith("Statement") || // astNodeType.endsWith("ConstructorInvocation") || astNodeType.endsWith("CatchClause") || astNodeType.endsWith("SwitchCase")) { @@ -198,22 +202,22 @@ public class HierarchicalRegrouperForC { parent = ((Addition) action).getParent(); // parent in the fixed source code tree } - if (parent.getType() == 55) { - int type = action.getNode().getType(); +// if (parent.getType() == 55) { +// int type = action.getNode().getType(); // Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation - if (type != 83 && type != 77 && type != 78 && type != 79 - && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 - && type != 76 && type != 84 && type != 87 && type != 88 && type != 42) { - // ArrayType, PrimitiveType, SimpleType, ParameterizedType, - // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName - return null; - } +// if (type != 83 && type != 77 && type != 78 && type != 79 +// && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 +// && type != 76 && type != 84 && type != 87 && type != 88 && type != 42) { +// // ArrayType, PrimitiveType, SimpleType, ParameterizedType, +// // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName +// return null; +// } // } else if (parent.getType() == 31) { // method declaration // int type = action.getNode().getType(); // if (Checker.isStatement(type)) {// statements // return null; // } - } +// } for (Action act : actions) { if (act.getNode().equals(parent)) { @@ -229,10 +233,10 @@ public class HierarchicalRegrouperForC { if (parent instanceof Move && !(child instanceof Move)) {// If action is MOV, its children must be MOV. return false; } - if (parent instanceof Delete && !(child instanceof Delete)) {// If action is INS, its children must be MOV or INS. + if (parent instanceof Delete && !(child instanceof Delete)) {// If action is DEL, its children must be DEL. return false; } - if (parent instanceof Insert && !(child instanceof Addition)) {// If action is DEL, its children must be DEL. + if (parent instanceof Insert && !(child instanceof Addition)) {// If action is INS, its children must be MOV or INS. return false; } return true; From 6afc11ae62430741b330ac67c2a2b48fd73af620 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 8 Feb 2018 17:27:03 +0100 Subject: [PATCH 004/127] extend node map --- .../uni/serval/FixPattern/utils/CNodeMap.java | 123 ++++++++++-------- 1 file changed, 70 insertions(+), 53 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java index 70db730..97f0638 100644 --- a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java @@ -9,63 +9,80 @@ public class CNodeMap { static { map = new HashMap(); - map.put(300100, "If"); - map.put(410100, "DefineFunc"); - map.put(340000, "Storage"); - map.put(240800, "Postfix"); - map.put(280100, "Goto"); - map.put(280003, "Return"); - map.put(300100, "If"); - map.put(270100, "Label"); - map.put(290001, "None"); - map.put(450200, "Definition"); - map.put(200000, "ParamList"); - map.put(310300, "For"); - map.put(241200, "ArrayAccess"); - map.put(240600, "Sequence"); - map.put(241600, "SizeOfType"); map.put(240500, "CondExpr"); - map.put(240100, "Ident"); - map.put(290100, "Some"); - map.put(280002, "Break"); - map.put(360100, "InitExpr"); - map.put(241300, "RecordAccess"); - map.put(280001, "Continue"); - map.put(470000, "GenericList"); - map.put(241500, "SizeOfExpr"); - map.put(310100, "While"); - map.put(240900, "Infix"); - map.put(460000, "Program"); - map.put(360200, "InitList"); - map.put(450300, "CppTop"); - map.put(380000, "Definition"); - map.put(330000, "Compound"); - map.put(240700, "Assignment"); - map.put(241000, "Unary"); - map.put(280200, "ReturnExpr"); - map.put(270400, "Default"); - map.put(420100, "DefineExpr"); - map.put(241400, "RecordPtAccess"); - map.put(450800, "FinalDef"); map.put(240400, "FunCall"); - map.put(241100, "Binary"); - map.put(20100, "Left"); - map.put(490100, "IfToken"); - map.put(300200, "Switch"); - map.put(400200, "Include"); - map.put(242000, "ParenExpr"); + map.put(241800, "StatementExpr"); + map.put(241300, "RecordAccess"); + map.put(420100, "DefineExpr"); + map.put(290001, "None"); + map.put(350200, "MacroDecl"); + map.put(280100, "Goto"); + map.put(60100, "BaseType"); map.put(410001, "DefineVar"); - map.put(310200, "DoWhile"); - map.put(420001, "DefineEmpty"); - map.put(241700, "Cast"); - map.put(270200, "Case"); - map.put(240200, "Constant"); - map.put(450100, "Declaration"); - map.put(480000, "GenericString"); - map.put(400100, "Define"); - map.put(450600, "EmptyDef"); - map.put(220100, "ParameterType"); + map.put(420200, "DefineStmt"); + map.put(450800, "FinalDef"); map.put(260300, "ExprStatement"); + map.put(340000, "Storage"); + map.put(290100, "Some"); + map.put(410100, "DefineFunc"); + map.put(420400, "DefineDoWhileZero"); + map.put(70100, "IntType"); + map.put(20100, "Left"); + map.put(480000, "GenericString"); + map.put(241600, "SizeOfType"); + map.put(241000, "Unary"); + map.put(300100, "If"); + map.put(450300, "CppTop"); + map.put(460000, "Program"); + map.put(241200, "ArrayAccess"); + map.put(450400, "IfdefTop"); + map.put(330000, "Compound"); + map.put(310200, "DoWhile"); + map.put(240700, "Assignment"); + map.put(270100, "Label"); + map.put(360100, "InitExpr"); + map.put(270400, "Default"); + map.put(450600, "EmptyDef"); + map.put(470000, "GenericList"); + map.put(490100, "IfToken"); + map.put(60900, "StructUnionName"); + map.put(240600, "Sequence"); + map.put(80100, "Si"); + map.put(360200, "InitList"); + map.put(370200, "DesignatorIndex"); + map.put(360300, "InitDesignators"); + map.put(280001, "Continue"); + map.put(420001, "DefineEmpty"); + map.put(310100, "While"); + map.put(270200, "Case"); + map.put(450700, "NotParsedCorrectly"); + map.put(400100, "Define"); + map.put(370100, "DesignatorField"); + map.put(280003, "Return"); + map.put(240800, "Postfix"); + map.put(100003, "CInt"); + map.put(240100, "Ident"); + map.put(310300, "For"); + map.put(400200, "Include"); + map.put(440100, "IfdefDirective"); + map.put(220100, "ParameterType"); + map.put(242000, "ParenExpr"); + map.put(200000, "ParamList"); + map.put(280002, "Break"); + map.put(241500, "SizeOfExpr"); + map.put(241400, "RecordPtAccess"); + map.put(380000, "Definition"); + map.put(50000, "TypeQualifier"); + map.put(450100, "Declaration"); + map.put(240900, "Infix"); + map.put(241100, "Binary"); + map.put(40000, "FullType"); + map.put(450200, "Definition"); + map.put(310400, "MacroIteration"); + map.put(280200, "ReturnExpr"); + map.put(300200, "Switch"); map.put(350100, "DeclList"); + map.put(240200, "Constant"); + map.put(241700, "Cast"); } } From eb2b9a0a05b200ece21623f4e5ca3775366b4fdb Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Fri, 9 Feb 2018 10:49:20 +0100 Subject: [PATCH 005/127] Create parent hierarchical actions for UPD actions at the statement level. --- .../regroup/HierarchicalRegrouperForC.java | 64 ++++++++++++------- 1 file changed, 42 insertions(+), 22 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index f636ded..bf2554c 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -27,6 +27,8 @@ public class HierarchicalRegrouperForC { System.out.println(actionSet); } + List actionSets = new ArrayList<>(); + public List regroupGumTreeResults(List actions) { /* * First, sort actions by their positions. @@ -39,12 +41,8 @@ public class HierarchicalRegrouperForC { /* * Second, group actions by their positions. */ - List actionSets = new ArrayList<>(); HierarchicalActionSet actionSet = null; for(Action act : actions){ - if (act.toString().startsWith("UPD")) { - System.out.println(); - } Action parentAct = findParentAction(act, actions); if (parentAct == null) { @@ -195,30 +193,15 @@ public class HierarchicalRegrouperForC { return false; } + List newParentActions = new ArrayList<>(); private Action findParentAction(Action action, List actions) { ITree parent = action.getNode().getParent(); + if (parent == null) return null; if (action instanceof Addition) { parent = ((Addition) action).getParent(); // parent in the fixed source code tree } -// if (parent.getType() == 55) { -// int type = action.getNode().getType(); - // Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation -// if (type != 83 && type != 77 && type != 78 && type != 79 -// && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 -// && type != 76 && type != 84 && type != 87 && type != 88 && type != 42) { -// // ArrayType, PrimitiveType, SimpleType, ParameterizedType, -// // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName -// return null; -// } -// } else if (parent.getType() == 31) { // method declaration -// int type = action.getNode().getType(); -// if (Checker.isStatement(type)) {// statements -// return null; -// } -// } - for (Action act : actions) { if (act.getNode().equals(parent)) { if (areRelatedActions(act, action)) { @@ -226,9 +209,46 @@ public class HierarchicalRegrouperForC { } } } - return null; + for (Action act : newParentActions) { + if (act.getNode().equals(parent)) { + if (areRelatedActions(act, action)) { + return act; + } + } + } + + ITree tree = action.getNode(); + Action parentAction = null; + if (!isStatement(tree)) { + parentAction = new Update(parent, action.getNode().getParent()); + newParentActions.add(parentAction); + + Action higherParentAct = findParentAction(parentAction, actions); + HierarchicalActionSet actionSet = null; + if (higherParentAct == null) { + actionSet = createActionSet(parentAction, higherParentAct, null); + actionSets.add(actionSet); + } else { + if (!addToAactionSet(parentAction, higherParentAct, actionSets)) { + // The index of the parent action in the actions' list is larger than the index of this action. + actionSet = createActionSet(parentAction, higherParentAct, null); + actionSets.add(actionSet); + } + } + } + return parentAction; } + private boolean isStatement(ITree tree) { + int nodeType = tree.getType(); + if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100 + || nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300 + || 260300 == nodeType || nodeType == 460000) {// TODO + return true; + } + return false; + } + private boolean areRelatedActions(Action parent, Action child) { if (parent instanceof Move && !(child instanceof Move)) {// If action is MOV, its children must be MOV. return false; From 0192d84ae9bcc91d07496275dcb886a107fb40ab Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 9 Feb 2018 11:59:44 +0100 Subject: [PATCH 006/127] new c node map --- .../uni/serval/FixPattern/utils/CNodeMap.java | 163 ++++++++++-------- .../MultipleThreadsParser/AkkaParser2.java | 2 +- .../regroup/HierarchicalRegrouperForC.java | 4 +- 3 files changed, 91 insertions(+), 78 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java index 97f0638..648449c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java @@ -9,80 +9,93 @@ public class CNodeMap { static { map = new HashMap(); - map.put(240500, "CondExpr"); - map.put(240400, "FunCall"); - map.put(241800, "StatementExpr"); - map.put(241300, "RecordAccess"); - map.put(420100, "DefineExpr"); - map.put(290001, "None"); - map.put(350200, "MacroDecl"); - map.put(280100, "Goto"); - map.put(60100, "BaseType"); - map.put(410001, "DefineVar"); - map.put(420200, "DefineStmt"); - map.put(450800, "FinalDef"); - map.put(260300, "ExprStatement"); - map.put(340000, "Storage"); - map.put(290100, "Some"); - map.put(410100, "DefineFunc"); - map.put(420400, "DefineDoWhileZero"); - map.put(70100, "IntType"); - map.put(20100, "Left"); - map.put(480000, "GenericString"); - map.put(241600, "SizeOfType"); - map.put(241000, "Unary"); - map.put(300100, "If"); - map.put(450300, "CppTop"); - map.put(460000, "Program"); - map.put(241200, "ArrayAccess"); - map.put(450400, "IfdefTop"); - map.put(330000, "Compound"); - map.put(310200, "DoWhile"); - map.put(240700, "Assignment"); - map.put(270100, "Label"); - map.put(360100, "InitExpr"); - map.put(270400, "Default"); - map.put(450600, "EmptyDef"); - map.put(470000, "GenericList"); - map.put(490100, "IfToken"); - map.put(60900, "StructUnionName"); - map.put(240600, "Sequence"); - map.put(80100, "Si"); - map.put(360200, "InitList"); - map.put(370200, "DesignatorIndex"); - map.put(360300, "InitDesignators"); - map.put(280001, "Continue"); - map.put(420001, "DefineEmpty"); - map.put(310100, "While"); - map.put(270200, "Case"); - map.put(450700, "NotParsedCorrectly"); - map.put(400100, "Define"); - map.put(370100, "DesignatorField"); - map.put(280003, "Return"); - map.put(240800, "Postfix"); - map.put(100003, "CInt"); - map.put(240100, "Ident"); - map.put(310300, "For"); - map.put(400200, "Include"); - map.put(440100, "IfdefDirective"); - map.put(220100, "ParameterType"); - map.put(242000, "ParenExpr"); - map.put(200000, "ParamList"); - map.put(280002, "Break"); - map.put(241500, "SizeOfExpr"); - map.put(241400, "RecordPtAccess"); - map.put(380000, "Definition"); - map.put(50000, "TypeQualifier"); - map.put(450100, "Declaration"); - map.put(240900, "Infix"); - map.put(241100, "Binary"); - map.put(40000, "FullType"); - map.put(450200, "Definition"); - map.put(310400, "MacroIteration"); - map.put(280200, "ReturnExpr"); - map.put(300200, "Switch"); - map.put(350100, "DeclList"); - map.put(240200, "Constant"); - map.put(241700, "Cast"); + map.put(20100,"Left"); + map.put(30100,"ActMisc"); + map.put(40000,"FullType"); + map.put(50000,"TypeQualifier"); + map.put(60100,"BaseType"); + map.put(60200,"Pointer"); + map.put(60800,"EnumName"); + map.put(60900,"StructUnionName"); + map.put(61000,"TypeName"); + map.put(70002,"SizeType"); + map.put(70100,"IntType"); + map.put(80001,"CChar"); + map.put(80100,"Si"); + map.put(90002,"UnSigned"); + map.put(100003,"CInt"); + map.put(200000,"ParamList"); + map.put(210000,"DotsParameter"); + map.put(220100,"ParameterType"); + map.put(240100,"Ident"); + map.put(240200,"Constant"); + map.put(240400,"FunCall"); + map.put(240500,"CondExpr"); + map.put(240600,"Sequence"); + map.put(240700,"Assignment"); + map.put(240800,"Postfix"); + map.put(240900,"Infix"); + map.put(241000,"Unary"); + map.put(241100,"Binary"); + map.put(241200,"ArrayAccess"); + map.put(241300,"RecordAccess"); + map.put(241400,"RecordPtAccess"); + map.put(241500,"SizeOfExpr"); + map.put(241600,"SizeOfType"); + map.put(241700,"Cast"); + map.put(241900,"Constructor"); + map.put(242000,"ParenExpr"); + map.put(260300,"ExprStatement"); + map.put(260800,"Asm"); + map.put(270100,"Label"); + map.put(270200,"Case"); + map.put(270300,"CaseRange"); + map.put(270400,"Default"); + map.put(280001,"Continue"); + map.put(280002,"Break"); + map.put(280003,"Return"); + map.put(280100,"Goto"); + map.put(280200,"ReturnExpr"); + map.put(290001,"None"); + map.put(290100,"Some"); + map.put(300100,"If"); + map.put(300200,"Switch"); + map.put(310100,"While"); + map.put(310200,"DoWhile"); + map.put(310300,"For"); + map.put(310400,"MacroIteration"); + map.put(330000,"Compound"); + map.put(340000,"Storage"); + map.put(350100,"DeclList"); + map.put(350200,"MacroDecl"); + map.put(360100,"InitExpr"); + map.put(360200,"InitList"); + map.put(360300,"InitDesignators"); + map.put(370100,"DesignatorField"); + map.put(370200,"DesignatorIndex"); + map.put(370300,"DesignatorRange"); + map.put(380000,"Definition"); + map.put(400100,"Define"); + map.put(400200,"Include"); + map.put(400400,"OtherDirective"); + map.put(410001,"DefineVar"); + map.put(410002,"Undef"); + map.put(410100,"DefineFunc"); + map.put(420001,"DefineEmpty"); + map.put(420100,"DefineExpr"); + map.put(420200,"DefineStmt"); + map.put(420400,"DefineDoWhileZero"); + map.put(420600,"DefineInit"); + map.put(440100,"IfdefDirective"); + map.put(450100,"Declaration"); + map.put(450200,"Definition"); + map.put(450300,"CppTop"); + map.put(450400,"IfdefTop"); + map.put(450700,"NotParsedCorrectly"); + map.put(450800,"FinalDef"); + map.put(460000,"Program"); + map.put(470000,"GenericList"); + map.put(480000,"GenericString"); + map.put(490100,"IfToken"); } } diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index ab1b332..fa07097 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -109,6 +109,6 @@ public class AkkaParser2 { // } } - return msgFiles.subList(10,20); + return msgFiles; //.subList(10,20); } } diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index bf2554c..268d014 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -20,8 +20,8 @@ public class HierarchicalRegrouperForC { public static void main(String[] args) { GumTreeComparer com = new GumTreeComparer(); - File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c"); - File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c"); + File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_7779c5_545624_drivers#gpu#drm#drm_dp_helper.c"); + File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/7779c5_545624_drivers#gpu#drm#drm_dp_helper.c"); List action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2); List actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action); System.out.println(actionSet); From cce03be0b7078c3fdcbacc6737a7f6ddc4c1a79d Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 10 Feb 2018 15:07:13 +0100 Subject: [PATCH 007/127] runnable jar --- pom.xml | 35 ++++++++++++++++--- .../MultipleThreadsParser/AkkaParser2.java | 11 +++--- .../lu/uni/serval/config/Configuration.java | 2 +- 3 files changed, 37 insertions(+), 11 deletions(-) diff --git a/pom.xml b/pom.xml index 6cb33af..5f2acdd 100644 --- a/pom.xml +++ b/pom.xml @@ -42,11 +42,11 @@ 2.0.0-SNAPSHOT - - edu.lu.uni.serval - SourceCodeParser - 0.0.1-SNAPSHOT - + + + + + edu.lu.uni.serval @@ -73,6 +73,31 @@ 1.8 + + + org.apache.maven.plugins + maven-assembly-plugin + + + package + + single + + + + + + edu.lu.uni.serval.MultipleThreadsParser.AkkaParser2 + + + + + jar-with-dependencies + + + + + diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index fa07097..ff4015c 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -31,16 +31,17 @@ public class AkkaParser2 { */ @SuppressWarnings("deprecation") public static void main(String[] args) { -// String inputRootPath = args[0]; - int numberOfWorkers = 10; //Integer.parseInt(args[1]); - int hunkThreshold = 5; + String inputRootPath = args[0]; + int numberOfWorkers = Integer.parseInt(args[1]); + int hunkThreshold = Integer.parseInt(args[2]); // try { // hunkThreshold = Integer.parseInt(args[2]); // } catch (NumberFormatException e1) { // hunkThreshold = 10; // } -// Configuration.ROOT_PATH = inputRootPath; + Configuration.ROOT_PATH = inputRootPath; + log.info(Configuration.ROOT_PATH); Configuration.HUNK_SIZE = hunkThreshold; @@ -51,7 +52,7 @@ public class AkkaParser2 { // String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; log.info(pjName); // input data - log.info("Get the input data..."); + log.info("Get the input data..." + Configuration.GUM_TREE_INPUT +pjName +"/"); final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"/"); log.info("MessageFiles: " + msgFiles.size()); diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 4ff7b50..1f9658c 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,7 +2,7 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 100L; + public static final long SECONDS_TO_WAIT = 300L; // public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. From 4c680d91a8e89d3684c0b013a1b306ae4d37a7d7 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 10 Feb 2018 15:16:14 +0100 Subject: [PATCH 008/127] longer timeout --- src/main/java/edu/lu/uni/serval/config/Configuration.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 1f9658c..816221f 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,7 +2,7 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 300L; + public static final long SECONDS_TO_WAIT = 900L; // public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. From a5f41de1a2454724794322e40b468cbcbccbb6fa Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 10 Feb 2018 15:35:51 +0100 Subject: [PATCH 009/127] case sensitive --- .../edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index ff4015c..7378af2 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -100,7 +100,7 @@ public class AkkaParser2 { String fileName = revFile.getName(); File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file // fileName = fileName.replace(".java", ".txt"); - File diffentryFile = new File(gumTreeInput + "diffentries/" + fileName); // DiffEntry file + File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); msgFile.setPositionFile(positionFile); From 6b00aabc271d2866727b6f426c28dc1ebaccd571 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 15 Feb 2018 14:45:03 +0100 Subject: [PATCH 010/127] line number change wip --- .../violations/FixedViolationHunkParser.java | 2 +- .../violations/TestHunkParser.java | 17 +++--- .../MultipleThreadsParser/AkkaParser2.java | 2 +- .../lu/uni/serval/config/Configuration.java | 4 +- .../regroup/HierarchicalRegrouperForC.java | 11 ++-- .../gumtree/regroup/HunkActionFilter.java | 55 +++++++++++++++++-- 6 files changed, 68 insertions(+), 23 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 1804185..b8d37f4 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -53,7 +53,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { //Filter out the modify actions, which are not in the DiffEntry hunks. HunkActionFilter hunkFilter = new HunkActionFilter(); - List selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile); + List selectedPatchHunks = hunkFilter.filterActionsByLineNumber4C(diffentryHunks, actionSets, revFile, prevFile); for (DiffEntryHunk patchHunk : selectedPatchHunks) { List hunkActionSets = patchHunk.getActionSets(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index a370e99..341ce17 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -28,7 +28,8 @@ public class TestHunkParser { public static void main(String[] args) { // input data - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); + String pjName = "linux"; + final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"/"); System.out.println(msgFiles.size()); // output path @@ -38,11 +39,11 @@ public class TestHunkParser { final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE; final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE; - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - FileHelper.deleteDirectory(alarmTypesFilePath); +// FileHelper.deleteDirectory(editScriptsFilePath); +// FileHelper.deleteDirectory(patchesSourceCodeFilePath); +// FileHelper.deleteDirectory(buggyTokensFilePath); +// FileHelper.deleteDirectory(editScriptSizesFilePath); +// FileHelper.deleteDirectory(alarmTypesFilePath); StringBuilder astEditScripts = new StringBuilder(); StringBuilder tokens = new StringBuilder(); @@ -120,7 +121,7 @@ public class TestHunkParser { List msgFiles = new ArrayList<>(); for (File revFile : revFiles) { - if (revFile.getName().endsWith(".java")) { +// if (revFile.getName().endsWith(".java")) { String fileName = revFile.getName(); File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file fileName = fileName.replace(".java", ".txt"); @@ -129,7 +130,7 @@ public class TestHunkParser { MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); msgFile.setPositionFile(positionFile); msgFiles.add(msgFile); - } +// } } return msgFiles; diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index 7378af2..a7df66c 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -46,7 +46,7 @@ public class AkkaParser2 { - String pjName = "linux-stable"; + String pjName = "linux"; // String rootPath = "/Volumes/data/bugStudy/"; // String DATASET_FILE_PATH = rootPath + "/dataset/GumTreeInput/" + pjName; // String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 816221f..d04c138 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -3,13 +3,13 @@ package edu.lu.uni.serval.config; public class Configuration { public static final long SECONDS_TO_WAIT = 900L; - + // public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. public static int HUNK_SIZE = 10; // The limitation of source code lines of each DiffEntry, which will be selected as training data. public static final String BUGGY_TREE_SIGNAL = "BUGGY_TREE###"; // The starting signal of the tree of buggy source code . - public static final String PATCH_SIGNAL = "PATCH###"; // The starting signal of each patch. + public static final String PATCH_SIGNAL = "PATCH###"; // Th starting signal of each patch. // input path of GumTree. (i.e., Fix patterns parser) public static final String GUM_TREE_INPUT = ROOT_PATH + "GumTreeInput/";// Buggy version file VS. Fixing version file, (DiffEntry File) diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index 268d014..d31dd40 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -20,8 +20,8 @@ public class HierarchicalRegrouperForC { public static void main(String[] args) { GumTreeComparer com = new GumTreeComparer(); - File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_7779c5_545624_drivers#gpu#drm#drm_dp_helper.c"); - File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/7779c5_545624_drivers#gpu#drm#drm_dp_helper.c"); + File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c"); + File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c"); List action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2); List actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action); System.out.println(actionSet); @@ -241,9 +241,10 @@ public class HierarchicalRegrouperForC { private boolean isStatement(ITree tree) { int nodeType = tree.getType(); - if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100 - || nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300 - || 260300 == nodeType || nodeType == 460000) {// TODO +// if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100 +// || nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300 +// || 260300 == nodeType || nodeType == 460000) {// TODO + if(nodeType == 460000){ return true; } return false; diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java index 6dbe24f..c564d20 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java @@ -351,7 +351,53 @@ public class HunkActionFilter { } return selectedViolations; } - + + + public List filterActionsByLineNumber4C(List diffentryHunks, + List actionSets, File revFile, File prevFile) { + + List selectedViolations = new ArrayList<>(); + + + for (DiffEntryHunk diffentryHunk : diffentryHunks) { +// int violationEndLine = violationStartLine + diffentryHunk.getBugRange(); + int bugHunkStartLine = diffentryHunk.getBugLineStartNum(); + int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1; + int fixHunkStartLine = diffentryHunk.getFixLineStartNum(); + int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1; + + for (HierarchicalActionSet actionSet : actionSets) { + int actionBugStartLine = actionSet.getBugStartLineNum(); +// if (actionBugStartLine == 0) { +// actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); +// } + int actionBugEndLine = actionSet.getBugEndLineNum(); + int actionFixStartLine = actionSet.getFixStartLineNum(); + int actionFixEndLine = actionSet.getFixEndLineNum(); + + String actionStr = actionSet.getActionString(); + if (actionStr.startsWith("INS")) { + if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) { + if (actionBugStartLine != 0) { + diffentryHunk.getActionSets().add(actionSet); + } + } + } else { + if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) { + diffentryHunk.getActionSets().add(actionSet); + } + } + } + + + if (diffentryHunk.getActionSets().size() > 0) { + selectedViolations.add(diffentryHunk); + } + } + return selectedViolations; + } + + /** * Filter out the modify actions, which are not in the DiffEntry hunks, with considering the same parent node. * @@ -440,11 +486,8 @@ public class HunkActionFilter { // ITree parent = null; // List actionSetsWithSameParent = new ArrayList<>(); //TODO for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - int actionBugEndLine = actionSet.getBugEndLineNum(); + int actionBugStartLine = actionSet.getStartPosition(); + int actionBugEndLine = actionSet.getLength(); int actionFixStartLine = actionSet.getFixStartLineNum(); int actionFixEndLine = actionSet.getFixEndLineNum(); From d31e9f9e2144cec16c89b1c8271571d37dbee266 Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Thu, 15 Feb 2018 15:26:42 +0100 Subject: [PATCH 011/127] Update regrouper for GumTree output of C code. --- .../violations/FixedViolationHunkParser.java | 2 +- .../regroup/HierarchicalRegrouperForC.java | 10 +++--- .../gumtree/regroup/HunkActionFilter.java | 31 ++++++++++--------- 3 files changed, 22 insertions(+), 21 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index b8d37f4..b6fdac3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -53,7 +53,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { //Filter out the modify actions, which are not in the DiffEntry hunks. HunkActionFilter hunkFilter = new HunkActionFilter(); - List selectedPatchHunks = hunkFilter.filterActionsByLineNumber4C(diffentryHunks, actionSets, revFile, prevFile); + List selectedPatchHunks = hunkFilter.matchActionsByDiffEntryForC(diffentryHunks, actionSets, revFile, prevFile); for (DiffEntryHunk patchHunk : selectedPatchHunks) { List hunkActionSets = patchHunk.getActionSets(); diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index d31dd40..57aa788 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -29,14 +29,14 @@ public class HierarchicalRegrouperForC { List actionSets = new ArrayList<>(); - public List regroupGumTreeResults(List actions) { + public List regroupGumTreeResults(List actionsArgu) { /* * First, sort actions by their positions. */ -// List actions = new ListSorter(actionsArgu).sortAscending(); -// if (actions == null) { -// actions = actionsArgu; -// } + List actions = new ListSorter(actionsArgu).sortAscending(); + if (actions == null) { + actions = actionsArgu; + } /* * Second, group actions by their positions. diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java index c564d20..fb1aa0b 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java @@ -352,37 +352,38 @@ public class HunkActionFilter { return selectedViolations; } - - public List filterActionsByLineNumber4C(List diffentryHunks, + /** + * Match hierarchical actions with code change diffs for C code. + * + * @param diffentryHunks + * @param actionSets + * @param revFile + * @param prevFile + * @return + */ + public List matchActionsByDiffEntryForC(List diffentryHunks, List actionSets, File revFile, File prevFile) { List selectedViolations = new ArrayList<>(); - for (DiffEntryHunk diffentryHunk : diffentryHunks) { -// int violationEndLine = violationStartLine + diffentryHunk.getBugRange(); int bugHunkStartLine = diffentryHunk.getBugLineStartNum(); int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1; int fixHunkStartLine = diffentryHunk.getFixLineStartNum(); int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1; for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); -// if (actionBugStartLine == 0) { -// actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); -// } - int actionBugEndLine = actionSet.getBugEndLineNum(); - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - String actionStr = actionSet.getActionString(); if (actionStr.startsWith("INS")) { + int actionFixStartLine = actionSet.getBugStartLineNum(); + int actionFixEndLine = actionSet.getBugEndLineNum(); if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) { - if (actionBugStartLine != 0) { - diffentryHunk.getActionSets().add(actionSet); - } + diffentryHunk.getActionSets().add(actionSet); } } else { + int actionBugStartLine = actionSet.getBugStartLineNum(); + int actionBugEndLine = actionSet.getBugEndLineNum(); + if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) { diffentryHunk.getActionSets().add(actionSet); } From 4c80cb43130290a487d7922e7e1f11acc5560a84 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 15 Feb 2018 15:59:21 +0100 Subject: [PATCH 012/127] start position and lenght for actions --- .../violations/FixedViolationHunkParser.java | 3 +++ .../gumtree/regroup/HierarchicalRegrouperForC.java | 9 ++++----- .../lu/uni/serval/gumtree/regroup/HunkActionFilter.java | 8 ++++---- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index b6fdac3..392b10b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -69,6 +69,9 @@ public class FixedViolationHunkParser extends FixedViolationParser { int bugEndPosition = 0; int fixEndPosition = 0; for (HierarchicalActionSet hunkActionSet : hunkActionSets) { + + + //TODO FIX ME int actionBugStart = hunkActionSet.getBugStartLineNum(); int actionBugEnd = hunkActionSet.getBugEndLineNum(); int actionFixStart = hunkActionSet.getFixStartLineNum(); diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index 57aa788..34db1c8 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -241,11 +241,10 @@ public class HierarchicalRegrouperForC { private boolean isStatement(ITree tree) { int nodeType = tree.getType(); -// if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100 -// || nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300 -// || 260300 == nodeType || nodeType == 460000) {// TODO - if(nodeType == 460000){ - return true; + if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100 + || nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300 + || 260300 == nodeType || nodeType == 460000) {// TODO + return true; } return false; } diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java index fb1aa0b..a9ac36b 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java @@ -375,14 +375,14 @@ public class HunkActionFilter { for (HierarchicalActionSet actionSet : actionSets) { String actionStr = actionSet.getActionString(); if (actionStr.startsWith("INS")) { - int actionFixStartLine = actionSet.getBugStartLineNum(); - int actionFixEndLine = actionSet.getBugEndLineNum(); + int actionFixStartLine = actionSet.getStartPosition(); + int actionFixEndLine = actionSet.getLength(); if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) { diffentryHunk.getActionSets().add(actionSet); } } else { - int actionBugStartLine = actionSet.getBugStartLineNum(); - int actionBugEndLine = actionSet.getBugEndLineNum(); + int actionBugStartLine = actionSet.getStartPosition(); + int actionBugEndLine = actionSet.getLength(); if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) { diffentryHunk.getActionSets().add(actionSet); From a9715cdc96a6bac9330962872e544b28affd5830 Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Thu, 15 Feb 2018 23:48:02 +0100 Subject: [PATCH 013/127] Match change actions for diffs of C code. --- .../violations/FixedViolationHunkParser.java | 13 +---- .../regroup/HierarchicalRegrouperForC.java | 50 +++++++++++++++---- .../gumtree/regroup/HunkActionFilter.java | 16 +++--- 3 files changed, 49 insertions(+), 30 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 392b10b..78bbc01 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -53,7 +53,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { //Filter out the modify actions, which are not in the DiffEntry hunks. HunkActionFilter hunkFilter = new HunkActionFilter(); - List selectedPatchHunks = hunkFilter.matchActionsByDiffEntryForC(diffentryHunks, actionSets, revFile, prevFile); + List selectedPatchHunks = hunkFilter.matchActionsByDiffEntryForC(diffentryHunks, actionSets); for (DiffEntryHunk patchHunk : selectedPatchHunks) { List hunkActionSets = patchHunk.getActionSets(); @@ -69,8 +69,6 @@ public class FixedViolationHunkParser extends FixedViolationParser { int bugEndPosition = 0; int fixEndPosition = 0; for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - - //TODO FIX ME int actionBugStart = hunkActionSet.getBugStartLineNum(); int actionBugEnd = hunkActionSet.getBugEndLineNum(); @@ -102,11 +100,6 @@ public class FixedViolationHunkParser extends FixedViolationParser { continue; } - if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions. - // get the exact buggy code by violation's position. TODO later - } - -// if (children.size() == 0) continue; boolean isPureInsert = false; if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) { bugStartLine = patchHunk.getBugLineStartNum(); @@ -141,10 +134,6 @@ public class FixedViolationHunkParser extends FixedViolationParser { String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; - //TODO uncomment the line below for more detailed gumtree input -// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; -// if (noUpdate(editScriptTokens)) { -// } this.patchesSourceCode += info; this.sizes += size + "\n"; diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index 34db1c8..d98ef8f 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -29,14 +29,14 @@ public class HierarchicalRegrouperForC { List actionSets = new ArrayList<>(); - public List regroupGumTreeResults(List actionsArgu) { + public List regroupGumTreeResults(List actions) { /* * First, sort actions by their positions. */ - List actions = new ListSorter(actionsArgu).sortAscending(); - if (actions == null) { - actions = actionsArgu; - } +// List actions = new ListSorter(actionsArgu).sortAscending(); +// if (actions == null) { +// actions = actionsArgu; +// } /* * Second, group actions by their positions. @@ -82,10 +82,42 @@ public class HierarchicalRegrouperForC { private HierarchicalActionSet createActionSet(Action act, Action parentAct, HierarchicalActionSet parent) { HierarchicalActionSet actionSet = new HierarchicalActionSet(); actionSet.setAction(act); - actionSet.setActionString(parseAction(act.toString())); + String actStr = parseAction(act.toString()); + actionSet.setActionString(actStr); actionSet.setParentAction(parentAct); actionSet.setNode(act.getNode()); actionSet.setParent(parent); + + int bugStartLineNum = 0; + int bugEndLineNum = 0; + int fixStartLineNum = 0; + int fixEndLineNum = 0; + if (actStr.startsWith("INS")) { + Insert insert = (Insert) act; +// int pos = insert.getPos();//index position of the new node in the children array list of its corresponding old parent node. + ITree newTree = insert.getNode(); + fixStartLineNum = newTree.getPos(); + fixEndLineNum = newTree.getLength(); + } else { + ITree tree = act.getNode(); + bugStartLineNum = tree.getPos(); + bugEndLineNum = tree.getLength(); + if (actStr.startsWith("UPD")) { + Update update = (Update) act; + ITree newTree = update.getNewNode(); + fixStartLineNum = newTree.getPos(); + fixEndLineNum = newTree.getLength(); + } else if (actStr.startsWith("MOV")) { + Move update = (Move) act; + ITree newTree = update.getNewNode(); + fixStartLineNum = newTree.getPos(); + fixEndLineNum = newTree.getLength(); + } + } + actionSet.setBugStartLineNum(bugStartLineNum); + actionSet.setBugEndLineNum(bugEndLineNum); + actionSet.setFixStartLineNum(fixStartLineNum); + actionSet.setFixEndLineNum(fixEndLineNum); return actionSet; } @@ -132,7 +164,7 @@ public class HierarchicalRegrouperForC { break; } else { if (isPossibileSubAction(action, act)) { - // SubAction range： startPosition2 <= startPosition && startPosition + length <= startPosition2 + length2 + // SubAction range： startPosition2 <= startPosition && length <= length2 addToActionSets(actionSet, parentAct, actSet.getSubActions()); } } @@ -148,7 +180,7 @@ public class HierarchicalRegrouperForC { int startPosition2 = parent.getPosition(); int length2 = parent.getLength(); - if (!(startPosition2 <= startPosition && startPosition + length <= startPosition2 + length2)) { + if (!(startPosition2 <= startPosition && length <= length2)) { // when act is not the sub-set of action. return false; } @@ -177,7 +209,7 @@ public class HierarchicalRegrouperForC { return true; } else { if (isPossibileSubAction(action, act)) { - // SubAction range： startPosition2 <= startPosition && startPosition + length <= startP + length2 + // SubAction range: startPosition2 <= startPosition && startPosition + length <= startP + length2 List subActionSets = actionSet.getSubActions(); if (subActionSets.size() > 0) { boolean added = addToAactionSet(act, parentAct, subActionSets); diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java index a9ac36b..f986f33 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java @@ -361,8 +361,7 @@ public class HunkActionFilter { * @param prevFile * @return */ - public List matchActionsByDiffEntryForC(List diffentryHunks, - List actionSets, File revFile, File prevFile) { + public List matchActionsByDiffEntryForC(List diffentryHunks, List actionSets) { List selectedViolations = new ArrayList<>(); @@ -375,22 +374,21 @@ public class HunkActionFilter { for (HierarchicalActionSet actionSet : actionSets) { String actionStr = actionSet.getActionString(); if (actionStr.startsWith("INS")) { - int actionFixStartLine = actionSet.getStartPosition(); - int actionFixEndLine = actionSet.getLength(); - if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) { + int actionFixStartLine = actionSet.getFixStartLineNum(); + int actionFixEndLine = actionSet.getFixEndLineNum(); + if (fixHunkStartLine <= actionFixEndLine && actionFixStartLine <= fixHunkEndLine ) { diffentryHunk.getActionSets().add(actionSet); } } else { - int actionBugStartLine = actionSet.getStartPosition(); - int actionBugEndLine = actionSet.getLength(); + int actionBugStartLine = actionSet.getBugStartLineNum(); + int actionBugEndLine = actionSet.getBugEndLineNum(); - if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) { + if (bugHunkStartLine <= actionBugEndLine && actionBugStartLine <= bugHunkEndLine) { diffentryHunk.getActionSets().add(actionSet); } } } - if (diffentryHunk.getActionSets().size() > 0) { selectedViolations.add(diffentryHunk); } From c6fa20645beea3ed604a0bab1a562147cc07e94f Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Fri, 16 Feb 2018 10:57:23 +0100 Subject: [PATCH 014/127] Rename a parameter. --- .../java/edu/lu/uni/serval/FixPatternParser/Parser.java | 7 ++++--- .../violations/FixedViolationHunkParser.java | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java index f5eb979..29ea314 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java @@ -148,6 +148,7 @@ public abstract class Parser implements ParserInterface { } private String handleSimpleNameNode(String singleEdit, String actionStr, int index) { + // TODO if (singleEdit.endsWith("SimpleName")) { actionStr = actionStr.substring(index + 2); if (actionStr.startsWith("MethodName")) { @@ -430,7 +431,7 @@ public abstract class Parser implements ParserInterface { return editScripts; } - private String getActionString(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition, String startStr) { + private String getActionString(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition, String hierarchicalLabel) { String editScripts = ""; String actionStr = actionSet.getActionString(); @@ -439,7 +440,7 @@ public abstract class Parser implements ParserInterface { singleEdit = handleSimpleNameNode(singleEdit, actionStr, index); - editScripts += startStr + singleEdit + "\n"; + editScripts += hierarchicalLabel + singleEdit + "\n"; for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) { int position = subActionSet.getAction().getPosition(); @@ -447,7 +448,7 @@ public abstract class Parser implements ParserInterface { if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) { continue; } - editScripts += getActionString(subActionSet, bugEndPosition, fixEndPosition, startStr + "---"); + editScripts += getActionString(subActionSet, bugEndPosition, fixEndPosition, hierarchicalLabel + "---"); } return editScripts; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 78bbc01..9ea9bb8 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -108,7 +108,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { // continue; } if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE && !isPureInsert) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { -// continue; +// continue; //TODO filter out the } From a1e96275660bdaa017d307b4e830f6f40b0e9bd4 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 21 Feb 2018 16:31:58 +0100 Subject: [PATCH 015/127] initial commit --- FixPatternMiner.iml | 1 - .../uni/serval/FixPatternParser/Parser.java | 3 +- .../violations/FixedViolationHunkParser.java | 50 ++-- .../violations/FixedViolationParser.java | 19 +- .../violations/TestHunkParser.java | 217 ++++++++++-------- .../MultipleThreadsParser/AkkaParser2.java | 4 +- .../uni/serval/diffentry/DiffEntryReader.java | 2 + .../edu/lu/uni/serval/diffentry/RegExp.java | 2 +- 8 files changed, 167 insertions(+), 131 deletions(-) diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index 1f288a8..2df3bc9 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -42,7 +42,6 @@ - diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java index 29ea314..d7f7dfb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java @@ -36,7 +36,8 @@ public abstract class Parser implements ParserInterface { protected List parseChangedSourceCodeWithGumTree(File prevFile, File revFile) { List actionSets = new ArrayList<>(); // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile); + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); +// List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile); if (gumTreeResults != null && gumTreeResults.size() > 0) { // Regroup GumTre results. List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 9ea9bb8..74aa543 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -49,17 +49,17 @@ public class FixedViolationHunkParser extends FixedViolationParser { // type = "#NoStatementChange:"; // } } else { - List diffentryHunks = new DiffEntryReader().readHunks2(diffentryFile); + List diffentryHunks = new DiffEntryReader().readHunks3(diffentryFile); //Filter out the modify actions, which are not in the DiffEntry hunks. HunkActionFilter hunkFilter = new HunkActionFilter(); - List selectedPatchHunks = hunkFilter.matchActionsByDiffEntryForC(diffentryHunks, actionSets); - + List selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile); + for (DiffEntryHunk patchHunk : selectedPatchHunks) { - List hunkActionSets = patchHunk.getActionSets(); + List hunkActionSets = patchHunk.getActionSets(); // multiple UPD, and some UPD contain other UPD. removeOverlapperdUPD(hunkActionSets); - + // Range of buggy source code int bugStartLine = 0; int bugEndLine = 0; @@ -69,7 +69,6 @@ public class FixedViolationHunkParser extends FixedViolationParser { int bugEndPosition = 0; int fixEndPosition = 0; for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - //TODO FIX ME int actionBugStart = hunkActionSet.getBugStartLineNum(); int actionBugEnd = hunkActionSet.getBugEndLineNum(); int actionFixStart = hunkActionSet.getFixStartLineNum(); @@ -93,13 +92,18 @@ public class FixedViolationHunkParser extends FixedViolationParser { fixEndPosition = hunkActionSet.getFixEndPosition(); } } - + if (fixStartLine == 0 && bugStartLine == 0) { this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; this.nullMappingGumTreeResult ++; continue; } - + + if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions. + // get the exact buggy code by violation's position. TODO later + } + +// if (children.size() == 0) continue; boolean isPureInsert = false; if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) { bugStartLine = patchHunk.getBugLineStartNum(); @@ -107,13 +111,15 @@ public class FixedViolationHunkParser extends FixedViolationParser { isPureInsert = true; // continue; } - if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE && !isPureInsert) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { -// continue; //TODO filter out the +// if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE ) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { +// continue; //TODO hunk size +// } + if(patchHunk.getBuggyHunkSize() > Configuration.HUNK_SIZE || patchHunk.getFixedHunkSize() > Configuration.HUNK_SIZE){ + continue; } - - + /** - * Select edit scripts for deep learning. + * Select edit scripts for deep learning. * Edit scripts will be used to mine common fix patterns. */ // 1. First level: AST node type. @@ -122,8 +128,8 @@ public class FixedViolationHunkParser extends FixedViolationParser { System.err.println("===+++===: " + revFile.getName() + ":" +patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize()); } // 2. source code: raw tokens - // 3. abstract identifiers: - // 4. semi-source code: + // 3. abstract identifiers: + // 4. semi-source code: String[] editScriptTokens = astEditScripts.split(" "); int size = editScriptTokens.length; if (size == 1) { @@ -131,17 +137,21 @@ public class FixedViolationHunkParser extends FixedViolationParser { this.unfixedViolations += "#NullMatchedGumTreeResult1:" + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; continue; } - + String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; +//TODO uncomment the line below for more detailed gumtree input. + // String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; +// if (noUpdate(editScriptTokens)) { +// } this.patchesSourceCode += info; this.sizes += size + "\n"; this.astEditScripts += astEditScripts + "\n"; - -// SimpleTree simpleTree = getBuggyCodeTree(patchHunk, bugEndPosition, prevFile, bugStartLine, bugEndLine); -// String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); -// this.tokensOfSourceCode += tokens + "\n"; + + SimpleTree simpleTree = getBuggyCodeTree(patchHunk, bugEndPosition, prevFile, bugStartLine, bugEndLine); + String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); + this.tokensOfSourceCode += tokens + "\n"; } } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java index 272560a..a94c1c0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java @@ -12,19 +12,18 @@ import com.github.gumtreediff.actions.model.Action; import edu.lu.uni.serval.FixPatternParser.Parser; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; - -import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouperForC; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; /** * Parse fix patterns with GumTree. - * + * * @author kui.liu * */ public class FixedViolationParser extends Parser { - + /* * ResultType: * 0: normal GumTree results. @@ -34,16 +33,16 @@ public class FixedViolationParser extends Parser { * 4: useless violations */ public int resultType = 0; - + protected String violationTypes = ""; - + @Override public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { } - + /** * Regroup GumTree results without remove the modification of variable names. - * + * * @param prevFile * @param revFile * @return @@ -51,7 +50,7 @@ public class FixedViolationParser extends Parser { protected List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { List actionSets = new ArrayList<>(); // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile); + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); if (gumTreeResults == null) { this.resultType = 1; return null; @@ -60,7 +59,7 @@ public class FixedViolationParser extends Parser { return actionSets; } else { // Regroup GumTre results. - List allActionSets = new HierarchicalRegrouperForC().regroupGumTreeResults(gumTreeResults); + List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); // for (HierarchicalActionSet actionSet : allActionSets) { // String astNodeType = actionSet.getAstNodeType(); // if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 341ce17..9837afb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -6,111 +6,132 @@ import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; +import java.util.*; import java.util.concurrent.ExecutionException; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Future; import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeoutException; +import java.util.stream.Collectors; +import java.util.stream.Stream; import edu.lu.uni.serval.FixPatternParser.RunnableParser; import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.utils.FileHelper; +import org.eclipse.jgit.revwalk.RevCommit; public class TestHunkParser { public static void main(String[] args) { // input data - String pjName = "linux"; - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"/"); - System.out.println(msgFiles.size()); + File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); - // output path - final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE; - final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE; - final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKENS_FILE; - final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE; - final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE; + List targetList = new ArrayList(); + for (File f:folders){ + for(File f1 :f.listFiles()){ + if (!f1.getName().startsWith(".")){ + targetList.add(f1); + } + } + } -// FileHelper.deleteDirectory(editScriptsFilePath); -// FileHelper.deleteDirectory(patchesSourceCodeFilePath); -// FileHelper.deleteDirectory(buggyTokensFilePath); -// FileHelper.deleteDirectory(editScriptSizesFilePath); -// FileHelper.deleteDirectory(alarmTypesFilePath); - - StringBuilder astEditScripts = new StringBuilder(); - StringBuilder tokens = new StringBuilder(); - StringBuilder sizes = new StringBuilder(); - StringBuilder patches = new StringBuilder(); - StringBuilder alarmTypes = new StringBuilder(); - - int a = 0; + for (File target : targetList) { + final List msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" + System.out.println(msgFiles.size()); + if(msgFiles.size() == 0) + continue; + String pjName = target.getName(); + // output path + String GUM_TREE_OUTPUT = Configuration.ROOT_PATH + pjName + "/"; + final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; + final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; + final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; + final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; + final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; + + + + FileHelper.deleteDirectory(editScriptsFilePath); + FileHelper.deleteDirectory(patchesSourceCodeFilePath); + FileHelper.deleteDirectory(buggyTokensFilePath); + FileHelper.deleteDirectory(editScriptSizesFilePath); + FileHelper.deleteDirectory(alarmTypesFilePath); + + StringBuilder astEditScripts = new StringBuilder(); + StringBuilder tokens = new StringBuilder(); + StringBuilder sizes = new StringBuilder(); + StringBuilder patches = new StringBuilder(); + StringBuilder alarmTypes = new StringBuilder(); + + int a = 0; // int counter = 0; - for (MessageFile msgFile : msgFiles) { - FixedViolationHunkParser parser = new FixedViolationHunkParser(); - - final ExecutorService executor = Executors.newSingleThreadExecutor(); - // schedule the work - final Future future = executor.submit(new RunnableParser(msgFile.getPrevFile(), - msgFile.getRevFile(), msgFile.getDiffEntryFile(), parser)); - try { - // where we wait for task to complete - future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); - String editScripts = parser.getAstEditScripts(); - if (!editScripts.equals("")) { - astEditScripts.append(editScripts); - tokens.append(parser.getTokensOfSourceCode()); - sizes.append(parser.getSizes()); - patches.append(parser.getPatchesSourceCode()); - alarmTypes.append(parser.getAlarmTypes()); + for (MessageFile msgFile : msgFiles) { + FixedViolationHunkParser parser = new FixedViolationHunkParser(); + + final ExecutorService executor = Executors.newSingleThreadExecutor(); + // schedule the work + final Future future = executor.submit(new RunnableParser(msgFile.getPrevFile(), + msgFile.getRevFile(), msgFile.getDiffEntryFile(), parser)); + try { + // where we wait for task to complete + future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); + String editScripts = parser.getAstEditScripts(); + if (!editScripts.equals("")) { + astEditScripts.append(editScripts); + tokens.append(parser.getTokensOfSourceCode()); + sizes.append(parser.getSizes()); + patches.append(parser.getPatchesSourceCode()); + alarmTypes.append(parser.getAlarmTypes()); + + a++; + if (a % 10 == 0) { + FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); + FileHelper.outputToFile(buggyTokensFilePath, tokens, true); + FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); + FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); + FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); + astEditScripts.setLength(0); + tokens.setLength(0); + sizes.setLength(0); + patches.setLength(0); + alarmTypes.setLength(0); + System.out.println("Finish of parsing " + a + " files......"); + } + } + } catch (TimeoutException e) { + err.println("task timed out"); + future.cancel(true /* mayInterruptIfRunning */); + } catch (InterruptedException e) { + err.println("task interrupted"); + } catch (ExecutionException e) { + err.println("task aborted"); + } finally { + executor.shutdownNow(); + } + } + + FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); + FileHelper.outputToFile(buggyTokensFilePath, tokens, true); + FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); + FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); + FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); + astEditScripts.setLength(0); + tokens.setLength(0); + sizes.setLength(0); + patches.setLength(0); + alarmTypes.setLength(0); + System.out.println(a); - a ++; - if (a % 100 == 0) { - FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); - FileHelper.outputToFile(buggyTokensFilePath, tokens, true); - FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); - FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); - FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); - astEditScripts.setLength(0); - tokens.setLength(0); - sizes.setLength(0); - patches.setLength(0); - alarmTypes.setLength(0); - System.out.println("Finish of parsing " + a + " files......"); - } - } - } catch (TimeoutException e) { - err.println("task timed out"); - future.cancel(true /* mayInterruptIfRunning */ ); - } catch (InterruptedException e) { - err.println("task interrupted"); - } catch (ExecutionException e) { - err.println("task aborted"); - } finally { - executor.shutdownNow(); - } - } - - FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); - FileHelper.outputToFile(buggyTokensFilePath, tokens, true); - FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); - FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); - FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); - astEditScripts.setLength(0); - tokens.setLength(0); - sizes.setLength(0); - patches.setLength(0); - alarmTypes.setLength(0); - System.out.println(a); - // classifyByAlarmTypes(); + } } @@ -119,21 +140,25 @@ public class TestHunkParser { File revFilesPath = new File(inputPath + "revFiles/"); File[] revFiles = revFilesPath.listFiles(); // project folders List msgFiles = new ArrayList<>(); - - for (File revFile : revFiles) { + if (revFiles.length >= 0) { + for (File revFile : revFiles) { // if (revFile.getName().endsWith(".java")) { - String fileName = revFile.getName(); - File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file - fileName = fileName.replace(".java", ".txt"); - File diffentryFile = new File(gumTreeInput + "diffentries/" + fileName); // DiffEntry file - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file - MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); + String fileName = revFile.getName(); + File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file + fileName = fileName.replace(".java", ".txt"); + File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file + File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); + msgFile.setPositionFile(positionFile); + msgFiles.add(msgFile); // } - } - - return msgFiles; + } + + return msgFiles; + } + else{ + return null; + } } public static void classifyByAlarmTypes() { diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index a7df66c..016746a 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -52,8 +52,8 @@ public class AkkaParser2 { // String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; log.info(pjName); // input data - log.info("Get the input data..." + Configuration.GUM_TREE_INPUT +pjName +"/"); - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"/"); + log.info("Get the input data..." + Configuration.GUM_TREE_INPUT ); + final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); log.info("MessageFiles: " + msgFiles.size()); // output path diff --git a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java b/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java index c0d9693..0e4806b 100644 --- a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java +++ b/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java @@ -6,6 +6,7 @@ import java.io.IOException; import java.io.StringReader; import java.util.ArrayList; import java.util.List; +import java.util.regex.Pattern; import edu.lu.uni.serval.utils.FileHelper; @@ -101,6 +102,7 @@ public class DiffEntryReader { while ((line = reader.readLine()) != null) { if (RegExp.filterSignal(line.trim())) { +// line = Pattern.compile("^@@\\s\\-\\d+,*\\d*\\s\\+\\d+,*\\d*\\s@@").split(line)[1]; sourceCode = true; if (hunk.length() > 0) { if (startLine > 0) { diff --git a/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java b/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java index ebcf9a8..b1d017d 100644 --- a/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java +++ b/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java @@ -9,7 +9,7 @@ public class RegExp { public static boolean filterSignal(String string) { boolean flag = false; - + Matcher res = pattern.matcher(string); if (res.matches()) { flag = true; From 832fdc0bd6f68b61a5fa7ce44f778cb1d2e68ba9 Mon Sep 17 00:00:00 2001 From: Kui LIU Date: Wed, 21 Feb 2018 17:34:21 +0100 Subject: [PATCH 016/127] Rename variables. --- .../violations/FixedViolationHunkParser.java | 91 +++++++++---------- .../serval/gumtree/regroup/SimplifyTree.java | 65 ++++++++++++- 2 files changed, 102 insertions(+), 54 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 74aa543..29bbcde 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -2,17 +2,17 @@ package edu.lu.uni.serval.FixPatternParser.violations; import java.io.File; import java.util.ArrayList; +import java.util.HashMap; import java.util.List; +import java.util.Map; import com.github.gumtreediff.tree.ITree; -import edu.lu.uni.serval.FixPatternParser.Tokenizer; import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.diffentry.DiffEntryHunk; import edu.lu.uni.serval.diffentry.DiffEntryReader; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; @@ -145,13 +145,13 @@ public class FixedViolationHunkParser extends FixedViolationParser { // if (noUpdate(editScriptTokens)) { // } + String canonicalVariableNames = getBuggyCodeTree(patchHunk, prevFile, revFile); this.patchesSourceCode += info; - this.sizes += size + "\n"; - this.astEditScripts += astEditScripts + "\n"; - - SimpleTree simpleTree = getBuggyCodeTree(patchHunk, bugEndPosition, prevFile, bugStartLine, bugEndLine); - String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); - this.tokensOfSourceCode += tokens + "\n"; + this.patchesSourceCode += "\nRenamed_Variables###:" + canonicalVariableNames; +// this.sizes += size + "\n"; +// this.astEditScripts += astEditScripts + "\n"; +// String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); +// this.tokensOfSourceCode += tokens + "\n"; } } } @@ -164,53 +164,44 @@ public class FixedViolationHunkParser extends FixedViolationParser { return scripts; } - private SimpleTree getBuggyCodeTree(DiffEntryHunk patchHunk, int bugEndPosition, File prevFile, int bugStartLine, int bugEndLine) { - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); + private String getBuggyCodeTree(DiffEntryHunk patchHunk, File prevFile, File revFile) { + int bugStartLine = patchHunk.getBugLineStartNum(); + int bugEndLine = bugStartLine + patchHunk.getBugRange() - 1; - int vStartLine = patchHunk.getBugLineStartNum(); - int vEndLine = vStartLine + patchHunk.getBuggyHunkSize() + 1; - if (bugStartLine < vStartLine && vEndLine < bugEndLine) { - ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, vStartLine, vEndLine); - parser.extract(); - List matchedTrees = parser.getViolationSourceCodeTrees(); - if (matchedTrees.size() > 0) { - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, simpleTree); - children.add(simpleT); - } + ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, bugStartLine, bugEndLine); + parser.extract(); + List matchedTrees = parser.getViolationSourceCodeTrees(); + Map renamedVariablesMap = new HashMap<>(); + Map canonicalVariables = new HashMap<>(); + if (matchedTrees.size() > 0) { + SimplifyTree st = new SimplifyTree(); + for (ITree matchedTree : matchedTrees) { + st.canonicalizeSourceCodeTree(matchedTree); } + renamedVariablesMap = st.canonicalVariableMap; + canonicalVariables = st.canonicalVariables; } - if (children.size() == 0) { - List hunkActionSets = patchHunk.getActionSets(); - /* - * Convert the ITree of buggy code to a simple tree. - * It will be used to compute the similarity. - */ - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - // TODO simplify buggy tree with buggy code. - /** - * Select edit scripts for deep learning. - * Edit scripts will be used to mine common fix patterns. - */ -// // 1. First level: AST node type. -// // 2. source code: raw tokens -// // 3. abstract identifiers: -// // 4. semi-source code: - SimplifyTree abstractIdentifier = new SimplifyTree(); - abstractIdentifier.abstractTree(hunkActionSet, bugEndPosition); - SimpleTree simpleT = hunkActionSet.getSimpleTree(); - if (simpleT == null) { // Failed to get the simple tree for INS actions. - continue; - } - children.add(simpleT); + + int fixStartLine = patchHunk.getFixLineStartNum(); + int fixEndLine = fixStartLine + patchHunk.getFixRange() - 1; + ViolationSourceCodeTree fixedParser = new ViolationSourceCodeTree(revFile, fixStartLine, fixEndLine); + fixedParser.extract(); + matchedTrees = fixedParser.getViolationSourceCodeTrees(); + if (matchedTrees.size() > 0) { + SimplifyTree st = new SimplifyTree(); + st.canonicalVariableMap = renamedVariablesMap; + st.canonicalVariables = canonicalVariables; + for (ITree matchedTree : matchedTrees) { + st.canonicalizeSourceCodeTree(matchedTree); } + renamedVariablesMap = st.canonicalVariableMap; } - simpleTree.setChildren(children); - simpleTree.setParent(null); - return simpleTree; + + StringBuilder builder = new StringBuilder(); + for (Map.Entry entry : renamedVariablesMap.entrySet()) { + builder.append(entry.getKey()).append(" = ").append(entry.getValue()).append("\n"); + } + return builder.toString(); } private void removeOverlapperdUPD(List actionSets) { diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java index 3ccf138..3dac976 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java @@ -254,6 +254,44 @@ public class SimplifyTree { return simpleTree; } + public void canonicalizeSourceCodeTree(ITree tree) { + String label = tree.getLabel(); + String astNode = ASTNodeMap.map.get(tree.getType()); + + List children = tree.getChildren(); + if (children.size() > 0) { + if (astNode.endsWith("Type")) { + } else { + if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) { + if (label.startsWith("MethodName:")) { + } else if (label.startsWith("ClassName:")) { + } + } else { + } + for (ITree child : children) { + canonicalizeSourceCodeTree(child); + } + } + } else { + if (astNode.endsWith("Name")) { + // variableName, methodName, QualifiedName + if (label.startsWith("MethodName:")) { // + } else if (label.startsWith("ClassName:")) { + } else if (label.startsWith("Name:")) { + label = label.substring(5); + char firstChar = label.charAt(0); + if (Character.isUpperCase(firstChar)) { +// simpleTree.setNodeType("Name"); + } else {// variableName: + canonicalVariableName(label, tree); + } + } else {// variableName: + canonicalVariableName(label, tree); + } + } + } + } + public SimpleTree canonicalizeSourceCodeTree(ITree tree, SimpleTree parent, int bugEndPosition) { SimpleTree simpleTree = new SimpleTree(); @@ -430,6 +468,9 @@ public class SimplifyTree { return null; } + public Map canonicalVariableMap = new HashMap<>(); + public Map canonicalVariables = new HashMap<>(); + private String matchVariableDeclarationExpression(ITree variable, String label) { List children = variable.getChildren(); ITree type = null; @@ -442,8 +483,7 @@ public class SimplifyTree { ITree simpleName = child.getChild(0); if (simpleName.getLabel().equals(label)) { String typeStr = canonicalizeTypeStr(type.getLabel()); - label = typeStr.toLowerCase() + "Var"; - return label; + return canonicalizeVariable(label, typeStr); } } } @@ -458,8 +498,7 @@ public class SimplifyTree { if (child.getLabel().equals(label)) { ITree type = children.get(i - 1); String typeStr = canonicalizeTypeStr(type.getLabel()); - label = typeStr.toLowerCase() + "Var"; - return label; + return canonicalizeVariable(label, typeStr); } break; } @@ -467,6 +506,24 @@ public class SimplifyTree { return null; } + private String canonicalizeVariable(String label, String typeStr) { + String key = label + "_" + typeStr; + if (canonicalVariableMap.containsKey(key)) { + label = canonicalVariableMap.get(key); + } else { + label = typeStr.toLowerCase() + "Var"; + Integer num = canonicalVariables.get(label); + if (num == null) { + num = 0; + } + num ++; + canonicalVariables.put(label, num); + label += "" + num; + canonicalVariableMap.put(key, label); + } + return label; + } + private String canonicalizeTypeStr(String label) { String typeStr = label; int index1 = typeStr.indexOf("<"); From 257a5a6443acd38c874fb0cd14a17a50894a1c21 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 22 Feb 2018 15:47:22 +0100 Subject: [PATCH 017/127] minor modifications on canonical form --- .../violations/FixedViolationHunkParser.java | 11 ++++++----- .../lu/uni/serval/gumtree/regroup/SimplifyTree.java | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 29bbcde..7056ea0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -8,6 +8,7 @@ import java.util.Map; import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPatternParser.Tokenizer; import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.diffentry.DiffEntryHunk; import edu.lu.uni.serval.diffentry.DiffEntryReader; @@ -139,17 +140,17 @@ public class FixedViolationHunkParser extends FixedViolationParser { } String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; - String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; +// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; //TODO uncomment the line below for more detailed gumtree input. - // String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; + String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; // if (noUpdate(editScriptTokens)) { // } String canonicalVariableNames = getBuggyCodeTree(patchHunk, prevFile, revFile); this.patchesSourceCode += info; - this.patchesSourceCode += "\nRenamed_Variables###:" + canonicalVariableNames; -// this.sizes += size + "\n"; -// this.astEditScripts += astEditScripts + "\n"; + this.patchesSourceCode += "\nRenamed_Variables###:\n" + canonicalVariableNames; + this.sizes += size + "\n"; + this.astEditScripts += astEditScripts + "\n"; // String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); // this.tokensOfSourceCode += tokens + "\n"; } diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java index 3dac976..317bf18 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java @@ -507,7 +507,7 @@ public class SimplifyTree { } private String canonicalizeVariable(String label, String typeStr) { - String key = label + "_" + typeStr; + String key = label + ":" + typeStr; if (canonicalVariableMap.containsKey(key)) { label = canonicalVariableMap.get(key); } else { From 6d173a854b671b2ad64e88a7982aa8872438506c Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 13:31:09 +0100 Subject: [PATCH 018/127] testhunkparser --- pom.xml | 2 +- .../violations/TestHunkParser.java | 29 ++++++++++++------- 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/pom.xml b/pom.xml index 5f2acdd..81e805a 100644 --- a/pom.xml +++ b/pom.xml @@ -87,7 +87,7 @@ - edu.lu.uni.serval.MultipleThreadsParser.AkkaParser2 + edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 9837afb..95919c3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -27,30 +27,37 @@ public class TestHunkParser { public static void main(String[] args) { // input data - File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput"); + +// String rootPath = "/Users/anilkoyuncu/bugStudy"; + String rootPath = args[0]; + String inputPath = args[1]; + String outputPath = args[0] + "/GumTreeOutputBug/"; + + + File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List folders = stream .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); - List targetList = new ArrayList(); - for (File f:folders){ - for(File f1 :f.listFiles()){ - if (!f1.getName().startsWith(".")){ - targetList.add(f1); - } - } - } +// List targetList = new ArrayList(); +// for (File f:folders){ +// for(File f1 :f.listFiles()){ +// if (!f1.getName().startsWith(".")){ +// targetList.add(f1); +// } +// } +// } - for (File target : targetList) { + for (File target : folders) { final List msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" System.out.println(msgFiles.size()); if(msgFiles.size() == 0) continue; String pjName = target.getName(); // output path - String GUM_TREE_OUTPUT = Configuration.ROOT_PATH + pjName + "/"; + String GUM_TREE_OUTPUT = outputPath + pjName + "/"; final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; From 9d3b5fe4e3156016d115d312d9568042f6d3acb1 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 15:12:08 +0100 Subject: [PATCH 019/127] server config --- pom.xml | 2 +- .../MultipleThreadsParser/AkkaParser2.java | 26 +++++++++---------- 2 files changed, 13 insertions(+), 15 deletions(-) diff --git a/pom.xml b/pom.xml index 81e805a..5f2acdd 100644 --- a/pom.xml +++ b/pom.xml @@ -87,7 +87,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser + edu.lu.uni.serval.MultipleThreadsParser.AkkaParser2 diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index 016746a..a4f5472 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -40,27 +40,25 @@ public class AkkaParser2 { // hunkThreshold = 10; // } - Configuration.ROOT_PATH = inputRootPath; - log.info(Configuration.ROOT_PATH); - Configuration.HUNK_SIZE = hunkThreshold; +// Configuration.ROOT_PATH = inputRootPath; +// log.info(Configuration.ROOT_PATH); +// Configuration.HUNK_SIZE = hunkThreshold; - String pjName = "linux"; -// String rootPath = "/Volumes/data/bugStudy/"; -// String DATASET_FILE_PATH = rootPath + "/dataset/GumTreeInput/" + pjName; -// String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; - log.info(pjName); // input data - log.info("Get the input data..." + Configuration.GUM_TREE_INPUT ); - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); + String GUM_TREE_INPUT = inputRootPath + "GumTreeInput/"; + log.info("Get the input data..." + GUM_TREE_INPUT ); + String GUM_TREE_OUTPUT = inputRootPath + "GumTreeResults/"; + log.info("Set the output data..." + GUM_TREE_OUTPUT ); + final List msgFiles = getMessageFiles(GUM_TREE_INPUT); log.info("MessageFiles: " + msgFiles.size()); // output path - final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH + pjName + "/"; - final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH+ pjName + "/"; - final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH+ pjName + "/"; - final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH+ pjName + "/"; + final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts/"; + final String patchesSourceCodeFilePath = GUM_TREE_OUTPUT + "patchSourceCode/"; + final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens/"; + final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes/"; FileHelper.deleteDirectory(editScriptsFilePath); FileHelper.deleteDirectory(patchesSourceCodeFilePath); FileHelper.deleteDirectory(buggyTokensFilePath); From ec9b8616a2afc0c97b47ea19c28bdc1bd0fe0ff9 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 15:17:32 +0100 Subject: [PATCH 020/127] server config --- .../MultipleThreadsParser/AkkaParser2.java | 70 ++++++++++++------- 1 file changed, 45 insertions(+), 25 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index a4f5472..0ec2eee 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -11,6 +11,8 @@ import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; /** * Multi-thread parser of parsing the difference between buggy code file and fixed code file. @@ -49,33 +51,51 @@ public class AkkaParser2 { // input data String GUM_TREE_INPUT = inputRootPath + "GumTreeInput/"; log.info("Get the input data..." + GUM_TREE_INPUT ); - String GUM_TREE_OUTPUT = inputRootPath + "GumTreeResults/"; - log.info("Set the output data..." + GUM_TREE_OUTPUT ); - final List msgFiles = getMessageFiles(GUM_TREE_INPUT); - log.info("MessageFiles: " + msgFiles.size()); + String outputPath = inputRootPath + "GumTreeResults/"; + log.info("Set the output data..." + outputPath ); - // output path - final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts/"; - final String patchesSourceCodeFilePath = GUM_TREE_OUTPUT + "patchSourceCode/"; - final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens/"; - final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes/"; - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - ActorSystem system = null; - ActorRef parsingActor = null; - final WorkMessage msg = new WorkMessage(0, msgFiles); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); + File folder = new File(GUM_TREE_INPUT); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + for (File target : folders) { + final List msgFiles = getMessageFiles(target.toString() + "/"); + log.info("MessageFiles: " + msgFiles.size()); + // output path + + + String pjName = target.getName(); + // output path + String GUM_TREE_OUTPUT = outputPath + pjName + "/"; + final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; + final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; + final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; + final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; + final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; + + FileHelper.deleteDirectory(editScriptsFilePath); + FileHelper.deleteDirectory(patchesSourceCodeFilePath); + FileHelper.deleteDirectory(buggyTokensFilePath); + FileHelper.deleteDirectory(editScriptSizesFilePath); + + ActorSystem system = null; + ActorRef parsingActor = null; + final WorkMessage msg = new WorkMessage(0, msgFiles); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Mining-FixPattern-System"); + parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, + patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } + } From 9fa41e6c1990467340810e16620f6a9260be2d48 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 15:22:26 +0100 Subject: [PATCH 021/127] server config --- .../edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index 0ec2eee..5176320 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -63,6 +63,7 @@ public class AkkaParser2 { .collect(Collectors.toList()); for (File target : folders) { + log.info("MessageFiles: " + target.toString()); final List msgFiles = getMessageFiles(target.toString() + "/"); log.info("MessageFiles: " + msgFiles.size()); // output path From b9efc501d24ea6575ef2c331291b002e93cb6d62 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 16:41:38 +0100 Subject: [PATCH 022/127] server --- .../violations/TestHunkParser.java | 13 ++++++-- .../MultipleThreadsParser/AkkaParser2.java | 31 +++++++++++++------ 2 files changed, 31 insertions(+), 13 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 95919c3..665cd29 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -29,9 +29,16 @@ public class TestHunkParser { // input data // String rootPath = "/Users/anilkoyuncu/bugStudy"; - String rootPath = args[0]; - String inputPath = args[1]; - String outputPath = args[0] + "/GumTreeOutputBug/"; + String inputPath; + String outputPath; + if(args.length > 0){ + inputPath = args[1]; + outputPath = args[0] + "/GumTreeOutputBug/"; + }else{ + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset" + "/GumTreeOutputBug/"; + } + File folder = new File(inputPath); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index 5176320..f159003 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -33,9 +33,19 @@ public class AkkaParser2 { */ @SuppressWarnings("deprecation") public static void main(String[] args) { - String inputRootPath = args[0]; - int numberOfWorkers = Integer.parseInt(args[1]); - int hunkThreshold = Integer.parseInt(args[2]); + String inputRootPath; + String outputRootPath; + int numberOfWorkers; + if(args.length > 0){ + inputRootPath = args[0]; + outputRootPath = args[1]; + numberOfWorkers = Integer.parseInt(args[2]); + }else{ + inputRootPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug"; + outputRootPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputBug/"; + numberOfWorkers = 1; + } + // try { // hunkThreshold = Integer.parseInt(args[2]); // } catch (NumberFormatException e1) { @@ -49,13 +59,13 @@ public class AkkaParser2 { // input data - String GUM_TREE_INPUT = inputRootPath + "GumTreeInput/"; - log.info("Get the input data..." + GUM_TREE_INPUT ); - String outputPath = inputRootPath + "GumTreeResults/"; - log.info("Set the output data..." + outputPath ); +// String GUM_TREE_INPUT = inputRootPath + "GumTreeInput/"; + log.info("Get the input data..." + inputRootPath ); + + log.info("Set the output data..." + outputRootPath ); - File folder = new File(GUM_TREE_INPUT); + File folder = new File(inputRootPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List folders = stream @@ -71,7 +81,7 @@ public class AkkaParser2 { String pjName = target.getName(); // output path - String GUM_TREE_OUTPUT = outputPath + pjName + "/"; + String GUM_TREE_OUTPUT = outputRootPath + pjName + "/"; final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; @@ -115,7 +125,8 @@ public class AkkaParser2 { List msgFiles = new ArrayList<>(); for (File revFile : revFiles) { - if (revFile.getName().endsWith(".c") || revFile.getName().endsWith(".h")) { +// if (revFile.getName().endsWith(".c") || revFile.getName().endsWith(".h")) { + if (revFile.getName().endsWith(".java")) { String fileName = revFile.getName(); File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file // fileName = fileName.replace(".java", ".txt"); From 55eaebc710303f8f2e368c3f3dcd049f3b2aeb18 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 17:26:15 +0100 Subject: [PATCH 023/127] file change txt 2 java --- .../edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index f159003..3ed0348 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -129,7 +129,7 @@ public class AkkaParser2 { if (revFile.getName().endsWith(".java")) { String fileName = revFile.getName(); File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file -// fileName = fileName.replace(".java", ".txt"); + fileName = fileName.replace(".java", ".txt"); File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); From 6a05ccb3350c11d4ae339c74e9297aee16dd3112 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 18:06:22 +0100 Subject: [PATCH 024/127] output fix --- .../uni/serval/MultipleThreadsParser/AkkaParser2.java | 11 ++++++----- .../MultipleThreadsParser/ParseFixPatternWorker.java | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index 3ed0348..c6de0ca 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -82,11 +82,11 @@ public class AkkaParser2 { String pjName = target.getName(); // output path String GUM_TREE_OUTPUT = outputRootPath + pjName + "/"; - final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; - final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; - final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; - final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; - final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; + final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts/"; + final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode/"; + final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens/"; + final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes/"; + final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes/"; FileHelper.deleteDirectory(editScriptsFilePath); FileHelper.deleteDirectory(patchesSourceCodeFilePath); @@ -107,6 +107,7 @@ public class AkkaParser2 { e.printStackTrace(); } + } diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index 0d81521..bc581c4 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -155,7 +155,7 @@ public class ParseFixPatternWorker extends UntypedActor { } if (sizes.length() > 0) { - FileHelper.outputToFile(editScriptsFilePath + "edistScripts_" + id + ".list", editScripts, true); + FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true); FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); From 9322b35b4807b0fddad8e901defe2db484a58250 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Feb 2018 19:19:16 +0100 Subject: [PATCH 025/127] single thread --- pom.xml | 2 +- .../uni/serval/FixPatternParser/violations/TestHunkParser.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 5f2acdd..81e805a 100644 --- a/pom.xml +++ b/pom.xml @@ -87,7 +87,7 @@ - edu.lu.uni.serval.MultipleThreadsParser.AkkaParser2 + edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 665cd29..45eb1d0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -36,7 +36,7 @@ public class TestHunkParser { outputPath = args[0] + "/GumTreeOutputBug/"; }else{ inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset" + "/GumTreeOutputBug/"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset" + "/GumTreeOutputBug2/"; } From 175d70b9c3822ff32b1afe9c86f1a677ec5d9a8c Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 11:45:46 +0100 Subject: [PATCH 026/127] treedumps --- pom.xml | 2 +- .../violations/FixedViolationHunkParser.java | 282 +++++++++++------- .../FixPatternParser/violations/Message.java | 32 ++ .../violations/MultiThreadTreeLoader.java | 168 +++++++++++ .../violations/TestHunkParser.java | 22 +- .../violations/TestTreeLoader.java | 229 ++++++++++++++ .../lu/uni/serval/config/Configuration.java | 2 +- .../regroup/HierarchicalActionSet.java | 3 +- .../regroup/HierarchicalRegrouper.java | 1 + 9 files changed, 619 insertions(+), 122 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java diff --git a/pom.xml b/pom.xml index 81e805a..b333845 100644 --- a/pom.xml +++ b/pom.xml @@ -87,7 +87,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser + edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 7056ea0..945a73c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -1,11 +1,12 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import java.io.File; +import java.io.*; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; +import com.github.gumtreediff.actions.model.Update; import com.github.gumtreediff.tree.ITree; import edu.lu.uni.serval.FixPatternParser.Tokenizer; @@ -38,124 +39,181 @@ public class FixedViolationHunkParser extends FixedViolationParser { @Override public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { - // GumTree results - List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); - if (this.resultType != 0) { -// String type = ""; -// if (this.resultType == 1) { -// type = "#NullGumTreeResult:"; -// } else if (this.resultType == 2) { -// type = "#NoSourceCodeChange:"; -// } else if (this.resultType == 3) { -// type = "#NoStatementChange:"; -// } - } else { - List diffentryHunks = new DiffEntryReader().readHunks3(diffentryFile); + List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); - //Filter out the modify actions, which are not in the DiffEntry hunks. - HunkActionFilter hunkFilter = new HunkActionFilter(); - List selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile); + boolean isUpdate = + actionSets.stream().allMatch(p -> p.getAction() instanceof Update); + int hunkSet = 0; + if(isUpdate){ + for (HierarchicalActionSet actionSet : actionSets) { - for (DiffEntryHunk patchHunk : selectedPatchHunks) { - List hunkActionSets = patchHunk.getActionSets(); - // multiple UPD, and some UPD contain other UPD. - removeOverlapperdUPD(hunkActionSets); - // Range of buggy source code - int bugStartLine = 0; - int bugEndLine = 0; - // Range of fixing source code - int fixStartLine = 0; - int fixEndLine = 0; - int bugEndPosition = 0; - int fixEndPosition = 0; - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - int actionBugStart = hunkActionSet.getBugStartLineNum(); - int actionBugEnd = hunkActionSet.getBugEndLineNum(); - int actionFixStart = hunkActionSet.getFixStartLineNum(); - int actionFixEnd = hunkActionSet.getFixEndLineNum(); - if (bugStartLine == 0) { - bugStartLine = actionBugStart; - } else if (actionBugStart != 0 && actionBugStart < bugStartLine) { - bugStartLine = actionBugStart; - } - if (fixStartLine == 0) { - fixStartLine = actionFixStart; - } else if (actionFixStart != 0 && actionFixStart < fixStartLine) { - fixStartLine = actionFixStart; - } - if (bugEndLine < actionBugEnd) { - bugEndLine = actionBugEnd; - bugEndPosition = hunkActionSet.getBugEndPosition(); - } - if (fixEndLine < actionFixEnd) { - fixEndLine = actionFixEnd; - fixEndPosition = hunkActionSet.getFixEndPosition(); - } + FileOutputStream f = null; + try { + String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; + String root = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + String hunkTreeFileName = root+pj.replace("DiffEntries","ASTDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + f = new FileOutputStream(new File(hunkTreeFileName)); + ObjectOutputStream o = new ObjectOutputStream(f); + o.writeObject(actionSet.getNode()); + + o.close(); + f.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); } - - if (fixStartLine == 0 && bugStartLine == 0) { - this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; - this.nullMappingGumTreeResult ++; - continue; - } - - if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions. - // get the exact buggy code by violation's position. TODO later - } - -// if (children.size() == 0) continue; - boolean isPureInsert = false; - if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) { - bugStartLine = patchHunk.getBugLineStartNum(); - bugEndLine = bugStartLine + patchHunk.getBuggyHunkSize() - 1; - isPureInsert = true; -// continue; - } -// if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE ) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { -// continue; //TODO hunk size -// } - if(patchHunk.getBuggyHunkSize() > Configuration.HUNK_SIZE || patchHunk.getFixedHunkSize() > Configuration.HUNK_SIZE){ - continue; - } - - /** - * Select edit scripts for deep learning. - * Edit scripts will be used to mine common fix patterns. - */ - // 1. First level: AST node type. - String astEditScripts = getASTEditScriptsDeepFirst(hunkActionSets, bugEndPosition, fixEndPosition); - if (astEditScripts.contains("\n") || astEditScripts.split(" ").length % 3 != 0) { - System.err.println("===+++===: " + revFile.getName() + ":" +patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize()); - } - // 2. source code: raw tokens - // 3. abstract identifiers: - // 4. semi-source code: - String[] editScriptTokens = astEditScripts.split(" "); - int size = editScriptTokens.length; - if (size == 1) { - this.nullMappingGumTreeResult ++; - this.unfixedViolations += "#NullMatchedGumTreeResult1:" + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; - continue; - } - - String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; -// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; -//TODO uncomment the line below for more detailed gumtree input. - String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; -// if (noUpdate(editScriptTokens)) { -// } - - String canonicalVariableNames = getBuggyCodeTree(patchHunk, prevFile, revFile); - this.patchesSourceCode += info; - this.patchesSourceCode += "\nRenamed_Variables###:\n" + canonicalVariableNames; - this.sizes += size + "\n"; - this.astEditScripts += astEditScripts + "\n"; -// String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); -// this.tokensOfSourceCode += tokens + "\n"; + hunkSet++; } + } + } +// public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { +// // GumTree results +// List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); +// +// +// if (this.resultType != 0) { +//// String type = ""; +//// if (this.resultType == 1) { +//// type = "#NullGumTreeResult:"; +//// } else if (this.resultType == 2) { +//// type = "#NoSourceCodeChange:"; +//// } else if (this.resultType == 3) { +//// type = "#NoStatementChange:"; +//// } +// } else { +// List diffentryHunks = new DiffEntryReader().readHunks3(diffentryFile); +// +// //Filter out the modify actions, which are not in the DiffEntry hunks. +// HunkActionFilter hunkFilter = new HunkActionFilter(); +// List selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile); +// +// for (DiffEntryHunk patchHunk : selectedPatchHunks) { +// List hunkActionSets = patchHunk.getActionSets(); +// // multiple UPD, and some UPD contain other UPD. +// removeOverlapperdUPD(hunkActionSets); +// +// // Range of buggy source code +// int bugStartLine = 0; +// int bugEndLine = 0; +// // Range of fixing source code +// int fixStartLine = 0; +// int fixEndLine = 0; +// int bugEndPosition = 0; +// int fixEndPosition = 0; +// int hunkSet = 0; +// for (HierarchicalActionSet hunkActionSet : hunkActionSets) { +// +// +// FileOutputStream f = null; +// try { +// String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; +// String root = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; +// String hunkTreeFileName = root+pj.replace("DiffEntries","ASTDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); +// f = new FileOutputStream(new File(hunkTreeFileName)); +// ObjectOutputStream o = new ObjectOutputStream(f); +// o.writeObject(hunkActionSet.getNode()); +// +// o.close(); +// f.close(); +// } catch (FileNotFoundException e) { +// e.printStackTrace(); +// } catch (IOException e) { +// e.printStackTrace(); +// } +// hunkSet++; +// +// +// +// int actionBugStart = hunkActionSet.getBugStartLineNum(); +// int actionBugEnd = hunkActionSet.getBugEndLineNum(); +// int actionFixStart = hunkActionSet.getFixStartLineNum(); +// int actionFixEnd = hunkActionSet.getFixEndLineNum(); +// if (bugStartLine == 0) { +// bugStartLine = actionBugStart; +// } else if (actionBugStart != 0 && actionBugStart < bugStartLine) { +// bugStartLine = actionBugStart; +// } +// if (fixStartLine == 0) { +// fixStartLine = actionFixStart; +// } else if (actionFixStart != 0 && actionFixStart < fixStartLine) { +// fixStartLine = actionFixStart; +// } +// if (bugEndLine < actionBugEnd) { +// bugEndLine = actionBugEnd; +// bugEndPosition = hunkActionSet.getBugEndPosition(); +// } +// if (fixEndLine < actionFixEnd) { +// fixEndLine = actionFixEnd; +// fixEndPosition = hunkActionSet.getFixEndPosition(); +// } +// } +// +// if (fixStartLine == 0 && bugStartLine == 0) { +// this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; +// this.nullMappingGumTreeResult ++; +// continue; +// } +// +// if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions. +// // get the exact buggy code by violation's position. TODO later +// } +// +//// if (children.size() == 0) continue; +// boolean isPureInsert = false; +// if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) { +// bugStartLine = patchHunk.getBugLineStartNum(); +// bugEndLine = bugStartLine + patchHunk.getBuggyHunkSize() - 1; +// isPureInsert = true; +//// continue; +// } +//// if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE ) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { +//// continue; //TODO hunk size +//// } +// if(patchHunk.getBuggyHunkSize() > Configuration.HUNK_SIZE || patchHunk.getFixedHunkSize() > Configuration.HUNK_SIZE){ +// continue; +// } +// +// /** +// * Select edit scripts for deep learning. +// * Edit scripts will be used to mine common fix patterns. +// */ +// // 1. First level: AST node type. +// String astEditScripts = getASTEditScriptsDeepFirst(hunkActionSets, bugEndPosition, fixEndPosition); +// if (astEditScripts.contains("\n") || astEditScripts.split(" ").length % 3 != 0) { +// System.err.println("===+++===: " + revFile.getName() + ":" +patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize()); +// } +// // 2. source code: raw tokens +// // 3. abstract identifiers: +// // 4. semi-source code: +// String[] editScriptTokens = astEditScripts.split(" "); +// int size = editScriptTokens.length; +// if (size == 1) { +// this.nullMappingGumTreeResult ++; +// this.unfixedViolations += "#NullMatchedGumTreeResult1:" + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; +// continue; +// } +// +// String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; +//// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; +////TODO uncomment the line below for more detailed gumtree input. +// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; +//// if (noUpdate(editScriptTokens)) { +//// } +// +// String canonicalVariableNames = getBuggyCodeTree(patchHunk, prevFile, revFile); +// this.patchesSourceCode += info; +// this.patchesSourceCode += "\nRenamed_Variables###:\n" + canonicalVariableNames; +// this.sizes += size + "\n"; +// this.astEditScripts += astEditScripts + "\n"; +//// String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); +//// this.tokensOfSourceCode += tokens + "\n"; +// } +// } +// } private String getAstEditScripts(List hunkActionSets) { String scripts = ""; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java new file mode 100644 index 0000000..6855e62 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java @@ -0,0 +1,32 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + + +import javafx.util.Pair; + +import java.io.Serializable; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class Message implements Serializable{ + Pair first; + Pair second; + Pair p; + + public Pair getPair() { + return p; + } + + public void setPair(Pair p) { + this.p = p; + } + + + + public Message(Integer keyFirst, String valueFirst, Integer keySecond, String valueSecond ){ + first = new Pair<>(keyFirst,valueFirst); + second = new Pair<>(keySecond,valueSecond); + p = new Pair<>(first,second); + } + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java new file mode 100644 index 0000000..cb7cb2b --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -0,0 +1,168 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import akka.actor.ActorRef; +import akka.actor.ActorSystem; +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; +import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class MultiThreadTreeLoader { + private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoader.class); + + public static void main(String[] args) { + + + String inputPath; + String outputPath; + if(args.length > 0){ + inputPath = args[0]; + outputPath = args[1]; + }else{ + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + } + + +// String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for (File pj : pjs) { + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ASTDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + final List msgFiles = readMessageFiles(fileToCompare); + + FileOutputStream f = null; + try { + + + f = new FileOutputStream(new File(outputPath + "messageFile")); + ObjectOutputStream o = new ObjectOutputStream(f); + o.writeObject(msgFiles); + + o.close(); + f.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + List loaded = null; + try { + FileInputStream fi = new FileInputStream(new File(outputPath + "messageFile")); + ObjectInputStream oi = new ObjectInputStream(fi); + loaded = (List) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + + log.info(String.valueOf(msgFiles.size())); + log.info(String.valueOf(loaded.size())); +// msgFiles.parallelStream() +// .forEach(m -> m.dosomething())); + } + +// private static coreLoop(){ +// try { +// BufferedWriter writer = new BufferedWriter(new FileWriter("output2.txt", true)); +// ITree oldTree = getSimpliedTree(treesFileNames.get(i)); +// +// ITree newTree = getSimpliedTree(treesFileNames.get(j)); +// +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); +// +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// writer.write(String.valueOf(i)); +// writer.write("\t"); +// writer.write(String.valueOf(j)); +// writer.write("\t"); +// +// writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.valueOf(actions.size())); +// writer.write("\t"); +// writer.write(treesFileNames.get(i)); +// writer.write("\t"); +// writer.write(treesFileNames.get(j)); +// writer.write("\n"); +// +// writer.close(); +// } catch (FileNotFoundException e) { +// System.out.println("File not found"); +// } catch (IOException e) { +// System.out.println("Error initializing stream"); +// +// } +// } + + private static List readMessageFiles(List folders) { + + List treesFileNames = new ArrayList<>(); + + List msgFiles = new ArrayList<>(); + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + log.info("Calculating pairs"); + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + Message msgFile = new Message(i, treesFileNames.get(i), j, treesFileNames.get(j)); + msgFiles.add(msgFile); + } + + } + return msgFiles; + } + + + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 45eb1d0..47d8318 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -35,8 +35,10 @@ public class TestHunkParser { inputPath = args[1]; outputPath = args[0] + "/GumTreeOutputBug/"; }else{ - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset" + "/GumTreeOutputBug2/"; +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; + inputPath = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4"; +// outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; } @@ -57,14 +59,20 @@ public class TestHunkParser { // } // } +// List pjList = Arrays.asList("DATAJPA","ZXing","PDE","SWS","SWT", "SWF", "COLLECTIONS", "JDT"); + for (File target : folders) { + String pjName = target.getName(); +// if (!pjList.contains(pjName)){ +// continue; +// } + final List msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" System.out.println(msgFiles.size()); if(msgFiles.size() == 0) continue; - String pjName = target.getName(); - // output path - String GUM_TREE_OUTPUT = outputPath + pjName + "/"; + + String GUM_TREE_OUTPUT = outputPath + "/"+ pjName + "/"; final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; @@ -72,7 +80,7 @@ public class TestHunkParser { final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; - + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ASTDumps"); FileHelper.deleteDirectory(editScriptsFilePath); FileHelper.deleteDirectory(patchesSourceCodeFilePath); FileHelper.deleteDirectory(buggyTokensFilePath); @@ -106,7 +114,7 @@ public class TestHunkParser { alarmTypes.append(parser.getAlarmTypes()); a++; - if (a % 10 == 0) { + if (a % 100 == 0) { FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); FileHelper.outputToFile(buggyTokensFilePath, tokens, true); FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java new file mode 100644 index 0000000..ad23b9c --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java @@ -0,0 +1,229 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.matchers.Mapping; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; + +import java.io.*; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Created by anilkoyuncu on 17/03/2018. + */ +public class TestTreeLoader { + public static void main(String[] args) { + + +// String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput/ENTESB/ASTDumps"; + String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for(File pj:pjs){ + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ASTDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + memoryFriendlyCompare(fileToCompare); + + + } + + + public static ITree getSimpliedTree(String fn) { + ITree tree = null; + try { + FileInputStream fi = new FileInputStream(new File(fn)); + ObjectInputStream oi = new ObjectInputStream(fi); + tree = (ITree) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + tree.setLabel(""); + tree.setParent(null); + List descendants = tree.getDescendants(); + for (ITree descendant : descendants) { + descendant.setLabel(""); + } + + return tree; + + } + public static void memoryFriendlyCompare(List folders){ + List treesFileNames = new ArrayList<>(); +// HashMap hmap = new HashMap(); + + for (File target : folders) { +// hmap.put(folders.indexOf(target), target.toString()); + treesFileNames.add(target.toString()); + } + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + // compare list.get(i) and list.get(j) + try { + BufferedWriter writer = new BufferedWriter(new FileWriter("output2.txt", true)); + ITree oldTree = getSimpliedTree(treesFileNames.get(i)); + + ITree newTree = getSimpliedTree(treesFileNames.get(j)); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(treesFileNames.get(i)); + writer.write("\t"); + writer.write(treesFileNames.get(j)); + writer.write("\n"); + + writer.close(); + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + + } + } + } + + + + + } + public static void compareAll(List folders){ + List trees = new ArrayList<>(); + HashMap hmap = new HashMap(); + for (File target : folders) { + + try { + FileInputStream fi = new FileInputStream(new File(target.toString())); + ObjectInputStream oi = new ObjectInputStream(fi); + ITree pr1 = (ITree) oi.readObject(); + oi.close(); + fi.close(); + trees.add(pr1); + hmap.put(folders.indexOf(target), target.toString()); + + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + + for (ITree tree : trees) { +// SimplifyTree simplifyTree = new SimplifyTree(); +// simplifyTree.canonicalizeSourceCodeTree(tree); + tree.setLabel(""); + tree.setParent(null); + List descendants = tree.getDescendants(); + for (ITree descendant : descendants) { + descendant.setLabel(""); + } + + } + System.out.println("a"); + + try { + + + + for (int i = 0; i < trees.size(); i++) { + for (int j = i + 1; j < trees.size(); j++) { + // compare list.get(i) and list.get(j) + BufferedWriter writer = new BufferedWriter(new FileWriter("output.txt",true)); + ITree oldTree = trees.get(i); + + ITree newTree = trees.get(j); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(hmap.get(i)); + writer.write("\t"); + writer.write(hmap.get(j)); + writer.write("\n"); + + writer.close(); + } + } + + + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + + } + + +// if (actions.size() > 1) { +// Matcher m1 = Matchers.getInstance().getMatcher(actions.get(0).getNode(), actions.get(0).getNode()); +// m1.match(); +// Set mappingSet1 = m1.getMappingSet(); +// +// } + } + +} diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index d04c138..3325840 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -16,7 +16,7 @@ public class Configuration { // the output path of GumTree results. - private static final String GUM_TREE_OUTPUT = ROOT_PATH + "GumTreeResults/"; + public static final String GUM_TREE_OUTPUT = ROOT_PATH + "GumTreeResults/"; public static final String EDITSCRIPTS_FILE_PATH = GUM_TREE_OUTPUT + "editScripts/"; public static final String PATCH_SOURCECODE_FILE_PATH = GUM_TREE_OUTPUT + "sourceCode/"; public static final String BUGGYTREE_FILE_PATH = GUM_TREE_OUTPUT + "buggyTrees/"; diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java index 7823826..1bff3ac 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java @@ -1,5 +1,6 @@ package edu.lu.uni.serval.gumtree.regroup; +import java.io.Serializable; import java.util.ArrayList; import java.util.List; @@ -12,7 +13,7 @@ import com.github.gumtreediff.tree.ITree; * @author kui.liu * */ -public class HierarchicalActionSet implements Comparable { +public class HierarchicalActionSet implements Comparable,Serializable { private String astNodeType; private Action action; diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java index 5590c48..6ccb32e 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java @@ -72,6 +72,7 @@ public class HierarchicalRegrouper { } } } + return reActionSets; } From 9df0b6c745f722974ae9124158d4892107dacb50 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 13:41:19 +0100 Subject: [PATCH 027/127] dumsp --- .../violations/MultiThreadTreeLoader.java | 203 ++++++++++++------ 1 file changed, 136 insertions(+), 67 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index cb7cb2b..d8f4eef 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -9,6 +9,8 @@ import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; +import edu.lu.uni.serval.utils.FileHelper; +import javafx.util.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -40,7 +42,37 @@ public class MultiThreadTreeLoader { } -// String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + + calculatePairs(inputPath,outputPath); + processMessages(outputPath ); + + +// List loaded = null; +// try { +// FileInputStream fi = new FileInputStream(new File(outputPath + "messageFile")); +// ObjectInputStream oi = new ObjectInputStream(fi); +// loaded = (List) oi.readObject(); +// oi.close(); +// fi.close(); +// +// +// } catch (FileNotFoundException e) { +// System.out.println("File not found"); +// } catch (IOException e) { +// System.out.println("Error initializing stream"); +// } catch (ClassNotFoundException e) { +// // TODO Auto-generated catch block +// e.printStackTrace(); +// } +// +// +// log.info(String.valueOf(msgFiles.size())); +// log.info(String.valueOf(loaded.size())); +// msgFiles.parallelStream() +// .forEach(m -> coreLoop(m,outputPath)); + } + + public static void calculatePairs(String inputPath,String outputPath){ File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); @@ -60,28 +92,27 @@ public class MultiThreadTreeLoader { } System.out.println("a"); // compareAll(fileToCompare); - final List msgFiles = readMessageFiles(fileToCompare); + readMessageFiles(fileToCompare,outputPath); + } - FileOutputStream f = null; + public static void processMessages(String outputPath){ + File folder = new File(outputPath+ "dumps/"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + FileHelper.createDirectory(outputPath + "comparison/"); + pjs.parallelStream() + .forEach(m -> coreLoop(m,outputPath)); + } + + public static ITree getSimpliedTree(String fn) { + ITree tree = null; try { - - - f = new FileOutputStream(new File(outputPath + "messageFile")); - ObjectOutputStream o = new ObjectOutputStream(f); - o.writeObject(msgFiles); - - o.close(); - f.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - } - List loaded = null; - try { - FileInputStream fi = new FileInputStream(new File(outputPath + "messageFile")); + FileInputStream fi = new FileInputStream(new File(fn)); ObjectInputStream oi = new ObjectInputStream(fi); - loaded = (List) oi.readObject(); + tree = (ITree) oi.readObject(); oi.close(); fi.close(); @@ -95,72 +126,110 @@ public class MultiThreadTreeLoader { e.printStackTrace(); } + tree.setLabel(""); + tree.setParent(null); + List descendants = tree.getDescendants(); + for (ITree descendant : descendants) { + descendant.setLabel(""); + } + + return tree; - log.info(String.valueOf(msgFiles.size())); - log.info(String.valueOf(loaded.size())); -// msgFiles.parallelStream() -// .forEach(m -> m.dosomething())); } -// private static coreLoop(){ -// try { -// BufferedWriter writer = new BufferedWriter(new FileWriter("output2.txt", true)); -// ITree oldTree = getSimpliedTree(treesFileNames.get(i)); -// -// ITree newTree = getSimpliedTree(treesFileNames.get(j)); -// -// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); -// m.match(); -// -// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); -// ag.generate(); -// List actions = ag.getActions(); -// writer.write(String.valueOf(i)); -// writer.write("\t"); -// writer.write(String.valueOf(j)); -// writer.write("\t"); -// -// writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); -// writer.write("\t"); -// writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); -// writer.write("\t"); -// writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); -// writer.write("\t"); -// writer.write(String.valueOf(actions.size())); -// writer.write("\t"); -// writer.write(treesFileNames.get(i)); -// writer.write("\t"); -// writer.write(treesFileNames.get(j)); -// writer.write("\n"); -// -// writer.close(); -// } catch (FileNotFoundException e) { -// System.out.println("File not found"); -// } catch (IOException e) { -// System.out.println("Error initializing stream"); -// -// } -// } + private static void coreLoop(File mes,String outputPath){ + try { + FileInputStream fi = new FileInputStream(mes); + ObjectInputStream oi = new ObjectInputStream(fi); + Message loaded = (Message) oi.readObject(); + oi.close(); + fi.close(); + Pair first = loaded.first; + Pair second = loaded.second; + int i = first.getKey(); + int j = second.getKey(); + String firstValue = first.getValue(); + String secondValue = second.getValue(); - private static List readMessageFiles(List folders) { + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath +"comparison/" + "output_"+String.valueOf(i)+"_"+String.valueOf(j)+".txt", true)); + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); + + writer.close(); + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + + private static void readMessageFiles(List folders,String outputPath) { List treesFileNames = new ArrayList<>(); - List msgFiles = new ArrayList<>(); + for (File target : folders) { treesFileNames.add(target.toString()); } + FileHelper.createDirectory(outputPath + "dumps/"); log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,10); for (int i = 0; i < treesFileNames.size(); i++) { for (int j = i + 1; j < treesFileNames.size(); j++) { Message msgFile = new Message(i, treesFileNames.get(i), j, treesFileNames.get(j)); - msgFiles.add(msgFile); +// msgFiles.add(msgFile); + + FileOutputStream f = null; + try { + + + f = new FileOutputStream(new File(outputPath + "dumps/" + "messageFile_"+String.valueOf(i)+"_"+String.valueOf(j))); + ObjectOutputStream o = new ObjectOutputStream(f); + o.writeObject(msgFile); + + o.close(); + f.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } } } - return msgFiles; + log.info("Done pairs"); +// return msgFiles; } From 8d21175d054152b02c245951226470837a3640e9 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 16:07:19 +0100 Subject: [PATCH 028/127] memory friendly --- .../FixPatternParser/violations/CSVUtils.java | 62 ++++++ .../FixPatternParser/violations/MMapper.java | 103 ++++++++++ .../violations/MultiThreadTreeLoader.java | 194 +++++++++--------- 3 files changed, 266 insertions(+), 93 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java new file mode 100644 index 0000000..1c5981b --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java @@ -0,0 +1,62 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import java.io.IOException; +import java.io.Writer; +import java.util.List; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class CSVUtils { + + private static final char DEFAULT_SEPARATOR = ','; + + public static void writeLine(Writer w, List values) throws IOException { + writeLine(w, values, DEFAULT_SEPARATOR, ' '); + } + + public static void writeLine(Writer w, List values, char separators) throws IOException { + writeLine(w, values, separators, ' '); + } + + //https://tools.ietf.org/html/rfc4180 + private static String followCVSformat(String value) { + + String result = value; + if (result.contains("\"")) { + result = result.replace("\"", "\"\""); + } + return result; + + } + + public static void writeLine(Writer w, List values, char separators, char customQuote) throws IOException { + + boolean first = true; + + //default customQuote is empty + + if (separators == ' ') { + separators = DEFAULT_SEPARATOR; + } + + StringBuilder sb = new StringBuilder(); + for (String value : values) { + if (!first) { + sb.append(separators); + } + if (customQuote == ' ') { + sb.append(followCVSformat(value)); + } else { + sb.append(customQuote).append(followCVSformat(value)).append(customQuote); + } + + first = false; + } + sb.append("\n"); + w.append(sb.toString()); + + + } + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java new file mode 100644 index 0000000..61b755c --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java @@ -0,0 +1,103 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +import java.io.RandomAccessFile; +import java.lang.reflect.Field; +import java.lang.reflect.Method; +import java.nio.channels.FileChannel; + +import sun.nio.ch.FileChannelImpl; +import sun.misc.Unsafe; + +@SuppressWarnings("restriction") +public class MMapper { + + private static final Unsafe unsafe; + private static final Method mmap; + private static final Method unmmap; + private static final int BYTE_ARRAY_OFFSET; + + private long addr, size; + private final String loc; + + static { + try { + Field singleoneInstanceField = Unsafe.class.getDeclaredField("theUnsafe"); + singleoneInstanceField.setAccessible(true); + unsafe = (Unsafe) singleoneInstanceField.get(null); + + mmap = getMethod(FileChannelImpl.class, "map0", int.class, long.class, long.class); + unmmap = getMethod(FileChannelImpl.class, "unmap0", long.class, long.class); + + BYTE_ARRAY_OFFSET = unsafe.arrayBaseOffset(byte[].class); + } catch (Exception e){ + throw new RuntimeException(e); + } + } + + //Bundle reflection calls to get access to the given method + private static Method getMethod(Class cls, String name, Class... params) throws Exception { + Method m = cls.getDeclaredMethod(name, params); + m.setAccessible(true); + return m; + } + + //Round to next 4096 bytes + private static long roundTo4096(long i) { + return (i + 0xfffL) & ~0xfffL; + } + + //Given that the location and size have been set, map that location + //for the given length and set this.addr to the returned offset + private void mapAndSetOffset() throws Exception{ + final RandomAccessFile backingFile = new RandomAccessFile(this.loc, "rw"); + backingFile.setLength(this.size); + + final FileChannel ch = backingFile.getChannel(); + this.addr = (long) mmap.invoke(ch, 1, 0L, this.size); + + ch.close(); + backingFile.close(); + } + + public MMapper(final String loc, long len) throws Exception { + this.loc = loc; + this.size = roundTo4096(len); + mapAndSetOffset(); + } + + //Callers should synchronize to avoid calls in the middle of this, but + //it is undesirable to synchronize w/ all access methods. + public void remap(long nLen) throws Exception{ + unmmap.invoke(null, addr, this.size); + this.size = roundTo4096(nLen); + mapAndSetOffset(); + } + + public int getInt(long pos){ + return unsafe.getInt(pos + addr); + } + + public long getLong(long pos){ + return unsafe.getLong(pos + addr); + } + + public void putInt(long pos, int val){ + unsafe.putInt(pos + addr, val); + } + + public void putLong(long pos, long val){ + unsafe.putLong(pos + addr, val); + } + + //May want to have offset & length within data as well, for both of these + public void getBytes(long pos, byte[] data){ + unsafe.copyMemory(null, pos + addr, data, BYTE_ARRAY_OFFSET, data.length); + } + + public void setBytes(long pos, byte[] data){ + unsafe.copyMemory(data, BYTE_ARRAY_OFFSET, null, pos + addr, data.length); + } +} \ No newline at end of file diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index d8f4eef..061d92e 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -15,12 +15,17 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.*; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; +import java.util.zip.Deflater; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; /** * Created by anilkoyuncu on 19/03/2018. @@ -33,46 +38,23 @@ public class MultiThreadTreeLoader { String inputPath; String outputPath; - if(args.length > 0){ + if (args.length > 0) { inputPath = args[0]; outputPath = args[1]; - }else{ + } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; } - - calculatePairs(inputPath,outputPath); - processMessages(outputPath ); + calculatePairs(inputPath, outputPath); + processMessages(inputPath,outputPath); + -// List loaded = null; -// try { -// FileInputStream fi = new FileInputStream(new File(outputPath + "messageFile")); -// ObjectInputStream oi = new ObjectInputStream(fi); -// loaded = (List) oi.readObject(); -// oi.close(); -// fi.close(); -// -// -// } catch (FileNotFoundException e) { -// System.out.println("File not found"); -// } catch (IOException e) { -// System.out.println("Error initializing stream"); -// } catch (ClassNotFoundException e) { -// // TODO Auto-generated catch block -// e.printStackTrace(); -// } -// -// -// log.info(String.valueOf(msgFiles.size())); -// log.info(String.valueOf(loaded.size())); -// msgFiles.parallelStream() -// .forEach(m -> coreLoop(m,outputPath)); } - public static void calculatePairs(String inputPath,String outputPath){ + public static void calculatePairs(String inputPath, String outputPath) { File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); @@ -92,11 +74,11 @@ public class MultiThreadTreeLoader { } System.out.println("a"); // compareAll(fileToCompare); - readMessageFiles(fileToCompare,outputPath); + readMessageFiles(fileToCompare, outputPath); } - public static void processMessages(String outputPath){ - File folder = new File(outputPath+ "dumps/"); + public static void processMessages(String inputPath, String outputPath) { + File folder = new File(outputPath + "pairs/"); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List pjs = stream @@ -104,7 +86,7 @@ public class MultiThreadTreeLoader { .collect(Collectors.toList()); FileHelper.createDirectory(outputPath + "comparison/"); pjs.parallelStream() - .forEach(m -> coreLoop(m,outputPath)); + .forEach(m -> coreLoop(m, outputPath,inputPath)); } public static ITree getSimpliedTree(String fn) { @@ -137,62 +119,68 @@ public class MultiThreadTreeLoader { } - private static void coreLoop(File mes,String outputPath){ + private static void coreLoop(File mes, String outputPath,String inputPath) { try { - FileInputStream fi = new FileInputStream(mes); - ObjectInputStream oi = new ObjectInputStream(fi); - Message loaded = (Message) oi.readObject(); - oi.close(); - fi.close(); - Pair first = loaded.first; - Pair second = loaded.second; - int i = first.getKey(); - int j = second.getKey(); - String firstValue = first.getValue(); - String secondValue = second.getValue(); - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath +"comparison/" + "output_"+String.valueOf(i)+"_"+String.valueOf(j)+".txt", true)); - ITree oldTree = getSimpliedTree(firstValue); + log.info("Starting in coreLoop"); - ITree newTree = getSimpliedTree(secondValue); + BufferedReader br = null; + String sCurrentLine = null; + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison/" + "output_" + mes.getName())); - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); + firstValue = inputPath + firstValue; + secondValue = inputPath + secondValue; - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(firstValue); - writer.write("\t"); - writer.write(secondValue); - writer.write("\n"); + ITree oldTree = getSimpliedTree(firstValue); + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); + + + } writer.close(); } catch (FileNotFoundException e) { System.out.println("File not found"); } catch (IOException e) { System.out.println("Error initializing stream"); - } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(); } } - private static void readMessageFiles(List folders,String outputPath) { + private static void readMessageFiles(List folders, String outputPath) { List treesFileNames = new ArrayList<>(); @@ -201,37 +189,57 @@ public class MultiThreadTreeLoader { treesFileNames.add(target.toString()); } - FileHelper.createDirectory(outputPath + "dumps/"); +// FileHelper.createDirectory(outputPath + "dumps/"); log.info("Calculating pairs"); -// treesFileNames = treesFileNames.subList(0,10); +// treesFileNames = treesFileNames.subList(0,100); + byte [] buf = new byte[0]; + String line = null; + try { + + FileChannel rwChannel = new RandomAccessFile(outputPath +"textfile.txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + fileCounter++; + rwChannel = new RandomAccessFile(outputPath +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + } - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - Message msgFile = new Message(i, treesFileNames.get(i), j, treesFileNames.get(j)); -// msgFiles.add(msgFile); - - FileOutputStream f = null; - try { - f = new FileOutputStream(new File(outputPath + "dumps/" + "messageFile_"+String.valueOf(i)+"_"+String.valueOf(j))); - ObjectOutputStream o = new ObjectOutputStream(f); - o.writeObject(msgFile); - o.close(); - f.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); } } - + rwChannel.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); } + log.info("Done pairs"); -// return msgFiles; } +// return msgFiles; } + + + + From 64c7d75df743375a042d4ba518985f67aadca844 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 16:10:14 +0100 Subject: [PATCH 029/127] paths --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 061d92e..ec806a7 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -189,14 +189,14 @@ public class MultiThreadTreeLoader { treesFileNames.add(target.toString()); } -// FileHelper.createDirectory(outputPath + "dumps/"); + FileHelper.createDirectory(outputPath + "pairs/"); log.info("Calculating pairs"); // treesFileNames = treesFileNames.subList(0,100); byte [] buf = new byte[0]; String line = null; try { - FileChannel rwChannel = new RandomAccessFile(outputPath +"textfile.txt", "rw").getChannel(); + FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); int fileCounter = 0; From 069b7173e704f890abd615cc796d23141636ad0d Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 16:29:57 +0100 Subject: [PATCH 030/127] log --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index ec806a7..f76421a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -211,6 +211,7 @@ public class MultiThreadTreeLoader { if(wrBuf.remaining() > 500) { wrBuf.put(buf); }else{ + log.info("Next pair dump"); fileCounter++; rwChannel = new RandomAccessFile(outputPath +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); From 2492d36dbe349b3e7d87906593aa92ed4253fd83 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 16:38:28 +0100 Subject: [PATCH 031/127] path correction --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index f76421a..6201b86 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -213,7 +213,7 @@ public class MultiThreadTreeLoader { }else{ log.info("Next pair dump"); fileCounter++; - rwChannel = new RandomAccessFile(outputPath +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); } From d7bd815ef609ebb85b6bad20708e3b37407b0cfe Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 17:38:55 +0100 Subject: [PATCH 032/127] paths; --- .../violations/MultiThreadTreeLoader.java | 50 ++++++++++++++++++- 1 file changed, 49 insertions(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 6201b86..32c7879 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -47,8 +47,9 @@ public class MultiThreadTreeLoader { } - calculatePairs(inputPath, outputPath); +// calculatePairs(inputPath, outputPath); processMessages(inputPath,outputPath); + evaluateResults(inputPath,outputPath); @@ -89,6 +90,17 @@ public class MultiThreadTreeLoader { .forEach(m -> coreLoop(m, outputPath,inputPath)); } + public static void evaluateResults(String inputPath, String outputPath){ + File folder = new File(outputPath + "comparison/"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + pjs.parallelStream() + .forEach(m -> coreEval(m, outputPath,inputPath)); + } + public static ITree getSimpliedTree(String fn) { ITree tree = null; try { @@ -119,6 +131,42 @@ public class MultiThreadTreeLoader { } + private static void coreEval(File mes, String outputPath,String inputPath) { + try { + + log.info("Starting in coreLoop"); + + BufferedReader br = null; + String sCurrentLine = null; + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "/" + "eval_" + mes.getName())); + + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + Double chawatheSimilarity = Double.valueOf(split[2]); + Double diceSimilarity = Double.valueOf(split[3]); + Double jaccardSimilarity = Double.valueOf(split[4]); + int actionSize = Integer.valueOf(split[5]); +// String firstValue = split[6]; +// String secondValue = split[7]; + if (chawatheSimilarity.equals(1.0) || diceSimilarity.equals(1.0) || jaccardSimilarity.equals(1.0) || actionSize == 0){ + writer.write(currentLine); + writer.write("\n"); + } + } + writer.close(); + } catch (FileNotFoundException e) { + System.out.println("File not found"); + } catch (IOException e) { + System.out.println("Error initializing stream"); + + } + } + private static void coreLoop(File mes, String outputPath,String inputPath) { try { From 182b000ad1e0e623ea42d4dfa3328f9a551230c2 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 18:30:48 +0100 Subject: [PATCH 033/127] filepath --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 32c7879..66538f2 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -186,8 +186,8 @@ public class MultiThreadTreeLoader { String firstValue = split[2]; String secondValue = split[3]; - firstValue = inputPath + firstValue; - secondValue = inputPath + secondValue; + firstValue = inputPath + firstValue.substring(1);; + secondValue = inputPath + secondValue.substring(1);; ITree oldTree = getSimpliedTree(firstValue); From 951303b43bc3aeaed2dd76812a3260d73bcf9003 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 18:36:42 +0100 Subject: [PATCH 034/127] error --- .../violations/MultiThreadTreeLoader.java | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 66538f2..fe98a0a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -112,9 +112,11 @@ public class MultiThreadTreeLoader { } catch (FileNotFoundException e) { - System.out.println("File not found"); + log.error("File not found"); + e.printStackTrace(); } catch (IOException e) { - System.out.println("Error initializing stream"); + log.error("Error initializing stream"); + e.printStackTrace(); } catch (ClassNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); @@ -160,9 +162,11 @@ public class MultiThreadTreeLoader { } writer.close(); } catch (FileNotFoundException e) { - System.out.println("File not found"); + log.error("File not found"); + e.printStackTrace(); } catch (IOException e) { - System.out.println("Error initializing stream"); + log.error("Error initializing stream"); + e.printStackTrace(); } } @@ -221,9 +225,11 @@ public class MultiThreadTreeLoader { } writer.close(); } catch (FileNotFoundException e) { - System.out.println("File not found"); + log.error("File not found"); + e.printStackTrace(); } catch (IOException e) { - System.out.println("Error initializing stream"); + log.error("Error initializing stream"); + e.printStackTrace(); } } From 5af57d23b241ccddb121e3fd7930dcea40dc3cbf Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 18:47:22 +0100 Subject: [PATCH 035/127] path fix --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index fe98a0a..6d2ad81 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -190,8 +190,8 @@ public class MultiThreadTreeLoader { String firstValue = split[2]; String secondValue = split[3]; - firstValue = inputPath + firstValue.substring(1);; - secondValue = inputPath + secondValue.substring(1);; + firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; + secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; ITree oldTree = getSimpliedTree(firstValue); From 75f6d5d996ebb7f9ea5dee36363b4e19c006a5b9 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 19 Mar 2018 22:01:21 +0100 Subject: [PATCH 036/127] splitted --- .../violations/MultiThreadTreeLoader.java | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 6d2ad81..3bb4556 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -79,24 +79,25 @@ public class MultiThreadTreeLoader { } public static void processMessages(String inputPath, String outputPath) { - File folder = new File(outputPath + "pairs/"); + File folder = new File(outputPath + "pairs_splitted/"); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List pjs = stream .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "comparison/"); + FileHelper.createDirectory(outputPath + "comparison_splitted/"); pjs.parallelStream() .forEach(m -> coreLoop(m, outputPath,inputPath)); } public static void evaluateResults(String inputPath, String outputPath){ - File folder = new File(outputPath + "comparison/"); + File folder = new File(outputPath + "comparison_splitted/"); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List pjs = stream .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); + FileHelper.createDirectory(outputPath + "eval_splitted/"); pjs.parallelStream() .forEach(m -> coreEval(m, outputPath,inputPath)); } @@ -140,7 +141,7 @@ public class MultiThreadTreeLoader { BufferedReader br = null; String sCurrentLine = null; - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "/" + "eval_" + mes.getName())); + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "eval_splitted/" + "eval_" + mes.getName())); br = new BufferedReader( new FileReader(mes)); @@ -178,7 +179,7 @@ public class MultiThreadTreeLoader { BufferedReader br = null; String sCurrentLine = null; - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison/" + "output_" + mes.getName())); + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); br = new BufferedReader( new FileReader(mes)); @@ -232,6 +233,7 @@ public class MultiThreadTreeLoader { e.printStackTrace(); } + log.info("Completed output_" + mes.getName()); } private static void readMessageFiles(List folders, String outputPath) { From ce634034e46ef965582177cc254825442982edc0 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 22 Mar 2018 23:03:22 +0100 Subject: [PATCH 037/127] rds --- FixPatternMiner.iml | 2 + pom.xml | 7 + .../violations/MultiThreadTreeLoader.java | 128 +++++++++++++++++- 3 files changed, 131 insertions(+), 6 deletions(-) diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index 2df3bc9..a1e4217 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -54,5 +54,7 @@ + + \ No newline at end of file diff --git a/pom.xml b/pom.xml index b333845..ad887f3 100644 --- a/pom.xml +++ b/pom.xml @@ -60,6 +60,13 @@ 4.12 test + + + redis.clients + jedis + 2.8.1 + + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 3bb4556..9a8dd78 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -13,14 +13,13 @@ import edu.lu.uni.serval.utils.FileHelper; import javafx.util.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; import java.io.*; import java.nio.ByteBuffer; import java.nio.channels.FileChannel; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; +import java.time.Duration; +import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; import java.util.zip.Deflater; @@ -48,13 +47,100 @@ public class MultiThreadTreeLoader { // calculatePairs(inputPath, outputPath); - processMessages(inputPath,outputPath); - evaluateResults(inputPath,outputPath); +// processMessages(inputPath,outputPath); +// evaluateResults(inputPath,outputPath); + + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + Set names = jedis.keys("*"); + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_*"); + ScanResult scan = jedis.scan("0",sc); + +// java.util.Iterator it = names.iterator(); +// while(it.hasNext()) { +// String s = it.next(); +// System.out.println(s + " : " + jedis.get(s)); +// } + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath)); + } } + private static void coreCompare(String name , String inputPath) { + + String value; + try (Jedis jedis = jedisPool.getResource()) { + + + value = jedis.get(name); + + + String[] split = value.split(","); + log.info("Starting in coreLoop"); + + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; + + String[] firstValueSplit = firstValue.split("GumTreeOutput2"); + String[] secondValueSplit = secondValue.split("GumTreeOutput2"); + + if (firstValueSplit.length == 1) { + firstValue = inputPath + firstValueSplit[0]; + } else { + firstValue = inputPath + firstValueSplit[1]; + } + + if (secondValueSplit.length == 1) { + secondValue = inputPath + secondValueSplit[0]; + } else { + secondValue = inputPath + secondValueSplit[1]; + } + + + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f",chawatheSimilarity1 ); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f",diceSimilarity1 ); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); + + String result = chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + jedis.set(resultKey, result); + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0){ + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.set(matchKey, result); + } + + + log.info("Completed " + resultKey); + } + } + + + public static void calculatePairs(String inputPath, String outputPath) { File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); @@ -141,6 +227,18 @@ public class MultiThreadTreeLoader { BufferedReader br = null; String sCurrentLine = null; + + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + Set names = jedis.keys("*"); + + java.util.Iterator it = names.iterator(); + while(it.hasNext()) { + String s = it.next(); + System.out.println(s + " : " + jedis.get(s)); + } + } + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "eval_splitted/" + "eval_" + mes.getName())); br = new BufferedReader( @@ -292,6 +390,24 @@ public class MultiThreadTreeLoader { log.info("Done pairs"); } + static final JedisPoolConfig poolConfig = buildPoolConfig(); + static JedisPool jedisPool = new JedisPool(poolConfig, "localhost"); + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofSeconds(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofSeconds(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + return poolConfig; + } + // return msgFiles; From c365ccb780d1c0feb963dacb52a6aea18a087f0c Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 22 Mar 2018 23:19:11 +0100 Subject: [PATCH 038/127] timeout --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 9a8dd78..6d5050b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -401,10 +401,11 @@ public class MultiThreadTreeLoader { poolConfig.setTestOnBorrow(true); poolConfig.setTestOnReturn(true); poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofSeconds(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofSeconds(30).toMillis()); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); poolConfig.setNumTestsPerEvictionRun(3); poolConfig.setBlockWhenExhausted(true); + return poolConfig; } From a2f67f6134718fdd7d5fa1c7438c81584665bddf Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 22 Mar 2018 23:30:39 +0100 Subject: [PATCH 039/127] address --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 6d5050b..5569749 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -391,7 +391,7 @@ public class MultiThreadTreeLoader { } static final JedisPoolConfig poolConfig = buildPoolConfig(); - static JedisPool jedisPool = new JedisPool(poolConfig, "localhost"); + static JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1"); private static JedisPoolConfig buildPoolConfig() { final JedisPoolConfig poolConfig = new JedisPoolConfig(); From 3f82ebd57db55a290f4ec8b50896cf70fad3de7d Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 23 Mar 2018 10:12:43 +0100 Subject: [PATCH 040/127] timeout --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 5569749..5e577b0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -391,7 +391,7 @@ public class MultiThreadTreeLoader { } static final JedisPoolConfig poolConfig = buildPoolConfig(); - static JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1"); + static JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",6379,20000000); private static JedisPoolConfig buildPoolConfig() { final JedisPoolConfig poolConfig = new JedisPoolConfig(); From 884016e612772eb9096cd4bc70a1ace284c9ec54 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Mar 2018 18:55:00 +0100 Subject: [PATCH 041/127] red --- .../violations/MultiThreadTreeLoader.java | 239 ++++++++++++------ 1 file changed, 155 insertions(+), 84 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 5e577b0..b7b6f76 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -20,6 +20,8 @@ import java.nio.ByteBuffer; import java.nio.channels.FileChannel; import java.time.Duration; import java.util.*; +import java.util.concurrent.Executors; +import java.util.function.Consumer; import java.util.stream.Collectors; import java.util.stream.Stream; import java.util.zip.Deflater; @@ -30,6 +32,23 @@ import java.util.zip.GZIPOutputStream; * Created by anilkoyuncu on 19/03/2018. */ public class MultiThreadTreeLoader { + + private static class StreamGobbler implements Runnable { + private InputStream inputStream; + private Consumer consumer; + + public StreamGobbler(InputStream inputStream, Consumer consumer) { + this.inputStream = inputStream; + this.consumer = consumer; + } + + @Override + public void run() { + new BufferedReader(new InputStreamReader(inputStream)).lines() + .forEach(consumer); + } + } + private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoader.class); public static void main(String[] args) { @@ -37,56 +56,107 @@ public class MultiThreadTreeLoader { String inputPath; String outputPath; + String port; + String pairsCSVPath; + String importScript; if (args.length > 0) { inputPath = args[0]; outputPath = args[1]; + port = args[2]; + pairsCSVPath = args[3]; + importScript = args[4]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6379"; + pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; + importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; } + String cmd; + cmd = "bash " + importScript +" %s"; + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); // calculatePairs(inputPath, outputPath); // processMessages(inputPath,outputPath); // evaluateResults(inputPath,outputPath); - try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - Set names = jedis.keys("*"); - ScanParams sc = new ScanParams(); - sc.count(150000000); - sc.match("pair_*"); - ScanResult scan = jedis.scan("0",sc); + File folder = new File(pairsCSVPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + for (File f:folders){ + + + Process process; + + try { + String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(comd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); + int exitCode = process.waitFor(); + assert exitCode == 0; + } catch (IOException e) { + e.printStackTrace(); + } catch (InterruptedException e) { + e.printStackTrace(); + } + + + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + // Set names = jedis.keys("*"); + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_*"); + jedis.configSet("dbfilename",f.getName()); + + ScanResult scan = jedis.scan("0",sc); + + // java.util.Iterator it = names.iterator(); + // while(it.hasNext()) { + // String s = it.next(); + // System.out.println(s + " : " + jedis.get(s)); + // } + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool)); + + jedis.save(); + } -// java.util.Iterator it = names.iterator(); -// while(it.hasNext()) { -// String s = it.next(); -// System.out.println(s + " : " + jedis.get(s)); -// } - scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath)); } } - private static void coreCompare(String name , String inputPath) { + private static void coreCompare(String name , String inputPath, JedisPool jedisPool) { + - String value; try (Jedis jedis = jedisPool.getResource()) { - value = jedis.get(name); + Map resultMap = jedis.hgetAll(name); + + resultMap.get("0"); - String[] split = value.split(","); + String[] split = name.split("_"); log.info("Starting in coreLoop"); - String i = split[0]; - String j = split[1]; - String firstValue = split[2]; - String secondValue = split[3]; + String i = split[1]; + String j = split[2]; + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); String[] firstValueSplit = firstValue.split("GumTreeOutput2"); String[] secondValueSplit = secondValue.split("GumTreeOutput2"); @@ -124,13 +194,14 @@ public class MultiThreadTreeLoader { String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); String editDistance = String.valueOf(actions.size()); - + jedis.select(1); String result = chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; jedis.set(resultKey, result); if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0){ String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.select(2); jedis.set(matchKey, result); } @@ -176,17 +247,17 @@ public class MultiThreadTreeLoader { .forEach(m -> coreLoop(m, outputPath,inputPath)); } - public static void evaluateResults(String inputPath, String outputPath){ - File folder = new File(outputPath + "comparison_splitted/"); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "eval_splitted/"); - pjs.parallelStream() - .forEach(m -> coreEval(m, outputPath,inputPath)); - } +// public static void evaluateResults(String inputPath, String outputPath){ +// File folder = new File(outputPath + "comparison_splitted/"); +// File[] listOfFiles = folder.listFiles(); +// Stream stream = Arrays.stream(listOfFiles); +// List pjs = stream +// .filter(x -> !x.getName().startsWith(".")) +// .collect(Collectors.toList()); +// FileHelper.createDirectory(outputPath + "eval_splitted/"); +// pjs.parallelStream() +// .forEach(m -> coreEval(m, outputPath,inputPath)); +// } public static ITree getSimpliedTree(String fn) { ITree tree = null; @@ -220,55 +291,55 @@ public class MultiThreadTreeLoader { } - private static void coreEval(File mes, String outputPath,String inputPath) { - try { - - log.info("Starting in coreLoop"); - - BufferedReader br = null; - String sCurrentLine = null; - - try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - Set names = jedis.keys("*"); - - java.util.Iterator it = names.iterator(); - while(it.hasNext()) { - String s = it.next(); - System.out.println(s + " : " + jedis.get(s)); - } - } - - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "eval_splitted/" + "eval_" + mes.getName())); - - br = new BufferedReader( - new FileReader(mes)); - while ((sCurrentLine = br.readLine()) != null) { - String currentLine = sCurrentLine; - String[] split = currentLine.split("\t"); - String i = split[0]; - String j = split[1]; - Double chawatheSimilarity = Double.valueOf(split[2]); - Double diceSimilarity = Double.valueOf(split[3]); - Double jaccardSimilarity = Double.valueOf(split[4]); - int actionSize = Integer.valueOf(split[5]); -// String firstValue = split[6]; -// String secondValue = split[7]; - if (chawatheSimilarity.equals(1.0) || diceSimilarity.equals(1.0) || jaccardSimilarity.equals(1.0) || actionSize == 0){ - writer.write(currentLine); - writer.write("\n"); - } - } - writer.close(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - - } - } +// private static void coreEval(File mes, String outputPath,String inputPath) { +// try { +// +// log.info("Starting in coreLoop"); +// +// BufferedReader br = null; +// String sCurrentLine = null; +// +// try (Jedis jedis = jedisPool.getResource()) { +// // do operations with jedis resource +// Set names = jedis.keys("*"); +// +// java.util.Iterator it = names.iterator(); +// while(it.hasNext()) { +// String s = it.next(); +// System.out.println(s + " : " + jedis.get(s)); +// } +// } +// +// BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "eval_splitted/" + "eval_" + mes.getName())); +// +// br = new BufferedReader( +// new FileReader(mes)); +// while ((sCurrentLine = br.readLine()) != null) { +// String currentLine = sCurrentLine; +// String[] split = currentLine.split("\t"); +// String i = split[0]; +// String j = split[1]; +// Double chawatheSimilarity = Double.valueOf(split[2]); +// Double diceSimilarity = Double.valueOf(split[3]); +// Double jaccardSimilarity = Double.valueOf(split[4]); +// int actionSize = Integer.valueOf(split[5]); +//// String firstValue = split[6]; +//// String secondValue = split[7]; +// if (chawatheSimilarity.equals(1.0) || diceSimilarity.equals(1.0) || jaccardSimilarity.equals(1.0) || actionSize == 0){ +// writer.write(currentLine); +// writer.write("\n"); +// } +// } +// writer.close(); +// } catch (FileNotFoundException e) { +// log.error("File not found"); +// e.printStackTrace(); +// } catch (IOException e) { +// log.error("Error initializing stream"); +// e.printStackTrace(); +// +// } +// } private static void coreLoop(File mes, String outputPath,String inputPath) { try { @@ -391,7 +462,7 @@ public class MultiThreadTreeLoader { } static final JedisPoolConfig poolConfig = buildPoolConfig(); - static JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",6379,20000000); + private static JedisPoolConfig buildPoolConfig() { final JedisPoolConfig poolConfig = new JedisPoolConfig(); From 37bf7e69c14d3f80c2e2f026e2459097c48934f6 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Mar 2018 19:40:52 +0100 Subject: [PATCH 042/127] flushdb --- .../violations/MultiThreadTreeLoader.java | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index b7b6f76..50a33b0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -92,7 +92,7 @@ public class MultiThreadTreeLoader { Process process; - + log.info(f.getName()); try { String comd = String.format(cmd, f.getAbsoluteFile()); process = Runtime.getRuntime() @@ -110,7 +110,7 @@ public class MultiThreadTreeLoader { } catch (InterruptedException e) { e.printStackTrace(); } - + log.info("Load done"); try (Jedis jedis = jedisPool.getResource()) { // do operations with jedis resource @@ -118,10 +118,10 @@ public class MultiThreadTreeLoader { ScanParams sc = new ScanParams(); sc.count(150000000); sc.match("pair_*"); - jedis.configSet("dbfilename",f.getName()); - +// jedis.configSet("dbfilename",f.getName()); + log.info("Scanning"); ScanResult scan = jedis.scan("0",sc); - + log.info("Scanning " + String.valueOf(scan.getResult().size())); // java.util.Iterator it = names.iterator(); // while(it.hasNext()) { // String s = it.next(); @@ -130,7 +130,11 @@ public class MultiThreadTreeLoader { scan.getResult().parallelStream() .forEach(m -> coreCompare(m, inputPath, jedisPool)); + jedis.select(0); + jedis.flushDB(); + jedis.save(); + } } From b7936f05a702b01e1ae95ba53e4a1533412c7abd Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Mar 2018 20:00:21 +0100 Subject: [PATCH 043/127] only %100 match --- .../violations/MultiThreadTreeLoader.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 50a33b0..821d3b1 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -198,14 +198,14 @@ public class MultiThreadTreeLoader { String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); String editDistance = String.valueOf(actions.size()); - jedis.select(1); - String result = chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; - jedis.set(resultKey, result); +// jedis.select(1); + String result = resultMap.get("0") + "," +resultMap.get("1") + "," +chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; +// jedis.set(resultKey, result); if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0){ String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - jedis.select(2); + jedis.select(1); jedis.set(matchKey, result); } From 25737ae3bb8abd94cbd12d5867e2cec37985d529 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 24 Mar 2018 22:39:05 +0100 Subject: [PATCH 044/127] error handling --- .../violations/MultiThreadTreeLoader.java | 63 +++++++++++-------- 1 file changed, 38 insertions(+), 25 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 821d3b1..de83b3f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -130,8 +130,8 @@ public class MultiThreadTreeLoader { scan.getResult().parallelStream() .forEach(m -> coreCompare(m, inputPath, jedisPool)); - jedis.select(0); - jedis.flushDB(); +// jedis.select(0); +// jedis.flushDB(); jedis.save(); @@ -155,7 +155,7 @@ public class MultiThreadTreeLoader { String[] split = name.split("_"); - log.info("Starting in coreLoop"); + String i = split[1]; String j = split[2]; @@ -177,40 +177,53 @@ public class MultiThreadTreeLoader { secondValue = inputPath + secondValueSplit[1]; } + try { + ITree oldTree = getSimpliedTree(firstValue); - ITree oldTree = getSimpliedTree(firstValue); + ITree newTree = getSimpliedTree(secondValue); - ITree newTree = getSimpliedTree(secondValue); + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); - String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); - double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); - String chawatheSimilarity = String.format("%1.2f",chawatheSimilarity1 ); - double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); - String diceSimilarity = String.format("%1.2f",diceSimilarity1 ); - double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); - String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - String editDistance = String.valueOf(actions.size()); + String editDistance = String.valueOf(actions.size()); // jedis.select(1); - String result = resultMap.get("0") + "," +resultMap.get("1") + "," +chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; // jedis.set(resultKey, result); - if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) - || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0){ - String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - jedis.select(1); - jedis.set(matchKey, result); + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.select(1); + jedis.set(matchKey, result); + } + jedis.select(0); + String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.del(pairKey); + +// log.info("Completed " + resultKey); + + }catch (Exception e){ + log.error(e.toString() + " {}",(name)); + + } - log.info("Completed " + resultKey); + + } } From 03899d217eb746f76bf28abd22f612cef1129fd8 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 28 Mar 2018 11:40:27 +0200 Subject: [PATCH 045/127] continue from checkpoint --- .../violations/MultiThreadTreeLoader.java | 135 ++++++------------ 1 file changed, 43 insertions(+), 92 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index de83b3f..4de8367 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -51,6 +51,30 @@ public class MultiThreadTreeLoader { private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoader.class); + + public static void loadRedis(String cmd, File f){ + Process process; + log.info(f.getName()); + try { + String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(comd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); + int exitCode = process.waitFor(); + assert exitCode == 0; + } catch (IOException e) { + e.printStackTrace(); + } catch (InterruptedException e) { + e.printStackTrace(); + } + log.info("Load done"); + } + public static void main(String[] args) { @@ -59,18 +83,21 @@ public class MultiThreadTreeLoader { String port; String pairsCSVPath; String importScript; + String pairsCompletedPath; if (args.length > 0) { inputPath = args[0]; outputPath = args[1]; port = args[2]; pairsCSVPath = args[3]; importScript = args[4]; + pairsCompletedPath = args[3]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; port = "6379"; pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; + pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; } String cmd; @@ -88,54 +115,37 @@ public class MultiThreadTreeLoader { .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); + //create dir + File file = new File(pairsCompletedPath); + file.mkdirs(); + for (File f:folders){ - Process process; - log.info(f.getName()); - try { - String comd = String.format(cmd, f.getAbsoluteFile()); - process = Runtime.getRuntime() - - .exec(comd); - - - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); - Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; - } catch (IOException e) { - e.printStackTrace(); - } catch (InterruptedException e) { - e.printStackTrace(); - } - log.info("Load done"); try (Jedis jedis = jedisPool.getResource()) { // do operations with jedis resource - // Set names = jedis.keys("*"); ScanParams sc = new ScanParams(); sc.count(150000000); sc.match("pair_*"); -// jedis.configSet("dbfilename",f.getName()); - log.info("Scanning"); + ScanResult scan = jedis.scan("0",sc); - log.info("Scanning " + String.valueOf(scan.getResult().size())); - // java.util.Iterator it = names.iterator(); - // while(it.hasNext()) { - // String s = it.next(); - // System.out.println(s + " : " + jedis.get(s)); - // } + int size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + if (size == 0){ + loadRedis(cmd,f); + + scan = jedis.scan("0",sc); + size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + } scan.getResult().parallelStream() .forEach(m -> coreCompare(m, inputPath, jedisPool)); -// jedis.select(0); -// jedis.flushDB(); - jedis.save(); } + f.renameTo(new File(pairsCompletedPath, f.getName())); } @@ -264,17 +274,6 @@ public class MultiThreadTreeLoader { .forEach(m -> coreLoop(m, outputPath,inputPath)); } -// public static void evaluateResults(String inputPath, String outputPath){ -// File folder = new File(outputPath + "comparison_splitted/"); -// File[] listOfFiles = folder.listFiles(); -// Stream stream = Arrays.stream(listOfFiles); -// List pjs = stream -// .filter(x -> !x.getName().startsWith(".")) -// .collect(Collectors.toList()); -// FileHelper.createDirectory(outputPath + "eval_splitted/"); -// pjs.parallelStream() -// .forEach(m -> coreEval(m, outputPath,inputPath)); -// } public static ITree getSimpliedTree(String fn) { ITree tree = null; @@ -308,55 +307,7 @@ public class MultiThreadTreeLoader { } -// private static void coreEval(File mes, String outputPath,String inputPath) { -// try { -// -// log.info("Starting in coreLoop"); -// -// BufferedReader br = null; -// String sCurrentLine = null; -// -// try (Jedis jedis = jedisPool.getResource()) { -// // do operations with jedis resource -// Set names = jedis.keys("*"); -// -// java.util.Iterator it = names.iterator(); -// while(it.hasNext()) { -// String s = it.next(); -// System.out.println(s + " : " + jedis.get(s)); -// } -// } -// -// BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "eval_splitted/" + "eval_" + mes.getName())); -// -// br = new BufferedReader( -// new FileReader(mes)); -// while ((sCurrentLine = br.readLine()) != null) { -// String currentLine = sCurrentLine; -// String[] split = currentLine.split("\t"); -// String i = split[0]; -// String j = split[1]; -// Double chawatheSimilarity = Double.valueOf(split[2]); -// Double diceSimilarity = Double.valueOf(split[3]); -// Double jaccardSimilarity = Double.valueOf(split[4]); -// int actionSize = Integer.valueOf(split[5]); -//// String firstValue = split[6]; -//// String secondValue = split[7]; -// if (chawatheSimilarity.equals(1.0) || diceSimilarity.equals(1.0) || jaccardSimilarity.equals(1.0) || actionSize == 0){ -// writer.write(currentLine); -// writer.write("\n"); -// } -// } -// writer.close(); -// } catch (FileNotFoundException e) { -// log.error("File not found"); -// e.printStackTrace(); -// } catch (IOException e) { -// log.error("Error initializing stream"); -// e.printStackTrace(); -// -// } -// } + private static void coreLoop(File mes, String outputPath,String inputPath) { try { From d6be9c73657905d1fd01201ed8291507e54f5dcb Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 28 Mar 2018 13:33:21 +0200 Subject: [PATCH 046/127] tree cluster --- .../serval/FixPattern/utils/ASTNodeMap.java | 7 + .../MultiThreadTreeLoaderCluster.java | 689 ++++++++++++++++++ 2 files changed, 696 insertions(+) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java index 29d2699..266063c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/ASTNodeMap.java @@ -105,5 +105,12 @@ public class ASTNodeMap { map.put(90, "ExpressionMethodReference"); map.put(91, "SuperMethodReference"); map.put(92, "TypeMethodReference"); + + + map.put(100,"Insert"); + map.put(101,"Update"); + map.put(102,"Delete"); + map.put(103,"Move"); + map.put(104,"NoChange"); } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java new file mode 100644 index 0000000..21ec977 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -0,0 +1,689 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.gumtree.GumTreeComparer; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; +import edu.lu.uni.serval.utils.FileHelper; +import edu.lu.uni.serval.utils.ListSorter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; + +import java.io.*; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; +import java.time.Duration; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.function.Consumer; +import java.util.regex.Pattern; +import java.util.stream.Collectors; +import java.util.stream.Stream; +import javafx.util.*; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class MultiThreadTreeLoaderCluster { + + private static int resultType; + + private static class StreamGobbler implements Runnable { + private InputStream inputStream; + private Consumer consumer; + + public StreamGobbler(InputStream inputStream, Consumer consumer) { + this.inputStream = inputStream; + this.consumer = consumer; + } + + @Override + public void run() { + new BufferedReader(new InputStreamReader(inputStream)).lines() + .forEach(consumer); + } + } + + private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster.class); + + public static void main(String[] args){ + + String inputPath; + String outputPath; + String port; + String pairsCSVPath; + String importScript; + if (args.length > 0) { + inputPath = args[0]; + outputPath = args[1]; + port = args[2]; + pairsCSVPath = args[3]; + importScript = args[4]; + } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + inputPath = "/Users/anilkoyuncu/bugStudy/code/python/clusterDumps"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6379"; + pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_csv/"; + importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; + } + +// calculatePairsOfClusters(inputPath, outputPath); + mainCompare(inputPath,port,pairsCSVPath,importScript); + // calculatePairs(inputPath, outputPath); +// processMessages(inputPath,outputPath); +// evaluateResults(inputPath,outputPath); + + } + + public static void loadRedis(String cmd, File f){ + Process process; + log.info(f.getName()); + try { + String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(comd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); + int exitCode = process.waitFor(); + assert exitCode == 0; + } catch (IOException e) { + e.printStackTrace(); + } catch (InterruptedException e) { + e.printStackTrace(); + } + log.info("Load done"); + } + + public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { + + String cmd; + cmd = "bash " + importScript +" %s"; + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + + + File folder = new File(pairsCSVPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + for (File f:folders){ + + + + + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_[0-9]*"); + + log.info("Scanning"); + ScanResult scan = jedis.scan("0",sc); + int size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + if (size == 0){ + loadRedis(cmd,f); + + scan = jedis.scan("0",sc); + size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + } + + + + String clusterName = f.getName().replaceAll("[^0-9]+", ""); + + + + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool,clusterName)); + + + + + jedis.save(); + + } + + + } + + + + } + + + + public static Pair getTree(String firstValue){ + String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; + String[] split2 = firstValue.split("/"); + String cluster = split2[1]; + + + File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) + .collect(Collectors.toList()); + + + + String[] split1 = folders.get(0).getName().split(".txt_"); + String s = split1[0]; + String[] splitPJ = split1[1].split("_"); + String project = splitPJ[1]; + String actionSetPosition = splitPJ[0]; + + File prevFile = new File(gumTreeInput + project+ "/" + "prevFiles/prev_" + s + ".java");// previous file + File revFile = new File(gumTreeInput + project+ "/" + "revFiles/" + s + ".java");//rev file + + List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); + + HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); +// for (HierarchicalActionSet actionSet : actionSets) { + + ITree test = getActionTree(actionSet); + test.getLabel(); + for (ITree descendant : test.getDescendants()) { +// descendant.setLabel(""); + if(!(descendant.getType() == 100 || descendant.getType() == 101 || descendant.getType() == 102 || descendant.getType() == 103)){ + descendant.setType(104); + } + } + test.getDescendants(); + test.setParent(null); +// } +// } + + Pair pair = new Pair<>(test,project); + return pair; + } + + public static ITree getActionTree(HierarchicalActionSet actionSet){ + + + int newType = 0; + + Action action = actionSet.getAction(); + if (action instanceof Update){ + newType = 101; + }else if(action instanceof Insert){ + newType =100; + }else if(action instanceof Move){ + newType = 102; + }else if(action instanceof Delete){ + newType=103; + }else{ + new Exception("unknow action"); + } + actionSet.getNode().setType(newType); +// actionSet.getNode().setLabel(""); + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + getActionTree(subAction); + } + + + } + return actionSet.getNode(); + } + + + + private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName) { + + + try (Jedis jedis = jedisPool.getResource()) { + + + Map resultMap = jedis.hgetAll(name); + + resultMap.get("0"); + + + String[] split = name.split("_"); + String i = null; + String j =null; + try { + i = split[1]; + j = split[2]; + } + catch (Exception e){ + e.printStackTrace(); + } + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + + + + + +// firstValue = inputPath + firstValue; +// secondValue = inputPath + secondValue; + +// String[] firstValueSplit = firstValue.split("/"); +// String[] secondValueSplit = secondValue.split("/"); +// +// if (firstValueSplit.length == 1) { +// firstValue = inputPath + firstValueSplit[0]; +// } else { +// firstValue = inputPath + firstValueSplit[1]; +// } +// +// if (secondValueSplit.length == 1) { +// secondValue = inputPath + secondValueSplit[0]; +// } else { +// secondValue = inputPath + secondValueSplit[1]; +// } + + try { + Pair oldPair = getTree(firstValue); + Pair newPair = getTree(secondValue); + + ITree oldTree = oldPair.getKey(); + ITree newTree = newPair.getKey(); + + String oldProject = oldPair.getValue(); + String newProject = newPair.getValue(); + + + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); +// jedis.select(1); + String result = resultMap.get("0") + "," + oldProject +"," + resultMap.get("1") + "," +newProject+ "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; +// jedis.set(resultKey, result); + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.select(1); + jedis.set(matchKey, result); + } + jedis.select(0); + String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.del(pairKey); + +// log.info("Completed " + resultKey); + + }catch (Exception e){ + log.error(e.toString() + " {}",(name)); + + + } + + + + + } + } + + + + protected static List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { + List actionSets = new ArrayList<>(); + // GumTree results + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); + if (gumTreeResults == null) { + resultType = 1; + return null; + } else if (gumTreeResults.size() == 0){ + resultType = 2; + return actionSets; + } else { + // Regroup GumTre results. + List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); +// for (HierarchicalActionSet actionSet : allActionSets) { +// String astNodeType = actionSet.getAstNodeType(); +// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { +// actionSets.add(actionSet); +// } +// } + + // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. + // variable effects range, sub-actions are these kinds of modification? +// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); + + ListSorter sorter = new ListSorter<>(allActionSets); + actionSets = sorter.sortAscending(); + + if (actionSets.size() == 0) { + resultType = 3; + } + + return actionSets; + } + } + + +/* +orginal calculate pairs, from all dumps of the projects + */ + public static void calculatePairs(String inputPath, String outputPath) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for (File pj : pjs) { + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ASTDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + readMessageFiles(fileToCompare, outputPath); + } + + /* + pairs of each cluster + */ + public static void calculatePairsOfClusters(String inputPath, String outputPath) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + FileHelper.createDirectory(outputPath + "pairs/"); + for (File pj : pjs) { + File[] files = pj.listFiles(); + List fileList = Arrays.asList(files); + + readMessageFilesCluster(fileList, outputPath,inputPath,pj.getName()); + + } + + } + + public static void processMessages(String inputPath, String outputPath) { + File folder = new File(outputPath + "pairs_splitted/"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + FileHelper.createDirectory(outputPath + "comparison_splitted/"); + pjs.parallelStream() + .forEach(m -> coreLoop(m, outputPath,inputPath)); + } + + private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + + String filename = "cluster" + cluster; + byte [] buf = new byte[0]; + String line = null; + try { + + FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +filename+".txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, 1000*treesFileNames.size()*treesFileNames.size()); + int fileCounter = 0; + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"pairs/" +filename+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + } + + + + + } + } + rwChannel.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); + } + + log.info("Done pairs"); + } + + + + public static ITree getSimpliedTree(String fn) { + ITree tree = null; + try { + FileInputStream fi = new FileInputStream(new File(fn)); + ObjectInputStream oi = new ObjectInputStream(fi); + tree = (ITree) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + +// tree.setLabel(""); + tree.setParent(null); +// List descendants = tree.getDescendants(); +// for (ITree descendant : descendants) { +// descendant.setLabel(""); +// } + + return tree; + + } + + + private static void coreLoop(File mes, String outputPath,String inputPath) { + try { + + log.info("Starting in coreLoop"); + + BufferedReader br = null; + String sCurrentLine = null; + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); + + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; + + firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; + secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; + + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); + + + } + writer.close(); + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + + } + log.info("Completed output_" + mes.getName()); + } + + private static void readMessageFiles(List folders, String outputPath) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + FileHelper.createDirectory(outputPath + "pairs/"); + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + byte [] buf = new byte[0]; + String line = null; + try { + + FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + } + + + + + } + } + rwChannel.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); + } + + log.info("Done pairs"); + } + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + + + +// return msgFiles; +} + + + + From e627d861402b5917eae147492e75b97eb4d1288b Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 28 Mar 2018 13:43:43 +0200 Subject: [PATCH 047/127] change lib --- .../FixPatternParser/violations/MMapper.java | 103 ------------------ .../FixPatternParser/violations/Message.java | 32 ------ .../violations/MultiThreadTreeLoader.java | 8 -- .../MultiThreadTreeLoaderCluster.java | 11 +- 4 files changed, 5 insertions(+), 149 deletions(-) delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java deleted file mode 100644 index 61b755c..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MMapper.java +++ /dev/null @@ -1,103 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -/** - * Created by anilkoyuncu on 19/03/2018. - */ -import java.io.RandomAccessFile; -import java.lang.reflect.Field; -import java.lang.reflect.Method; -import java.nio.channels.FileChannel; - -import sun.nio.ch.FileChannelImpl; -import sun.misc.Unsafe; - -@SuppressWarnings("restriction") -public class MMapper { - - private static final Unsafe unsafe; - private static final Method mmap; - private static final Method unmmap; - private static final int BYTE_ARRAY_OFFSET; - - private long addr, size; - private final String loc; - - static { - try { - Field singleoneInstanceField = Unsafe.class.getDeclaredField("theUnsafe"); - singleoneInstanceField.setAccessible(true); - unsafe = (Unsafe) singleoneInstanceField.get(null); - - mmap = getMethod(FileChannelImpl.class, "map0", int.class, long.class, long.class); - unmmap = getMethod(FileChannelImpl.class, "unmap0", long.class, long.class); - - BYTE_ARRAY_OFFSET = unsafe.arrayBaseOffset(byte[].class); - } catch (Exception e){ - throw new RuntimeException(e); - } - } - - //Bundle reflection calls to get access to the given method - private static Method getMethod(Class cls, String name, Class... params) throws Exception { - Method m = cls.getDeclaredMethod(name, params); - m.setAccessible(true); - return m; - } - - //Round to next 4096 bytes - private static long roundTo4096(long i) { - return (i + 0xfffL) & ~0xfffL; - } - - //Given that the location and size have been set, map that location - //for the given length and set this.addr to the returned offset - private void mapAndSetOffset() throws Exception{ - final RandomAccessFile backingFile = new RandomAccessFile(this.loc, "rw"); - backingFile.setLength(this.size); - - final FileChannel ch = backingFile.getChannel(); - this.addr = (long) mmap.invoke(ch, 1, 0L, this.size); - - ch.close(); - backingFile.close(); - } - - public MMapper(final String loc, long len) throws Exception { - this.loc = loc; - this.size = roundTo4096(len); - mapAndSetOffset(); - } - - //Callers should synchronize to avoid calls in the middle of this, but - //it is undesirable to synchronize w/ all access methods. - public void remap(long nLen) throws Exception{ - unmmap.invoke(null, addr, this.size); - this.size = roundTo4096(nLen); - mapAndSetOffset(); - } - - public int getInt(long pos){ - return unsafe.getInt(pos + addr); - } - - public long getLong(long pos){ - return unsafe.getLong(pos + addr); - } - - public void putInt(long pos, int val){ - unsafe.putInt(pos + addr, val); - } - - public void putLong(long pos, long val){ - unsafe.putLong(pos + addr, val); - } - - //May want to have offset & length within data as well, for both of these - public void getBytes(long pos, byte[] data){ - unsafe.copyMemory(null, pos + addr, data, BYTE_ARRAY_OFFSET, data.length); - } - - public void setBytes(long pos, byte[] data){ - unsafe.copyMemory(data, BYTE_ARRAY_OFFSET, null, pos + addr, data.length); - } -} \ No newline at end of file diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java deleted file mode 100644 index 6855e62..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java +++ /dev/null @@ -1,32 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - - -import javafx.util.Pair; - -import java.io.Serializable; - -/** - * Created by anilkoyuncu on 19/03/2018. - */ -public class Message implements Serializable{ - Pair first; - Pair second; - Pair p; - - public Pair getPair() { - return p; - } - - public void setPair(Pair p) { - this.p = p; - } - - - - public Message(Integer keyFirst, String valueFirst, Integer keySecond, String valueSecond ){ - first = new Pair<>(keyFirst,valueFirst); - second = new Pair<>(keySecond,valueSecond); - p = new Pair<>(first,second); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 4de8367..0104ea6 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -1,16 +1,11 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import akka.actor.ActorRef; -import akka.actor.ActorSystem; import com.github.gumtreediff.actions.ActionGenerator; import com.github.gumtreediff.actions.model.Action; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; import edu.lu.uni.serval.utils.FileHelper; -import javafx.util.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; @@ -24,9 +19,6 @@ import java.util.concurrent.Executors; import java.util.function.Consumer; import java.util.stream.Collectors; import java.util.stream.Stream; -import java.util.zip.Deflater; -import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; /** * Created by anilkoyuncu on 19/03/2018. diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index 21ec977..6ee554a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -10,6 +10,7 @@ import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; +import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; @@ -21,10 +22,8 @@ import java.time.Duration; import java.util.*; import java.util.concurrent.Executors; import java.util.function.Consumer; -import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; -import javafx.util.*; /** * Created by anilkoyuncu on 19/03/2018. @@ -296,11 +295,11 @@ public class MultiThreadTreeLoaderCluster { Pair oldPair = getTree(firstValue); Pair newPair = getTree(secondValue); - ITree oldTree = oldPair.getKey(); - ITree newTree = newPair.getKey(); + ITree oldTree = oldPair.getValue0(); + ITree newTree = newPair.getValue0(); - String oldProject = oldPair.getValue(); - String newProject = newPair.getValue(); + String oldProject = oldPair.getValue1(); + String newProject = newPair.getValue1(); From dc46b5eb38b58e2f3917c76f4da2f9ca5055a633 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 2 Apr 2018 18:08:36 +0200 Subject: [PATCH 048/127] new dumper --- FixPatternMiner.iml | 1 + pom.xml | 10 +- .../violations/FixedViolationHunkParser.java | 4 +- .../violations/MultiThreadTreeLoader.java | 2 +- .../MultiThreadTreeLoaderCluster.java | 155 ++-- .../MultiThreadTreeLoaderCluster3.java | 832 ++++++++++++++++++ .../violations/TestHunkParser.java | 113 ++- .../lu/uni/serval/config/Configuration.java | 2 +- 8 files changed, 1009 insertions(+), 110 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index a1e4217..05d2946 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -56,5 +56,6 @@ + \ No newline at end of file diff --git a/pom.xml b/pom.xml index ad887f3..58211fc 100644 --- a/pom.xml +++ b/pom.xml @@ -67,6 +67,14 @@ 2.8.1 + + + org.apache.commons + commons-text + 1.3 + + + @@ -94,7 +102,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader + edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 945a73c..b768994 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -52,10 +52,10 @@ public class FixedViolationHunkParser extends FixedViolationParser { try { String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; String root = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; - String hunkTreeFileName = root+pj.replace("DiffEntries","ASTDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + String hunkTreeFileName = root+pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); f = new FileOutputStream(new File(hunkTreeFileName)); ObjectOutputStream o = new ObjectOutputStream(f); - o.writeObject(actionSet.getNode()); + o.writeObject(actionSet); o.close(); f.close(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 0104ea6..9fe832f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -243,7 +243,7 @@ public class MultiThreadTreeLoader { for (File pj : pjs) { File[] files = pj.listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { - return name.startsWith("ASTDumps"); + return name.startsWith("ActionSetDumps"); } }); Collections.addAll(fileToCompare, files[0].listFiles()); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index 6ee554a..be1a7c0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -5,6 +5,7 @@ import com.github.gumtreediff.actions.model.*; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.Tree; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; @@ -68,7 +69,7 @@ public class MultiThreadTreeLoaderCluster { inputPath = "/Users/anilkoyuncu/bugStudy/code/python/clusterDumps"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; port = "6379"; - pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_csv/"; + pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs-csv/"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; } @@ -120,41 +121,41 @@ public class MultiThreadTreeLoaderCluster { for (File f:folders){ + if(f.getName().startsWith("cluster76")) { + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_[0-9]*"); - try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - ScanParams sc = new ScanParams(); - sc.count(150000000); - sc.match("pair_[0-9]*"); + log.info("Scanning"); + ScanResult scan = jedis.scan("0", sc); + int size = scan.getResult().size(); - log.info("Scanning"); - ScanResult scan = jedis.scan("0",sc); - int size = scan.getResult().size(); - log.info("Scanning " + String.valueOf(size)); - if (size == 0){ - loadRedis(cmd,f); + if (size == 0) { + loadRedis(cmd, f); + + scan = jedis.scan("0", sc); + size = scan.getResult().size(); + + } + log.info("Scanned " + String.valueOf(size)); + + + String clusterName = f.getName().replaceAll("[^0-9]+", ""); + + + //76 + + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName)); + + + jedis.save(); - scan = jedis.scan("0",sc); - size = scan.getResult().size(); - log.info("Scanning " + String.valueOf(size)); } - - - - String clusterName = f.getName().replaceAll("[^0-9]+", ""); - - - - scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool,clusterName)); - - - - - jedis.save(); - } @@ -166,6 +167,8 @@ public class MultiThreadTreeLoaderCluster { + + public static Pair getTree(String firstValue){ String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; String[] split2 = firstValue.split("/"); @@ -195,24 +198,30 @@ public class MultiThreadTreeLoaderCluster { HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); // for (HierarchicalActionSet actionSet : actionSets) { - ITree test = getActionTree(actionSet); - test.getLabel(); - for (ITree descendant : test.getDescendants()) { -// descendant.setLabel(""); - if(!(descendant.getType() == 100 || descendant.getType() == 101 || descendant.getType() == 102 || descendant.getType() == 103)){ - descendant.setType(104); - } + + + ITree actionTree= null; + ITree test2 = null; + getActionTree(actionSet); + ITree node = actionSet.getNode(); + List descendants = node.getDescendants(); + for (ITree descendant : descendants) { + if(descendant.getType() <= 100){ + descendant.setType(104); } - test.getDescendants(); - test.setParent(null); -// } + } + node.setParent(null); + + + // } // } - Pair pair = new Pair<>(test,project); + Pair pair = new Pair<>(node,project); return pair; } - public static ITree getActionTree(HierarchicalActionSet actionSet){ + + public static void getActionTree(HierarchicalActionSet actionSet){ int newType = 0; @@ -239,8 +248,47 @@ public class MultiThreadTreeLoaderCluster { } - return actionSet.getNode(); + } +// public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ +// +// int newType = 0; +// +// Action action = actionSet.getAction(); +// if (action instanceof Update){ +// newType = 101; +// }else if(action instanceof Insert){ +// newType =100; +// }else if(action instanceof Move){ +// newType = 102; +// }else if(action instanceof Delete){ +// newType=103; +// }else{ +// new Exception("unknow action"); +// } +// if(actionSet.getParent() == null){ +// //root +// +// parent = new Tree(newType,""); +// }else{ +// children = new Tree(newType,""); +// parent.addChild(children); +// } +// List subActions = actionSet.getSubActions(); +// if (subActions.size() != 0){ +// for (HierarchicalActionSet subAction : subActions) { +// +// if(actionSet.getParent() == null){ +// children = parent; +// } +// getActionTree(subAction,children,null); +// +// } +// +// +// } +// return parent; +// } @@ -464,9 +512,9 @@ orginal calculate pairs, from all dumps of the projects String line = null; try { - FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +filename+".txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, 1000*treesFileNames.size()*treesFileNames.size()); - int fileCounter = 0; + FileOutputStream fos = new FileOutputStream(outputPath + "pairs/" +filename+".txt"); + DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); + for (int i = 0; i < treesFileNames.size(); i++) { @@ -475,22 +523,11 @@ orginal calculate pairs, from all dumps of the projects line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"pairs/" +filename+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - } - - - + outStream.write(line.getBytes()); } } - rwChannel.close(); + outStream.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java new file mode 100644 index 0000000..4ac21e9 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -0,0 +1,832 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.gumtree.GumTreeComparer; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; +import edu.lu.uni.serval.utils.FileHelper; +import edu.lu.uni.serval.utils.ListSorter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; + +import java.io.*; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; +import java.time.Duration; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.function.Consumer; +import java.util.stream.Collectors; +import java.util.stream.Stream; +import org.apache.commons.text.similarity.*; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class MultiThreadTreeLoaderCluster3 { + + private static int resultType; + + private static class StreamGobbler implements Runnable { + private InputStream inputStream; + private Consumer consumer; + + public StreamGobbler(InputStream inputStream, Consumer consumer) { + this.inputStream = inputStream; + this.consumer = consumer; + } + + @Override + public void run() { + new BufferedReader(new InputStreamReader(inputStream)).lines() + .forEach(consumer); + } + } + + private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster3.class); + + public static void main(String[] args){ + + String inputPath; + String outputPath; + String port; + String pairsCSVPath; + String importScript; + String csvScript; + if (args.length > 0) { + inputPath = args[0]; + outputPath = args[1]; + port = args[2]; + pairsCSVPath = args[3]; + importScript = args[4]; + csvScript = args[5]; + } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + inputPath = "/Users/anilkoyuncu/bugStudy/code/python/cluster2L"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6379"; + pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs-2l-csv/"; + importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; + csvScript = "/Users/anilkoyuncu/bugStudy/dataset/transformCSV.sh"; + } + + calculatePairsOfClusters(inputPath, outputPath); + +// createCSV(csvScript,outputPath + "pairs-2l/",pairsCSVPath); + + //create csv file and move + + mainCompare(inputPath,port,pairsCSVPath,importScript); + // calculatePairs(inputPath, outputPath); +// processMessages(inputPath,outputPath); +// evaluateResults(inputPath,outputPath); + + } + + public static void createCSV(String csvScript, String f1, String f2){ + String cmd; + cmd = "bash " + csvScript +" %s %s"; + Process process = null; + File source = new File(f1); + File dest = new File(f2); + log.info(source.getName()); + log.info(dest.getName()); + try { + String comd = String.format(cmd, source.getAbsoluteFile() ,dest.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(comd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); + int exitCode = process.waitFor(); + assert exitCode == 0; + } catch (IOException e) { + e.printStackTrace(); + } catch (InterruptedException e) { + e.printStackTrace(); + }finally { + process.destroyForcibly(); + } + log.info("Load done"); + + } + + public static void loadRedis(String cmd, File f){ + Process process; + log.info(f.getName()); + try { + String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(comd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); + int exitCode = process.waitFor(); + assert exitCode == 0; + } catch (IOException e) { + e.printStackTrace(); + } catch (InterruptedException e) { + e.printStackTrace(); + } + log.info("Load done"); + } + + public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { + + String cmd; + cmd = "bash " + importScript +" %s"; + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + + + File folder = new File(pairsCSVPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + for (File f:folders){ + + + + + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_[0-9]*"); + + log.info("Scanning"); + ScanResult scan = jedis.scan("0",sc); + int size = scan.getResult().size(); + + if (size == 0){ + loadRedis(cmd,f); + + scan = jedis.scan("0",sc); + size = scan.getResult().size(); + + } + log.info("Scanned " + String.valueOf(size)); + + + String clusterName = f.getName().split("\\.")[0].replace("cluster",""); + + + + + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool,clusterName)); + + + + + jedis.save(); + + } + + + + + } + + + + } + + + + + + public static ITree getTree(String firstValue){ + String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; + String[] split2 = firstValue.split("/"); + String cluster = split2[1]; + String subCluster = split2[2]; + String filename = split2[3]; + String[] split1= filename.split(".txt_"); + String s = split1[0]; + String[] splitPJ = split1[1].split("_"); + String project = splitPJ[1]; + String actionSetPosition = splitPJ[0]; + + + File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/clusterDumps/"+cluster + "/" + s + ".txt_" + actionSetPosition); + + + ITree tree = null; + try { + FileInputStream fi = new FileInputStream(folder); + ObjectInputStream oi = new ObjectInputStream(fi); + tree = (ITree) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + return tree; + +// File[] listOfFiles = folder.listFiles(); +// Stream stream = Arrays.stream(listOfFiles); +// List folders = stream +// .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) +// .collect(Collectors.toList()); +// +// +// +//// String[] split1 = folders.get(0).getName().split(".txt_"); +//// String s = split1[0]; +//// String[] splitPJ = split1[1].split("_"); +//// String project = splitPJ[1]; +//// String actionSetPosition = splitPJ[0]; +// +// File prevFile = new File(gumTreeInput + project+ "/" + "prevFiles/prev_" + s + ".java");// previous file +// File revFile = new File(gumTreeInput + project+ "/" + "revFiles/" + s + ".java");//rev file +// +// List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); +// +// HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); +//// for (HierarchicalActionSet actionSet : actionSets) { +// +// ITree test = getActionTree(actionSet); +// test.getLabel(); +// for (ITree descendant : test.getDescendants()) { +//// descendant.setLabel(""); +// if(!(descendant.getType() == 100 || descendant.getType() == 101 || descendant.getType() == 102 || descendant.getType() == 103)){ +// descendant.setType(104); +// } +// } +// test.getDescendants(); +// test.setParent(null); +//// } +//// } +// +// Pair pair = new Pair<>(test,project); +// return pair; + } + + public static ITree getActionTree(HierarchicalActionSet actionSet){ + + + int newType = 0; + + Action action = actionSet.getAction(); + if (action instanceof Update){ + newType = 101; + }else if(action instanceof Insert){ + newType =100; + }else if(action instanceof Move){ + newType = 102; + }else if(action instanceof Delete){ + newType=103; + }else{ + new Exception("unknow action"); + } + actionSet.getNode().setType(newType); +// actionSet.getNode().setLabel(""); + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + getActionTree(subAction); + } + + + } + return actionSet.getNode(); + } + + private static List getNames(ITree oldTree, List oldTokens){ + if((oldTree.getType() == 42 && oldTree.getLabel().startsWith("Name:")) || oldTree.getType() == 42 && oldTree.getParent().getType() == 59 || oldTree.getType() == 43 || (oldTree.getType() == 41 && oldTree.getLabel().startsWith("SimpleName:")) ){ + + oldTokens.add(oldTree.getLabel()); + + } + for (ITree oldDescendant : oldTree.getDescendants()) { + if ((oldDescendant.getType() == 42 && oldDescendant.getLabel().startsWith("Name:") ) || oldDescendant.getType() == 42 && oldDescendant.getParent().getType() == 59 ||oldDescendant.getType() == 43 || (oldDescendant.getType() == 41 && oldDescendant.getLabel().startsWith("SimpleName:"))){ + + oldTokens.add(oldDescendant.getLabel()); + + } + } + return oldTokens; + } + + private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName) { + + + try (Jedis jedis = jedisPool.getResource()) { + + + Map resultMap = jedis.hgetAll(name); + + + + + String[] split = name.split("_"); + String i = null; + String j =null; + try { + i = split[1]; + j = split[2]; + } + catch (Exception e){ + e.printStackTrace(); + } + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + ///35/1/22b5f7_84bf27_ui#org.eclipse.pde.runtime#src#org#eclipse#pde#internal#runtime#registry#RegistryBrowserLabelProvider.txt_2_PDE + + + +// firstValue = inputPath + firstValue; +// secondValue = inputPath + secondValue; + +// String[] firstValueSplit = firstValue.split("/"); +// String[] secondValueSplit = secondValue.split("/"); +// +// if (firstValueSplit.length == 1) { +// firstValue = inputPath + firstValueSplit[0]; +// } else { +// firstValue = inputPath + firstValueSplit[1]; +// } +// +// if (secondValueSplit.length == 1) { +// secondValue = inputPath + secondValueSplit[0]; +// } else { +// secondValue = inputPath + secondValueSplit[1]; +// } + + try { + ITree oldTree = getTree(firstValue); + ITree newTree = getTree(secondValue); + +// ITree oldTree = oldPair.getValue0(); +// ITree newTree = newPair.getValue0(); +// +// String oldProject = oldPair.getValue1(); +// String newProject = newPair.getValue1(); + + List oldTokens = new ArrayList<>(); + List newTokens = new ArrayList<>(); + + +// if(secondValue.startsWith("/2/")){ +// log.info("newss"); +// } + + // 41 return statement + + oldTokens = getNames(oldTree,oldTokens); + newTokens = getNames(newTree,newTokens); + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); + CharSequence[] newSequences = newTokens.toArray(new CharSequence[newTokens.size()]); + JaroWinklerDistance jwd = new JaroWinklerDistance(); + Double overallSimi = Double.valueOf(1); + if(oldSequences.length > 0 && (oldSequences.length == newSequences.length)){ + for (int idx = 0; idx < newSequences.length; idx++) { + Double simi = jwd.apply(newSequences[idx], oldSequences[idx]); + overallSimi = simi * overallSimi; + } + }else{ + overallSimi = Double.valueOf(0); + if(oldSequences.length != 0) { + log.info("ERROR"); + } + } + if(overallSimi.equals(1.0)){ + +// log.info("YES"); +// log.info(name); +// log.info(firstValue); +// log.info(secondValue); +// log.info("************"); + String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); + String result = firstValue + "," + secondValue; + jedis.select(1); + jedis.set(matchKey, result); + } + jedis.select(0); + String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.del(pairKey); + + + + +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// +// String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); +// double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); +// String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); +// double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); +// String diceSimilarity = String.format("%1.2f", diceSimilarity1); +// double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); +// String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); +// +// String editDistance = String.valueOf(actions.size()); +// jedis.select(1); +// String result = resultMap.get("0") + "," + oldProject +"," + resultMap.get("1") + "," +newProject+ "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; +//// jedis.set(resultKey, result); +// +// if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) +// || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { +// String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); +// jedis.select(1); +// jedis.set(matchKey, result); +// } +// jedis.select(0); + +// +//// log.info("Completed " + resultKey); + + }catch (Exception e){ + log.error(e.toString() + " {}",(name)); + + + } + + + + + } + } + + + + protected static List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { + List actionSets = new ArrayList<>(); + // GumTree results + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); + if (gumTreeResults == null) { + resultType = 1; + return null; + } else if (gumTreeResults.size() == 0){ + resultType = 2; + return actionSets; + } else { + // Regroup GumTre results. + List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); +// for (HierarchicalActionSet actionSet : allActionSets) { +// String astNodeType = actionSet.getAstNodeType(); +// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { +// actionSets.add(actionSet); +// } +// } + + // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. + // variable effects range, sub-actions are these kinds of modification? +// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); + + ListSorter sorter = new ListSorter<>(allActionSets); + actionSets = sorter.sortAscending(); + + if (actionSets.size() == 0) { + resultType = 3; + } + + return actionSets; + } + } + + +/* +orginal calculate pairs, from all dumps of the projects + */ + public static void calculatePairs(String inputPath, String outputPath) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for (File pj : pjs) { + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ASTDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + readMessageFiles(fileToCompare, outputPath); + } + + /* + pairs of each cluster + */ + public static void calculatePairsOfClusters(String inputPath, String outputPath) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + FileHelper.createDirectory(outputPath + "pairs-2l/"); + + for (File pj : pjs) { + File[] files = pj.listFiles(); + List fileList = Arrays.asList(files); + for (File cluster:fileList) { + if (cluster.getName().startsWith(".")){ + continue; + } + File[] clusterFiles = cluster.listFiles(); + List clusterFilesL = Arrays.asList(clusterFiles); + readMessageFilesCluster(clusterFilesL, outputPath, inputPath, pj.getName(), cluster.getName()); + + + + + } + + } + + } + + public static void processMessages(String inputPath, String outputPath) { + File folder = new File(outputPath + "pairs_splitted/"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + FileHelper.createDirectory(outputPath + "comparison_splitted/"); + pjs.parallelStream() + .forEach(m -> coreLoop(m, outputPath,inputPath)); + } + + private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster, String subCluster) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + + String filename = "cluster" + cluster + "_" + subCluster; + byte [] buf = new byte[0]; + String line = null; + try { + +// FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs-2l/" +filename+".txt", "rw").getChannel(); +// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, 1000*treesFileNames.size()*treesFileNames.size()); +// int fileCounter = 0; + + FileOutputStream fos = new FileOutputStream(outputPath + "pairs-2l/" +filename+".txt"); + DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); + + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; + outStream.write(line.getBytes()); +// buf = line.getBytes(); +// if(wrBuf.remaining() > 500) { +// wrBuf.put(buf); +// }else{ +// log.info("Next pair dump"); +// fileCounter++; +// rwChannel = new RandomAccessFile(outputPath+"pairs/" +filename+String.valueOf(fileCounter)+".txt", "rw").getChannel(); +// wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); +// } + + + + + } + } + outStream.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); + } + + log.info("Done pairs"); + } + + + + public static ITree getSimpliedTree(String fn) { + ITree tree = null; + try { + FileInputStream fi = new FileInputStream(new File(fn)); + ObjectInputStream oi = new ObjectInputStream(fi); + tree = (ITree) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + +// tree.setLabel(""); + tree.setParent(null); +// List descendants = tree.getDescendants(); +// for (ITree descendant : descendants) { +// descendant.setLabel(""); +// } + + return tree; + + } + + + private static void coreLoop(File mes, String outputPath,String inputPath) { + try { + + log.info("Starting in coreLoop"); + + BufferedReader br = null; + String sCurrentLine = null; + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); + + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; + + firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; + secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; + + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); + + + } + writer.close(); + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + + } + log.info("Completed output_" + mes.getName()); + } + + private static void readMessageFiles(List folders, String outputPath) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + FileHelper.createDirectory(outputPath + "pairs/"); + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + byte [] buf = new byte[0]; + String line = null; + try { + + FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + } + + + + + } + } + rwChannel.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); + } + + log.info("Done pairs"); + } + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + + + +// return msgFiles; +} + + + + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 47d8318..d705c3b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -16,15 +16,22 @@ import java.util.concurrent.TimeoutException; import java.util.stream.Collectors; import java.util.stream.Stream; +import akka.actor.ActorRef; +import akka.actor.ActorSystem; import edu.lu.uni.serval.FixPatternParser.RunnableParser; +import edu.lu.uni.serval.MultipleThreadsParser.AkkaParser; import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; +import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor; +import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.utils.FileHelper; import org.eclipse.jgit.revwalk.RevCommit; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class TestHunkParser { - + private static Logger log = LoggerFactory.getLogger(TestHunkParser.class); public static void main(String[] args) { // input data @@ -80,7 +87,7 @@ public class TestHunkParser { final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; - FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ASTDumps"); + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ActionSetDumps"); FileHelper.deleteDirectory(editScriptsFilePath); FileHelper.deleteDirectory(patchesSourceCodeFilePath); FileHelper.deleteDirectory(buggyTokensFilePath); @@ -94,51 +101,65 @@ public class TestHunkParser { StringBuilder alarmTypes = new StringBuilder(); int a = 0; + + ActorSystem system = null; + ActorRef parsingActor = null; + final WorkMessage msg = new WorkMessage(0, msgFiles); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Mining-FixPattern-System"); + parsingActor = system.actorOf(ParseFixPatternActor.props(20, editScriptsFilePath, + patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } // int counter = 0; - for (MessageFile msgFile : msgFiles) { - FixedViolationHunkParser parser = new FixedViolationHunkParser(); - - final ExecutorService executor = Executors.newSingleThreadExecutor(); - // schedule the work - final Future future = executor.submit(new RunnableParser(msgFile.getPrevFile(), - msgFile.getRevFile(), msgFile.getDiffEntryFile(), parser)); - try { - // where we wait for task to complete - future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); - String editScripts = parser.getAstEditScripts(); - if (!editScripts.equals("")) { - astEditScripts.append(editScripts); - tokens.append(parser.getTokensOfSourceCode()); - sizes.append(parser.getSizes()); - patches.append(parser.getPatchesSourceCode()); - alarmTypes.append(parser.getAlarmTypes()); - - a++; - if (a % 100 == 0) { - FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); - FileHelper.outputToFile(buggyTokensFilePath, tokens, true); - FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); - FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); - FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); - astEditScripts.setLength(0); - tokens.setLength(0); - sizes.setLength(0); - patches.setLength(0); - alarmTypes.setLength(0); - System.out.println("Finish of parsing " + a + " files......"); - } - } - } catch (TimeoutException e) { - err.println("task timed out"); - future.cancel(true /* mayInterruptIfRunning */); - } catch (InterruptedException e) { - err.println("task interrupted"); - } catch (ExecutionException e) { - err.println("task aborted"); - } finally { - executor.shutdownNow(); - } - } +// for (MessageFile msgFile : msgFiles) { +// FixedViolationHunkParser parser = new FixedViolationHunkParser(); +// +// final ExecutorService executor = Executors.newSingleThreadExecutor(); +// // schedule the work +// final Future future = executor.submit(new RunnableParser(msgFile.getPrevFile(), +// msgFile.getRevFile(), msgFile.getDiffEntryFile(), parser)); +// try { +// // where we wait for task to complete +// future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); +// String editScripts = parser.getAstEditScripts(); +// if (!editScripts.equals("")) { +// astEditScripts.append(editScripts); +// tokens.append(parser.getTokensOfSourceCode()); +// sizes.append(parser.getSizes()); +// patches.append(parser.getPatchesSourceCode()); +// alarmTypes.append(parser.getAlarmTypes()); +// +// a++; +// if (a % 100 == 0) { +// FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); +// FileHelper.outputToFile(buggyTokensFilePath, tokens, true); +// FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); +// FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); +// astEditScripts.setLength(0); +// tokens.setLength(0); +// sizes.setLength(0); +// patches.setLength(0); +// alarmTypes.setLength(0); +// System.out.println("Finish of parsing " + a + " files......"); +// } +// } +// } catch (TimeoutException e) { +// err.println("task timed out"); +// future.cancel(true /* mayInterruptIfRunning */); +// } catch (InterruptedException e) { +// err.println("task interrupted"); +// } catch (ExecutionException e) { +// err.println("task aborted"); +// } finally { +// executor.shutdownNow(); +// } +// } FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); FileHelper.outputToFile(buggyTokensFilePath, tokens, true); diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 3325840..45e21f7 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,7 +2,7 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 900L; + public static final long SECONDS_TO_WAIT = 9000L; // public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. From 444be41cd83f122120ac217210b7d9869136fea7 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 2 Apr 2018 18:13:48 +0200 Subject: [PATCH 049/127] output --- .../uni/serval/FixPatternParser/violations/TestHunkParser.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index d705c3b..30bcd06 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -40,7 +40,7 @@ public class TestHunkParser { String outputPath; if(args.length > 0){ inputPath = args[1]; - outputPath = args[0] + "/GumTreeOutputBug/"; + outputPath = args[0]; }else{ // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; inputPath = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4"; From a0d23eafa431fbf99c47daee91566d4238d8fcb7 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 2 Apr 2018 18:18:57 +0200 Subject: [PATCH 050/127] test --- .../FixPatternParser/violations/FixedViolationHunkParser.java | 2 +- .../uni/serval/FixPatternParser/violations/TestHunkParser.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index b768994..0fcbda8 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -51,7 +51,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { FileOutputStream f = null; try { String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; - String root = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + String root = diffentryFile.getParent().split("GumTreeInputBug4")[0]; String hunkTreeFileName = root+pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); f = new FileOutputStream(new File(hunkTreeFileName)); ObjectOutputStream o = new ObjectOutputStream(f); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 30bcd06..36863a5 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -108,7 +108,7 @@ public class TestHunkParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(20, editScriptsFilePath, + parsingActor = system.actorOf(ParseFixPatternActor.props(1, editScriptsFilePath, patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { From d9bb4aac243c60e28ac039e444ec4994d22a7237 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 2 Apr 2018 18:23:35 +0200 Subject: [PATCH 051/127] test --- .../FixPatternParser/violations/FixedViolationHunkParser.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 0fcbda8..1f4290c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -52,7 +52,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { try { String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; String root = diffentryFile.getParent().split("GumTreeInputBug4")[0]; - String hunkTreeFileName = root+pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + String hunkTreeFileName = root+"GumTreeOutput2/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); f = new FileOutputStream(new File(hunkTreeFileName)); ObjectOutputStream o = new ObjectOutputStream(f); o.writeObject(actionSet); From 0555731517dc56c7fb4dfd35e3933c8c14e0c1c9 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 2 Apr 2018 19:50:00 +0200 Subject: [PATCH 052/127] redisload --- pom.xml | 2 +- .../violations/MultiThreadTreeLoader.java | 173 +++++++++++------- 2 files changed, 108 insertions(+), 67 deletions(-) diff --git a/pom.xml b/pom.xml index 58211fc..d080fee 100644 --- a/pom.xml +++ b/pom.xml @@ -102,7 +102,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser + edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 9fe832f..f6f4ec8 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -13,6 +13,8 @@ import redis.clients.jedis.*; import java.io.*; import java.nio.ByteBuffer; import java.nio.channels.FileChannel; +import java.nio.file.Files; +import java.nio.file.StandardCopyOption; import java.time.Duration; import java.util.*; import java.util.concurrent.Executors; @@ -80,9 +82,9 @@ public class MultiThreadTreeLoader { inputPath = args[0]; outputPath = args[1]; port = args[2]; - pairsCSVPath = args[3]; - importScript = args[4]; - pairsCompletedPath = args[3]; +// pairsCSVPath = args[3]; +// importScript = args[4]; +// pairsCompletedPath = args[3]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; @@ -92,57 +94,91 @@ public class MultiThreadTreeLoader { pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; } - String cmd; - cmd = "bash " + importScript +" %s"; + + calculatePairs(inputPath, outputPath,port); +// comparePairs(port,inputPath); + + + } + + public static void comparePairs(String port,String inputPath){ +// String cmd; +// cmd = "bash " + importScript +" %s"; JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); // calculatePairs(inputPath, outputPath); // processMessages(inputPath,outputPath); // evaluateResults(inputPath,outputPath); - File folder = new File(pairsCSVPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List folders = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); +// File folder = new File(pairsCSVPath); +// File[] listOfFiles = folder.listFiles(); +// Stream stream = Arrays.stream(listOfFiles); +// List folders = stream +// .filter(x -> !x.getName().startsWith(".")) +// .collect(Collectors.toList()); +// +// //create dir +// File file = new File(pairsCompletedPath); +// file.mkdirs(); - //create dir - File file = new File(pairsCompletedPath); - file.mkdirs(); +// for (File f:folders){ - for (File f:folders){ try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - ScanParams sc = new ScanParams(); - sc.count(150000000); - sc.match("pair_*"); - ScanResult scan = jedis.scan("0",sc); - int size = scan.getResult().size(); - log.info("Scanning " + String.valueOf(size)); - if (size == 0){ - loadRedis(cmd,f); - scan = jedis.scan("0",sc); - size = scan.getResult().size(); + + List dir = jedis.configGet("dir"); + List path = jedis.configGet("dbfilename"); + File dbDir = new File(dir.get(1)); + String orgDbname = path.get(1); + File[] files = dbDir.listFiles(); + Stream stream = Arrays.stream(files); + List folders = stream + .filter(x -> !x.getName().startsWith(orgDbname)).filter(x -> x.getName().endsWith(".rdb")) + .collect(Collectors.toList()); + for (File folder : folders) { + + + File dbPath = new File(dir.get(1) + "/" + path.get(1)); + File savePath = new File(dir.get(1) + "/" + folder.getName()); + try { + Files.copy(savePath.toPath(),dbPath.toPath(), StandardCopyOption.REPLACE_EXISTING); + } catch (IOException e) { + + e.printStackTrace(); + } + + jedis.configSet("dbfilename",folder.getName()); + + + // do operations with jedis resource + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_*"); + + ScanResult scan = jedis.scan("0", sc); + int size = scan.getResult().size(); log.info("Scanning " + String.valueOf(size)); +// if (size == 0){ +// loadRedis(cmd,f); +// +// scan = jedis.scan("0",sc); +// size = scan.getResult().size(); +// log.info("Scanning " + String.valueOf(size)); +// } + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool)); + + jedis.save(); } - scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool)); - jedis.save(); - - } - f.renameTo(new File(pairsCompletedPath, f.getName())); +// } +// f.renameTo(new File(pairsCompletedPath, f.getName())); } - - - } private static void coreCompare(String name , String inputPath, JedisPool jedisPool) { @@ -231,7 +267,7 @@ public class MultiThreadTreeLoader { - public static void calculatePairs(String inputPath, String outputPath) { + public static void calculatePairs(String inputPath, String outputPath,String port) { File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); @@ -251,7 +287,7 @@ public class MultiThreadTreeLoader { } System.out.println("a"); // compareAll(fileToCompare); - readMessageFiles(fileToCompare, outputPath); + readMessageFiles(fileToCompare, outputPath,port); } public static void processMessages(String inputPath, String outputPath) { @@ -365,7 +401,7 @@ public class MultiThreadTreeLoader { log.info("Completed output_" + mes.getName()); } - private static void readMessageFiles(List folders, String outputPath) { + private static void readMessageFiles(List folders, String outputPath,String port) { List treesFileNames = new ArrayList<>(); @@ -379,44 +415,49 @@ public class MultiThreadTreeLoader { // treesFileNames = treesFileNames.subList(0,100); byte [] buf = new byte[0]; String line = null; - try { - - FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - int fileCounter = 0; +// FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); +// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); for (int i = 0; i < treesFileNames.size(); i++) { for (int j = i + 1; j < treesFileNames.size(); j++) { + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + + String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); +// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; +// jedis.set(key,value); + + jedis.hset(key,"0",treesFileNames.get(i).split("GumTreeOutput2")[1]); + jedis.hset(key,"1",treesFileNames.get(j).split("GumTreeOutput2")[1]); + //10000000 + if(Integer.compare(jedis.dbSize().intValue(),10000000) == 0){ + List dir = jedis.configGet("dir"); + List path = jedis.configGet("dbfilename"); + File dbPath = new File(dir.get(1)+"/"+path.get(1)); + File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); + try { + Files.copy(dbPath.toPath(),savePath.toPath()); + } catch (IOException e) { + + e.printStackTrace(); + } + fileCounter++; + jedis.flushDB(); + + } - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); } - - - - } } - rwChannel.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - }catch (java.nio.BufferOverflowException e) { - log.error(line); - log.error(String.valueOf(buf.length)); - e.printStackTrace(); - } + + + log.info("Done pairs"); } From 017ac2d1691154af4ffc848745dd7a4fe9f94aa6 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 09:37:30 +0200 Subject: [PATCH 053/127] test --- .../violations/MultiThreadTreeLoader.java | 490 +++++++++++------- 1 file changed, 293 insertions(+), 197 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index f6f4ec8..1181567 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -1,10 +1,13 @@ package edu.lu.uni.serval.FixPatternParser.violations; import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.actions.model.*; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.Tree; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.utils.FileHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -15,6 +18,7 @@ import java.nio.ByteBuffer; import java.nio.channels.FileChannel; import java.nio.file.Files; import java.nio.file.StandardCopyOption; +import java.sql.Timestamp; import java.time.Duration; import java.util.*; import java.util.concurrent.Executors; @@ -46,26 +50,27 @@ public class MultiThreadTreeLoader { private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoader.class); - public static void loadRedis(String cmd, File f){ + public static void loadRedis(String cmd){ Process process; - log.info(f.getName()); + try { - String comd = String.format(cmd, f.getAbsoluteFile()); +// String comd = String.format(cmd, f.getAbsoluteFile()); process = Runtime.getRuntime() - .exec(comd); + .exec(cmd); StreamGobbler streamGobbler = new StreamGobbler(process.getInputStream(), System.out::println); Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; +// int exitCode = process.waitFor(); +// assert exitCode == 0; } catch (IOException e) { e.printStackTrace(); - } catch (InterruptedException e) { - e.printStackTrace(); } +// } catch (InterruptedException e) { +// e.printStackTrace(); +// } log.info("Load done"); } @@ -75,6 +80,7 @@ public class MultiThreadTreeLoader { String inputPath; String outputPath; String port; + String portInner; String pairsCSVPath; String importScript; String pairsCompletedPath; @@ -82,192 +88,173 @@ public class MultiThreadTreeLoader { inputPath = args[0]; outputPath = args[1]; port = args[2]; + portInner = args[3]; // pairsCSVPath = args[3]; // importScript = args[4]; // pairsCompletedPath = args[3]; } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; port = "6379"; + portInner = "6380"; pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; } - calculatePairs(inputPath, outputPath,port); -// comparePairs(port,inputPath); + calculatePairs(inputPath, port); + log.info("Calculate pairs done"); + comparePairs(port,inputPath,portInner); } - public static void comparePairs(String port,String inputPath){ + + public static void comparePairs(String port,String inputPath, String innerPort){ // String cmd; // cmd = "bash " + importScript +" %s"; JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); -// calculatePairs(inputPath, outputPath); -// processMessages(inputPath,outputPath); -// evaluateResults(inputPath,outputPath); -// File folder = new File(pairsCSVPath); -// File[] listOfFiles = folder.listFiles(); -// Stream stream = Arrays.stream(listOfFiles); -// List folders = stream -// .filter(x -> !x.getName().startsWith(".")) -// .collect(Collectors.toList()); -// -// //create dir -// File file = new File(pairsCompletedPath); -// file.mkdirs(); - -// for (File f:folders){ + List dir; + List path; + File[] files; + String orgDbname; + File dbDir; + try (Jedis jedis = jedisPool.getResource()) { + dir = jedis.configGet("dir"); + path = jedis.configGet("dbfilename"); + dbDir = new File(dir.get(1)); + orgDbname = path.get(1); + files = dbDir.listFiles(); + } - try (Jedis jedis = jedisPool.getResource()) { - - - - List dir = jedis.configGet("dir"); - List path = jedis.configGet("dbfilename"); - File dbDir = new File(dir.get(1)); - String orgDbname = path.get(1); - File[] files = dbDir.listFiles(); - Stream stream = Arrays.stream(files); - List folders = stream + Stream stream = Arrays.stream(files); + List folders = stream .filter(x -> !x.getName().startsWith(orgDbname)).filter(x -> x.getName().endsWith(".rdb")) .collect(Collectors.toList()); - for (File folder : folders) { + for (File folder : folders) { - File dbPath = new File(dir.get(1) + "/" + path.get(1)); - File savePath = new File(dir.get(1) + "/" + folder.getName()); - try { - Files.copy(savePath.toPath(),dbPath.toPath(), StandardCopyOption.REPLACE_EXISTING); - } catch (IOException e) { - - e.printStackTrace(); - } - - jedis.configSet("dbfilename",folder.getName()); - // do operations with jedis resource + String cmd = "bash "+dir.get(1) + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,folder.getName(),Integer.valueOf(innerPort)); + loadRedis(cmd); + + + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + try (Jedis inner = pool.getResource()) { ScanParams sc = new ScanParams(); sc.count(150000000); sc.match("pair_*"); - ScanResult scan = jedis.scan("0", sc); + ScanResult scan = inner.scan("0", sc); int size = scan.getResult().size(); log.info("Scanning " + String.valueOf(size)); -// if (size == 0){ -// loadRedis(cmd,f); -// -// scan = jedis.scan("0",sc); -// size = scan.getResult().size(); -// log.info("Scanning " + String.valueOf(size)); -// } + scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool)); + .forEach(m -> coreCompare(m, inputPath, jedisPool,pool)); - jedis.save(); + }finally { + pool.close(); } + String stopServer = "bash "+dir.get(1) + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(innerPort)); + loadRedis(stopServer); + + } + + -// } -// f.renameTo(new File(pairsCompletedPath, f.getName())); - } } - private static void coreCompare(String name , String inputPath, JedisPool jedisPool) { + private static void coreCompare(String name , String inputPath, JedisPool jedisPool,JedisPool innerPool) { + + Map resultMap; + try (Jedis jedis = innerPool.getResource()) { + resultMap = jedis.hgetAll(name); + } + String[] split = name.split("_"); - try (Jedis jedis = jedisPool.getResource()) { + String i = split[1]; + String j = split[2]; + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + String[] firstValueSplit = firstValue.split("GumTreeOutput2"); + String[] secondValueSplit = secondValue.split("GumTreeOutput2"); + + if (firstValueSplit.length == 1) { + firstValue = inputPath + firstValueSplit[0]; + } else { + firstValue = inputPath + firstValueSplit[1]; + } + + if (secondValueSplit.length == 1) { + secondValue = inputPath + secondValueSplit[0]; + } else { + secondValue = inputPath + secondValueSplit[1]; + } + + try { + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); - Map resultMap = jedis.hgetAll(name); + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); - resultMap.get("0"); + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); + + String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; - String[] split = name.split("_"); - - - String i = split[1]; - String j = split[2]; - String firstValue = resultMap.get("0"); - String secondValue = resultMap.get("1"); - - String[] firstValueSplit = firstValue.split("GumTreeOutput2"); - String[] secondValueSplit = secondValue.split("GumTreeOutput2"); - - if (firstValueSplit.length == 1) { - firstValue = inputPath + firstValueSplit[0]; - } else { - firstValue = inputPath + firstValueSplit[1]; - } - - if (secondValueSplit.length == 1) { - secondValue = inputPath + secondValueSplit[0]; - } else { - secondValue = inputPath + secondValueSplit[1]; - } - - try { - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - - String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); - double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); - String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); - double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); - String diceSimilarity = String.format("%1.2f", diceSimilarity1); - double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); - String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - - String editDistance = String.valueOf(actions.size()); -// jedis.select(1); - String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; -// jedis.set(resultKey, result); - - if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) - || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { - String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - jedis.select(1); - jedis.set(matchKey, result); + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + try (Jedis outer = jedisPool.getResource()) { + outer.select(1); + outer.set(matchKey, result); } - jedis.select(0); - String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); - jedis.del(pairKey); - -// log.info("Completed " + resultKey); - - }catch (Exception e){ - log.error(e.toString() + " {}",(name)); - - } + }catch (Exception e){ + log.error(e.toString() + " {}",(name)); + + } + + + + + } - public static void calculatePairs(String inputPath, String outputPath,String port) { + public static void calculatePairs(String inputPath,String port) { File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); @@ -287,7 +274,7 @@ public class MultiThreadTreeLoader { } System.out.println("a"); // compareAll(fileToCompare); - readMessageFiles(fileToCompare, outputPath,port); + readMessageFiles(fileToCompare,port); } public static void processMessages(String inputPath, String outputPath) { @@ -304,11 +291,11 @@ public class MultiThreadTreeLoader { public static ITree getSimpliedTree(String fn) { - ITree tree = null; + HierarchicalActionSet actionSet = null; try { FileInputStream fi = new FileInputStream(new File(fn)); ObjectInputStream oi = new ObjectInputStream(fi); - tree = (ITree) oi.readObject(); + actionSet = (HierarchicalActionSet) oi.readObject(); oi.close(); fi.close(); @@ -324,17 +311,98 @@ public class MultiThreadTreeLoader { e.printStackTrace(); } - tree.setLabel(""); + ITree parent = null; + ITree children =null; + ITree tree = getASTTree(actionSet, parent, children); tree.setParent(null); - List descendants = tree.getDescendants(); - for (ITree descendant : descendants) { - descendant.setLabel(""); - } return tree; } + public static List getKeysByValue(Map map, E value) { + return map.entrySet() + .stream() + .filter(entry -> Objects.equals(entry.getValue(), value)) + .map(Map.Entry::getKey) + .collect(Collectors.toList()); + } + + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("Birden cok astnodemapmapping"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + + parent = new Tree(newType,""); + }else{ + children = new Tree(newType,""); + parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null); + + } + + + } + return parent; + } + + public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ + + int newType = 0; + + Action action = actionSet.getAction(); + if (action instanceof Update){ + newType = 101; + }else if(action instanceof Insert){ + newType =100; + }else if(action instanceof Move){ + newType = 102; + }else if(action instanceof Delete){ + newType=103; + }else{ + new Exception("unknow action"); + } + if(actionSet.getParent() == null){ + //root + + parent = new Tree(newType,""); + }else{ + children = new Tree(newType,""); + parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getActionTree(subAction,children,null); + + } + + + } + return parent; + } + private static void coreLoop(File mes, String outputPath,String inputPath) { @@ -346,49 +414,49 @@ public class MultiThreadTreeLoader { String sCurrentLine = null; BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); - br = new BufferedReader( - new FileReader(mes)); - while ((sCurrentLine = br.readLine()) != null) { - String currentLine = sCurrentLine; - String[] split = currentLine.split("\t"); - String i = split[0]; - String j = split[1]; - String firstValue = split[2]; - String secondValue = split[3]; + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; - firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; - secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; + firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; + secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; - ITree oldTree = getSimpliedTree(firstValue); + ITree oldTree = getSimpliedTree(firstValue); - ITree newTree = getSimpliedTree(secondValue); + ITree newTree = getSimpliedTree(secondValue); - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(firstValue); - writer.write("\t"); - writer.write(secondValue); - writer.write("\n"); + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); - } + } writer.close(); } catch (FileNotFoundException e) { log.error("File not found"); @@ -401,7 +469,7 @@ public class MultiThreadTreeLoader { log.info("Completed output_" + mes.getName()); } - private static void readMessageFiles(List folders, String outputPath,String port) { + private static void readMessageFiles(List folders,String port) { List treesFileNames = new ArrayList<>(); @@ -410,7 +478,7 @@ public class MultiThreadTreeLoader { treesFileNames.add(target.toString()); } - FileHelper.createDirectory(outputPath + "pairs/"); +// FileHelper.createDirectory(outputPath + "pairs/"); log.info("Calculating pairs"); // treesFileNames = treesFileNames.subList(0,100); byte [] buf = new byte[0]; @@ -422,39 +490,67 @@ public class MultiThreadTreeLoader { int fileCounter = 0; JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + try (Jedis jedis = jedisPool.getResource()) { + List dir = null; + List path = null; for (int i = 0; i < treesFileNames.size(); i++) { for (int j = i + 1; j < treesFileNames.size(); j++) { - try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); + // do operations with jedis resource + + String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); // String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; // jedis.set(key,value); - jedis.hset(key,"0",treesFileNames.get(i).split("GumTreeOutput2")[1]); - jedis.hset(key,"1",treesFileNames.get(j).split("GumTreeOutput2")[1]); - //10000000 - if(Integer.compare(jedis.dbSize().intValue(),10000000) == 0){ - List dir = jedis.configGet("dir"); - List path = jedis.configGet("dbfilename"); - File dbPath = new File(dir.get(1)+"/"+path.get(1)); - File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); - try { - Files.copy(dbPath.toPath(),savePath.toPath()); - } catch (IOException e) { - - e.printStackTrace(); + jedis.hset(key,"0",treesFileNames.get(i).split("GumTreeOutput2")[1]); + jedis.hset(key,"1",treesFileNames.get(j).split("GumTreeOutput2")[1]); + //10000000 + if(Integer.compare(jedis.dbSize().intValue(),100000) == 0){ + dir = jedis.configGet("dir"); + path = jedis.configGet("dbfilename"); + File dbPath = new File(dir.get(1)+"/"+path.get(1)); + File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); + try { + jedis.save(); + while (jedis.ping()== "PONG"){ + log.info("wait"); } - fileCounter++; - jedis.flushDB(); + + + Files.copy(dbPath.toPath(),savePath.toPath()); + } catch (IOException e) { + + e.printStackTrace(); } - + fileCounter++; + jedis.flushDB(); } + + } } + jedis.save(); + fileCounter++; + File dbPath = new File(dir.get(1)+"/"+path.get(1)); + File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); + try { + + while (jedis.ping()== "PONG"){ + log.info("wait"); + } + + + + Files.copy(dbPath.toPath(),savePath.toPath()); + } catch (IOException e) { + + e.printStackTrace(); + } + jedis.flushDB(); + } From 1ded43b34b56244a621d23820547d46359c33694 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 09:54:33 +0200 Subject: [PATCH 054/127] chunksize --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 1181567..00c60a5 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -506,7 +506,7 @@ public class MultiThreadTreeLoader { jedis.hset(key,"0",treesFileNames.get(i).split("GumTreeOutput2")[1]); jedis.hset(key,"1",treesFileNames.get(j).split("GumTreeOutput2")[1]); //10000000 - if(Integer.compare(jedis.dbSize().intValue(),100000) == 0){ + if(Integer.compare(jedis.dbSize().intValue(),10000000) == 0){ dir = jedis.configGet("dir"); path = jedis.configGet("dbfilename"); File dbPath = new File(dir.get(1)+"/"+path.get(1)); From 3abb41a0b7dee7f78d0ca990e2f639ea4987d27f Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 11:38:11 +0200 Subject: [PATCH 055/127] test --- .../violations/MultiThreadTreeLoader.java | 49 +++++++++++-------- 1 file changed, 29 insertions(+), 20 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 00c60a5..dbd2179 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -50,7 +50,7 @@ public class MultiThreadTreeLoader { private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoader.class); - public static void loadRedis(String cmd){ + public static void loadRedis(String cmd,String serverWait){ Process process; try { @@ -65,12 +65,14 @@ public class MultiThreadTreeLoader { Executors.newSingleThreadExecutor().submit(streamGobbler); // int exitCode = process.waitFor(); // assert exitCode == 0; + Thread.sleep(Integer.valueOf(serverWait)); + } catch (IOException e) { e.printStackTrace(); } -// } catch (InterruptedException e) { -// e.printStackTrace(); -// } + catch (InterruptedException e) { + e.printStackTrace(); + } log.info("Load done"); } @@ -84,11 +86,12 @@ public class MultiThreadTreeLoader { String pairsCSVPath; String importScript; String pairsCompletedPath; + String serverWait; if (args.length > 0) { inputPath = args[0]; - outputPath = args[1]; port = args[2]; portInner = args[3]; + serverWait = args[4]; // pairsCSVPath = args[3]; // importScript = args[4]; // pairsCompletedPath = args[3]; @@ -97,21 +100,22 @@ public class MultiThreadTreeLoader { outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; port = "6379"; portInner = "6380"; + serverWait = "10000"; pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; } - calculatePairs(inputPath, port); +// calculatePairs(inputPath, port); log.info("Calculate pairs done"); - comparePairs(port,inputPath,portInner); + comparePairs(port,inputPath,portInner,serverWait); } - public static void comparePairs(String port,String inputPath, String innerPort){ + public static void comparePairs(String port,String inputPath, String innerPort,String serverWait){ // String cmd; // cmd = "bash " + importScript +" %s"; @@ -144,28 +148,27 @@ public class MultiThreadTreeLoader { String cmd = "bash "+dir.get(1) + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,folder.getName(),Integer.valueOf(innerPort)); - loadRedis(cmd); + loadRedis(cmd,serverWait); JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + ScanResult scan; try (Jedis inner = pool.getResource()) { ScanParams sc = new ScanParams(); sc.count(150000000); sc.match("pair_*"); - ScanResult scan = inner.scan("0", sc); + scan = inner.scan("0", sc); int size = scan.getResult().size(); log.info("Scanning " + String.valueOf(size)); - - scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool,pool)); - - }finally { - pool.close(); } + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, port,innerPort)); + + String stopServer = "bash "+dir.get(1) + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(innerPort)); - loadRedis(stopServer); + loadRedis(stopServer,serverWait); } @@ -174,10 +177,10 @@ public class MultiThreadTreeLoader { } - private static void coreCompare(String name , String inputPath, JedisPool jedisPool,JedisPool innerPool) { - + private static void coreCompare(String name , String inputPath, String port,String innerPort) { + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); Map resultMap; - try (Jedis jedis = innerPool.getResource()) { + try (Jedis jedis = pool.getResource()) { resultMap = jedis.hgetAll(name); } String[] split = name.split("_"); @@ -231,6 +234,7 @@ public class MultiThreadTreeLoader { if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + JedisPool jedisPool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(port), 20000000); try (Jedis outer = jedisPool.getResource()) { outer.select(1); outer.set(matchKey, result); @@ -238,6 +242,11 @@ public class MultiThreadTreeLoader { } + try (Jedis jedis = pool.getResource()) { + jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); + } + + }catch (Exception e){ From 9014d235a55f787cbadbfe95b3fcd69350425e60 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 11:43:51 +0200 Subject: [PATCH 056/127] all phse --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index dbd2179..f25ce40 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -107,7 +107,7 @@ public class MultiThreadTreeLoader { } -// calculatePairs(inputPath, port); + calculatePairs(inputPath, port); log.info("Calculate pairs done"); comparePairs(port,inputPath,portInner,serverWait); From b8a9c3024f1e446f144b1ec9d3b64e0b6936dc2a Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 14:10:02 +0200 Subject: [PATCH 057/127] call option --- FixPatternMiner.iml | 1 + pom.xml | 6 + .../FixPatternParser/violations/Consumer.java | 226 ++++++++++++++++++ .../violations/MultiThreadTreeLoader.java | 19 +- .../FixPatternParser/violations/Producer.java | 154 ++++++++++++ 5 files changed, 399 insertions(+), 7 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index 05d2946..76bff5b 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -57,5 +57,6 @@ + \ No newline at end of file diff --git a/pom.xml b/pom.xml index d080fee..5c9389c 100644 --- a/pom.xml +++ b/pom.xml @@ -74,6 +74,12 @@ 1.3 + + com.rabbitmq + amqp-client + 4.0.0 + + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java new file mode 100644 index 0000000..9cda090 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java @@ -0,0 +1,226 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.Tree; +import com.rabbitmq.client.*; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.JedisPoolConfig; + +import java.io.*; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.concurrent.TimeoutException; +import java.util.stream.Collectors; + +/** + * Created by anilkoyuncu on 03/04/2018. + */ +public class Consumer { + + private static Logger log = LoggerFactory.getLogger(Consumer.class); + private static String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + + public static void main(String[] args) { + + ConnectionFactory factory = new ConnectionFactory(); + factory.setHost("10.240.5.10"); +// factory.setVirtualHost("treeCompare"); + factory.setPort(5672); + factory.setUsername("anil"); + factory.setPassword("changeme2018"); + factory.setConnectionTimeout(1000); + Connection connection = null; + Channel channel = null; + try { + connection = factory.newConnection(); + + channel = connection.createChannel(); + channel.queueDeclare("tree_queue", false, false, false, null); + + + boolean autoAck = false; + Channel finalChannel = channel; + channel.basicConsume("tree_queue", autoAck,"myConsumerTag", + new DefaultConsumer(finalChannel) { + @Override + public void handleDelivery( + String consumerTag, + Envelope envelope, + AMQP.BasicProperties properties, + byte[] body) throws IOException { + + String message = new String(body, "UTF-8"); + String[] split = message.split(","); + String key = split[0]; + String firstV = split[1]; + String secondV = split[2]; + try{ + calculateSimi(firstV,secondV,key); + }catch (Exception e){ + finalChannel.basicNack(envelope.getDeliveryTag(),false,false); + } + finalChannel.basicAck(envelope.getDeliveryTag(),false); + + // process the message + } + }); + +// channel.basicConsume("tree_queue", true, consumer); + + } catch (IOException e) { + e.printStackTrace(); + } catch (TimeoutException e) { + e.printStackTrace(); + } + } + + public static void calculateSimi(String firstVal,String secondVal, String key){ + + String[] split = key.split("_"); + + + String i = split[1]; + String j = split[2]; + + String[] firstValueSplit = firstVal.split("GumTreeOutput2"); + String[] secondValueSplit = secondVal.split("GumTreeOutput2"); + + String firstValue; + if (firstValueSplit.length == 1) { + firstValue = inputPath + firstValueSplit[0]; + } else { + firstValue = inputPath + firstValueSplit[1]; + } + + String secondValue; + if (secondValueSplit.length == 1) { + secondValue = inputPath + secondValueSplit[0]; + } else { + secondValue = inputPath + secondValueSplit[1]; + } + + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); + + String result = firstVal + "," + secondVal + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + log.info(matchKey); +// JedisPool jedisPool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(port), 20000000); +// try (Jedis outer = jedisPool.getResource()) { +// outer.select(1); +// outer.set(matchKey, result); +// } + } + + +// try (Jedis jedis = pool.getResource()) { +// jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); +// } + + } + + public static ITree getSimpliedTree(String fn) { + HierarchicalActionSet actionSet = null; + try { + FileInputStream fi = new FileInputStream(new File(fn)); + ObjectInputStream oi = new ObjectInputStream(fi); + actionSet = (HierarchicalActionSet) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + ITree parent = null; + ITree children =null; + ITree tree = getASTTree(actionSet, parent, children); + tree.setParent(null); + + return tree; + + } + + public static List getKeysByValue(Map map, E value) { + return map.entrySet() + .stream() + .filter(entry -> Objects.equals(entry.getValue(), value)) + .map(Map.Entry::getKey) + .collect(Collectors.toList()); + } + + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("Birden cok astnodemapmapping"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + + parent = new Tree(newType,""); + }else{ + children = new Tree(newType,""); + parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null); + + } + + + } + return parent; + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index f25ce40..1a8297d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -87,11 +87,13 @@ public class MultiThreadTreeLoader { String importScript; String pairsCompletedPath; String serverWait; + String option; if (args.length > 0) { inputPath = args[0]; - port = args[2]; - portInner = args[3]; - serverWait = args[4]; + port = args[1]; + portInner = args[2]; + serverWait = args[3]; + option = args[4]; // pairsCSVPath = args[3]; // importScript = args[4]; // pairsCompletedPath = args[3]; @@ -101,15 +103,18 @@ public class MultiThreadTreeLoader { port = "6379"; portInner = "6380"; serverWait = "10000"; + option = "COMP"; pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; } - - calculatePairs(inputPath, port); - log.info("Calculate pairs done"); - comparePairs(port,inputPath,portInner,serverWait); + if (option.equals("CALC")) { + calculatePairs(inputPath, port); + log.info("Calculate pairs done"); + }else { + comparePairs(port, inputPath, portInner, serverWait); + } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java new file mode 100644 index 0000000..339f28b --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java @@ -0,0 +1,154 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.oracle.tools.packager.Log; +import com.rabbitmq.client.Channel; +import com.rabbitmq.client.Connection; +import com.rabbitmq.client.ConnectionFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; + +import java.io.File; +import java.io.FilenameFilter; +import java.io.IOException; +import java.nio.file.Files; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.concurrent.TimeoutException; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Created by anilkoyuncu on 03/04/2018. + */ +public class Producer { + private static Logger log = LoggerFactory.getLogger(Producer.class); + public static void main(String[] args) { + + + String inputPath; + String outputPath; + String port; + String portInner; + String pairsCSVPath; + String importScript; + String pairsCompletedPath; + String serverWait; + if (args.length > 0) { + inputPath = args[0]; + port = args[1]; + portInner = args[2]; + serverWait = args[3]; +// pairsCSVPath = args[3]; +// importScript = args[4]; +// pairsCompletedPath = args[3]; + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6379"; + portInner = "6380"; + serverWait = "10000"; + pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; + importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; + pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; + } + + + calculatePairs(inputPath, port); + log.info("Calculate pairs done"); + + + + } + public static void calculatePairs(String inputPath,String port) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for (File pj : pjs) { + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ActionSetDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + readMessageFiles(fileToCompare, port); + } + + private static void readMessageFiles(List folders, String port) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + + + log.info("Calculating pairs"); + + int fileCounter = 0; + + ConnectionFactory factory = new ConnectionFactory(); + factory.setHost("10.240.5.10"); +// factory.setVirtualHost("treeCompare"); + factory.setPort(5672); + factory.setUsername("anil"); + factory.setPassword("changeme2018"); + factory.setConnectionTimeout(1000); + Connection connection = null; + Channel channel = null; + try { + connection = factory.newConnection(); + + channel = connection.createChannel(); + channel.queueDeclare("tree_queue", false, false, false, null); + + } catch (IOException e) { + e.printStackTrace(); + } catch (TimeoutException e) { + e.printStackTrace(); + } + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + // do operations with jedis resource + + String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); +// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; +// jedis.set(key,value); + + String message = key +","+treesFileNames.get(i).split("GumTreeOutput2")[1] + "," + treesFileNames.get(j).split("GumTreeOutput2")[1]; + try { + channel.basicPublish("", "tree_queue", null, message.getBytes()); + } catch (IOException e) { + e.printStackTrace(); + } + + + + + } + } + + + + + log.info("Done pairs"); + } +} From 43c69855bb3bb43288e3ff9a5905f7a0ab6b5adf Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 14:15:35 +0200 Subject: [PATCH 058/127] ping --- .../FixPatternParser/violations/MultiThreadTreeLoader.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 1a8297d..97153cb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -159,6 +159,10 @@ public class MultiThreadTreeLoader { JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); ScanResult scan; try (Jedis inner = pool.getResource()) { + while (inner.ping()== "PONG"){ + log.info("wait"); + } + ScanParams sc = new ScanParams(); sc.count(150000000); sc.match("pair_*"); From 59c81bf824e0b2539dc3f4ee41d54d275f73b81d Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 14:49:09 +0200 Subject: [PATCH 059/127] multi --- .../violations/MultiThreadTreeLoader.java | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index 97153cb..ff550f9 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -88,12 +88,16 @@ public class MultiThreadTreeLoader { String pairsCompletedPath; String serverWait; String option; + String dbDir; + String chunkName; if (args.length > 0) { inputPath = args[0]; port = args[1]; portInner = args[2]; serverWait = args[3]; option = args[4]; + chunkName = args[5]; + dbDir = args[6]; // pairsCSVPath = args[3]; // importScript = args[4]; // pairsCompletedPath = args[3]; @@ -107,51 +111,47 @@ public class MultiThreadTreeLoader { pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; + chunkName ="chunk0.rdb"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; } if (option.equals("CALC")) { calculatePairs(inputPath, port); log.info("Calculate pairs done"); }else { - comparePairs(port, inputPath, portInner, serverWait); + comparePairs(port, inputPath, portInner, serverWait,chunkName,dbDir); } } - public static void comparePairs(String port,String inputPath, String innerPort,String serverWait){ + public static void comparePairs(String port,String inputPath, String innerPort,String serverWait,String chunkName, String dbDir){ // String cmd; // cmd = "bash " + importScript +" %s"; - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + List dir; List path; - File[] files; + String orgDbname; - File dbDir; - try (Jedis jedis = jedisPool.getResource()) { - dir = jedis.configGet("dir"); - path = jedis.configGet("dbfilename"); - dbDir = new File(dir.get(1)); - orgDbname = path.get(1); - files = dbDir.listFiles(); - } + File files = new File(dbDir); + File[] listFiles = files.listFiles(); - Stream stream = Arrays.stream(files); + Stream stream = Arrays.stream(listFiles); List folders = stream - .filter(x -> !x.getName().startsWith(orgDbname)).filter(x -> x.getName().endsWith(".rdb")) + .filter(x -> x.getName().equals(chunkName)) .collect(Collectors.toList()); for (File folder : folders) { - String cmd = "bash "+dir.get(1) + "/" + "startServer.sh" +" %s %s %s"; + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,folder.getName(),Integer.valueOf(innerPort)); loadRedis(cmd,serverWait); @@ -172,10 +172,10 @@ public class MultiThreadTreeLoader { log.info("Scanning " + String.valueOf(size)); } scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, port,innerPort)); + .forEach(m -> coreCompare(m, inputPath, innerPort)); - String stopServer = "bash "+dir.get(1) + "/" + "stopServer.sh" +" %s"; + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(innerPort)); loadRedis(stopServer,serverWait); @@ -186,7 +186,7 @@ public class MultiThreadTreeLoader { } - private static void coreCompare(String name , String inputPath, String port,String innerPort) { + private static void coreCompare(String name , String inputPath, String innerPort) { JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); Map resultMap; try (Jedis jedis = pool.getResource()) { @@ -243,10 +243,10 @@ public class MultiThreadTreeLoader { if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - JedisPool jedisPool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(port), 20000000); - try (Jedis outer = jedisPool.getResource()) { - outer.select(1); - outer.set(matchKey, result); + + try (Jedis jedis = pool.getResource()) { + jedis.select(1); + jedis.set(matchKey, result); } } From 61b6c7a8405c8d18ca7ba5443d3d1ace74514da1 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 3 Apr 2018 22:23:16 +0200 Subject: [PATCH 060/127] akka --- pom.xml | 2 +- .../violations/AkkaTreeLoader.java | 651 ++++++++++++++++++ .../FixPatternParser/violations/Compare.java | 102 +++ .../FixPatternParser/violations/Message.java | 20 + .../violations/MultiThreadTreeLoader.java | 2 +- .../violations/RunnableCompare.java | 25 + .../violations/TreeActor.java | 82 +++ .../violations/TreeWorker.java | 206 ++++++ .../violations/WorkMessage.java | 53 ++ 9 files changed, 1141 insertions(+), 2 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java diff --git a/pom.xml b/pom.xml index 5c9389c..1378d5b 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader + edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java new file mode 100644 index 0000000..bdbcef0 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -0,0 +1,651 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import akka.actor.ActorRef; +import akka.actor.ActorSystem; +import akka.actor.Props; +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.Tree; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.MultipleThreadsParser.*; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import edu.lu.uni.serval.utils.FileHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; + +import java.io.*; +import java.nio.file.Files; +import java.time.Duration; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.function.Consumer; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class AkkaTreeLoader { + + private static class StreamGobbler implements Runnable { + private InputStream inputStream; + private Consumer consumer; + + public StreamGobbler(InputStream inputStream, Consumer consumer) { + this.inputStream = inputStream; + this.consumer = consumer; + } + + @Override + public void run() { + new BufferedReader(new InputStreamReader(inputStream)).lines() + .forEach(consumer); + } + } + + private static Logger log = LoggerFactory.getLogger(AkkaTreeLoader.class); + + + public static void loadRedis(String cmd,String serverWait){ + Process process; + + try { +// String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(cmd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); +// int exitCode = process.waitFor(); +// assert exitCode == 0; + Thread.sleep(Integer.valueOf(serverWait)); + + } catch (IOException e) { + e.printStackTrace(); + } + catch (InterruptedException e) { + e.printStackTrace(); + } + log.info("Load done"); + } + + public static void main(String[] args) { + + + String inputPath; + String outputPath; + String port; + String portInner; + String pairsCSVPath; + String importScript; + String pairsCompletedPath; + String serverWait; + String option; + String dbDir; + String chunkName; + String numOfWorkers; + if (args.length > 0) { + inputPath = args[0]; + port = args[1]; + portInner = args[2]; + serverWait = args[3]; + option = args[4]; + chunkName = args[5]; + dbDir = args[6]; + numOfWorkers = args[7]; +// pairsCSVPath = args[3]; +// importScript = args[4]; +// pairsCompletedPath = args[3]; + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6379"; + portInner = "6380"; + serverWait = "10000"; + option = "COMP"; + pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; + importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; + pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; + chunkName ="chunk5.rdb"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + numOfWorkers = "16"; + } + + if (option.equals("CALC")) { + calculatePairs(inputPath, port); + log.info("Calculate pairs done"); + }else { + comparePairs(port, inputPath, portInner, serverWait,chunkName,dbDir,numOfWorkers); + } + + + } + + + public static void comparePairs(String port,String inputPath, String innerPort,String serverWait,String chunkName, String dbDir,String numOfWorkers){ +// String cmd; +// cmd = "bash " + importScript +" %s"; + + + + List dir; + List path; + + String orgDbname; + + + File files = new File(dbDir); + File[] listFiles = files.listFiles(); + + + Stream stream = Arrays.stream(listFiles); + List folders = stream + .filter(x -> x.getName().equals(chunkName)) + .collect(Collectors.toList()); + for (File folder : folders) { + + + + + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,folder.getName(),Integer.valueOf(innerPort)); + loadRedis(cmd,serverWait); + + + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + ScanResult scan; + try (Jedis inner = pool.getResource()) { + while (inner.ping()== "PONG"){ + log.info("wait"); + } + + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_*"); + + scan = inner.scan("0", sc); + int size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + } + List result = scan.getResult(); + + + ActorSystem system = null; + ActorRef parsingActor = null; + final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Tree-System"); + parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers)), "tree-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } +// greeter.tell(); + +// .parallelStream() +// .forEach(m -> coreCompare(m, inputPath, innerPort)); + + +// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; +// stopServer = String.format(stopServer,Integer.valueOf(innerPort)); +// loadRedis(stopServer,serverWait); + + } + + + + + } + + private static void coreCompare(String name , String inputPath, String innerPort) { + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + Map resultMap; + try (Jedis jedis = pool.getResource()) { + resultMap = jedis.hgetAll(name); + } + String[] split = name.split("_"); + + + String i = split[1]; + String j = split[2]; + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + String[] firstValueSplit = firstValue.split("GumTreeOutput2"); + String[] secondValueSplit = secondValue.split("GumTreeOutput2"); + + if (firstValueSplit.length == 1) { + firstValue = inputPath + firstValueSplit[0]; + } else { + firstValue = inputPath + firstValueSplit[1]; + } + + if (secondValueSplit.length == 1) { + secondValue = inputPath + secondValueSplit[0]; + } else { + secondValue = inputPath + secondValueSplit[1]; + } + + try { + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); + + String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + + try (Jedis jedis = pool.getResource()) { + jedis.select(1); + jedis.set(matchKey, result); + } + } + + + try (Jedis jedis = pool.getResource()) { + jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); + } + + + + + }catch (Exception e){ + log.error(e.toString() + " {}",(name)); + + + } + + + + + + } + + + + public static void calculatePairs(String inputPath,String port) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for (File pj : pjs) { + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ActionSetDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + readMessageFiles(fileToCompare,port); + } + + public static void processMessages(String inputPath, String outputPath) { + File folder = new File(outputPath + "pairs_splitted/"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + FileHelper.createDirectory(outputPath + "comparison_splitted/"); + pjs.parallelStream() + .forEach(m -> coreLoop(m, outputPath,inputPath)); + } + + + public static ITree getSimpliedTree(String fn) { + HierarchicalActionSet actionSet = null; + try { + FileInputStream fi = new FileInputStream(new File(fn)); + ObjectInputStream oi = new ObjectInputStream(fi); + actionSet = (HierarchicalActionSet) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + ITree parent = null; + ITree children =null; + ITree tree = getASTTree(actionSet, parent, children); + tree.setParent(null); + + return tree; + + } + + public static List getKeysByValue(Map map, E value) { + return map.entrySet() + .stream() + .filter(entry -> Objects.equals(entry.getValue(), value)) + .map(Map.Entry::getKey) + .collect(Collectors.toList()); + } + + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("Birden cok astnodemapmapping"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + + parent = new Tree(newType,""); + }else{ + children = new Tree(newType,""); + parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null); + + } + + + } + return parent; + } + + public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ + + int newType = 0; + + Action action = actionSet.getAction(); + if (action instanceof Update){ + newType = 101; + }else if(action instanceof Insert){ + newType =100; + }else if(action instanceof Move){ + newType = 102; + }else if(action instanceof Delete){ + newType=103; + }else{ + new Exception("unknow action"); + } + if(actionSet.getParent() == null){ + //root + + parent = new Tree(newType,""); + }else{ + children = new Tree(newType,""); + parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getActionTree(subAction,children,null); + + } + + + } + return parent; + } + + + + private static void coreLoop(File mes, String outputPath,String inputPath) { + try { + + log.info("Starting in coreLoop"); + + BufferedReader br = null; + String sCurrentLine = null; + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); + + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; + + firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; + secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; + + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); + + + } + writer.close(); + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + + } + log.info("Completed output_" + mes.getName()); + } + + private static void readMessageFiles(List folders,String port) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } +// FileHelper.createDirectory(outputPath + "pairs/"); + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + byte [] buf = new byte[0]; + String line = null; + + +// FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); +// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + try (Jedis jedis = jedisPool.getResource()) { + List dir = null; + List path = null; + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + // do operations with jedis resource + + String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); +// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; +// jedis.set(key,value); + + jedis.hset(key,"0",treesFileNames.get(i).split("GumTreeOutput2")[1]); + jedis.hset(key,"1",treesFileNames.get(j).split("GumTreeOutput2")[1]); + //10000000 + if(Integer.compare(jedis.dbSize().intValue(),10000000) == 0){ + dir = jedis.configGet("dir"); + path = jedis.configGet("dbfilename"); + File dbPath = new File(dir.get(1)+"/"+path.get(1)); + File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); + try { + jedis.save(); + while (jedis.ping()== "PONG"){ + log.info("wait"); + } + + + + Files.copy(dbPath.toPath(),savePath.toPath()); + } catch (IOException e) { + + e.printStackTrace(); + } + fileCounter++; + jedis.flushDB(); + + } + + + } + } + jedis.save(); + fileCounter++; + File dbPath = new File(dir.get(1)+"/"+path.get(1)); + File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); + try { + + while (jedis.ping()== "PONG"){ + log.info("wait"); + } + + + + Files.copy(dbPath.toPath(),savePath.toPath()); + } catch (IOException e) { + + e.printStackTrace(); + } + jedis.flushDB(); + } + + + + + log.info("Done pairs"); + } + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + + private static List getMessageFiles(String gumTreeInput) { + String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile + File revFilesPath = new File(inputPath + "revFiles/"); + File[] revFiles = revFilesPath.listFiles(); // project folders + List msgFiles = new ArrayList<>(); + if (revFiles.length >= 0) { + for (File revFile : revFiles) { +// if (revFile.getName().endsWith(".java")) { + String fileName = revFile.getName(); + File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file + fileName = fileName.replace(".java", ".txt"); + File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file + File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + edu.lu.uni.serval.MultipleThreadsParser.MessageFile msgFile = new edu.lu.uni.serval.MultipleThreadsParser.MessageFile(revFile, prevFile, diffentryFile); + msgFile.setPositionFile(positionFile); + msgFiles.add(msgFile); +// } + } + + return msgFiles; + } + else{ + return null; + } + } + + + +// return msgFiles; +} + + + + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java new file mode 100644 index 0000000..6c4d11b --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java @@ -0,0 +1,102 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.JedisPoolConfig; + +import java.util.List; +import java.util.Map; + +import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; + +/** + * Created by anilkoyuncu on 03/04/2018. + */ +public class Compare { + + private Logger log = LoggerFactory.getLogger(Compare.class); + + public void coreCompare(String name , String inputPath, String innerPort) { + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + Map resultMap; + try (Jedis jedis = pool.getResource()) { + resultMap = jedis.hgetAll(name); + } + String[] split = name.split("_"); + + + String i = split[1]; + String j = split[2]; + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + String[] firstValueSplit = firstValue.split("GumTreeOutput2"); + String[] secondValueSplit = secondValue.split("GumTreeOutput2"); + + if (firstValueSplit.length == 1) { + firstValue = inputPath + firstValueSplit[0]; + } else { + firstValue = inputPath + firstValueSplit[1]; + } + + if (secondValueSplit.length == 1) { + secondValue = inputPath + secondValueSplit[0]; + } else { + secondValue = inputPath + secondValueSplit[1]; + } + + try { + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); + + String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + log.info(matchKey); + try (Jedis jedis = pool.getResource()) { + jedis.select(1); + jedis.set(matchKey, result); + } + } + + + try (Jedis jedis = pool.getResource()) { + jedis.del("pair_" + (String.valueOf(i)) + "_" + String.valueOf(j)); + } + + + } catch (Exception e) { + log.error(e.toString() + " {}", (name)); + + + } + } + } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java new file mode 100644 index 0000000..969a4c2 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java @@ -0,0 +1,20 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import java.io.File; + +public class Message { + + private String name; + private String inputPath; + private String innerPort; + + public Message(String name , String inputPath, String innerPort) { + super(); + this.name = name; + this.inputPath = inputPath; + this.innerPort = innerPort; + } + + + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index ff550f9..a30d3fc 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -111,7 +111,7 @@ public class MultiThreadTreeLoader { pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; - chunkName ="chunk0.rdb"; + chunkName ="chunk5.rdb"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java new file mode 100644 index 0000000..0ff319f --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java @@ -0,0 +1,25 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import edu.lu.uni.serval.FixPatternParser.Parser; + +import java.io.File; + +public class RunnableCompare implements Runnable { + + private String name; + private String inputPath; + private String innerPort; + private Compare comparer; + + public RunnableCompare(String name , String inputPath, String innerPort, Compare comp) { + this.name = name; + this.inputPath = inputPath; + this.innerPort = innerPort; + this.comparer = comp; + } + + @Override + public void run() { + comparer.coreCompare(name, inputPath, innerPort); + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java new file mode 100644 index 0000000..a72c1f0 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java @@ -0,0 +1,82 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import akka.actor.ActorRef; +import akka.actor.Props; +import akka.actor.UntypedActor; +import akka.japi.Creator; +import akka.routing.RoundRobinPool; + +import edu.lu.uni.serval.FixPatternParser.violations.WorkMessage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.List; + +public class TreeActor extends UntypedActor { + + private static Logger logger = LoggerFactory.getLogger(TreeActor.class); + + private ActorRef mineRouter; + private final int numberOfWorkers; + private int counter = 0; + + public TreeActor(int numberOfWorkers) { + mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) + .props(TreeWorker.props()), "tree-router"); + this.numberOfWorkers = numberOfWorkers; + } + + public static Props props(final int numberOfWorkers) { + + return Props.create(new Creator() { + + private static final long serialVersionUID = 9207427376110704705L; + + @Override + public TreeActor create() throws Exception { + return new TreeActor(numberOfWorkers); + } + + }); + } + + @SuppressWarnings("deprecation") + @Override + public void onReceive(Object message) throws Exception { + if (message instanceof WorkMessage) { + List files = ((WorkMessage) message).getMsgFiles(); + String innerPort = ((WorkMessage) message).getInnerPort(); + String inputPath = ((WorkMessage) message).getInputPath(); + String dbDir = ((WorkMessage) message).getDbDir(); + String serverWait = ((WorkMessage) message).getServerWait(); + + int size = files.size(); + int average = size / numberOfWorkers; + int reminder = size % numberOfWorkers; + int counter = 0; + + for (int i = 0; i < numberOfWorkers; i ++) { + int fromIndex = i * average + counter; + if (counter < reminder) counter ++; + int toIndex = (i + 1) * average + counter; + + List filesOfWorkers = files.subList(fromIndex, toIndex); + final WorkMessage workMsg = new WorkMessage(i + 1, filesOfWorkers,innerPort,inputPath,dbDir,serverWait); + mineRouter.tell(workMsg, getSelf()); + logger.info("Assign a task to worker #" + (i + 1) + "..."); + } + } else if ("STOP".equals(message.toString())) { + counter ++; + logger.info(counter + " workers finailized their work..."); + if (counter >= numberOfWorkers) { + logger.info("All workers finailized their work..."); + this.getContext().stop(mineRouter); + this.getContext().stop(getSelf()); + this.getContext().system().shutdown(); + } + } else { + unhandled(message); + } + } + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java new file mode 100644 index 0000000..f9ae8a4 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -0,0 +1,206 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import akka.actor.Props; +import akka.actor.UntypedActor; +import akka.japi.Creator; +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPatternParser.RunnableParser; +import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; + +import edu.lu.uni.serval.FixPatternParser.violations.WorkMessage; +import edu.lu.uni.serval.config.Configuration; +import edu.lu.uni.serval.utils.FileHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.JedisPoolConfig; + +import java.io.BufferedReader; +import java.io.File; +import java.io.IOException; +import java.io.StringReader; +import java.util.List; +import java.util.Map; +import java.util.concurrent.*; + +import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; +import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; + +public class TreeWorker extends UntypedActor { + private static Logger log = LoggerFactory.getLogger(TreeWorker.class); + + + + public TreeWorker() { + + + } + + public static Props props() { + return Props.create(new Creator() { + + private static final long serialVersionUID = -7615153844097275009L; + + @Override + public TreeWorker create() throws Exception { + return new TreeWorker(); + } + + }); + } + + @Override + public void onReceive(Object message) throws Exception { + if(message instanceof edu.lu.uni.serval.FixPatternParser.violations.WorkMessage) { + + log.info("do sometihng"); +// if (message instanceof edu.lu.uni.serval.MultipleThreadsParser.WorkMessage) { + edu.lu.uni.serval.FixPatternParser.violations.WorkMessage msg = (WorkMessage) message; + List files = msg.getMsgFiles(); + String innerPort = msg.getInnerPort(); + String inputPath = msg.getInputPath(); + String dbDir = msg.getDbDir(); + String serverWait = msg.getServerWait(); +// StringBuilder editScripts = new StringBuilder(); +// StringBuilder patchesSourceCode = new StringBuilder(); +// StringBuilder sizes = new StringBuilder(); +// StringBuilder tokens = new StringBuilder(); +// StringBuilder testingInfo = new StringBuilder(); +// +// int id = msg.getId(); +// int counter = 0; +// +// int nullGumTreeResults = 0; +// int noSourceCodeChanges = 0; +// int noStatementChanges = 0; +// int nullDiffEntry = 0; +// int nullMappingGumTreeResults = 0; +// int pureDeletion = 0; +// int largeHunk = 0; +// int nullSourceCode = 0; +// int testInfos = 0; +// int timeouts = 0; +// StringBuilder builder = new StringBuilder(); +// + for (String name : files) { + +// log.info(name); +// File revFile = msgFile.getRevFile(); +// File prevFile = msgFile.getPrevFile(); +// File diffentryFile = msgFile.getDiffEntryFile(); +//// File positionFile = msgFile.getPositionFile(); +// /*if (revFile.getName().toLowerCase().contains("test")) { +// continue; +// }*/ +// FixedViolationHunkParser parser = new FixedViolationHunkParser(); +// + final ExecutorService executor = Executors.newSingleThreadExecutor(); +// // schedule the work + final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare())); + try { + // wait for task to complete + future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); +// +// nullDiffEntry += parser.nullMatchedDiffEntry; +// nullMappingGumTreeResults += parser.nullMappingGumTreeResult; +// pureDeletion += parser.pureDeletions; +// largeHunk += parser.largeHunk; +// nullSourceCode += parser.nullSourceCode; +// testInfos += parser.testInfos; +// testingInfo.append(parser.testingInfo); +// builder.append(parser.unfixedViolations); +// +// String editScript = parser.getAstEditScripts(); +// if ("".equals(editScript)) { +//// if (parser.resultType == 1) { +//// nullGumTreeResults += countAlarms(positionFile, ""); +//// } else if (parser.resultType == 2) { +//// noSourceCodeChanges += countAlarms(positionFile, ""); +//// } else if (parser.resultType == 3) { +//// noStatementChanges += countAlarms(positionFile, ""); +//// } +// } else { +// editScripts.append(editScript); +// patchesSourceCode.append(parser.getPatchesSourceCode()); +// sizes.append(parser.getSizes()); +// tokens.append(parser.getTokensOfSourceCode()); +// +// counter ++; +// if (counter % 100 == 0) { +// FileHelper.outputToFile(editScriptsFilePath + "edistScripts_" + id + ".list", editScripts, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); +// FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); +// FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); +// editScripts.setLength(0); +// patchesSourceCode.setLength(0); +// sizes.setLength(0); +// tokens.setLength(0); +// log.info("Worker #" + id +" finialized parsing " + counter + " files..."); +// FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); +// testingInfo.setLength(0); +// } +// } + } catch (TimeoutException e) { + future.cancel(true); +//// timeouts += countAlarms(positionFile, "#Timeout:"); +// System.err.println("#Timeout: " + revFile.getName()); + } catch (InterruptedException e) { +//// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); +// System.err.println("#TimeInterrupted: " + revFile.getName()); + e.printStackTrace(); + } catch (ExecutionException e) { +//// timeouts += countAlarms(positionFile, "#TimeAborted:"); +// System.err.println("#TimeAborted: " + revFile.getName()); + e.printStackTrace(); + } finally { + executor.shutdownNow(); + } + } + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(innerPort)); + loadRedis(stopServer,serverWait); +// +// if (sizes.length() > 0) { +// FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); +// FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); +// FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); +// editScripts.setLength(0); +// patchesSourceCode.setLength(0); +// sizes.setLength(0); +// tokens.setLength(0); +// +// FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); +// testingInfo.setLength(0); +// } +// String statistic = "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + +// "\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults + +// "\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + +// "\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts; +// FileHelper.outputToFile("OUTPUT/statistic_" + id + ".list", statistic, false); +// FileHelper.outputToFile("OUTPUT/UnfixedV_" + id + ".list", builder, false); +// +// log.info("Worker #" + id +"finialized parsing " + counter + " files..."); +// log.info("Worker #" + id + " finialized the work..."); +// this.getSender().tell("STOP", getSelf()); +// } else { + }else{ + unhandled(message); + } + } + + + + + + + + + + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java new file mode 100644 index 0000000..6343c51 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java @@ -0,0 +1,53 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; + +import java.util.List; + +public class WorkMessage { + + private int id; + private List msgFiles; + + public String getDbDir() { + return dbDir; + } + + public String getServerWait() { + return serverWait; + } + + private String dbDir; + private String serverWait; + + public String getInputPath() { + return inputPath; + } + + private String inputPath; + + public String getInnerPort() { + return innerPort; + } + + private String innerPort; + + public WorkMessage(int id, List msgFiles,String innerPort,String inputPath,String dbDir,String serverWait) { + super(); + this.id = id; + this.msgFiles = msgFiles; + this.innerPort = innerPort; + this.inputPath = inputPath; + this.dbDir = dbDir; + this.serverWait = serverWait; + } + + public int getId() { + return id; + } + + public List getMsgFiles() { + return msgFiles; + } + +} \ No newline at end of file From 8aedc4ec40788f9a6aa3a31b9b6de055a0af62c8 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 11:14:52 +0200 Subject: [PATCH 061/127] akka --- .../violations/AkkaTreeLoader.java | 3 +- .../violations/TreeActor.java | 18 +++++-- .../violations/TreeWorker.java | 48 ++++++------------- 3 files changed, 31 insertions(+), 38 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index bdbcef0..296fe0c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -167,6 +167,7 @@ public class AkkaTreeLoader { } ScanParams sc = new ScanParams(); + //150000000 sc.count(150000000); sc.match("pair_*"); @@ -183,7 +184,7 @@ public class AkkaTreeLoader { try { log.info("Akka begins..."); system = ActorSystem.create("Tree-System"); - parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers)), "tree-actor"); + parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { system.shutdown(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java index a72c1f0..c9f0edb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java @@ -12,6 +12,8 @@ import org.slf4j.LoggerFactory; import java.util.List; +import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; + public class TreeActor extends UntypedActor { private static Logger logger = LoggerFactory.getLogger(TreeActor.class); @@ -20,13 +22,20 @@ public class TreeActor extends UntypedActor { private final int numberOfWorkers; private int counter = 0; - public TreeActor(int numberOfWorkers) { + private String innerPort; + private String dbDir; + private String serverWait; + + public TreeActor(int numberOfWorkers,String dbDir,String innerPort,String serverWait) { mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) .props(TreeWorker.props()), "tree-router"); this.numberOfWorkers = numberOfWorkers; + this.innerPort = innerPort; + this.dbDir = dbDir; + this.serverWait = serverWait; } - public static Props props(final int numberOfWorkers) { + public static Props props(final int numberOfWorkers, final String dbDir,final String innerPort, final String serverWait) { return Props.create(new Creator() { @@ -34,7 +43,7 @@ public class TreeActor extends UntypedActor { @Override public TreeActor create() throws Exception { - return new TreeActor(numberOfWorkers); + return new TreeActor(numberOfWorkers,dbDir,innerPort,serverWait); } }); @@ -73,6 +82,9 @@ public class TreeActor extends UntypedActor { this.getContext().stop(mineRouter); this.getContext().stop(getSelf()); this.getContext().system().shutdown(); + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(innerPort)); + loadRedis(stopServer,serverWait); } } else { unhandled(message); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index f9ae8a4..2e01109 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -58,7 +58,7 @@ public class TreeWorker extends UntypedActor { public void onReceive(Object message) throws Exception { if(message instanceof edu.lu.uni.serval.FixPatternParser.violations.WorkMessage) { - log.info("do sometihng"); + // if (message instanceof edu.lu.uni.serval.MultipleThreadsParser.WorkMessage) { edu.lu.uni.serval.FixPatternParser.violations.WorkMessage msg = (WorkMessage) message; List files = msg.getMsgFiles(); @@ -66,38 +66,13 @@ public class TreeWorker extends UntypedActor { String inputPath = msg.getInputPath(); String dbDir = msg.getDbDir(); String serverWait = msg.getServerWait(); -// StringBuilder editScripts = new StringBuilder(); -// StringBuilder patchesSourceCode = new StringBuilder(); -// StringBuilder sizes = new StringBuilder(); -// StringBuilder tokens = new StringBuilder(); -// StringBuilder testingInfo = new StringBuilder(); -// -// int id = msg.getId(); -// int counter = 0; -// -// int nullGumTreeResults = 0; -// int noSourceCodeChanges = 0; -// int noStatementChanges = 0; -// int nullDiffEntry = 0; -// int nullMappingGumTreeResults = 0; -// int pureDeletion = 0; -// int largeHunk = 0; -// int nullSourceCode = 0; -// int testInfos = 0; -// int timeouts = 0; -// StringBuilder builder = new StringBuilder(); + int id = msg.getId(); + int counter = 0; + // for (String name : files) { -// log.info(name); -// File revFile = msgFile.getRevFile(); -// File prevFile = msgFile.getPrevFile(); -// File diffentryFile = msgFile.getDiffEntryFile(); -//// File positionFile = msgFile.getPositionFile(); -// /*if (revFile.getName().toLowerCase().contains("test")) { -// continue; -// }*/ -// FixedViolationHunkParser parser = new FixedViolationHunkParser(); + // final ExecutorService executor = Executors.newSingleThreadExecutor(); // // schedule the work @@ -105,7 +80,7 @@ public class TreeWorker extends UntypedActor { try { // wait for task to complete future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); -// + counter++; // nullDiffEntry += parser.nullMatchedDiffEntry; // nullMappingGumTreeResults += parser.nullMappingGumTreeResult; // pureDeletion += parser.pureDeletions; @@ -161,9 +136,14 @@ public class TreeWorker extends UntypedActor { executor.shutdownNow(); } } - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(innerPort)); - loadRedis(stopServer,serverWait); + + log.info("bitti"); + log.info("Worker #" + id +"finialized parsing " + counter + " files..."); + log.info("Worker #" + id + " finialized the work..."); + this.getSender().tell("STOP", getSelf()); +// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; +// stopServer = String.format(stopServer,Integer.valueOf(innerPort)); +// loadRedis(stopServer,serverWait); // // if (sizes.length() > 0) { // FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true); From 01a5206f3ff9cff2f709eff04d1c3f15f1fc0a7e Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 11:38:10 +0200 Subject: [PATCH 062/127] params --- .../violations/AkkaTreeLoader.java | 50 ++++++++++--------- 1 file changed, 26 insertions(+), 24 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 296fe0c..08290fc 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -80,56 +80,58 @@ public class AkkaTreeLoader { String inputPath; - String outputPath; +// String outputPath; String port; String portInner; - String pairsCSVPath; +// String pairsCSVPath; String importScript; - String pairsCompletedPath; +// String pairsCompletedPath; String serverWait; - String option; +// String option; String dbDir; String chunkName; String numOfWorkers; if (args.length > 0) { inputPath = args[0]; - port = args[1]; - portInner = args[2]; - serverWait = args[3]; - option = args[4]; - chunkName = args[5]; - dbDir = args[6]; - numOfWorkers = args[7]; +// port = args[1]; + portInner = args[1]; + serverWait = args[2]; +// option = args[4]; + chunkName = args[3]; + numOfWorkers = args[4]; + dbDir = args[5]; // pairsCSVPath = args[3]; // importScript = args[4]; // pairsCompletedPath = args[3]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6379"; +// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; +// port = "6379"; portInner = "6380"; serverWait = "10000"; - option = "COMP"; - pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; - importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; - pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; +// option = "COMP"; +// pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; +// importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; +// pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; chunkName ="chunk5.rdb"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "16"; } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + log.info(parameters); - if (option.equals("CALC")) { - calculatePairs(inputPath, port); - log.info("Calculate pairs done"); - }else { - comparePairs(port, inputPath, portInner, serverWait,chunkName,dbDir,numOfWorkers); - } +// if (option.equals("CALC")) { +// calculatePairs(inputPath, port); +// log.info("Calculate pairs done"); +// }else { + comparePairs(inputPath, portInner, serverWait,chunkName,dbDir,numOfWorkers); +// } } - public static void comparePairs(String port,String inputPath, String innerPort,String serverWait,String chunkName, String dbDir,String numOfWorkers){ + public static void comparePairs(String inputPath, String innerPort,String serverWait,String chunkName, String dbDir,String numOfWorkers){ // String cmd; // cmd = "bash " + importScript +" %s"; From d59e196973525735d6c7670dd2933f61b9c9dfa6 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 16:20:13 +0200 Subject: [PATCH 063/127] storefile --- pom.xml | 2 +- .../violations/AkkaTreeLoader.java | 48 ++-- .../FixPatternParser/violations/Compare.java | 30 +-- .../violations/StoreFile.java | 237 ++++++++++++++++++ 4 files changed, 286 insertions(+), 31 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java diff --git a/pom.xml b/pom.xml index 1378d5b..5753a75 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader + edu.lu.uni.serval.FixPatternParser.violations.StoreFile diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 08290fc..1a215fa 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -115,7 +115,7 @@ public class AkkaTreeLoader { // pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; chunkName ="chunk5.rdb"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "16"; + numOfWorkers = "1"; } String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); log.info(parameters); @@ -330,27 +330,45 @@ public class AkkaTreeLoader { .forEach(m -> coreLoop(m, outputPath,inputPath)); } - + /** Read the object from Base64 string. */ + private static Object fromString( String s ) throws IOException , + ClassNotFoundException { + byte [] data = Base64.getDecoder().decode( s ); + ObjectInputStream ois = new ObjectInputStream( + new ByteArrayInputStream( data ) ); + Object o = ois.readObject(); + ois.close(); + return o; + } public static ITree getSimpliedTree(String fn) { + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(6399), 20000000); HierarchicalActionSet actionSet = null; - try { - FileInputStream fi = new FileInputStream(new File(fn)); - ObjectInputStream oi = new ObjectInputStream(fi); - actionSet = (HierarchicalActionSet) oi.readObject(); - oi.close(); - fi.close(); - - - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); + try (Jedis inner = pool.getResource()) { + String s = inner.get(fn.substring(1)); + actionSet = (HierarchicalActionSet) fromString(s); } catch (IOException e) { - log.error("Error initializing stream"); e.printStackTrace(); } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block e.printStackTrace(); } +// try { +// FileInputStream fi = new FileInputStream(new File(fn)); +// ObjectInputStream oi = new ObjectInputStream(fi); +// actionSet = (HierarchicalActionSet) oi.readObject(); +// oi.close(); +// fi.close(); +// +// +// } catch (FileNotFoundException e) { +// log.error("File not found"); +// e.printStackTrace(); +// } catch (IOException e) { +// log.error("Error initializing stream"); +// e.printStackTrace(); +// } catch (ClassNotFoundException e) { +// // TODO Auto-generated catch block +// e.printStackTrace(); +// } ITree parent = null; ITree children =null; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java index 6c4d11b..514f515 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java @@ -14,7 +14,7 @@ import redis.clients.jedis.JedisPoolConfig; import java.util.List; import java.util.Map; -import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; +import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.getSimpliedTree; /** * Created by anilkoyuncu on 03/04/2018. @@ -37,20 +37,20 @@ public class Compare { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); - String[] firstValueSplit = firstValue.split("GumTreeOutput2"); - String[] secondValueSplit = secondValue.split("GumTreeOutput2"); - - if (firstValueSplit.length == 1) { - firstValue = inputPath + firstValueSplit[0]; - } else { - firstValue = inputPath + firstValueSplit[1]; - } - - if (secondValueSplit.length == 1) { - secondValue = inputPath + secondValueSplit[0]; - } else { - secondValue = inputPath + secondValueSplit[1]; - } +// String[] firstValueSplit = firstValue.split("GumTreeOutput2"); +// String[] secondValueSplit = secondValue.split("GumTreeOutput2"); +// +// if (firstValueSplit.length == 1) { +// firstValue = inputPath + firstValueSplit[0]; +// } else { +// firstValue = inputPath + firstValueSplit[1]; +// } +// +// if (secondValueSplit.length == 1) { +// secondValue = inputPath + secondValueSplit[0]; +// } else { +// secondValue = inputPath + secondValueSplit[1]; +// } try { ITree oldTree = getSimpliedTree(firstValue); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java new file mode 100644 index 0000000..588b099 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java @@ -0,0 +1,237 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.JedisPoolConfig; +import redis.clients.jedis.ScanResult; + +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; +import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; + +/** + * Created by anilkoyuncu on 03/04/2018. + */ +public class StoreFile { + + private static Logger log = LoggerFactory.getLogger(StoreFile.class); + + public static void main(String[] args) { + + String inputPath; + String portInner; + String serverWait; + String dbDir; + String chunkName; + String numOfWorkers; + if (args.length > 0) { + inputPath = args[0]; + portInner = args[1]; + serverWait = args[2]; + chunkName = args[3]; + numOfWorkers = args[4]; + dbDir = args[5]; + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + portInner = "6399"; + serverWait = "10000"; + chunkName ="dumps.rdb"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + numOfWorkers = "1"; + } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + + + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner)); + loadRedis(cmd,serverWait); + + File folder = new File(inputPath); + File[] subFolders = folder.listFiles(); + Stream stream = Arrays.stream(subFolders); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + List workList = new ArrayList(); + for (File pj : pjs) { + String pjName = pj.getName(); + File[] files = pj.listFiles(); + Stream fileStream = Arrays.stream(files); + List fs = fileStream + .filter(x -> x.getName().startsWith("ActionSetDumps")) + .collect(Collectors.toList()); + + File[] dumps = fs.get(0).listFiles(); + for (File f : dumps) { + String name = f.getName(); + + String key = pjName + "/"+ "ActionSetDumps/" + name; + String result = key +","+f.getPath(); + workList.add(result); + } + + } + workList.stream().parallel() + .forEach(m -> storeCore(portInner, m.split(",")[1],m.split(",")[0])); + + log.info(parameters); + } + + public static void storeCore(String portInner,String path,String key){ + try { + + + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(portInner), 20000000); + ScanResult scan; + + + HierarchicalActionSet actionSet = null; + HierarchicalActionSet NewactionSet = null; + try { + FileInputStream fi = new FileInputStream(new File(path)); + ObjectInputStream oi = new ObjectInputStream(fi); + actionSet = (HierarchicalActionSet) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + + try (Jedis inner = pool.getResource()) { + inner.set(key,toString(actionSet)); + } + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } + } + + + /** Read the object from Base64 string. */ + private static Object fromString( String s ) throws IOException , + ClassNotFoundException { + byte [] data = Base64.getDecoder().decode( s ); + ObjectInputStream ois = new ObjectInputStream( + new ByteArrayInputStream( data ) ); + Object o = ois.readObject(); + ois.close(); + return o; + } + + /** Write the object to a Base64 string. */ + private static String toString( Serializable o ) throws IOException { + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + ObjectOutputStream oos = new ObjectOutputStream( baos ); + oos.writeObject( o ); + oos.close(); + return Base64.getEncoder().encodeToString(baos.toByteArray()); + } + + public void storeBinary(String name , String inputPath, String innerPort) { + JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + Map resultMap; + try (Jedis jedis = pool.getResource()) { + resultMap = jedis.hgetAll(name); + } + String[] split = name.split("_"); + + + String i = split[1]; + String j = split[2]; + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + String[] firstValueSplit = firstValue.split("GumTreeOutput2"); + String[] secondValueSplit = secondValue.split("GumTreeOutput2"); + + + + if (firstValueSplit.length == 1) { + firstValue = inputPath + firstValueSplit[0]; + } else { + firstValue = inputPath + firstValueSplit[1]; + } + + if (secondValueSplit.length == 1) { + secondValue = inputPath + secondValueSplit[0]; + } else { + secondValue = inputPath + secondValueSplit[1]; + } + + try { + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); + + String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); + log.info(matchKey); + try (Jedis jedis = pool.getResource()) { + jedis.select(1); + jedis.set(matchKey, result); + } + } + + + try (Jedis jedis = pool.getResource()) { + jedis.del("pair_" + (String.valueOf(i)) + "_" + String.valueOf(j)); + } + + + } catch (Exception e) { + log.error(e.toString() + " {}", (name)); + + + } + } + } From c6d0ce9ab02fa58f6774a457dbd07c47861a8b02 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 16:37:49 +0200 Subject: [PATCH 064/127] akka loader --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 5753a75..1378d5b 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.StoreFile + edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader From 11607ca2b336b3df051f9c4c101aa592053a00ec Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 16:51:42 +0200 Subject: [PATCH 065/127] ports --- .../FixPatternParser/violations/AkkaTreeLoader.java | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 1a215fa..5f34090 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -93,20 +93,20 @@ public class AkkaTreeLoader { String numOfWorkers; if (args.length > 0) { inputPath = args[0]; -// port = args[1]; portInner = args[1]; serverWait = args[2]; // option = args[4]; chunkName = args[3]; numOfWorkers = args[4]; dbDir = args[5]; + port = args[6]; // pairsCSVPath = args[3]; // importScript = args[4]; // pairsCompletedPath = args[3]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; // outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; -// port = "6379"; + port = "6399"; portInner = "6380"; serverWait = "10000"; // option = "COMP"; @@ -116,6 +116,7 @@ public class AkkaTreeLoader { chunkName ="chunk5.rdb"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "1"; + } String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); log.info(parameters); @@ -124,6 +125,10 @@ public class AkkaTreeLoader { // calculatePairs(inputPath, port); // log.info("Calculate pairs done"); // }else { + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); + loadRedis(cmd,serverWait); + comparePairs(inputPath, portInner, serverWait,chunkName,dbDir,numOfWorkers); // } From 7248d3cf831b74f0ef212db4cc52c1f7e1777fb1 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 17:45:58 +0200 Subject: [PATCH 066/127] timeout --- .../lu/uni/serval/FixPatternParser/violations/TreeWorker.java | 2 +- src/main/java/edu/lu/uni/serval/config/Configuration.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index 2e01109..b07cb2d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -123,7 +123,7 @@ public class TreeWorker extends UntypedActor { } catch (TimeoutException e) { future.cancel(true); //// timeouts += countAlarms(positionFile, "#Timeout:"); -// System.err.println("#Timeout: " + revFile.getName()); + System.err.println("#Timeout: " + name); } catch (InterruptedException e) { //// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); // System.err.println("#TimeInterrupted: " + revFile.getName()); diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 45e21f7..9c60ae1 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,7 +2,7 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 9000L; + public static final long SECONDS_TO_WAIT = 90L; // public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. From 73b6d767e4df70cce7030fe63982230074b50c62 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 18:10:24 +0200 Subject: [PATCH 067/127] config --- .../violations/AkkaTreeLoader.java | 8 ++ .../lu/uni/serval/config/Configuration.java | 2 +- src/main/resource/application.conf | 73 +++++++++++++++++++ 3 files changed, 82 insertions(+), 1 deletion(-) create mode 100644 src/main/resource/application.conf diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 5f34090..2684f2b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -9,6 +9,7 @@ import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.Tree; +import com.typesafe.config.ConfigFactory; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; import edu.lu.uni.serval.MultipleThreadsParser.*; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; @@ -189,6 +190,13 @@ public class AkkaTreeLoader { ActorRef parsingActor = null; final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); try { + + + + system = ActorSystem.create("my-dispatcher", + ConfigFactory.load().getConfig("MyDispatcherExample")); + + log.info("Akka begins..."); system = ActorSystem.create("Tree-System"); parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 9c60ae1..3325840 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -2,7 +2,7 @@ package edu.lu.uni.serval.config; public class Configuration { - public static final long SECONDS_TO_WAIT = 90L; + public static final long SECONDS_TO_WAIT = 900L; // public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. diff --git a/src/main/resource/application.conf b/src/main/resource/application.conf new file mode 100644 index 0000000..079b1d8 --- /dev/null +++ b/src/main/resource/application.conf @@ -0,0 +1,73 @@ +MyDispatcherExample{ + defaultDispatcher { + type = Dispatcher + executor = "fork-join-executor" + fork-join-executor { + parallelism-min = 2 + parallelism-factor = 2.0 + parallelism-max = 6 + } + } + + defaultDispatcher1 { + type = Dispatcher + executor = "thread-pool-executor" + thread-pool-executor { + core-pool-size-min = 1 + core-pool-size-factor = 2.0 + core-pool-size-max = 6 + } + } + pinnedDispatcher { + type = PinnedDispatcher + executor = "thread-pool-executor" + thread-pool-executor { + core-pool-size-min = 2 + core-pool-size-factor = 2.0 + core-pool-size-max = 10 + } + throughput = 5 + } + balancingDispatcher { + type = BalancingDispatcher + executor = "thread-pool-executor" + thread-pool-executor { + core-pool-size-min = 1 + core-pool-size-factor = 2.0 + core-pool-size-max = 2 + } + throughput = 5 + } + balancingDispatcher1 { + type = BalancingDispatcher + executor = "fork-join-executor" + fork-join-executor { + parallelism-min = 2 + parallelism-factor = 2.0 + parallelism-max = 6 + } + throughput = 5 + } + my-dispatcher { + # Dispatcher is the name of the event-based dispatcher + type = Dispatcher + # What kind of ExecutionService to use + executor = "fork-join-executor" + # Configuration for the fork join pool + fork-join-executor { + # Min number of threads to cap factor-based parallelism number to + parallelism-min = 2 + # Parallelism (threads) ... ceil(available processors * factor) + parallelism-factor = 2.0 + # Max number of threads to cap factor-based parallelism number to + parallelism-max = 10 + } + # Throughput defines the maximum number of messages to be + # processed per actor before the thread jumps to the next actor. + # Set to 1 for as fair as possible. + throughput = 100 + } + CallingThreadDispatcher { + type = akka.testkit.CallingThreadDispatcherConfigurator + } +} \ No newline at end of file From 3173c46a847ba35a98c64af5b6f9dbebb16d03bf Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 18:22:12 +0200 Subject: [PATCH 068/127] remove akka conf --- .../violations/AkkaTreeLoader.java | 7 -- src/main/resource/application.conf | 73 ------------------- 2 files changed, 80 deletions(-) delete mode 100644 src/main/resource/application.conf diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 2684f2b..88ca42e 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -9,7 +9,6 @@ import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.Tree; -import com.typesafe.config.ConfigFactory; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; import edu.lu.uni.serval.MultipleThreadsParser.*; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; @@ -191,12 +190,6 @@ public class AkkaTreeLoader { final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); try { - - - system = ActorSystem.create("my-dispatcher", - ConfigFactory.load().getConfig("MyDispatcherExample")); - - log.info("Akka begins..."); system = ActorSystem.create("Tree-System"); parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); diff --git a/src/main/resource/application.conf b/src/main/resource/application.conf deleted file mode 100644 index 079b1d8..0000000 --- a/src/main/resource/application.conf +++ /dev/null @@ -1,73 +0,0 @@ -MyDispatcherExample{ - defaultDispatcher { - type = Dispatcher - executor = "fork-join-executor" - fork-join-executor { - parallelism-min = 2 - parallelism-factor = 2.0 - parallelism-max = 6 - } - } - - defaultDispatcher1 { - type = Dispatcher - executor = "thread-pool-executor" - thread-pool-executor { - core-pool-size-min = 1 - core-pool-size-factor = 2.0 - core-pool-size-max = 6 - } - } - pinnedDispatcher { - type = PinnedDispatcher - executor = "thread-pool-executor" - thread-pool-executor { - core-pool-size-min = 2 - core-pool-size-factor = 2.0 - core-pool-size-max = 10 - } - throughput = 5 - } - balancingDispatcher { - type = BalancingDispatcher - executor = "thread-pool-executor" - thread-pool-executor { - core-pool-size-min = 1 - core-pool-size-factor = 2.0 - core-pool-size-max = 2 - } - throughput = 5 - } - balancingDispatcher1 { - type = BalancingDispatcher - executor = "fork-join-executor" - fork-join-executor { - parallelism-min = 2 - parallelism-factor = 2.0 - parallelism-max = 6 - } - throughput = 5 - } - my-dispatcher { - # Dispatcher is the name of the event-based dispatcher - type = Dispatcher - # What kind of ExecutionService to use - executor = "fork-join-executor" - # Configuration for the fork join pool - fork-join-executor { - # Min number of threads to cap factor-based parallelism number to - parallelism-min = 2 - # Parallelism (threads) ... ceil(available processors * factor) - parallelism-factor = 2.0 - # Max number of threads to cap factor-based parallelism number to - parallelism-max = 10 - } - # Throughput defines the maximum number of messages to be - # processed per actor before the thread jumps to the next actor. - # Set to 1 for as fair as possible. - throughput = 100 - } - CallingThreadDispatcher { - type = akka.testkit.CallingThreadDispatcherConfigurator - } -} \ No newline at end of file From 592af5a0f41cdd52b560984d01f020abae941d25 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 18:39:28 +0200 Subject: [PATCH 069/127] log --- .../lu/uni/serval/FixPatternParser/violations/Compare.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java index 514f515..a6c2269 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java @@ -53,10 +53,11 @@ public class Compare { // } try { + log.info("start simplied tree"); ITree oldTree = getSimpliedTree(firstValue); - + log.info("start simplied2 tree"); ITree newTree = getSimpliedTree(secondValue); - + log.info("start matcher"); Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); m.match(); @@ -71,7 +72,7 @@ public class Compare { String diceSimilarity = String.format("%1.2f", diceSimilarity1); double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - + log.info("end simi"); String editDistance = String.valueOf(actions.size()); String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; From 6b7e5b1cb369b7502a05ecb793b2f132be6408c7 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 18:47:49 +0200 Subject: [PATCH 070/127] test --- .../violations/AkkaTreeLoader.java | 318 +++++++++--------- .../FixPatternParser/violations/Compare.java | 23 +- .../violations/TreeWorker.java | 22 +- 3 files changed, 195 insertions(+), 168 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 88ca42e..c82b801 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -215,89 +215,89 @@ public class AkkaTreeLoader { } - private static void coreCompare(String name , String inputPath, String innerPort) { - JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); - Map resultMap; - try (Jedis jedis = pool.getResource()) { - resultMap = jedis.hgetAll(name); - } - String[] split = name.split("_"); - - - String i = split[1]; - String j = split[2]; - String firstValue = resultMap.get("0"); - String secondValue = resultMap.get("1"); - - String[] firstValueSplit = firstValue.split("GumTreeOutput2"); - String[] secondValueSplit = secondValue.split("GumTreeOutput2"); - - if (firstValueSplit.length == 1) { - firstValue = inputPath + firstValueSplit[0]; - } else { - firstValue = inputPath + firstValueSplit[1]; - } - - if (secondValueSplit.length == 1) { - secondValue = inputPath + secondValueSplit[0]; - } else { - secondValue = inputPath + secondValueSplit[1]; - } - - try { - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - - double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); - String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); - double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); - String diceSimilarity = String.format("%1.2f", diceSimilarity1); - double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); - String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - - String editDistance = String.valueOf(actions.size()); - - String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; - - - if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) - || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { - String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - - try (Jedis jedis = pool.getResource()) { - jedis.select(1); - jedis.set(matchKey, result); - } - } - - - try (Jedis jedis = pool.getResource()) { - jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); - } - - - - - }catch (Exception e){ - log.error(e.toString() + " {}",(name)); - - - } - - - - - - } +// private static void coreCompare(String name , String inputPath, String innerPort) { +// JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); +// Map resultMap; +// try (Jedis jedis = pool.getResource()) { +// resultMap = jedis.hgetAll(name); +// } +// String[] split = name.split("_"); +// +// +// String i = split[1]; +// String j = split[2]; +// String firstValue = resultMap.get("0"); +// String secondValue = resultMap.get("1"); +// +// String[] firstValueSplit = firstValue.split("GumTreeOutput2"); +// String[] secondValueSplit = secondValue.split("GumTreeOutput2"); +// +// if (firstValueSplit.length == 1) { +// firstValue = inputPath + firstValueSplit[0]; +// } else { +// firstValue = inputPath + firstValueSplit[1]; +// } +// +// if (secondValueSplit.length == 1) { +// secondValue = inputPath + secondValueSplit[0]; +// } else { +// secondValue = inputPath + secondValueSplit[1]; +// } +// +// try { +// ITree oldTree = getSimpliedTree(firstValue); +// +// ITree newTree = getSimpliedTree(secondValue); +// +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); +// +// +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// +// double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); +// String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); +// double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); +// String diceSimilarity = String.format("%1.2f", diceSimilarity1); +// double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); +// String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); +// +// String editDistance = String.valueOf(actions.size()); +// +// String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; +// +// +// if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) +// || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { +// String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); +// +// try (Jedis jedis = pool.getResource()) { +// jedis.select(1); +// jedis.set(matchKey, result); +// } +// } +// +// +// try (Jedis jedis = pool.getResource()) { +// jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); +// } +// +// +// +// +// }catch (Exception e){ +// log.error(e.toString() + " {}",(name)); +// +// +// } +// +// +// +// +// +// } @@ -324,17 +324,17 @@ public class AkkaTreeLoader { readMessageFiles(fileToCompare,port); } - public static void processMessages(String inputPath, String outputPath) { - File folder = new File(outputPath + "pairs_splitted/"); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "comparison_splitted/"); - pjs.parallelStream() - .forEach(m -> coreLoop(m, outputPath,inputPath)); - } +// public static void processMessages(String inputPath, String outputPath) { +// File folder = new File(outputPath + "pairs_splitted/"); +// File[] listOfFiles = folder.listFiles(); +// Stream stream = Arrays.stream(listOfFiles); +// List pjs = stream +// .filter(x -> !x.getName().startsWith(".")) +// .collect(Collectors.toList()); +// FileHelper.createDirectory(outputPath + "comparison_splitted/"); +// pjs.parallelStream() +// .forEach(m -> coreLoop(m, outputPath,inputPath)); +// } /** Read the object from Base64 string. */ private static Object fromString( String s ) throws IOException , @@ -346,8 +346,8 @@ public class AkkaTreeLoader { ois.close(); return o; } - public static ITree getSimpliedTree(String fn) { - JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(6399), 20000000); + public static ITree getSimpliedTree(String fn,JedisPoolConfig config) { + JedisPool pool = new JedisPool(config, "127.0.0.1", Integer.valueOf(6399), 20000000); HierarchicalActionSet actionSet = null; try (Jedis inner = pool.getResource()) { String s = inner.get(fn.substring(1)); @@ -470,69 +470,69 @@ public class AkkaTreeLoader { - private static void coreLoop(File mes, String outputPath,String inputPath) { - try { - - log.info("Starting in coreLoop"); - - BufferedReader br = null; - String sCurrentLine = null; - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); - - br = new BufferedReader( - new FileReader(mes)); - while ((sCurrentLine = br.readLine()) != null) { - String currentLine = sCurrentLine; - String[] split = currentLine.split("\t"); - String i = split[0]; - String j = split[1]; - String firstValue = split[2]; - String secondValue = split[3]; - - firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; - secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; - - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); - - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(firstValue); - writer.write("\t"); - writer.write(secondValue); - writer.write("\n"); - - - } - writer.close(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - - } - log.info("Completed output_" + mes.getName()); - } +// private static void coreLoop(File mes, String outputPath,String inputPath) { +// try { +// +// log.info("Starting in coreLoop"); +// +// BufferedReader br = null; +// String sCurrentLine = null; +// BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); +// +// br = new BufferedReader( +// new FileReader(mes)); +// while ((sCurrentLine = br.readLine()) != null) { +// String currentLine = sCurrentLine; +// String[] split = currentLine.split("\t"); +// String i = split[0]; +// String j = split[1]; +// String firstValue = split[2]; +// String secondValue = split[3]; +// +// firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; +// secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; +// +// ITree oldTree = getSimpliedTree(firstValue); +// +// ITree newTree = getSimpliedTree(secondValue); +// +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); +// +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// writer.write(String.valueOf(i)); +// writer.write("\t"); +// writer.write(String.valueOf(j)); +// writer.write("\t"); +// +// writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.valueOf(actions.size())); +// writer.write("\t"); +// writer.write(firstValue); +// writer.write("\t"); +// writer.write(secondValue); +// writer.write("\n"); +// +// +// } +// writer.close(); +// } catch (FileNotFoundException e) { +// log.error("File not found"); +// e.printStackTrace(); +// } catch (IOException e) { +// log.error("Error initializing stream"); +// e.printStackTrace(); +// +// } +// log.info("Completed output_" + mes.getName()); +// } private static void readMessageFiles(List folders,String port) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java index a6c2269..4c245fc 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java @@ -11,6 +11,7 @@ import redis.clients.jedis.Jedis; import redis.clients.jedis.JedisPool; import redis.clients.jedis.JedisPoolConfig; +import java.time.Duration; import java.util.List; import java.util.Map; @@ -22,9 +23,13 @@ import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.getSi public class Compare { private Logger log = LoggerFactory.getLogger(Compare.class); + private JedisPoolConfig poolConfig; + public Compare(JedisPoolConfig pool) { + this.poolConfig = pool; + } public void coreCompare(String name , String inputPath, String innerPort) { - JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); + JedisPool pool = new JedisPool(poolConfig, "127.0.0.1", Integer.valueOf(innerPort), 20000000); Map resultMap; try (Jedis jedis = pool.getResource()) { resultMap = jedis.hgetAll(name); @@ -53,11 +58,11 @@ public class Compare { // } try { - log.info("start simplied tree"); - ITree oldTree = getSimpliedTree(firstValue); - log.info("start simplied2 tree"); - ITree newTree = getSimpliedTree(secondValue); - log.info("start matcher"); + + ITree oldTree = getSimpliedTree(firstValue,poolConfig); + + ITree newTree = getSimpliedTree(secondValue,poolConfig); + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); m.match(); @@ -72,7 +77,7 @@ public class Compare { String diceSimilarity = String.format("%1.2f", diceSimilarity1); double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - log.info("end simi"); + String editDistance = String.valueOf(actions.size()); String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; @@ -100,4 +105,6 @@ public class Compare { } } - } + + +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index b07cb2d..5163af6 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -24,6 +24,7 @@ import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.StringReader; +import java.time.Duration; import java.util.List; import java.util.Map; import java.util.concurrent.*; @@ -76,7 +77,7 @@ public class TreeWorker extends UntypedActor { // final ExecutorService executor = Executors.newSingleThreadExecutor(); // // schedule the work - final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare())); + final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare(poolConfig))); try { // wait for task to complete future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); @@ -174,6 +175,25 @@ public class TreeWorker extends UntypedActor { } } + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + From d0fd259646b560a5db54171dea6aaf1e982bba70 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 18:59:14 +0200 Subject: [PATCH 071/127] test --- .../lu/uni/serval/FixPatternParser/violations/TreeWorker.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index 5163af6..b215e04 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -75,7 +75,7 @@ public class TreeWorker extends UntypedActor { // - final ExecutorService executor = Executors.newSingleThreadExecutor(); + final ExecutorService executor = Executors.newFixedThreadPool(20); // // schedule the work final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare(poolConfig))); try { From 37b36051fcfba901725ac4c138836295ac3ff4fc Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 19:18:19 +0200 Subject: [PATCH 072/127] test --- .../violations/TreeWorker.java | 68 ++++++++++++------- 1 file changed, 42 insertions(+), 26 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index b215e04..c5b2205 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -29,6 +29,7 @@ import java.util.List; import java.util.Map; import java.util.concurrent.*; +import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.comparePairs; import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; @@ -68,20 +69,35 @@ public class TreeWorker extends UntypedActor { String dbDir = msg.getDbDir(); String serverWait = msg.getServerWait(); int id = msg.getId(); - int counter = 0; + int counter = new Object() { + int counter = 0; + + // +// for (String name : files) + { + files.stream(). + parallel(). + peek(x -> counter++). + forEach(m -> + { + Compare compare = new Compare(poolConfig); + compare.coreCompare(m, inputPath, innerPort); + ; + } + ); + } + }.counter; // - for (String name : files) { - - -// - final ExecutorService executor = Executors.newFixedThreadPool(20); +// final ExecutorService executor = Executors.newFixedThreadPool(20); // // schedule the work - final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare(poolConfig))); - try { +// final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare(poolConfig))); +// try { // wait for task to complete - future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); - counter++; +// future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); +// Compare compare = new Compare(poolConfig); +// compare.coreCompare(name, inputPath, innerPort); +// counter++; // nullDiffEntry += parser.nullMatchedDiffEntry; // nullMappingGumTreeResults += parser.nullMappingGumTreeResult; // pureDeletion += parser.pureDeletions; @@ -121,22 +137,22 @@ public class TreeWorker extends UntypedActor { // testingInfo.setLength(0); // } // } - } catch (TimeoutException e) { - future.cancel(true); -//// timeouts += countAlarms(positionFile, "#Timeout:"); - System.err.println("#Timeout: " + name); - } catch (InterruptedException e) { -//// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); -// System.err.println("#TimeInterrupted: " + revFile.getName()); - e.printStackTrace(); - } catch (ExecutionException e) { -//// timeouts += countAlarms(positionFile, "#TimeAborted:"); -// System.err.println("#TimeAborted: " + revFile.getName()); - e.printStackTrace(); - } finally { - executor.shutdownNow(); - } - } +// } catch (TimeoutException e) { +// future.cancel(true); +////// timeouts += countAlarms(positionFile, "#Timeout:"); +// System.err.println("#Timeout: " + name); +// } catch (InterruptedException e) { +////// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); +//// System.err.println("#TimeInterrupted: " + revFile.getName()); +// e.printStackTrace(); +// } catch (ExecutionException e) { +////// timeouts += countAlarms(positionFile, "#TimeAborted:"); +//// System.err.println("#TimeAborted: " + revFile.getName()); +// e.printStackTrace(); +// } finally { +// executor.shutdownNow(); +// } +// } log.info("bitti"); log.info("Worker #" + id +"finialized parsing " + counter + " files..."); From 5c27c2c87b4a0b78a7656bb42c600c2c8779c49f Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 19:24:25 +0200 Subject: [PATCH 073/127] no akka --- .../violations/AkkaTreeLoader.java | 58 ++++++++++--------- 1 file changed, 32 insertions(+), 26 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index c82b801..963730a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -152,17 +152,17 @@ public class AkkaTreeLoader { File[] listFiles = files.listFiles(); - Stream stream = Arrays.stream(listFiles); - List folders = stream - .filter(x -> x.getName().equals(chunkName)) - .collect(Collectors.toList()); - for (File folder : folders) { +// Stream stream = Arrays.stream(listFiles); +// List folders = stream +// .filter(x -> x.getName().equals(chunkName)) +// .collect(Collectors.toList()); +// for (File folder : folders) { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,folder.getName(),Integer.valueOf(innerPort)); + cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(innerPort)); loadRedis(cmd,serverWait); @@ -185,30 +185,36 @@ public class AkkaTreeLoader { List result = scan.getResult(); - ActorSystem system = null; - ActorRef parsingActor = null; - final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); - try { - - log.info("Akka begins..."); - system = ActorSystem.create("Tree-System"); - parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); - } +// ActorSystem system = null; +// ActorRef parsingActor = null; +// final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); +// try { +// +// log.info("Akka begins..."); +// system = ActorSystem.create("Tree-System"); +// parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); +// parsingActor.tell(msg, ActorRef.noSender()); +// } catch (Exception e) { +// system.shutdown(); +// e.printStackTrace(); +// } // greeter.tell(); - -// .parallelStream() -// .forEach(m -> coreCompare(m, inputPath, innerPort)); + result + .parallelStream() + .forEach(m -> + { + Compare compare = new Compare(poolConfig); + compare.coreCompare(m, inputPath, innerPort); + ; + } + ); -// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; -// stopServer = String.format(stopServer,Integer.valueOf(innerPort)); -// loadRedis(stopServer,serverWait); + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(innerPort)); + loadRedis(stopServer,serverWait); - } +// } From a28043bf2c04953ca942158c3cfe39753a39d8f2 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 21:51:15 +0200 Subject: [PATCH 074/127] pool --- .../violations/AkkaTreeLoader.java | 48 +++++++---------- .../FixPatternParser/violations/Compare.java | 54 ++++++++----------- 2 files changed, 40 insertions(+), 62 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index 963730a..d37dfe3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -354,39 +354,27 @@ public class AkkaTreeLoader { } public static ITree getSimpliedTree(String fn,JedisPoolConfig config) { JedisPool pool = new JedisPool(config, "127.0.0.1", Integer.valueOf(6399), 20000000); - HierarchicalActionSet actionSet = null; - try (Jedis inner = pool.getResource()) { + ITree tree = null; + Jedis inner = null; + try { + inner = pool.getResource(); String s = inner.get(fn.substring(1)); - actionSet = (HierarchicalActionSet) fromString(s); + HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); + + ITree parent = null; + ITree children =null; + tree = getASTTree(actionSet, parent, children); + tree.setParent(null); + } catch (IOException e) { e.printStackTrace(); } catch (ClassNotFoundException e) { e.printStackTrace(); + }finally { + if (inner != null) { + inner.close(); + } } -// try { -// FileInputStream fi = new FileInputStream(new File(fn)); -// ObjectInputStream oi = new ObjectInputStream(fi); -// actionSet = (HierarchicalActionSet) oi.readObject(); -// oi.close(); -// fi.close(); -// -// -// } catch (FileNotFoundException e) { -// log.error("File not found"); -// e.printStackTrace(); -// } catch (IOException e) { -// log.error("Error initializing stream"); -// e.printStackTrace(); -// } catch (ClassNotFoundException e) { -// // TODO Auto-generated catch block -// e.printStackTrace(); -// } - - ITree parent = null; - ITree children =null; - ITree tree = getASTTree(actionSet, parent, children); - tree.setParent(null); - return tree; } @@ -637,12 +625,12 @@ public class AkkaTreeLoader { poolConfig.setMaxTotal(128); poolConfig.setMaxIdle(128); poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(true); - poolConfig.setTestOnReturn(true); + poolConfig.setTestOnBorrow(false); + poolConfig.setTestOnReturn(false); poolConfig.setTestWhileIdle(true); poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); - poolConfig.setNumTestsPerEvictionRun(3); +// poolConfig.setNumTestsPerEvictionRun(3); poolConfig.setBlockWhenExhausted(true); return poolConfig; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java index 4c245fc..61beeba 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java @@ -31,33 +31,19 @@ public class Compare { public void coreCompare(String name , String inputPath, String innerPort) { JedisPool pool = new JedisPool(poolConfig, "127.0.0.1", Integer.valueOf(innerPort), 20000000); Map resultMap; - try (Jedis jedis = pool.getResource()) { - resultMap = jedis.hgetAll(name); - } - String[] split = name.split("_"); - - - String i = split[1]; - String j = split[2]; - String firstValue = resultMap.get("0"); - String secondValue = resultMap.get("1"); - -// String[] firstValueSplit = firstValue.split("GumTreeOutput2"); -// String[] secondValueSplit = secondValue.split("GumTreeOutput2"); -// -// if (firstValueSplit.length == 1) { -// firstValue = inputPath + firstValueSplit[0]; -// } else { -// firstValue = inputPath + firstValueSplit[1]; -// } -// -// if (secondValueSplit.length == 1) { -// secondValue = inputPath + secondValueSplit[0]; -// } else { -// secondValue = inputPath + secondValueSplit[1]; -// } + Jedis jedis = null; try { + jedis = pool.getResource(); + resultMap = jedis.hgetAll(name); + + String[] split = name.split("_"); + + + String i = split[1]; + String j = split[2]; + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); ITree oldTree = getSimpliedTree(firstValue,poolConfig); @@ -87,22 +73,26 @@ public class Compare { || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); log.info(matchKey); - try (Jedis jedis = pool.getResource()) { - jedis.select(1); - jedis.set(matchKey, result); - } + + jedis.select(1); + jedis.set(matchKey, result); + } - try (Jedis jedis = pool.getResource()) { - jedis.del("pair_" + (String.valueOf(i)) + "_" + String.valueOf(j)); - } + + jedis.del("pair_" + (String.valueOf(i)) + "_" + String.valueOf(j)); + } catch (Exception e) { log.error(e.toString() + " {}", (name)); + }finally { + if (jedis != null) { + jedis.close(); + } } } From 9807eb913ccfa813f98896c3f8105b3171e05564 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 22:35:34 +0200 Subject: [PATCH 075/127] poolfix --- .../violations/AkkaTreeLoader.java | 61 +++++++------------ .../FixPatternParser/violations/Compare.java | 15 ++--- 2 files changed, 28 insertions(+), 48 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java index d37dfe3..8c32167 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java @@ -129,46 +129,31 @@ public class AkkaTreeLoader { cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); loadRedis(cmd,serverWait); - comparePairs(inputPath, portInner, serverWait,chunkName,dbDir,numOfWorkers); + String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); + loadRedis(cmd,serverWait); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + + + comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); + + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(portInner)); + loadRedis(stopServer,serverWait); // } } - public static void comparePairs(String inputPath, String innerPort,String serverWait,String chunkName, String dbDir,String numOfWorkers){ -// String cmd; -// cmd = "bash " + importScript +" %s"; + public static void comparePairs(String inputPath, JedisPool innerPool,JedisPool outerPool,String serverWait,String chunkName, String dbDir,String numOfWorkers){ - - List dir; - List path; - - String orgDbname; - - - File files = new File(dbDir); - File[] listFiles = files.listFiles(); - - -// Stream stream = Arrays.stream(listFiles); -// List folders = stream -// .filter(x -> x.getName().equals(chunkName)) -// .collect(Collectors.toList()); -// for (File folder : folders) { - - - - - String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(innerPort)); - loadRedis(cmd,serverWait); - - - JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); ScanResult scan; - try (Jedis inner = pool.getResource()) { + try (Jedis inner = innerPool.getResource()) { while (inner.ping()== "PONG"){ log.info("wait"); } @@ -203,16 +188,14 @@ public class AkkaTreeLoader { .parallelStream() .forEach(m -> { - Compare compare = new Compare(poolConfig); - compare.coreCompare(m, inputPath, innerPort); + Compare compare = new Compare(); + compare.coreCompare(m, innerPool, outerPool); ; } ); - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(innerPort)); - loadRedis(stopServer,serverWait); + // } @@ -352,12 +335,12 @@ public class AkkaTreeLoader { ois.close(); return o; } - public static ITree getSimpliedTree(String fn,JedisPoolConfig config) { - JedisPool pool = new JedisPool(config, "127.0.0.1", Integer.valueOf(6399), 20000000); + public static ITree getSimpliedTree(String fn,JedisPool outerPool) { + ITree tree = null; Jedis inner = null; try { - inner = pool.getResource(); + inner = outerPool.getResource(); String s = inner.get(fn.substring(1)); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java index 61beeba..813c982 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java @@ -23,18 +23,15 @@ import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.getSi public class Compare { private Logger log = LoggerFactory.getLogger(Compare.class); - private JedisPoolConfig poolConfig; - public Compare(JedisPoolConfig pool) { - this.poolConfig = pool; - } - public void coreCompare(String name , String inputPath, String innerPort) { - JedisPool pool = new JedisPool(poolConfig, "127.0.0.1", Integer.valueOf(innerPort), 20000000); + + public void coreCompare(String name , JedisPool innerPool, JedisPool outerPool) { + Map resultMap; Jedis jedis = null; try { - jedis = pool.getResource(); + jedis = innerPool.getResource(); resultMap = jedis.hgetAll(name); String[] split = name.split("_"); @@ -45,9 +42,9 @@ public class Compare { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); - ITree oldTree = getSimpliedTree(firstValue,poolConfig); + ITree oldTree = getSimpliedTree(firstValue,outerPool); - ITree newTree = getSimpliedTree(secondValue,poolConfig); + ITree newTree = getSimpliedTree(secondValue,outerPool); Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); m.match(); From 1b383675cd719b095e0c0c76a7e6dc745e1f3082 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 4 Apr 2018 22:38:14 +0200 Subject: [PATCH 076/127] poolfix --- .../violations/RunnableCompare.java | 13 +++++++------ .../FixPatternParser/violations/TreeWorker.java | 5 ++--- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java index 0ff319f..3079eb3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java @@ -1,25 +1,26 @@ package edu.lu.uni.serval.FixPatternParser.violations; import edu.lu.uni.serval.FixPatternParser.Parser; +import redis.clients.jedis.JedisPool; import java.io.File; public class RunnableCompare implements Runnable { private String name; - private String inputPath; - private String innerPort; + private JedisPool innerPool; + private JedisPool outerPool; private Compare comparer; - public RunnableCompare(String name , String inputPath, String innerPort, Compare comp) { + public RunnableCompare(String name , JedisPool innerPool, JedisPool outerPool, Compare comp) { this.name = name; - this.inputPath = inputPath; - this.innerPort = innerPort; + this.innerPool = innerPool; + this.outerPool = outerPool; this.comparer = comp; } @Override public void run() { - comparer.coreCompare(name, inputPath, innerPort); + comparer.coreCompare(name, innerPool, outerPool); } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index c5b2205..f6839b5 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -80,9 +80,8 @@ public class TreeWorker extends UntypedActor { peek(x -> counter++). forEach(m -> { - Compare compare = new Compare(poolConfig); - compare.coreCompare(m, inputPath, innerPort); - ; + Compare compare = new Compare(); +// compare.coreCompare(m, inputPath, innerPort); } ); } From 4c5570dd05887717eb9a6874de571ad8d0c8428a Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 13:36:06 +0200 Subject: [PATCH 077/127] calculate pairs --- pom.xml | 4 +- .../cluster/AkkaTreeLoader.java | 327 ++++++++ .../cluster/CalculatePairs.java | 153 ++++ .../{violations => cluster}/Compare.java | 6 +- .../{violations => cluster}/StoreFile.java | 94 +-- .../cluster/TreeLoaderClusterL1.java | 767 ++++++++++++++++++ .../violations/AkkaTreeLoader.java | 655 --------------- .../violations/RunnableCompare.java | 4 +- .../violations/TreeActor.java | 3 +- .../violations/TreeWorker.java | 23 +- 10 files changed, 1260 insertions(+), 776 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java rename src/main/java/edu/lu/uni/serval/FixPatternParser/{violations => cluster}/Compare.java (92%) rename src/main/java/edu/lu/uni/serval/FixPatternParser/{violations => cluster}/StoreFile.java (58%) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java diff --git a/pom.xml b/pom.xml index 1378d5b..09f7d2d 100644 --- a/pom.xml +++ b/pom.xml @@ -108,8 +108,8 @@ - edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader - + edu.lu.uni.serval.FixPatternParser.cluster.CalculatePairs + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java new file mode 100644 index 0000000..1e2e76e --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -0,0 +1,327 @@ +package edu.lu.uni.serval.FixPatternParser.cluster; + +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.Tree; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; + +import java.io.*; +import java.time.Duration; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.function.Consumer; +import java.util.stream.Collectors; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class AkkaTreeLoader { + + private static class StreamGobbler implements Runnable { + private InputStream inputStream; + private Consumer consumer; + + public StreamGobbler(InputStream inputStream, Consumer consumer) { + this.inputStream = inputStream; + this.consumer = consumer; + } + + @Override + public void run() { + new BufferedReader(new InputStreamReader(inputStream)).lines() + .forEach(consumer); + } + } + + private static Logger log = LoggerFactory.getLogger(AkkaTreeLoader.class); + + + public static void loadRedis(String cmd,String serverWait){ + Process process; + + try { +// String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(cmd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); +// int exitCode = process.waitFor(); +// assert exitCode == 0; + Thread.sleep(Integer.valueOf(serverWait)); + + } catch (IOException e) { + e.printStackTrace(); + } + catch (InterruptedException e) { + e.printStackTrace(); + } + log.info("Load done"); + } + + public static void main(String[] args) { + + + String inputPath; +// String outputPath; + String port; + String portInner; +// String pairsCSVPath; + String importScript; +// String pairsCompletedPath; + String serverWait; +// String option; + String dbDir; + String chunkName; + String numOfWorkers; + if (args.length > 0) { + inputPath = args[0]; + portInner = args[1]; + serverWait = args[2]; +// option = args[4]; + chunkName = args[3]; + numOfWorkers = args[4]; + dbDir = args[5]; + port = args[6]; +// pairsCSVPath = args[3]; +// importScript = args[4]; +// pairsCompletedPath = args[3]; + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; +// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6399"; + portInner = "6380"; + serverWait = "10000"; +// option = "COMP"; +// pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; +// importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; +// pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; + chunkName ="chunk3.rdb"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + numOfWorkers = "1"; + + } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + log.info(parameters); + +// if (option.equals("CALC")) { +// calculatePairs(inputPath, port); +// log.info("Calculate pairs done"); +// }else { + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); + loadRedis(cmd,serverWait); + + String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); + loadRedis(cmd,serverWait); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + + + comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); + + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(portInner)); + loadRedis(stopServer,serverWait); +// } + + + } + + + public static void comparePairs(String inputPath, JedisPool innerPool,JedisPool outerPool,String serverWait,String chunkName, String dbDir,String numOfWorkers){ + + + ScanResult scan; + try (Jedis inner = innerPool.getResource()) { + while (inner.ping()== "PONG"){ + log.info("wait"); + } + + ScanParams sc = new ScanParams(); + //150000000 + sc.count(150000000); + sc.match("pair_*"); + + scan = inner.scan("0", sc); + int size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + } + List result = scan.getResult(); + + +// ActorSystem system = null; +// ActorRef parsingActor = null; +// final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); +// try { +// +// log.info("Akka begins..."); +// system = ActorSystem.create("Tree-System"); +// parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); +// parsingActor.tell(msg, ActorRef.noSender()); +// } catch (Exception e) { +// system.shutdown(); +// e.printStackTrace(); +// } +// greeter.tell(); + result + .parallelStream() + .forEach(m -> + { + Compare compare = new Compare(); + compare.coreCompare(m, innerPool, outerPool); + ; + } + ); + + + + +// } + + + + + } + + /** Read the object from Base64 string. */ + private static Object fromString( String s ) throws IOException , + ClassNotFoundException { + byte [] data = Base64.getDecoder().decode( s ); + ObjectInputStream ois = new ObjectInputStream( + new ByteArrayInputStream( data ) ); + Object o = ois.readObject(); + ois.close(); + return o; + } + public static ITree getSimpliedTree(String fn,JedisPool outerPool) { + + ITree tree = null; + Jedis inner = null; + try { + inner = outerPool.getResource(); + String s = inner.get(fn.substring(1)); + HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); + + ITree parent = null; + ITree children =null; + tree = getASTTree(actionSet, parent, children); + tree.setParent(null); + + } catch (IOException e) { + e.printStackTrace(); + } catch (ClassNotFoundException e) { + e.printStackTrace(); + }finally { + if (inner != null) { + inner.close(); + } + } + return tree; + + } + + public static List getKeysByValue(Map map, E value) { + return map.entrySet() + .stream() + .filter(entry -> Objects.equals(entry.getValue(), value)) + .map(Map.Entry::getKey) + .collect(Collectors.toList()); + } + + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("Birden cok astnodemapmapping"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + + parent = new Tree(newType,""); + }else{ + children = new Tree(newType,""); + parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null); + + } + + + } + return parent; + } + + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(false); + poolConfig.setTestOnReturn(false); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); +// poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + + private static List getMessageFiles(String gumTreeInput) { + String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile + File revFilesPath = new File(inputPath + "revFiles/"); + File[] revFiles = revFilesPath.listFiles(); // project folders + List msgFiles = new ArrayList<>(); + if (revFiles.length >= 0) { + for (File revFile : revFiles) { +// if (revFile.getName().endsWith(".java")) { + String fileName = revFile.getName(); + File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file + fileName = fileName.replace(".java", ".txt"); + File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file + File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + edu.lu.uni.serval.MultipleThreadsParser.MessageFile msgFile = new edu.lu.uni.serval.MultipleThreadsParser.MessageFile(revFile, prevFile, diffentryFile); + msgFile.setPositionFile(positionFile); + msgFiles.add(msgFile); +// } + } + + return msgFiles; + } + else{ + return null; + } + } + + +} + + + + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java new file mode 100644 index 0000000..8f8c558 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -0,0 +1,153 @@ +package edu.lu.uni.serval.FixPatternParser.cluster; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.ScanParams; +import redis.clients.jedis.ScanResult; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.StandardCopyOption; +import java.util.List; + +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; +import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poolConfig; + +/** + * Created by anilkoyuncu on 05/04/2018. + */ +public class CalculatePairs { + private static Logger log = LoggerFactory.getLogger(CalculatePairs.class); + public static void main(String[] args) { + + + String inputPath; + String port; + String portInner; + String serverWait; + String dbDir; + String chunkName; + + if (args.length > 0) { + inputPath = args[0]; + portInner = args[1]; + serverWait = args[2]; + chunkName = args[3]; + + dbDir = args[5]; + port = args[6]; + + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + + port = "6399"; + portInner = "6380"; + serverWait = "10000"; + + chunkName ="chunk"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + + + } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir); + log.info(parameters); + + + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); + loadRedis(cmd,serverWait); + + String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); + loadRedis(cmd,serverWait); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + + ScanResult scan; + try (Jedis outer = outerPool.getResource()) { + while (outer.ping()== "PONG"){ + log.info("wait"); + } + + ScanParams sc = new ScanParams(); + //150000000 + sc.count(150000000); + sc.match("*"); + + scan = outer.scan("0", sc); + int size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + } + List result = scan.getResult(); + + int fileCounter = 0; + int pairCounter = 0; + for (int i = 0; i < result.size(); i++) { + for (int j = i + 1; j < result.size(); j++) { + Jedis jedis = null; + String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); + try { + jedis = innerPool.getResource(); + key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); +// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; +// jedis.set(key,value); + + jedis.hset(key, "0", result.get(i)); + jedis.hset(key, "1", result.get(j)); + pairCounter ++; + + //10000000 + if (pairCounter % 10000000 == 0) { + + File dbPath = new File(dbDir + "/" + chunkName); + File savePath = new File(dbDir + "/" + "chunk" + String.valueOf(fileCounter) + ".rdb"); + try { + jedis.save(); + log.info("saving key {} chunk {}",key,fileCounter); + while (jedis.ping() == "PONG") { + log.info("wait"); + } + + + Files.copy(dbPath.toPath(), savePath.toPath(), StandardCopyOption.REPLACE_EXISTING); + fileCounter++; + jedis.flushDB(); + while (jedis.ping() == "PONG") { + log.info("wait"); + } + + } catch (IOException e) { + + e.printStackTrace(); + } + + + } + }catch (Exception e) { + log.error(e.toString() + " {}", (key)); + + + }finally { + if (jedis != null) { + jedis.close(); + } + } + } + } + + +// comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); + + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(portInner)); + loadRedis(stopServer,serverWait); +// } + + + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java similarity index 92% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java rename to src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java index 813c982..76350e0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java @@ -1,4 +1,4 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.FixPatternParser.cluster; import com.github.gumtreediff.actions.ActionGenerator; import com.github.gumtreediff.actions.model.Action; @@ -9,13 +9,11 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.Jedis; import redis.clients.jedis.JedisPool; -import redis.clients.jedis.JedisPoolConfig; -import java.time.Duration; import java.util.List; import java.util.Map; -import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.getSimpliedTree; +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getSimpliedTree; /** * Created by anilkoyuncu on 03/04/2018. diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java similarity index 58% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java rename to src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java index 588b099..a8ff74a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java @@ -1,10 +1,5 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.FixPatternParser.cluster; -import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.matchers.Matcher; -import com.github.gumtreediff.matchers.Matchers; -import com.github.gumtreediff.tree.ITree; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -14,14 +9,14 @@ import redis.clients.jedis.JedisPoolConfig; import redis.clients.jedis.ScanResult; import java.io.*; -import java.nio.file.Files; -import java.nio.file.Paths; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Base64; +import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; -import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; /** * Created by anilkoyuncu on 03/04/2018. @@ -156,82 +151,5 @@ public class StoreFile { return Base64.getEncoder().encodeToString(baos.toByteArray()); } - public void storeBinary(String name , String inputPath, String innerPort) { - JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); - Map resultMap; - try (Jedis jedis = pool.getResource()) { - resultMap = jedis.hgetAll(name); - } - String[] split = name.split("_"); - - String i = split[1]; - String j = split[2]; - String firstValue = resultMap.get("0"); - String secondValue = resultMap.get("1"); - - String[] firstValueSplit = firstValue.split("GumTreeOutput2"); - String[] secondValueSplit = secondValue.split("GumTreeOutput2"); - - - - if (firstValueSplit.length == 1) { - firstValue = inputPath + firstValueSplit[0]; - } else { - firstValue = inputPath + firstValueSplit[1]; - } - - if (secondValueSplit.length == 1) { - secondValue = inputPath + secondValueSplit[0]; - } else { - secondValue = inputPath + secondValueSplit[1]; - } - - try { - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - - double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); - String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); - double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); - String diceSimilarity = String.format("%1.2f", diceSimilarity1); - double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); - String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - - String editDistance = String.valueOf(actions.size()); - - String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; - - - if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) - || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { - String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - log.info(matchKey); - try (Jedis jedis = pool.getResource()) { - jedis.select(1); - jedis.set(matchKey, result); - } - } - - - try (Jedis jedis = pool.getResource()) { - jedis.del("pair_" + (String.valueOf(i)) + "_" + String.valueOf(j)); - } - - - } catch (Exception e) { - log.error(e.toString() + " {}", (name)); - - - } - } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java new file mode 100644 index 0000000..dd82e21 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -0,0 +1,767 @@ +package edu.lu.uni.serval.FixPatternParser.cluster; + +import com.github.gumtreediff.actions.ActionGenerator; +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.matchers.Matcher; +import com.github.gumtreediff.matchers.Matchers; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.gumtree.GumTreeComparer; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; +import edu.lu.uni.serval.utils.FileHelper; +import edu.lu.uni.serval.utils.ListSorter; +import org.javatuples.Pair; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; + +import java.io.*; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; +import java.time.Duration; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.function.Consumer; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; + +/** + * Created by anilkoyuncu on 19/03/2018. + */ +public class TreeLoaderClusterL1 { + + private static int resultType; + + + private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); + + public static void main(String[] args){ + + String inputPath; + String outputPath; + String port; + String portInner; + String serverWait; + if (args.length > 0) { + inputPath = args[0]; + outputPath = args[1]; + port = args[2]; + serverWait = args[3]; + portInner = args[4]; + + } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; + port = "6379"; + portInner = "6380"; + serverWait = "10000"; + + + } + + String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, inputPath,"level1.rdb",Integer.valueOf(port)); + loadRedis(cmd,serverWait); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + + + String level1Path = inputPath + "/level1"; + File chunks = new File(level1Path); + File[] listFiles = chunks.listFiles(); + Stream stream = Arrays.stream(listFiles); + List dbs = stream + .filter(x -> x.getName().endsWith(".rdb")) + .collect(Collectors.toList()); + for (File db : dbs) { + String cmdInner = "bash "+level1Path + "/" + "startServer.sh" +" %s %s %s"; + cmdInner = String.format(cmdInner, level1Path,db.getName(),Integer.valueOf(portInner)); + loadRedis(cmdInner,serverWait); + JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + Jedis inner = null; + + try { + inner = innerPool.getResource(); + + inner.select(1); + ScanParams sc = new ScanParams(); + //150000000 + sc.count(150000000); + sc.match("match_*"); + + ScanResult scan; scan = inner.scan("0", sc); + int size = scan.getResult().size(); + log.info("Scanning " + String.valueOf(size)); + + List result = scan.getResult(); + + for (String key : result) { + String value = inner.get(key); + Jedis outer = null; + try { + outer = outerPool.getResource(); + outer.set(key,value); + } catch (Exception e) { + log.error(e.toString() + " {}", (key)); + + + }finally { + if (outer != null) { + outer.close(); + } + } + + + } + + + } catch (Exception e) { + log.error(e.toString() + " {}", (db.getName())); + + + }finally { + if (inner != null) { + inner.close(); + } + innerPool.close(); + } + + String stopServer = "bash "+level1Path + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(portInner)); + loadRedis(stopServer,serverWait); + + } + + +// calculatePairsOfClusters(inputPath, outputPath); +// mainCompare(inputPath,port,pairsCSVPath,importScript); + // calculatePairs(inputPath, outputPath); +// processMessages(inputPath,outputPath); +// evaluateResults(inputPath,outputPath); + + } + + + public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { + + String cmd; + cmd = "bash " + importScript +" %s"; + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + + + File folder = new File(pairsCSVPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + for (File f:folders){ + + if(f.getName().startsWith("cluster76")) { + + + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_[0-9]*"); + + log.info("Scanning"); + ScanResult scan = jedis.scan("0", sc); + int size = scan.getResult().size(); + + if (size == 0) { +// loadRedis(cmd, f); + + scan = jedis.scan("0", sc); + size = scan.getResult().size(); + + } + log.info("Scanned " + String.valueOf(size)); + + + String clusterName = f.getName().replaceAll("[^0-9]+", ""); + + + //76 + + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName)); + + + jedis.save(); + + } + } + + + } + + + + } + + + + + + public static Pair getTree(String firstValue){ + String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; + String[] split2 = firstValue.split("/"); + String cluster = split2[1]; + + + File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) + .collect(Collectors.toList()); + + + + String[] split1 = folders.get(0).getName().split(".txt_"); + String s = split1[0]; + String[] splitPJ = split1[1].split("_"); + String project = splitPJ[1]; + String actionSetPosition = splitPJ[0]; + + File prevFile = new File(gumTreeInput + project+ "/" + "prevFiles/prev_" + s + ".java");// previous file + File revFile = new File(gumTreeInput + project+ "/" + "revFiles/" + s + ".java");//rev file + + List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); + + HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); +// for (HierarchicalActionSet actionSet : actionSets) { + + + + ITree actionTree= null; + ITree test2 = null; + getActionTree(actionSet); + ITree node = actionSet.getNode(); + List descendants = node.getDescendants(); + for (ITree descendant : descendants) { + if(descendant.getType() <= 100){ + descendant.setType(104); + } + } + node.setParent(null); + + + // } +// } + + Pair pair = new Pair<>(node,project); + return pair; + } + + + public static void getActionTree(HierarchicalActionSet actionSet){ + + + int newType = 0; + + Action action = actionSet.getAction(); + if (action instanceof Update){ + newType = 101; + }else if(action instanceof Insert){ + newType =100; + }else if(action instanceof Move){ + newType = 102; + }else if(action instanceof Delete){ + newType=103; + }else{ + new Exception("unknow action"); + } + actionSet.getNode().setType(newType); +// actionSet.getNode().setLabel(""); + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + getActionTree(subAction); + } + + + } + + } +// public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ +// +// int newType = 0; +// +// Action action = actionSet.getAction(); +// if (action instanceof Update){ +// newType = 101; +// }else if(action instanceof Insert){ +// newType =100; +// }else if(action instanceof Move){ +// newType = 102; +// }else if(action instanceof Delete){ +// newType=103; +// }else{ +// new Exception("unknow action"); +// } +// if(actionSet.getParent() == null){ +// //root +// +// parent = new Tree(newType,""); +// }else{ +// children = new Tree(newType,""); +// parent.addChild(children); +// } +// List subActions = actionSet.getSubActions(); +// if (subActions.size() != 0){ +// for (HierarchicalActionSet subAction : subActions) { +// +// if(actionSet.getParent() == null){ +// children = parent; +// } +// getActionTree(subAction,children,null); +// +// } +// +// +// } +// return parent; +// } + + + + private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName) { + + + try (Jedis jedis = jedisPool.getResource()) { + + + Map resultMap = jedis.hgetAll(name); + + resultMap.get("0"); + + + String[] split = name.split("_"); + String i = null; + String j =null; + try { + i = split[1]; + j = split[2]; + } + catch (Exception e){ + e.printStackTrace(); + } + String firstValue = resultMap.get("0"); + String secondValue = resultMap.get("1"); + + + + + + +// firstValue = inputPath + firstValue; +// secondValue = inputPath + secondValue; + +// String[] firstValueSplit = firstValue.split("/"); +// String[] secondValueSplit = secondValue.split("/"); +// +// if (firstValueSplit.length == 1) { +// firstValue = inputPath + firstValueSplit[0]; +// } else { +// firstValue = inputPath + firstValueSplit[1]; +// } +// +// if (secondValueSplit.length == 1) { +// secondValue = inputPath + secondValueSplit[0]; +// } else { +// secondValue = inputPath + secondValueSplit[1]; +// } + + try { + Pair oldPair = getTree(firstValue); + Pair newPair = getTree(secondValue); + + ITree oldTree = oldPair.getValue0(); + ITree newTree = newPair.getValue0(); + + String oldProject = oldPair.getValue1(); + String newProject = newPair.getValue1(); + + + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + + String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); + double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); + String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); + double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); + String diceSimilarity = String.format("%1.2f", diceSimilarity1); + double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); + String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); + + String editDistance = String.valueOf(actions.size()); +// jedis.select(1); + String result = resultMap.get("0") + "," + oldProject +"," + resultMap.get("1") + "," +newProject+ "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; +// jedis.set(resultKey, result); + + if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) + || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { + String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.select(1); + jedis.set(matchKey, result); + } + jedis.select(0); + String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.del(pairKey); + +// log.info("Completed " + resultKey); + + }catch (Exception e){ + log.error(e.toString() + " {}",(name)); + + + } + + + + + } + } + + + + protected static List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { + List actionSets = new ArrayList<>(); + // GumTree results + List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); + if (gumTreeResults == null) { + resultType = 1; + return null; + } else if (gumTreeResults.size() == 0){ + resultType = 2; + return actionSets; + } else { + // Regroup GumTre results. + List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); +// for (HierarchicalActionSet actionSet : allActionSets) { +// String astNodeType = actionSet.getAstNodeType(); +// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { +// actionSets.add(actionSet); +// } +// } + + // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. + // variable effects range, sub-actions are these kinds of modification? +// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); + + ListSorter sorter = new ListSorter<>(allActionSets); + actionSets = sorter.sortAscending(); + + if (actionSets.size() == 0) { + resultType = 3; + } + + return actionSets; + } + } + + +/* +orginal calculate pairs, from all dumps of the projects + */ + public static void calculatePairs(String inputPath, String outputPath) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + List fileToCompare = new ArrayList<>(); + for (File pj : pjs) { + File[] files = pj.listFiles(new FilenameFilter() { + public boolean accept(File dir, String name) { + return name.startsWith("ASTDumps"); + } + }); + Collections.addAll(fileToCompare, files[0].listFiles()); + + } + System.out.println("a"); +// compareAll(fileToCompare); + readMessageFiles(fileToCompare, outputPath); + } + + /* + pairs of each cluster + */ + public static void calculatePairsOfClusters(String inputPath, String outputPath) { + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + + FileHelper.createDirectory(outputPath + "pairs/"); + for (File pj : pjs) { + File[] files = pj.listFiles(); + List fileList = Arrays.asList(files); + + readMessageFilesCluster(fileList, outputPath,inputPath,pj.getName()); + + } + + } + + public static void processMessages(String inputPath, String outputPath) { + File folder = new File(outputPath + "pairs_splitted/"); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List pjs = stream + .filter(x -> !x.getName().startsWith(".")) + .collect(Collectors.toList()); + FileHelper.createDirectory(outputPath + "comparison_splitted/"); + pjs.parallelStream() + .forEach(m -> coreLoop(m, outputPath,inputPath)); + } + + private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + + String filename = "cluster" + cluster; + byte [] buf = new byte[0]; + String line = null; + try { + + FileOutputStream fos = new FileOutputStream(outputPath + "pairs/" +filename+".txt"); + DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); + + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; + outStream.write(line.getBytes()); + + } + } + outStream.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); + } + + log.info("Done pairs"); + } + + + + public static ITree getSimpliedTree(String fn) { + ITree tree = null; + try { + FileInputStream fi = new FileInputStream(new File(fn)); + ObjectInputStream oi = new ObjectInputStream(fi); + tree = (ITree) oi.readObject(); + oi.close(); + fi.close(); + + + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + } catch (ClassNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + +// tree.setLabel(""); + tree.setParent(null); +// List descendants = tree.getDescendants(); +// for (ITree descendant : descendants) { +// descendant.setLabel(""); +// } + + return tree; + + } + + + private static void coreLoop(File mes, String outputPath,String inputPath) { + try { + + log.info("Starting in coreLoop"); + + BufferedReader br = null; + String sCurrentLine = null; + BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); + + br = new BufferedReader( + new FileReader(mes)); + while ((sCurrentLine = br.readLine()) != null) { + String currentLine = sCurrentLine; + String[] split = currentLine.split("\t"); + String i = split[0]; + String j = split[1]; + String firstValue = split[2]; + String secondValue = split[3]; + + firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; + secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; + + ITree oldTree = getSimpliedTree(firstValue); + + ITree newTree = getSimpliedTree(secondValue); + + Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); + m.match(); + + ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); + ag.generate(); + List actions = ag.getActions(); + writer.write(String.valueOf(i)); + writer.write("\t"); + writer.write(String.valueOf(j)); + writer.write("\t"); + + writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); + writer.write("\t"); + writer.write(String.valueOf(actions.size())); + writer.write("\t"); + writer.write(firstValue); + writer.write("\t"); + writer.write(secondValue); + writer.write("\n"); + + + } + writer.close(); + } catch (FileNotFoundException e) { + log.error("File not found"); + e.printStackTrace(); + } catch (IOException e) { + log.error("Error initializing stream"); + e.printStackTrace(); + + } + log.info("Completed output_" + mes.getName()); + } + + private static void readMessageFiles(List folders, String outputPath) { + + List treesFileNames = new ArrayList<>(); + + + for (File target : folders) { + + treesFileNames.add(target.toString()); + } + FileHelper.createDirectory(outputPath + "pairs/"); + log.info("Calculating pairs"); +// treesFileNames = treesFileNames.subList(0,100); + byte [] buf = new byte[0]; + String line = null; + try { + + FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + + for (int i = 0; i < treesFileNames.size(); i++) { + for (int j = i + 1; j < treesFileNames.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + } + + + + + } + } + rwChannel.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); + } + + log.info("Done pairs"); + } + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + + + +// return msgFiles; +} + + + + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java deleted file mode 100644 index 8c32167..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/AkkaTreeLoader.java +++ /dev/null @@ -1,655 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import akka.actor.Props; -import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.*; -import com.github.gumtreediff.matchers.Matcher; -import com.github.gumtreediff.matchers.Matchers; -import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.Tree; -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.MultipleThreadsParser.*; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.utils.FileHelper; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import redis.clients.jedis.*; - -import java.io.*; -import java.nio.file.Files; -import java.time.Duration; -import java.util.*; -import java.util.concurrent.Executors; -import java.util.function.Consumer; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -/** - * Created by anilkoyuncu on 19/03/2018. - */ -public class AkkaTreeLoader { - - private static class StreamGobbler implements Runnable { - private InputStream inputStream; - private Consumer consumer; - - public StreamGobbler(InputStream inputStream, Consumer consumer) { - this.inputStream = inputStream; - this.consumer = consumer; - } - - @Override - public void run() { - new BufferedReader(new InputStreamReader(inputStream)).lines() - .forEach(consumer); - } - } - - private static Logger log = LoggerFactory.getLogger(AkkaTreeLoader.class); - - - public static void loadRedis(String cmd,String serverWait){ - Process process; - - try { -// String comd = String.format(cmd, f.getAbsoluteFile()); - process = Runtime.getRuntime() - - .exec(cmd); - - - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); - Executors.newSingleThreadExecutor().submit(streamGobbler); -// int exitCode = process.waitFor(); -// assert exitCode == 0; - Thread.sleep(Integer.valueOf(serverWait)); - - } catch (IOException e) { - e.printStackTrace(); - } - catch (InterruptedException e) { - e.printStackTrace(); - } - log.info("Load done"); - } - - public static void main(String[] args) { - - - String inputPath; -// String outputPath; - String port; - String portInner; -// String pairsCSVPath; - String importScript; -// String pairsCompletedPath; - String serverWait; -// String option; - String dbDir; - String chunkName; - String numOfWorkers; - if (args.length > 0) { - inputPath = args[0]; - portInner = args[1]; - serverWait = args[2]; -// option = args[4]; - chunkName = args[3]; - numOfWorkers = args[4]; - dbDir = args[5]; - port = args[6]; -// pairsCSVPath = args[3]; -// importScript = args[4]; -// pairsCompletedPath = args[3]; - } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; -// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6399"; - portInner = "6380"; - serverWait = "10000"; -// option = "COMP"; -// pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; -// importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; -// pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; - chunkName ="chunk5.rdb"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "1"; - - } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); - log.info(parameters); - -// if (option.equals("CALC")) { -// calculatePairs(inputPath, port); -// log.info("Calculate pairs done"); -// }else { - String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); - loadRedis(cmd,serverWait); - - String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); - loadRedis(cmd,serverWait); - - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); - - - - comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); - - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(portInner)); - loadRedis(stopServer,serverWait); -// } - - - } - - - public static void comparePairs(String inputPath, JedisPool innerPool,JedisPool outerPool,String serverWait,String chunkName, String dbDir,String numOfWorkers){ - - - ScanResult scan; - try (Jedis inner = innerPool.getResource()) { - while (inner.ping()== "PONG"){ - log.info("wait"); - } - - ScanParams sc = new ScanParams(); - //150000000 - sc.count(150000000); - sc.match("pair_*"); - - scan = inner.scan("0", sc); - int size = scan.getResult().size(); - log.info("Scanning " + String.valueOf(size)); - } - List result = scan.getResult(); - - -// ActorSystem system = null; -// ActorRef parsingActor = null; -// final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); -// try { -// -// log.info("Akka begins..."); -// system = ActorSystem.create("Tree-System"); -// parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); -// parsingActor.tell(msg, ActorRef.noSender()); -// } catch (Exception e) { -// system.shutdown(); -// e.printStackTrace(); -// } -// greeter.tell(); - result - .parallelStream() - .forEach(m -> - { - Compare compare = new Compare(); - compare.coreCompare(m, innerPool, outerPool); - ; - } - ); - - - - -// } - - - - - } - -// private static void coreCompare(String name , String inputPath, String innerPort) { -// JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(innerPort), 20000000); -// Map resultMap; -// try (Jedis jedis = pool.getResource()) { -// resultMap = jedis.hgetAll(name); -// } -// String[] split = name.split("_"); -// -// -// String i = split[1]; -// String j = split[2]; -// String firstValue = resultMap.get("0"); -// String secondValue = resultMap.get("1"); -// -// String[] firstValueSplit = firstValue.split("GumTreeOutput2"); -// String[] secondValueSplit = secondValue.split("GumTreeOutput2"); -// -// if (firstValueSplit.length == 1) { -// firstValue = inputPath + firstValueSplit[0]; -// } else { -// firstValue = inputPath + firstValueSplit[1]; -// } -// -// if (secondValueSplit.length == 1) { -// secondValue = inputPath + secondValueSplit[0]; -// } else { -// secondValue = inputPath + secondValueSplit[1]; -// } -// -// try { -// ITree oldTree = getSimpliedTree(firstValue); -// -// ITree newTree = getSimpliedTree(secondValue); -// -// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); -// m.match(); -// -// -// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); -// ag.generate(); -// List actions = ag.getActions(); -// -// double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); -// String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); -// double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); -// String diceSimilarity = String.format("%1.2f", diceSimilarity1); -// double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); -// String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); -// -// String editDistance = String.valueOf(actions.size()); -// -// String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; -// -// -// if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) -// || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { -// String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); -// -// try (Jedis jedis = pool.getResource()) { -// jedis.select(1); -// jedis.set(matchKey, result); -// } -// } -// -// -// try (Jedis jedis = pool.getResource()) { -// jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); -// } -// -// -// -// -// }catch (Exception e){ -// log.error(e.toString() + " {}",(name)); -// -// -// } -// -// -// -// -// -// } - - - - public static void calculatePairs(String inputPath,String port) { - File folder = new File(inputPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - List fileToCompare = new ArrayList<>(); - for (File pj : pjs) { - File[] files = pj.listFiles(new FilenameFilter() { - public boolean accept(File dir, String name) { - return name.startsWith("ActionSetDumps"); - } - }); - Collections.addAll(fileToCompare, files[0].listFiles()); - - } - System.out.println("a"); -// compareAll(fileToCompare); - readMessageFiles(fileToCompare,port); - } - -// public static void processMessages(String inputPath, String outputPath) { -// File folder = new File(outputPath + "pairs_splitted/"); -// File[] listOfFiles = folder.listFiles(); -// Stream stream = Arrays.stream(listOfFiles); -// List pjs = stream -// .filter(x -> !x.getName().startsWith(".")) -// .collect(Collectors.toList()); -// FileHelper.createDirectory(outputPath + "comparison_splitted/"); -// pjs.parallelStream() -// .forEach(m -> coreLoop(m, outputPath,inputPath)); -// } - - /** Read the object from Base64 string. */ - private static Object fromString( String s ) throws IOException , - ClassNotFoundException { - byte [] data = Base64.getDecoder().decode( s ); - ObjectInputStream ois = new ObjectInputStream( - new ByteArrayInputStream( data ) ); - Object o = ois.readObject(); - ois.close(); - return o; - } - public static ITree getSimpliedTree(String fn,JedisPool outerPool) { - - ITree tree = null; - Jedis inner = null; - try { - inner = outerPool.getResource(); - String s = inner.get(fn.substring(1)); - HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); - - ITree parent = null; - ITree children =null; - tree = getASTTree(actionSet, parent, children); - tree.setParent(null); - - } catch (IOException e) { - e.printStackTrace(); - } catch (ClassNotFoundException e) { - e.printStackTrace(); - }finally { - if (inner != null) { - inner.close(); - } - } - return tree; - - } - - public static List getKeysByValue(Map map, E value) { - return map.entrySet() - .stream() - .filter(entry -> Objects.equals(entry.getValue(), value)) - .map(Map.Entry::getKey) - .collect(Collectors.toList()); - } - - public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ - - int newType = 0; - - String astNodeType = actionSet.getAstNodeType(); - List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); - - if(keysByValue.size() != 1){ - log.error("Birden cok astnodemapmapping"); - } - newType = keysByValue.get(0); - if(actionSet.getParent() == null){ - //root - - parent = new Tree(newType,""); - }else{ - children = new Tree(newType,""); - parent.addChild(children); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getASTTree(subAction,children,null); - - } - - - } - return parent; - } - - public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ - - int newType = 0; - - Action action = actionSet.getAction(); - if (action instanceof Update){ - newType = 101; - }else if(action instanceof Insert){ - newType =100; - }else if(action instanceof Move){ - newType = 102; - }else if(action instanceof Delete){ - newType=103; - }else{ - new Exception("unknow action"); - } - if(actionSet.getParent() == null){ - //root - - parent = new Tree(newType,""); - }else{ - children = new Tree(newType,""); - parent.addChild(children); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getActionTree(subAction,children,null); - - } - - - } - return parent; - } - - - -// private static void coreLoop(File mes, String outputPath,String inputPath) { -// try { -// -// log.info("Starting in coreLoop"); -// -// BufferedReader br = null; -// String sCurrentLine = null; -// BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); -// -// br = new BufferedReader( -// new FileReader(mes)); -// while ((sCurrentLine = br.readLine()) != null) { -// String currentLine = sCurrentLine; -// String[] split = currentLine.split("\t"); -// String i = split[0]; -// String j = split[1]; -// String firstValue = split[2]; -// String secondValue = split[3]; -// -// firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; -// secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; -// -// ITree oldTree = getSimpliedTree(firstValue); -// -// ITree newTree = getSimpliedTree(secondValue); -// -// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); -// m.match(); -// -// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); -// ag.generate(); -// List actions = ag.getActions(); -// writer.write(String.valueOf(i)); -// writer.write("\t"); -// writer.write(String.valueOf(j)); -// writer.write("\t"); -// -// writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); -// writer.write("\t"); -// writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); -// writer.write("\t"); -// writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); -// writer.write("\t"); -// writer.write(String.valueOf(actions.size())); -// writer.write("\t"); -// writer.write(firstValue); -// writer.write("\t"); -// writer.write(secondValue); -// writer.write("\n"); -// -// -// } -// writer.close(); -// } catch (FileNotFoundException e) { -// log.error("File not found"); -// e.printStackTrace(); -// } catch (IOException e) { -// log.error("Error initializing stream"); -// e.printStackTrace(); -// -// } -// log.info("Completed output_" + mes.getName()); -// } - - private static void readMessageFiles(List folders,String port) { - - List treesFileNames = new ArrayList<>(); - - - for (File target : folders) { - - treesFileNames.add(target.toString()); - } -// FileHelper.createDirectory(outputPath + "pairs/"); - log.info("Calculating pairs"); -// treesFileNames = treesFileNames.subList(0,100); - byte [] buf = new byte[0]; - String line = null; - - -// FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); -// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - int fileCounter = 0; - - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - try (Jedis jedis = jedisPool.getResource()) { - List dir = null; - List path = null; - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - - - // do operations with jedis resource - - String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); -// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; -// jedis.set(key,value); - - jedis.hset(key,"0",treesFileNames.get(i).split("GumTreeOutput2")[1]); - jedis.hset(key,"1",treesFileNames.get(j).split("GumTreeOutput2")[1]); - //10000000 - if(Integer.compare(jedis.dbSize().intValue(),10000000) == 0){ - dir = jedis.configGet("dir"); - path = jedis.configGet("dbfilename"); - File dbPath = new File(dir.get(1)+"/"+path.get(1)); - File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); - try { - jedis.save(); - while (jedis.ping()== "PONG"){ - log.info("wait"); - } - - - - Files.copy(dbPath.toPath(),savePath.toPath()); - } catch (IOException e) { - - e.printStackTrace(); - } - fileCounter++; - jedis.flushDB(); - - } - - - } - } - jedis.save(); - fileCounter++; - File dbPath = new File(dir.get(1)+"/"+path.get(1)); - File savePath = new File(dir.get(1)+"/"+"chunk"+String.valueOf(fileCounter)+ ".rdb"); - try { - - while (jedis.ping()== "PONG"){ - log.info("wait"); - } - - - - Files.copy(dbPath.toPath(),savePath.toPath()); - } catch (IOException e) { - - e.printStackTrace(); - } - jedis.flushDB(); - } - - - - - log.info("Done pairs"); - } - - static final JedisPoolConfig poolConfig = buildPoolConfig(); - - - private static JedisPoolConfig buildPoolConfig() { - final JedisPoolConfig poolConfig = new JedisPoolConfig(); - poolConfig.setMaxTotal(128); - poolConfig.setMaxIdle(128); - poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(false); - poolConfig.setTestOnReturn(false); - poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); -// poolConfig.setNumTestsPerEvictionRun(3); - poolConfig.setBlockWhenExhausted(true); - - return poolConfig; - } - - private static List getMessageFiles(String gumTreeInput) { - String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile - File revFilesPath = new File(inputPath + "revFiles/"); - File[] revFiles = revFilesPath.listFiles(); // project folders - List msgFiles = new ArrayList<>(); - if (revFiles.length >= 0) { - for (File revFile : revFiles) { -// if (revFile.getName().endsWith(".java")) { - String fileName = revFile.getName(); - File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file - fileName = fileName.replace(".java", ".txt"); - File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file - edu.lu.uni.serval.MultipleThreadsParser.MessageFile msgFile = new edu.lu.uni.serval.MultipleThreadsParser.MessageFile(revFile, prevFile, diffentryFile); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); -// } - } - - return msgFiles; - } - else{ - return null; - } - } - - - -// return msgFiles; -} - - - - diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java index 3079eb3..7f75eb5 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java @@ -1,10 +1,8 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import edu.lu.uni.serval.FixPatternParser.Parser; +import edu.lu.uni.serval.FixPatternParser.cluster.Compare; import redis.clients.jedis.JedisPool; -import java.io.File; - public class RunnableCompare implements Runnable { private String name; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java index c9f0edb..4b74489 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java @@ -6,13 +6,12 @@ import akka.actor.UntypedActor; import akka.japi.Creator; import akka.routing.RoundRobinPool; -import edu.lu.uni.serval.FixPatternParser.violations.WorkMessage; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.util.List; -import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; public class TreeActor extends UntypedActor { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java index f6839b5..37d5226 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java @@ -3,35 +3,14 @@ package edu.lu.uni.serval.FixPatternParser.violations; import akka.actor.Props; import akka.actor.UntypedActor; import akka.japi.Creator; -import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.matchers.Matcher; -import com.github.gumtreediff.matchers.Matchers; -import com.github.gumtreediff.tree.ITree; -import edu.lu.uni.serval.FixPatternParser.RunnableParser; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.FixPatternParser.violations.WorkMessage; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; +import edu.lu.uni.serval.FixPatternParser.cluster.Compare; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.Jedis; -import redis.clients.jedis.JedisPool; import redis.clients.jedis.JedisPoolConfig; -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; import java.time.Duration; import java.util.List; -import java.util.Map; -import java.util.concurrent.*; - -import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.comparePairs; -import static edu.lu.uni.serval.FixPatternParser.violations.AkkaTreeLoader.loadRedis; -import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getSimpliedTree; public class TreeWorker extends UntypedActor { private static Logger log = LoggerFactory.getLogger(TreeWorker.class); From deaa2f9364e470addb51b420ce388efec8f27f22 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 14:57:34 +0200 Subject: [PATCH 078/127] sleep --- .../lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index 8f8c558..2f3e116 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -112,7 +112,7 @@ public class CalculatePairs { while (jedis.ping() == "PONG") { log.info("wait"); } - + Thread.sleep(Integer.valueOf(serverWait)); Files.copy(dbPath.toPath(), savePath.toPath(), StandardCopyOption.REPLACE_EXISTING); fileCounter++; From 655ca0337438e483cb7a42379f69f0972a3a47d1 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 14:59:33 +0200 Subject: [PATCH 079/127] sleep --- .../lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index 2f3e116..5e9e693 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -120,6 +120,7 @@ public class CalculatePairs { while (jedis.ping() == "PONG") { log.info("wait"); } + Thread.sleep(Integer.valueOf(serverWait)); } catch (IOException e) { From cc3fd2af1200720aa7b729f05fb7e5b35e94f220 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 15:54:11 +0200 Subject: [PATCH 080/127] file --- .../cluster/CalculatePairs.java | 179 ++++++++++++------ 1 file changed, 122 insertions(+), 57 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index 5e9e693..500445e 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -1,5 +1,8 @@ package edu.lu.uni.serval.FixPatternParser.cluster; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.utils.FileHelper; +import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.Jedis; @@ -8,9 +11,14 @@ import redis.clients.jedis.ScanParams; import redis.clients.jedis.ScanResult; import java.io.File; +import java.io.FileNotFoundException; import java.io.IOException; +import java.io.RandomAccessFile; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; import java.nio.file.Files; import java.nio.file.StandardCopyOption; +import java.util.ArrayList; import java.util.List; import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; @@ -30,6 +38,7 @@ public class CalculatePairs { String serverWait; String dbDir; String chunkName; + String outputPath; if (args.length > 0) { inputPath = args[0]; @@ -39,6 +48,7 @@ public class CalculatePairs { dbDir = args[5]; port = args[6]; + outputPath = args[7]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; @@ -46,7 +56,7 @@ public class CalculatePairs { port = "6399"; portInner = "6380"; serverWait = "10000"; - + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; chunkName ="chunk"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; @@ -60,13 +70,10 @@ public class CalculatePairs { cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); loadRedis(cmd,serverWait); - String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); - loadRedis(cmd,serverWait); + FileHelper.createDirectory(outputPath); + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); - ScanResult scan; try (Jedis outer = outerPool.getResource()) { @@ -85,70 +92,128 @@ public class CalculatePairs { } List result = scan.getResult(); - int fileCounter = 0; - int pairCounter = 0; - for (int i = 0; i < result.size(); i++) { - for (int j = i + 1; j < result.size(); j++) { - Jedis jedis = null; - String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); - try { - jedis = innerPool.getResource(); - key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); -// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; -// jedis.set(key,value); - - jedis.hset(key, "0", result.get(i)); - jedis.hset(key, "1", result.get(j)); - pairCounter ++; - - //10000000 - if (pairCounter % 10000000 == 0) { - - File dbPath = new File(dbDir + "/" + chunkName); - File savePath = new File(dbDir + "/" + "chunk" + String.valueOf(fileCounter) + ".rdb"); - try { - jedis.save(); - log.info("saving key {} chunk {}",key,fileCounter); - while (jedis.ping() == "PONG") { - log.info("wait"); - } - Thread.sleep(Integer.valueOf(serverWait)); - - Files.copy(dbPath.toPath(), savePath.toPath(), StandardCopyOption.REPLACE_EXISTING); - fileCounter++; - jedis.flushDB(); - while (jedis.ping() == "PONG") { - log.info("wait"); - } - Thread.sleep(Integer.valueOf(serverWait)); - - } catch (IOException e) { - - e.printStackTrace(); - } + + byte [] buf = new byte[0]; + String line = null; + try { + + FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +"textfile.txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int fileCounter = 0; + + + for (int i = 0; i < result.size(); i++) { + for (int j = i + 1; j < result.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); } - }catch (Exception e) { - log.error(e.toString() + " {}", (key)); - }finally { - if (jedis != null) { - jedis.close(); + + } } - } + rwChannel.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + }catch (java.nio.BufferOverflowException e) { + log.error(line); + log.error(String.valueOf(buf.length)); + e.printStackTrace(); } + log.info("Done pairs"); + } + + + + + // comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(portInner)); - loadRedis(stopServer,serverWait); +// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; +// stopServer = String.format(stopServer,Integer.valueOf(portInner)); +// loadRedis(stopServer,serverWait); // } - } + + + +// public static void corePairs(,ArrayList> list){ +// String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; +// cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); +// loadRedis(cmd,serverWait); +// JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); +// +// +// +// Jedis jedis = null; +// for (Pair objects : list) { +// +// try { +// String key = objects.getValue0(); +// String value = objects.getValue1(); +// jedis = innerPool.getResource(); +// +// +// String[] split = value.split(","); +// +// +// jedis.hset(key, "0", split[0]); +// jedis.hset(key, "1", split[1]); +// +// +// //10000000 +// if (pairCounter % 10000000 == 0) { +// +// File dbPath = new File(dbDir + "/" + chunkName); +// File savePath = new File(dbDir + "/" + "chunk" + String.valueOf(fileCounter) + ".rdb"); +// try { +// jedis.save(); +// log.info("saving key {} chunk {}",key,fileCounter); +// while (jedis.ping() == "PONG") { +// log.info("wait"); +// } +// Thread.sleep(Integer.valueOf(serverWait)); +// +// Files.copy(dbPath.toPath(), savePath.toPath(), StandardCopyOption.REPLACE_EXISTING); +// fileCounter++; +// jedis.flushDB(); +// while (jedis.ping() == "PONG") { +// log.info("wait"); +// } +// Thread.sleep(Integer.valueOf(serverWait)); +// +// } catch (IOException e) { +// +// e.printStackTrace(); +// } +// +// +// } +// }catch (Exception e) { +// log.error(e.toString() + " {}", (key)); +// }finally { +// if (jedis != null) { +// jedis.close(); +// } +// } +// } +// } } From 90206c37215f021a7a8d843507f30cd6b81e614a Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:12:46 +0200 Subject: [PATCH 081/127] import --- .../cluster/ImportPairs2DB.java | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java new file mode 100644 index 0000000..9aacc1b --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -0,0 +1,71 @@ +package edu.lu.uni.serval.FixPatternParser.cluster; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; +import static jdk.nashorn.internal.runtime.regexp.joni.Config.log; + +/** + * Created by anilkoyuncu on 05/04/2018. + */ +public class ImportPairs2DB { + private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); + public static void main(String[] args) { + + String inputPath; + String portInner; + String serverWait; + String dbDir; + String chunkName; + String numOfWorkers; + if (args.length > 0) { + inputPath = args[0]; + portInner = args[1]; + serverWait = args[2]; + chunkName = args[3]; + numOfWorkers = args[4]; + dbDir = args[5]; + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; + portInner = "6380"; + serverWait = "10000"; + chunkName ="dumps.rdb"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + numOfWorkers = "1"; + } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + + + + File folder = new File(inputPath); + File[] subFolders = folder.listFiles(); + Stream stream = Arrays.stream(subFolders); + List pjs = stream + .filter(x -> x.getName().endsWith(".csv")) + .collect(Collectors.toList()); + + + for (File pj : pjs) { + Integer portInt = Integer.valueOf(portInner); + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); + loadRedis(cmd,serverWait); + + cmd = "bash "+dbDir + "/" + "redisImportSingle.sh" +" %s %s"; + cmd = String.format(cmd, dbDir,pj.getPath(), portInt); + loadRedis(cmd,serverWait); + + } + + + log.info(parameters); + } +} From 56c0cb3d3f0c710d67693bf45d18edb253d1fd40 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:13:59 +0200 Subject: [PATCH 082/127] import --- .../lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 9aacc1b..a12e796 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -63,6 +63,8 @@ public class ImportPairs2DB { cmd = String.format(cmd, dbDir,pj.getPath(), portInt); loadRedis(cmd,serverWait); + portInt++; + } From 15d34396fca6102418b9ea97d94a51aa6d2a00cb Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:17:21 +0200 Subject: [PATCH 083/127] pom --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 09f7d2d..a091669 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.cluster.CalculatePairs + edu.lu.uni.serval.FixPatternParser.cluster.ImportPairs2DB From fcf8ffd7fe01c7a027a30fe4c60e3aacad3a5fc4 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:22:16 +0200 Subject: [PATCH 084/127] port --- .../uni/serval/FixPatternParser/cluster/ImportPairs2DB.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index a12e796..60d5ed6 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -51,10 +51,10 @@ public class ImportPairs2DB { List pjs = stream .filter(x -> x.getName().endsWith(".csv")) .collect(Collectors.toList()); - + Integer portInt = Integer.valueOf(portInner); for (File pj : pjs) { - Integer portInt = Integer.valueOf(portInner); + log.info(String.valueOf(portInt)); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); loadRedis(cmd,serverWait); From 5cb3998baf8b5e10f35378bb4f0fc3459d74eeb3 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:25:23 +0200 Subject: [PATCH 085/127] port --- .../lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 60d5ed6..1af3ff1 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -60,6 +60,7 @@ public class ImportPairs2DB { loadRedis(cmd,serverWait); cmd = "bash "+dbDir + "/" + "redisImportSingle.sh" +" %s %s"; + log.info(cmd); cmd = String.format(cmd, dbDir,pj.getPath(), portInt); loadRedis(cmd,serverWait); From a47c5ddfb8cc6507d673702f6ab834a72aaa9ed4 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:29:54 +0200 Subject: [PATCH 086/127] port --- .../uni/serval/FixPatternParser/cluster/ImportPairs2DB.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 1af3ff1..420482f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -59,9 +59,10 @@ public class ImportPairs2DB { cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); loadRedis(cmd,serverWait); - cmd = "bash "+dbDir + "/" + "redisImportSingle.sh" +" %s %s"; - log.info(cmd); + cmd = "bash "+dbDir + "redisImportSingle.sh" +" %s %s"; + cmd = String.format(cmd, dbDir,pj.getPath(), portInt); + log.info(cmd); loadRedis(cmd,serverWait); portInt++; From e92c10846f595cef191389546d13a2dbc475c0ba Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 17:33:58 +0200 Subject: [PATCH 087/127] port --- .../lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 420482f..2bb5d5a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -61,7 +61,7 @@ public class ImportPairs2DB { cmd = "bash "+dbDir + "redisImportSingle.sh" +" %s %s"; - cmd = String.format(cmd, dbDir,pj.getPath(), portInt); + cmd = String.format(cmd, pj.getPath(), portInt); log.info(cmd); loadRedis(cmd,serverWait); From 55d7c7a1921d1773f25789dcbb9041320ba9ec2a Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 18:29:56 +0200 Subject: [PATCH 088/127] deneme --- .../cluster/AkkaTreeLoader.java | 26 +++++++++++++++++++ .../cluster/ImportPairs2DB.java | 12 ++++++--- 2 files changed, 34 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 1e2e76e..3a718bc 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -65,6 +65,32 @@ public class AkkaTreeLoader { log.info("Load done"); } + public static void loadRedisWait(String cmd){ + Process process; + + try { +// String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() + + .exec(cmd); + + + StreamGobbler streamGobbler = + new StreamGobbler(process.getInputStream(), System.out::println); + Executors.newSingleThreadExecutor().submit(streamGobbler); + int exitCode = process.waitFor(); + assert exitCode == 0; + + + } catch (IOException e) { + e.printStackTrace(); + } + catch (InterruptedException e) { + e.printStackTrace(); + } + log.info("Load done"); + } + public static void main(String[] args) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 2bb5d5a..a5a54ed 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -11,7 +11,8 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; -import static jdk.nashorn.internal.runtime.regexp.joni.Config.log; +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedisWait; + /** * Created by anilkoyuncu on 05/04/2018. @@ -54,16 +55,17 @@ public class ImportPairs2DB { Integer portInt = Integer.valueOf(portInner); for (File pj : pjs) { - log.info(String.valueOf(portInt)); + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); - loadRedis(cmd,serverWait); + log.info(cmd); + loadRedisWait(cmd); cmd = "bash "+dbDir + "redisImportSingle.sh" +" %s %s"; cmd = String.format(cmd, pj.getPath(), portInt); log.info(cmd); - loadRedis(cmd,serverWait); + loadRedisWait(cmd); portInt++; @@ -72,4 +74,6 @@ public class ImportPairs2DB { log.info(parameters); } + + } From c689157c43a7f39e20236424eeb15d19e402ccdb Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 19:05:09 +0200 Subject: [PATCH 089/127] akka --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a091669..aa97426 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.cluster.ImportPairs2DB + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader From 230f60c89f19ebbffeb352cb749a95b249ac2362 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 19:19:02 +0200 Subject: [PATCH 090/127] index fix --- .../lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 3a718bc..57c5fcd 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -235,7 +235,7 @@ public class AkkaTreeLoader { Jedis inner = null; try { inner = outerPool.getResource(); - String s = inner.get(fn.substring(1)); + String s = inner.get(fn); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); ITree parent = null; From 100485c5497177085279b6d27955d5d7f85ba521 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Thu, 5 Apr 2018 19:30:07 +0200 Subject: [PATCH 091/127] treecontext --- .../cluster/AkkaTreeLoader.java | 44 ++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 57c5fcd..3bfa772 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -2,6 +2,7 @@ package edu.lu.uni.serval.FixPatternParser.cluster; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.Tree; +import com.github.gumtreediff.tree.TreeContext; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; @@ -240,8 +241,10 @@ public class AkkaTreeLoader { ITree parent = null; ITree children =null; - tree = getASTTree(actionSet, parent, children); + TreeContext tc = new TreeContext(); + tree = getASTTree(actionSet, parent, children,tc); tree.setParent(null); + tc.validate(); } catch (IOException e) { e.printStackTrace(); @@ -264,6 +267,45 @@ public class AkkaTreeLoader { .collect(Collectors.toList()); } + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("Birden cok astnodemapmapping"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + +// parent = new Tree(newType,""); + parent = tc.createTree(newType, "", null); + tc.setRoot(parent); + }else{ +// children = new Tree(newType,""); +// parent.addChild(children); + children = tc.createTree(newType, "", null); + children.setParentAndUpdateChildren(parent); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null,tc); + + } + + + } + return parent; + } + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ int newType = 0; From 445b4477af3c8acc4e024280163ecbdd70ddbcb2 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Tue, 10 Apr 2018 11:13:32 +0200 Subject: [PATCH 092/127] initial working version --- .../cluster/AkkaTreeLoader.java | 4 + .../cluster/ImportPairs2DB.java | 2 + .../MultiThreadTreeLoaderCluster.java | 208 ++++++++--- .../MultiThreadTreeLoaderCluster3.java | 345 +++++++++++++++--- 4 files changed, 457 insertions(+), 102 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 3bfa772..8f6eee2 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -159,6 +159,10 @@ public class AkkaTreeLoader { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(portInner)); loadRedis(stopServer,serverWait); + + stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(port)); + loadRedis(stopServer,serverWait); // } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index a5a54ed..8922c67 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -69,6 +69,8 @@ public class ImportPairs2DB { portInt++; + //TODO missing kill server script + } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index be1a7c0..c4e73ba 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -6,6 +6,7 @@ import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.Tree; +import com.github.gumtreediff.tree.TreeContext; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; @@ -26,6 +27,8 @@ import java.util.function.Consumer; import java.util.stream.Collectors; import java.util.stream.Stream; +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; + /** * Created by anilkoyuncu on 19/03/2018. */ @@ -58,37 +61,49 @@ public class MultiThreadTreeLoaderCluster { String port; String pairsCSVPath; String importScript; + String dbDir; if (args.length > 0) { inputPath = args[0]; outputPath = args[1]; port = args[2]; pairsCSVPath = args[3]; importScript = args[4]; + dbDir = args[5]; } else { // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; inputPath = "/Users/anilkoyuncu/bugStudy/code/python/clusterDumps"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6379"; + port = "6381"; pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs-csv/"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; } -// calculatePairsOfClusters(inputPath, outputPath); - mainCompare(inputPath,port,pairsCSVPath,importScript); + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"cluster1.rdb",Integer.valueOf(port)); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); + + + cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"10000"); + + calculatePairsOfClusters(inputPath, outputPath); +// mainCompare(inputPath,port,pairsCSVPath,importScript); // calculatePairs(inputPath, outputPath); // processMessages(inputPath,outputPath); // evaluateResults(inputPath,outputPath); } - public static void loadRedis(String cmd, File f){ + public static void loadRedis(String cmd){ Process process; - log.info(f.getName()); + try { - String comd = String.format(cmd, f.getAbsoluteFile()); + process = Runtime.getRuntime() - .exec(comd); + .exec(cmd); StreamGobbler streamGobbler = @@ -107,10 +122,13 @@ public class MultiThreadTreeLoaderCluster { public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { String cmd; - cmd = "bash " + importScript +" %s"; + cmd = "bash " + importScript +" %s %s"; + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf("6399"),20000000); + File folder = new File(pairsCSVPath); File[] listOfFiles = folder.listFiles(); @@ -121,7 +139,7 @@ public class MultiThreadTreeLoaderCluster { for (File f:folders){ - if(f.getName().startsWith("cluster76")) { + if(f.getName().startsWith("cluster0")) { try (Jedis jedis = jedisPool.getResource()) { @@ -135,7 +153,8 @@ public class MultiThreadTreeLoaderCluster { int size = scan.getResult().size(); if (size == 0) { - loadRedis(cmd, f); + String comd = String.format(cmd,f.getPath(),port); + loadRedis(comd); scan = jedis.scan("0", sc); size = scan.getResult().size(); @@ -150,7 +169,7 @@ public class MultiThreadTreeLoaderCluster { //76 scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName)); + .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName,outerPool)); jedis.save(); @@ -166,15 +185,46 @@ public class MultiThreadTreeLoaderCluster { } + /** Read the object from Base64 string. */ + public static Object fromString( String s ) throws IOException , + ClassNotFoundException { + byte [] data = Base64.getDecoder().decode( s ); + ObjectInputStream ois = new ObjectInputStream( + new ByteArrayInputStream( data ) ); + Object o = ois.readObject(); + ois.close(); + return o; + } + public static Pair getTree(String firstValue, JedisPool outerPool){ - public static Pair getTree(String firstValue){ - String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; + +// HierarchicalActionSet actionSet = null; +// try { +// FileInputStream fi = new FileInputStream(new File(dumps + firstValue)); +// ObjectInputStream oi = new ObjectInputStream(fi); +// actionSet = (HierarchicalActionSet) oi.readObject(); +// oi.close(); +// fi.close(); +// +// +// } catch (FileNotFoundException e) { +// log.error("File not found"); +// e.printStackTrace(); +// } catch (IOException e) { +// log.error("Error initializing stream"); +// e.printStackTrace(); +// } catch (ClassNotFoundException e) { +// // TODO Auto-generated catch block +// e.printStackTrace(); +// } + + ITree tree = null; + Jedis inner = null; String[] split2 = firstValue.split("/"); String cluster = split2[1]; - File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); @@ -182,47 +232,59 @@ public class MultiThreadTreeLoaderCluster { .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) .collect(Collectors.toList()); - - String[] split1 = folders.get(0).getName().split(".txt_"); String s = split1[0]; String[] splitPJ = split1[1].split("_"); String project = splitPJ[1]; String actionSetPosition = splitPJ[0]; - File prevFile = new File(gumTreeInput + project+ "/" + "prevFiles/prev_" + s + ".java");// previous file - File revFile = new File(gumTreeInput + project+ "/" + "revFiles/" + s + ".java");//rev file - - List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); - - HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); -// for (HierarchicalActionSet actionSet : actionSets) { + try { + inner = outerPool.getResource(); + String filename = project + "/ActionSetDumps/" + split2[2]; + String si= inner.get(filename); + HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); + ITree parent = null; + ITree children =null; + TreeContext tc = new TreeContext(); + tree = getActionTree(actionSet, parent, children,tc); + tree.setParent(null); + tc.validate(); - ITree actionTree= null; - ITree test2 = null; - getActionTree(actionSet); - ITree node = actionSet.getNode(); - List descendants = node.getDescendants(); - for (ITree descendant : descendants) { - if(descendant.getType() <= 100){ - descendant.setType(104); +// log.info(tc.toString()); + +// ITree newTree = ((Update)actionSet.getAction()).getNewNode(); +// ITree oldTree = ((Update)actionSet.getAction()).getNode(); +// +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// log.info(actions.toString()); + + } catch (IOException e) { + e.printStackTrace(); + } catch (ClassNotFoundException e) { + e.printStackTrace(); + }finally { + if (inner != null) { + inner.close(); } } - node.setParent(null); - - - // } -// } - - Pair pair = new Pair<>(node,project); + Pair pair = new Pair<>(tree,project); return pair; + + + + + + } - public static void getActionTree(HierarchicalActionSet actionSet){ - + public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ int newType = 0; @@ -238,18 +300,64 @@ public class MultiThreadTreeLoaderCluster { }else{ new Exception("unknow action"); } - actionSet.getNode().setType(newType); -// actionSet.getNode().setLabel(""); + if(actionSet.getParent() == null){ + //root + + parent = tc.createTree(newType, "", null); + tc.setRoot(parent); + +// parent = new Tree(newType,""); + }else{ + children = tc.createTree(newType, "", null); + children.setParentAndUpdateChildren(parent); +// children = new Tree(newType,""); +// parent.addChild(children); + } List subActions = actionSet.getSubActions(); if (subActions.size() != 0){ for (HierarchicalActionSet subAction : subActions) { - getActionTree(subAction); + + if(actionSet.getParent() == null){ + children = parent; + } + getActionTree(subAction,children,null,tc); + } } - + return parent; } + +// public static void getActionTree(HierarchicalActionSet actionSet){ +// +// +// int newType = 0; +// +// Action action = actionSet.getAction(); +// if (action instanceof Update){ +// newType = 101; +// }else if(action instanceof Insert){ +// newType =100; +// }else if(action instanceof Move){ +// newType = 102; +// }else if(action instanceof Delete){ +// newType=103; +// }else{ +// new Exception("unknow action"); +// } +// actionSet.getNode().setType(newType); +//// actionSet.getNode().setLabel(""); +// List subActions = actionSet.getSubActions(); +// if (subActions.size() != 0){ +// for (HierarchicalActionSet subAction : subActions) { +// getActionTree(subAction); +// } +// +// +// } +// +// } // public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ // // int newType = 0; @@ -292,7 +400,7 @@ public class MultiThreadTreeLoaderCluster { - private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName) { + private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName,JedisPool outerPool) { try (Jedis jedis = jedisPool.getResource()) { @@ -316,6 +424,12 @@ public class MultiThreadTreeLoaderCluster { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); +// if (firstValue.equals("71d453_0b5934_hbase-server#src#main#java#org#apache#hadoop#hbase#regionserver#RSRpcServices.txt_0")){ +// //3f70d6_9ee9c5_camel-core#src#main#java#org#apache#camel#builder#NotifyBuilder.txt_0_CAMEL +// //29ea3e_71c614_spring-batch-core#src#test#java#org#springframework#batch#core#domain#JobExecutionTests.txt_0_BATCH +// log.info(firstValue); +// } + @@ -340,8 +454,8 @@ public class MultiThreadTreeLoaderCluster { // } try { - Pair oldPair = getTree(firstValue); - Pair newPair = getTree(secondValue); + Pair oldPair = getTree(firstValue, outerPool); + Pair newPair = getTree(secondValue, outerPool); ITree oldTree = oldPair.getValue0(); ITree newTree = newPair.getValue0(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 4ac21e9..ee301d2 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -5,11 +5,14 @@ import com.github.gumtreediff.actions.model.*; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.TreeContext; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; +import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; @@ -21,10 +24,14 @@ import java.time.Duration; import java.util.*; import java.util.concurrent.Executors; import java.util.function.Consumer; +import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.text.similarity.*; +import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getKeysByValue; +import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster.fromString; + /** * Created by anilkoyuncu on 19/03/2018. */ @@ -58,6 +65,7 @@ public class MultiThreadTreeLoaderCluster3 { String pairsCSVPath; String importScript; String csvScript; + String dbDir; if (args.length > 0) { inputPath = args[0]; outputPath = args[1]; @@ -65,6 +73,7 @@ public class MultiThreadTreeLoaderCluster3 { pairsCSVPath = args[3]; importScript = args[4]; csvScript = args[5]; + dbDir = args[6]; } else { // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; inputPath = "/Users/anilkoyuncu/bugStudy/code/python/cluster2L"; @@ -73,13 +82,21 @@ public class MultiThreadTreeLoaderCluster3 { pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs-2l-csv/"; importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; csvScript = "/Users/anilkoyuncu/bugStudy/dataset/transformCSV.sh"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; } - calculatePairsOfClusters(inputPath, outputPath); +// calculatePairsOfClusters(inputPath, outputPath); // createCSV(csvScript,outputPath + "pairs-2l/",pairsCSVPath); //create csv file and move + String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"cluster2.rdb",Integer.valueOf(port)); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); + + cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"10000"); mainCompare(inputPath,port,pairsCSVPath,importScript); // calculatePairs(inputPath, outputPath); @@ -145,9 +162,10 @@ public class MultiThreadTreeLoaderCluster3 { public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { String cmd; - cmd = "bash " + importScript +" %s"; + cmd = "bash " + importScript +" %s %s"; JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf("6399"),20000000); File folder = new File(pairsCSVPath); @@ -159,42 +177,41 @@ public class MultiThreadTreeLoaderCluster3 { for (File f:folders){ + if(f.getName().startsWith("cluster7_0")) { + try (Jedis jedis = jedisPool.getResource()) { + // do operations with jedis resource + ScanParams sc = new ScanParams(); + sc.count(150000000); + sc.match("pair_[0-9]*"); - try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - ScanParams sc = new ScanParams(); - sc.count(150000000); - sc.match("pair_[0-9]*"); + log.info("Scanning"); + ScanResult scan = jedis.scan("0", sc); + int size = scan.getResult().size(); - log.info("Scanning"); - ScanResult scan = jedis.scan("0",sc); - int size = scan.getResult().size(); + if (size == 0) { + String comd = String.format(cmd, f.getPath(), port); + edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster. + loadRedis(comd); - if (size == 0){ - loadRedis(cmd,f); + scan = jedis.scan("0", sc); + size = scan.getResult().size(); - scan = jedis.scan("0",sc); - size = scan.getResult().size(); + } + log.info("Scanned " + String.valueOf(size)); + + + String clusterName = f.getName().split("\\.")[0].replace("cluster", ""); + + + scan.getResult().parallelStream() + .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName, outerPool)); + + + jedis.save(); } - log.info("Scanned " + String.valueOf(size)); - - - String clusterName = f.getName().split("\\.")[0].replace("cluster",""); - - - - - scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool,clusterName)); - - - - - jedis.save(); - } @@ -210,8 +227,8 @@ public class MultiThreadTreeLoaderCluster3 { - public static ITree getTree(String firstValue){ - String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; + public static ITree getTree(String firstValue, JedisPool outerPool){ +// String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; String[] split2 = firstValue.split("/"); String cluster = split2[1]; String subCluster = split2[2]; @@ -222,29 +239,90 @@ public class MultiThreadTreeLoaderCluster3 { String project = splitPJ[1]; String actionSetPosition = splitPJ[0]; + Integer asp = Integer.valueOf(actionSetPosition); + if (asp > 1){ + return null; + } - File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/clusterDumps/"+cluster + "/" + s + ".txt_" + actionSetPosition); +// File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/clusterDumps/"+cluster + "/" + s + ".txt_" + actionSetPosition); +// +// +// ITree tree = null; +// try { +// FileInputStream fi = new FileInputStream(folder); +// ObjectInputStream oi = new ObjectInputStream(fi); +// tree = (ITree) oi.readObject(); +// oi.close(); +// fi.close(); +// +// +// } catch (FileNotFoundException e) { +// log.error("File not found"); +// e.printStackTrace(); +// } catch (IOException e) { +// log.error("Error initializing stream"); +// e.printStackTrace(); +// } catch (ClassNotFoundException e) { +// // TODO Auto-generated catch block +// e.printStackTrace(); +// } +// return tree; ITree tree = null; + Jedis inner = null; +// String[] split2 = firstValue.split("/"); +// String cluster = split2[1]; +// +// String[] split1 = folders.get(0).getName().split(".txt_"); +// String s = split1[0]; +// String[] splitPJ = split1[1].split("_"); +// String project = splitPJ[1]; +// String actionSetPosition = splitPJ[0]; + +// File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); +// File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/clusterDumps/"+cluster + "/" + s + ".txt_" + actionSetPosition); +// File[] listOfFiles = folder.listFiles(); +// Stream stream = Arrays.stream(listOfFiles); +// List folders = stream +// .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) +// .collect(Collectors.toList()); + + + try { - FileInputStream fi = new FileInputStream(folder); - ObjectInputStream oi = new ObjectInputStream(fi); - tree = (ITree) oi.readObject(); - oi.close(); - fi.close(); + inner = outerPool.getResource(); + String fn = project + "/ActionSetDumps/" + s + ".txt_" + actionSetPosition; + String si= inner.get(fn); + HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); +// ITree newTree = ((Update)actionSet.getAction()).getNewNode(); +// ITree oldTree = ((Update)actionSet.getAction()).getNode(); +// +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// log.info(actions.toString()); + + ITree parent = null; + ITree children =null; + TreeContext tc = new TreeContext(); + tree = getASTTree(actionSet, parent, children,tc); +// tree.setParent(null); + tc.validate(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); } catch (IOException e) { - log.error("Error initializing stream"); e.printStackTrace(); } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block e.printStackTrace(); + }finally { + if (inner != null) { + inner.close(); + } } +// Pair pair = new Pair<>(tree,project); return tree; // File[] listOfFiles = folder.listFiles(); @@ -286,6 +364,47 @@ public class MultiThreadTreeLoaderCluster3 { // return pair; } + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + + String label = actionSet.getAction().toString(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("Birden cok astnodemapmapping"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + +// parent = new Tree(newType,""); + parent = tc.createTree(newType, label, null); + tc.setRoot(parent); + }else{ +// children = new Tree(newType,""); +// parent.addChild(children); + children = tc.createTree(newType, label, null); + children.setParentAndUpdateChildren(parent); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null,tc); + + } + + + } + return parent; + } + public static ITree getActionTree(HierarchicalActionSet actionSet){ @@ -317,22 +436,127 @@ public class MultiThreadTreeLoaderCluster3 { } private static List getNames(ITree oldTree, List oldTokens){ - if((oldTree.getType() == 42 && oldTree.getLabel().startsWith("Name:")) || oldTree.getType() == 42 && oldTree.getParent().getType() == 59 || oldTree.getType() == 43 || (oldTree.getType() == 41 && oldTree.getLabel().startsWith("SimpleName:")) ){ +// if((oldTree.getType() == 42 && oldTree.getLabel().startsWith("Name:")) || oldTree.getType() == 42 && oldTree.getParent().getType() == 59 || oldTree.getType() == 43 || (oldTree.getType() == 41 && oldTree.getLabel().startsWith("SimpleName:")) ){ +// +// oldTokens.add(oldTree.getLabel()); +// +// } +// for (ITree oldDescendant : oldTree.getDescendants()) { +// if ((oldDescendant.getType() == 42 && oldDescendant.getLabel().startsWith("Name:") ) || oldDescendant.getType() == 42 && oldDescendant.getParent().getType() == 59 ||oldDescendant.getType() == 43 || (oldDescendant.getType() == 41 && oldDescendant.getLabel().startsWith("SimpleName:"))){ +// +// oldTokens.add(oldDescendant.getLabel()); +// +// } +// } + List descendants = oldTree.getDescendants(); + descendants.add(0,oldTree); + boolean upd=false; + for (ITree oldDescendant : descendants) { + int type = oldDescendant.getType(); - oldTokens.add(oldTree.getLabel()); + String sType = String.valueOf(type); - } - for (ITree oldDescendant : oldTree.getDescendants()) { - if ((oldDescendant.getType() == 42 && oldDescendant.getLabel().startsWith("Name:") ) || oldDescendant.getType() == 42 && oldDescendant.getParent().getType() == 59 ||oldDescendant.getType() == 43 || (oldDescendant.getType() == 41 && oldDescendant.getLabel().startsWith("SimpleName:"))){ + if((sType.equals("42") || oldDescendant.getChildren().size() ==0)|| + (sType.equals("32") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || + (sType.equals("59") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || + (sType.equals("43") && oldDescendant.getHeight() == 0 && oldDescendant.getChildren().size() == 0) || + (sType.equals("14") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || + (sType.equals("7") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || + (sType.equals("27") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) + ){ - oldTokens.add(oldDescendant.getLabel()); + int depth = oldDescendant.getChildren().size(); + String label = oldDescendant.getLabel(); + + if(sType.equals("32") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1){ + log.info(""); + } + + + label = label.split("@AT@")[0]; + String[] split = label.split(" "+sType); + String[] split2 = split[1].split("@"); + List m = new ArrayList(); + if(label.startsWith("UPD")){ + upd = true; + String timeRegex = "@@(.*)@TO@(.*)"; + Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); + java.util.regex.Matcher matcher = pattern.matcher(split[1]); + + if (matcher.matches()) { + String hours = matcher.group(1); + String to = matcher.group(2); + m.add(hours.trim()); + m.add(to.trim()); + + } + }else if(label.startsWith("INS") && upd == false){ + String timeRegex = "@@(.*)@TO@(.*)"; + Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); + java.util.regex.Matcher matcher = pattern.matcher(split[1]); + + if (matcher.matches()) { + String hours = matcher.group(1); + if (hours.startsWith("MethodName:")){ + String methodName = hours.split(":")[1]; + oldTokens.add(methodName); + }else { + oldTokens.add(hours.trim()); + } + } + + }else if(label.startsWith("DEL") && upd == false){ + String timeRegex = "@@(.*)"; + Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); + java.util.regex.Matcher matcher = pattern.matcher(split[1]); + + if (matcher.matches()) { + String hours = matcher.group(1); + if (hours.startsWith("MethodName:")){ + String methodName = hours.split(":")[1]; + oldTokens.add(methodName); + }else { + oldTokens.add(hours.trim()); + } + } + } + + for (String s : m) { + // if(s.isEmpty()){ + // continue; + // } + //TODO remove 44 + if(s.startsWith("SimpleName:") || s.startsWith("Name:")){ + oldTokens.add(s); + }else if (s.startsWith("MethodName:")){ + String methodName = s.split(":")[1]; + oldTokens.add(methodName); + }else if( sType.equals("59") || sType.equals("43")|| sType.equals("14") || sType.equals("7") || sType.equals("27") || sType.equals("83") || sType.equals("44")){ + if(sType.equals("27") || sType.equals("83") || sType.equals("44")){ + oldTokens.add(s); + } + else { + String s1 = s.split("=")[0]; + oldTokens.add(s1); + } + } +// else +// if(oldTokens.size() < 2){ +// oldTokens.add(s); +// } + + } } } + + if (oldTokens.size() == 0){ + log.info("dur bakalim nereye!???"); + } return oldTokens; } - private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName) { + private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName,JedisPool outerPool) { try (Jedis jedis = jedisPool.getResource()) { @@ -356,6 +580,10 @@ public class MultiThreadTreeLoaderCluster3 { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); + if(firstValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL") || secondValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL")){ + log.info(""); + } + ///35/1/22b5f7_84bf27_ui#org.eclipse.pde.runtime#src#org#eclipse#pde#internal#runtime#registry#RegistryBrowserLabelProvider.txt_2_PDE @@ -379,8 +607,15 @@ public class MultiThreadTreeLoaderCluster3 { // } try { - ITree oldTree = getTree(firstValue); - ITree newTree = getTree(secondValue); + ITree oldTree = getTree(firstValue,outerPool); + ITree newTree = getTree(secondValue,outerPool); + + if(oldTree == null || newTree == null) { + jedis.select(0); + String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); + jedis.del(pairKey); + return; + } // ITree oldTree = oldPair.getValue0(); // ITree newTree = newPair.getValue0(); @@ -400,8 +635,8 @@ public class MultiThreadTreeLoaderCluster3 { oldTokens = getNames(oldTree,oldTokens); newTokens = getNames(newTree,newTokens); - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); CharSequence[] newSequences = newTokens.toArray(new CharSequence[newTokens.size()]); JaroWinklerDistance jwd = new JaroWinklerDistance(); @@ -425,7 +660,7 @@ public class MultiThreadTreeLoaderCluster3 { // log.info(secondValue); // log.info("************"); String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); - String result = firstValue + "," + secondValue; + String result = firstValue + "," + secondValue + ","+String.join(",", oldTokens); jedis.select(1); jedis.set(matchKey, result); } From 6c16f82a1bdce91548efe4f6789fe5e8b99b8fbb Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 14 Apr 2018 12:52:02 +0200 Subject: [PATCH 093/127] new --- pom.xml | 2 +- .../violations/FixedViolationHunkParser.java | 14 +++++++------- .../violations/TestHunkParser.java | 6 +++--- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/pom.xml b/pom.xml index aa97426..e4506d2 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader + edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 1f4290c..eaa7a53 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -41,18 +41,18 @@ public class FixedViolationHunkParser extends FixedViolationParser { public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); - boolean isUpdate = - actionSets.stream().allMatch(p -> p.getAction() instanceof Update); +// boolean isUpdate = +// actionSets.stream().allMatch(p -> p.getAction() instanceof Update); int hunkSet = 0; - if(isUpdate){ +// if(isUpdate){ for (HierarchicalActionSet actionSet : actionSets) { FileOutputStream f = null; try { - String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; - String root = diffentryFile.getParent().split("GumTreeInputBug4")[0]; - String hunkTreeFileName = root+"GumTreeOutput2/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + String pj = diffentryFile.getParent().split("GumTreeInputBug13April")[1]; + String root = diffentryFile.getParent().split("GumTreeInputBug13April")[0]; + String hunkTreeFileName = root+"GumTreeOutput13April/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); f = new FileOutputStream(new File(hunkTreeFileName)); ObjectOutputStream o = new ObjectOutputStream(f); o.writeObject(actionSet); @@ -67,7 +67,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { hunkSet++; } - } +// } } // public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 36863a5..61f3125 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -43,9 +43,9 @@ public class TestHunkParser { outputPath = args[0]; }else{ // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; - inputPath = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4"; + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug13April"; // outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput13April"; } @@ -108,7 +108,7 @@ public class TestHunkParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(1, editScriptsFilePath, + parsingActor = system.actorOf(ParseFixPatternActor.props(100, editScriptsFilePath, patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { From 713f8f8e8bf5240177379f90ec2bff8cb2c40306 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 14 Apr 2018 13:40:20 +0200 Subject: [PATCH 094/127] store --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e4506d2..263489f 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser + edu.lu.uni.serval.FixPatternParser.cluster.StoreFile From dd9ab3ba5a406d1d95e2f1e1b8ef71104258865b Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 14 Apr 2018 16:35:47 +0200 Subject: [PATCH 095/127] calcpairs --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 263489f..09f7d2d 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.cluster.StoreFile + edu.lu.uni.serval.FixPatternParser.cluster.CalculatePairs From ae0c548e203dd264f7783b9e956a4cc0a85dcd1c Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 14 Apr 2018 17:19:39 +0200 Subject: [PATCH 096/127] calcpairs --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 09f7d2d..a091669 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.cluster.CalculatePairs + edu.lu.uni.serval.FixPatternParser.cluster.ImportPairs2DB From c03061db694d08682a938b52bcb33b9940366901 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 14 Apr 2018 19:07:53 +0200 Subject: [PATCH 097/127] launcher --- pom.xml | 2 +- .../cluster/AkkaTreeLoader.java | 82 ++-- .../cluster/CalculatePairs.java | 64 +-- .../cluster/ImportPairs2DB.java | 48 +-- .../FixPatternParser/cluster/StoreFile.java | 48 +-- .../MultiThreadTreeLoaderCluster3.java | 291 ++++++-------- .../violations/TestHunkParserSingleFile.java | 363 ++++++++++++++++++ src/main/java/edu/lu/uni/serval/Launcher.java | 60 +++ .../regroup/HierarchicalRegrouper.java | 4 +- 9 files changed, 677 insertions(+), 285 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java create mode 100644 src/main/java/edu/lu/uni/serval/Launcher.java diff --git a/pom.xml b/pom.xml index a091669..393feb7 100644 --- a/pom.xml +++ b/pom.xml @@ -108,7 +108,7 @@ - edu.lu.uni.serval.FixPatternParser.cluster.ImportPairs2DB + edu.lu.uni.serval.Launcher diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 8f6eee2..b27459f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -92,48 +92,48 @@ public class AkkaTreeLoader { log.info("Load done"); } - public static void main(String[] args) { +// public static void main(String[] args) { + public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers,String port){ - - String inputPath; -// String outputPath; - String port; - String portInner; -// String pairsCSVPath; - String importScript; -// String pairsCompletedPath; - String serverWait; -// String option; - String dbDir; - String chunkName; - String numOfWorkers; - if (args.length > 0) { - inputPath = args[0]; - portInner = args[1]; - serverWait = args[2]; -// option = args[4]; - chunkName = args[3]; - numOfWorkers = args[4]; - dbDir = args[5]; - port = args[6]; -// pairsCSVPath = args[3]; -// importScript = args[4]; -// pairsCompletedPath = args[3]; - } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; -// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6399"; - portInner = "6380"; - serverWait = "10000"; -// option = "COMP"; -// pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; -// importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; -// pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; - chunkName ="chunk3.rdb"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "1"; - - } +// String inputPath; +//// String outputPath; +// String port; +// String portInner; +//// String pairsCSVPath; +// String importScript; +//// String pairsCompletedPath; +// String serverWait; +//// String option; +// String dbDir; +// String chunkName; +// String numOfWorkers; +// if (args.length > 0) { +// inputPath = args[0]; +// portInner = args[1]; +// serverWait = args[2]; +//// option = args[4]; +// chunkName = args[3]; +// numOfWorkers = args[4]; +// dbDir = args[5]; +// port = args[6]; +//// pairsCSVPath = args[3]; +//// importScript = args[4]; +//// pairsCompletedPath = args[3]; +// } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; +//// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; +// port = "6399"; +// portInner = "6380"; +// serverWait = "10000"; +//// option = "COMP"; +//// pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; +//// importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; +//// pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; +// chunkName ="chunk3.rdb"; +// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; +// numOfWorkers = "1"; +// +// } String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); log.info(parameters); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index 500445e..ccc4e95 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -29,39 +29,39 @@ import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poo */ public class CalculatePairs { private static Logger log = LoggerFactory.getLogger(CalculatePairs.class); - public static void main(String[] args) { +// public static void main(String[] args) { + public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers,String port,String outputPath){ - - String inputPath; - String port; - String portInner; - String serverWait; - String dbDir; - String chunkName; - String outputPath; - - if (args.length > 0) { - inputPath = args[0]; - portInner = args[1]; - serverWait = args[2]; - chunkName = args[3]; - - dbDir = args[5]; - port = args[6]; - outputPath = args[7]; - - } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; - - port = "6399"; - portInner = "6380"; - serverWait = "10000"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; - chunkName ="chunk"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - - - } +// String inputPath; +// String port; +// String portInner; +// String serverWait; +// String dbDir; +// String chunkName; +// String outputPath; +// +// if (args.length > 0) { +// inputPath = args[0]; +// portInner = args[1]; +// serverWait = args[2]; +// chunkName = args[3]; +// +// dbDir = args[5]; +// port = args[6]; +// outputPath = args[7]; +// +// } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; +// +// port = "6399"; +// portInner = "6380"; +// serverWait = "10000"; +// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; +// chunkName ="chunk"; +// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; +// +// +// } String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir); log.info(parameters); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 8922c67..a0fa800 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -19,31 +19,33 @@ import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedi */ public class ImportPairs2DB { private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); - public static void main(String[] args) { +// public static void main(String[] args) { - String inputPath; - String portInner; - String serverWait; - String dbDir; - String chunkName; - String numOfWorkers; - if (args.length > 0) { - inputPath = args[0]; - portInner = args[1]; - serverWait = args[2]; - chunkName = args[3]; - numOfWorkers = args[4]; - dbDir = args[5]; - } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; - portInner = "6380"; - serverWait = "10000"; - chunkName ="dumps.rdb"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "1"; - } + public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers){ + +// String inputPath; +// String portInner; +// String serverWait; +// String dbDir; +// String chunkName; +// String numOfWorkers; +// if (args.length > 0) { +// inputPath = args[0]; +// portInner = args[1]; +// serverWait = args[2]; +// chunkName = args[3]; +// numOfWorkers = args[4]; +// dbDir = args[5]; +// } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; +// portInner = "6380"; +// serverWait = "10000"; +// chunkName ="dumps.rdb"; +// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; +// numOfWorkers = "1"; +// } String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); - + log.info(parameters); File folder = new File(inputPath); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java index a8ff74a..c680d96 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java @@ -25,31 +25,31 @@ public class StoreFile { private static Logger log = LoggerFactory.getLogger(StoreFile.class); - public static void main(String[] args) { - - String inputPath; - String portInner; - String serverWait; - String dbDir; - String chunkName; - String numOfWorkers; - if (args.length > 0) { - inputPath = args[0]; - portInner = args[1]; - serverWait = args[2]; - chunkName = args[3]; - numOfWorkers = args[4]; - dbDir = args[5]; - } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; - portInner = "6399"; - serverWait = "10000"; - chunkName ="dumps.rdb"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "1"; - } +// public static void main(String[] args) { + public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers){ +// String inputPath; +// String portInner; +// String serverWait; +// String dbDir; +// String chunkName; +// String numOfWorkers; +// if (args.length > 0) { +// inputPath = args[0]; +// portInner = args[1]; +// serverWait = args[2]; +// chunkName = args[3]; +// numOfWorkers = args[4]; +// dbDir = args[5]; +// } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; +// portInner = "6399"; +// serverWait = "10000"; +// chunkName ="dumps.rdb"; +// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; +// numOfWorkers = "1"; +// } String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); - + log.info(parameters); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner)); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index ee301d2..65d7f04 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -12,6 +12,7 @@ import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; +import org.apache.commons.lang3.StringUtils; import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -96,7 +97,7 @@ public class MultiThreadTreeLoaderCluster3 { cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"10000"); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); mainCompare(inputPath,port,pairsCSVPath,importScript); // calculatePairs(inputPath, outputPath); @@ -176,8 +177,8 @@ public class MultiThreadTreeLoaderCluster3 { .collect(Collectors.toList()); for (File f:folders){ - - if(f.getName().startsWith("cluster7_0")) { + //36_0,119_0,4_0 +// if(f.getName().startsWith("cluster1_0")) { try (Jedis jedis = jedisPool.getResource()) { @@ -217,7 +218,7 @@ public class MultiThreadTreeLoaderCluster3 { - } +// } @@ -245,48 +246,9 @@ public class MultiThreadTreeLoaderCluster3 { } -// File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/clusterDumps/"+cluster + "/" + s + ".txt_" + actionSetPosition); -// -// -// ITree tree = null; -// try { -// FileInputStream fi = new FileInputStream(folder); -// ObjectInputStream oi = new ObjectInputStream(fi); -// tree = (ITree) oi.readObject(); -// oi.close(); -// fi.close(); -// -// -// } catch (FileNotFoundException e) { -// log.error("File not found"); -// e.printStackTrace(); -// } catch (IOException e) { -// log.error("Error initializing stream"); -// e.printStackTrace(); -// } catch (ClassNotFoundException e) { -// // TODO Auto-generated catch block -// e.printStackTrace(); -// } -// return tree; - ITree tree = null; Jedis inner = null; -// String[] split2 = firstValue.split("/"); -// String cluster = split2[1]; -// -// String[] split1 = folders.get(0).getName().split(".txt_"); -// String s = split1[0]; -// String[] splitPJ = split1[1].split("_"); -// String project = splitPJ[1]; -// String actionSetPosition = splitPJ[0]; -// File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); -// File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/clusterDumps/"+cluster + "/" + s + ".txt_" + actionSetPosition); -// File[] listOfFiles = folder.listFiles(); -// Stream stream = Arrays.stream(listOfFiles); -// List folders = stream -// .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) -// .collect(Collectors.toList()); @@ -296,15 +258,6 @@ public class MultiThreadTreeLoaderCluster3 { String si= inner.get(fn); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); -// ITree newTree = ((Update)actionSet.getAction()).getNewNode(); -// ITree oldTree = ((Update)actionSet.getAction()).getNode(); -// -// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); -// m.match(); -// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); -// ag.generate(); -// List actions = ag.getActions(); -// log.info(actions.toString()); ITree parent = null; ITree children =null; @@ -322,46 +275,10 @@ public class MultiThreadTreeLoaderCluster3 { inner.close(); } } -// Pair pair = new Pair<>(tree,project); + return tree; -// File[] listOfFiles = folder.listFiles(); -// Stream stream = Arrays.stream(listOfFiles); -// List folders = stream -// .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) -// .collect(Collectors.toList()); -// -// -// -//// String[] split1 = folders.get(0).getName().split(".txt_"); -//// String s = split1[0]; -//// String[] splitPJ = split1[1].split("_"); -//// String project = splitPJ[1]; -//// String actionSetPosition = splitPJ[0]; -// -// File prevFile = new File(gumTreeInput + project+ "/" + "prevFiles/prev_" + s + ".java");// previous file -// File revFile = new File(gumTreeInput + project+ "/" + "revFiles/" + s + ".java");//rev file -// -// List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); -// -// HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); -//// for (HierarchicalActionSet actionSet : actionSets) { -// -// ITree test = getActionTree(actionSet); -// test.getLabel(); -// for (ITree descendant : test.getDescendants()) { -//// descendant.setLabel(""); -// if(!(descendant.getType() == 100 || descendant.getType() == 101 || descendant.getType() == 102 || descendant.getType() == 103)){ -// descendant.setType(104); -// } -// } -// test.getDescendants(); -// test.setParent(null); -//// } -//// } -// -// Pair pair = new Pair<>(test,project); -// return pair; + } public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ @@ -436,22 +353,14 @@ public class MultiThreadTreeLoaderCluster3 { } private static List getNames(ITree oldTree, List oldTokens){ -// if((oldTree.getType() == 42 && oldTree.getLabel().startsWith("Name:")) || oldTree.getType() == 42 && oldTree.getParent().getType() == 59 || oldTree.getType() == 43 || (oldTree.getType() == 41 && oldTree.getLabel().startsWith("SimpleName:")) ){ -// -// oldTokens.add(oldTree.getLabel()); -// -// } -// for (ITree oldDescendant : oldTree.getDescendants()) { -// if ((oldDescendant.getType() == 42 && oldDescendant.getLabel().startsWith("Name:") ) || oldDescendant.getType() == 42 && oldDescendant.getParent().getType() == 59 ||oldDescendant.getType() == 43 || (oldDescendant.getType() == 41 && oldDescendant.getLabel().startsWith("SimpleName:"))){ -// -// oldTokens.add(oldDescendant.getLabel()); -// -// } -// } + List descendants = oldTree.getDescendants(); descendants.add(0,oldTree); boolean upd=false; + for (ITree oldDescendant : descendants) { + + boolean addToken = false; int type = oldDescendant.getType(); String sType = String.valueOf(type); @@ -460,18 +369,18 @@ public class MultiThreadTreeLoaderCluster3 { (sType.equals("32") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || (sType.equals("59") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || (sType.equals("43") && oldDescendant.getHeight() == 0 && oldDescendant.getChildren().size() == 0) || - (sType.equals("14") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || + (sType.equals("53") )|| //&& oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || (sType.equals("7") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || - (sType.equals("27") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) + (sType.equals("41") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) ){ - int depth = oldDescendant.getChildren().size(); +// int depth = oldDescendant.getChildren().size(); String label = oldDescendant.getLabel(); - if(sType.equals("32") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1){ - log.info(""); - } +// if(sType.equals("32") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1){ +// log.info(""); +// } label = label.split("@AT@")[0]; @@ -480,15 +389,50 @@ public class MultiThreadTreeLoaderCluster3 { List m = new ArrayList(); if(label.startsWith("UPD")){ upd = true; - String timeRegex = "@@(.*)@TO@(.*)"; - Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); - java.util.regex.Matcher matcher = pattern.matcher(split[1]); - + java.util.regex.Matcher matcher; + if(sType.equals("53")){ + String timeRegex = ".*@@(ClassInstanceCreation:new [a-zA-Z0-9]+).*@TO@\\s(ClassInstanceCreation:new [a-zA-Z0-9]+).*"; + Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); + matcher= pattern.matcher(split[1]); + }else { + String timeRegex = "@@(.*)@TO@(.*)"; + Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); + matcher = pattern.matcher(split[1]); + } if (matcher.matches()) { String hours = matcher.group(1); String to = matcher.group(2); - m.add(hours.trim()); - m.add(to.trim()); + if(sType.equals("31")){ + + String commonPrefix = StringUtils.getCommonPrefix(hours.trim(), to.trim()); + if(commonPrefix.isEmpty()){ + log.info("PREFIX EMPTY"); + }else { + String s = hours.trim().replace(commonPrefix, ""); + String s1 = to.trim().replace(commonPrefix, ""); + String[] split1 = s.split(","); + String[] split3 = s1.split(","); + Set set = new TreeSet<>(); + for (String s2 : split1) { + if(!s2.isEmpty()) { + set.add(s2.trim()); + } + } + for (String s2 : split3) { + if(!s2.isEmpty()) { + set.add(s2.trim()); + } + } + + List list = set.stream().collect(Collectors.toList()); + m.addAll(list); + addToken = true; + + } + }else{ + m.add(hours.trim()); + m.add(to.trim()); + } } }else if(label.startsWith("INS") && upd == false){ @@ -521,25 +465,67 @@ public class MultiThreadTreeLoaderCluster3 { } } } - + boolean alreadyAddParentMethodName = false; for (String s : m) { // if(s.isEmpty()){ // continue; // } //TODO remove 44 if(s.startsWith("SimpleName:") || s.startsWith("Name:")){ - oldTokens.add(s); - }else if (s.startsWith("MethodName:")){ String methodName = s.split(":")[1]; oldTokens.add(methodName); - }else if( sType.equals("59") || sType.equals("43")|| sType.equals("14") || sType.equals("7") || sType.equals("27") || sType.equals("83") || sType.equals("44")){ - if(sType.equals("27") || sType.equals("83") || sType.equals("44")){ - oldTokens.add(s); - } - else { - String s1 = s.split("=")[0]; - oldTokens.add(s1); + }else if (s.startsWith("MethodName:")){ + String methodName = s.split(":")[1]; +// ITree parent = oldDescendant.getParent(); +// +// if(parent!= null && parent.getType() == 32 && !alreadyAddParentMethodName){ //parent is method invocation statement +// String parentLabel = parent.getLabel(); +// String[] pns = parentLabel.split("\\." + methodName); +// if(pns.length > 1) { +// String parentName = pns[0]; +// String[] parentNameSplit = parentName.split("@@"); +// if (parentNameSplit.length > 1) { +// String parentMethodName = parentNameSplit[1]; +// String s1 = parentMethodName.split("@TO@")[0]; +// oldTokens.add(s1.trim()); +// alreadyAddParentMethodName = true; +// } +// } +// +// } + oldTokens.add(methodName); + }else if( sType.equals("59") || sType.equals("43")|| sType.equals("53") || sType.equals("7") || sType.equals("27") || sType.equals("83") || sType.equals("44") ||sType.equals("78") || sType.equals("41") || addToken){ +// if(sType.equals("27") || sType.equals("83") || sType.equals("44")){ +// String parentLabel = oldDescendant.getParent().getLabel(); +// List parentM = new ArrayList(); +// if(parentLabel.startsWith("UPD")) { +// upd = true; +// String timeRegex = "@@(.*)@TO@(.*)"; +// Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); +// java.util.regex.Matcher matcher = pattern.matcher(split[1]); +// +// if (matcher.matches()) { +// String hours = matcher.group(1); +// String to = matcher.group(2); +// parentM.add(hours.trim()); +// parentM.add(to.trim()); +// +// } +// } +// +// +// oldTokens.add(s); +// }else + if(sType.equals("53") || sType.equals("78") || addToken){//sType.equals("41") || + + oldTokens.add(s); + + } +// else { +// String s1 = s.split("=")[0]; +// oldTokens.add(s1); +// } } // else // if(oldTokens.size() < 2){ @@ -550,9 +536,9 @@ public class MultiThreadTreeLoaderCluster3 { } } - if (oldTokens.size() == 0){ - log.info("dur bakalim nereye!???"); - } +// if (oldTokens.size() == 0 || oldTokens.size() > 3) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){ +// log.info("dur bakalim nereye!???"); +// } return oldTokens; } @@ -580,9 +566,9 @@ public class MultiThreadTreeLoaderCluster3 { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); - if(firstValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL") || secondValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL")){ - log.info(""); - } +// if(firstValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL") || secondValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL")){ +// log.info(""); +// } ///35/1/22b5f7_84bf27_ui#org.eclipse.pde.runtime#src#org#eclipse#pde#internal#runtime#registry#RegistryBrowserLabelProvider.txt_2_PDE @@ -635,6 +621,10 @@ public class MultiThreadTreeLoaderCluster3 { oldTokens = getNames(oldTree,oldTokens); newTokens = getNames(newTree,newTokens); + + if(oldTokens.size() == 0 || newTokens.size() == 0){ + log.error("Cluster {} has no tokens on pair {}",clusterName , name); + } // Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); // m.match(); CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); @@ -648,17 +638,21 @@ public class MultiThreadTreeLoaderCluster3 { } }else{ overallSimi = Double.valueOf(0); - if(oldSequences.length != 0) { - log.info("ERROR"); - } +// if(oldSequences.length != 0) { +// log.info("ERROR"); +// } } - if(overallSimi.equals(1.0)){ + int retval = Double.compare(overallSimi, Double.valueOf(0.8)); + if(retval >= 0){ // log.info("YES"); // log.info(name); // log.info(firstValue); // log.info(secondValue); // log.info("************"); + if(!overallSimi.equals(1.0)){ + log.info(""); + } String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); String result = firstValue + "," + secondValue + ","+String.join(",", oldTokens); jedis.select(1); @@ -670,35 +664,6 @@ public class MultiThreadTreeLoaderCluster3 { - -// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); -// ag.generate(); -// List actions = ag.getActions(); -// -// String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); -// double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); -// String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); -// double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); -// String diceSimilarity = String.format("%1.2f", diceSimilarity1); -// double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); -// String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); -// -// String editDistance = String.valueOf(actions.size()); -// jedis.select(1); -// String result = resultMap.get("0") + "," + oldProject +"," + resultMap.get("1") + "," +newProject+ "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; -//// jedis.set(resultKey, result); -// -// if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) -// || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { -// String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); -// jedis.select(1); -// jedis.set(matchKey, result); -// } -// jedis.select(0); - -// -//// log.info("Completed " + resultKey); - }catch (Exception e){ log.error(e.toString() + " {}",(name)); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java new file mode 100644 index 0000000..0266e2a --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java @@ -0,0 +1,363 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +import akka.actor.ActorRef; +import akka.actor.ActorSystem; +import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; +import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor; +import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; +import edu.lu.uni.serval.config.Configuration; +import edu.lu.uni.serval.utils.FileHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +public class TestHunkParserSingleFile { + + private static Logger log = LoggerFactory.getLogger(TestHunkParserSingleFile.class); + public static void main(String[] args) { + // input data + +// String rootPath = "/Users/anilkoyuncu/bugStudy"; + String inputPath; + String outputPath; + if(args.length > 0){ + inputPath = args[1]; + outputPath = args[0]; + }else{ +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; + inputPath = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4"; +// outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputSingle"; + } + + //5d9d60_76f5be_components#camel-jaxb#src#test#java#org#apache#camel#jaxb#FallbackTypeConverterShouldNotThrowExceptionTest.txt_1_CAMEL + + File folder = new File(inputPath); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List folders = stream + .filter(x -> !x.getName().startsWith(".")) + + .collect(Collectors.toList()); + +// List targetList = new ArrayList(); +// for (File f:folders){ +// for(File f1 :f.listFiles()){ +// if (!f1.getName().startsWith(".")){ +// targetList.add(f1); +// } +// } +// } + +// List pjList = Arrays.asList("DATAJPA","ZXing","PDE","SWS","SWT", "SWF", "COLLECTIONS", "JDT"); + List files = new ArrayList(); +// files.add("5d9d60_76f5be_components#camel-jaxb#src#test#java#org#apache#camel#jaxb#FallbackTypeConverterShouldNotThrowExceptionTest.java"); + files.add("49821e_3cc787_components#camel-infinispan#src#main#java#org#apache#camel#component#infinispan#InfinispanConstants.java"); + for(String f : files){ + String pjName = "CAMEL"; +// for (File target : folders) { +// String pjName = target.getName(); +// if (!pjList.contains(pjName)){ +// continue; +// } + +// final List msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" + MessageFile messageFile = getMessageFile(inputPath + "/" + pjName +"/", f); + + List msgFiles = new ArrayList<>(); + msgFiles.add(messageFile); + String GUM_TREE_OUTPUT = outputPath + "/"+ pjName + "/"; + final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; + final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; + final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; + final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; + final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; + + + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ActionSetDumps"); + FileHelper.deleteDirectory(editScriptsFilePath); + FileHelper.deleteDirectory(patchesSourceCodeFilePath); + FileHelper.deleteDirectory(buggyTokensFilePath); + FileHelper.deleteDirectory(editScriptSizesFilePath); + FileHelper.deleteDirectory(alarmTypesFilePath); + + StringBuilder astEditScripts = new StringBuilder(); + StringBuilder tokens = new StringBuilder(); + StringBuilder sizes = new StringBuilder(); + StringBuilder patches = new StringBuilder(); + StringBuilder alarmTypes = new StringBuilder(); + +// int a = 0; + + ActorSystem system = null; + ActorRef parsingActor = null; + final WorkMessage msg = new WorkMessage(0, msgFiles); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Mining-FixPattern-System"); + parsingActor = system.actorOf(ParseFixPatternActor.props(1, editScriptsFilePath, + patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } + +// int counter = 0; +// for (MessageFile msgFile : msgFiles) { +// FixedViolationHunkParser parser = new FixedViolationHunkParser(); +// +// final ExecutorService executor = Executors.newSingleThreadExecutor(); +// // schedule the work +// final Future future = executor.submit(new RunnableParser(msgFile.getPrevFile(), +// msgFile.getRevFile(), msgFile.getDiffEntryFile(), parser)); +// try { +// // where we wait for task to complete +// future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); +// String editScripts = parser.getAstEditScripts(); +// if (!editScripts.equals("")) { +// astEditScripts.append(editScripts); +// tokens.append(parser.getTokensOfSourceCode()); +// sizes.append(parser.getSizes()); +// patches.append(parser.getPatchesSourceCode()); +// alarmTypes.append(parser.getAlarmTypes()); +// +// a++; +// if (a % 100 == 0) { +// FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); +// FileHelper.outputToFile(buggyTokensFilePath, tokens, true); +// FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); +// FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); +// astEditScripts.setLength(0); +// tokens.setLength(0); +// sizes.setLength(0); +// patches.setLength(0); +// alarmTypes.setLength(0); +// System.out.println("Finish of parsing " + a + " files......"); +// } +// } +// } catch (TimeoutException e) { +// err.println("task timed out"); +// future.cancel(true /* mayInterruptIfRunning */); +// } catch (InterruptedException e) { +// err.println("task interrupted"); +// } catch (ExecutionException e) { +// err.println("task aborted"); +// } finally { +// executor.shutdownNow(); +// } +// } + + FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); + FileHelper.outputToFile(buggyTokensFilePath, tokens, true); + FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); + FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); + FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); + astEditScripts.setLength(0); + tokens.setLength(0); + sizes.setLength(0); + patches.setLength(0); + alarmTypes.setLength(0); + + +// classifyByAlarmTypes(); + } + } + + + private static List getMessageFiles(String gumTreeInput) { + String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile + File revFilesPath = new File(inputPath + "revFiles/"); + File[] revFiles = revFilesPath.listFiles(); // project folders + List msgFiles = new ArrayList<>(); + + // gumTreeInput = /Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/AMQP/ + // fileName = 01534a_df5570_spring-rabbit#src#test#java#org#springframework#amqp#rabbit#listener#LocallyTransactedTests.java + if (revFiles.length >= 0) { + for (File revFile : revFiles) { +// if (revFile.getName().endsWith(".java")) { + String fileName = revFile.getName(); + File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file + fileName = fileName.replace(".java", ".txt"); + File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file + File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); + msgFile.setPositionFile(positionFile); + msgFiles.add(msgFile); +// } + } + + return msgFiles; + } + else{ + return null; + } + } + + private static MessageFile getMessageFile(String gumTreeInput, String fileName) { +// String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile +// File revFilesPath = new File(inputPath + "revFiles/"); +// File[] revFiles = revFilesPath.listFiles(); // project folders +// List msgFiles = new ArrayList<>(); + + // gumTreeInput = /Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/AMQP/ + // fileName = 01534a_df5570_spring-rabbit#src#test#java#org#springframework#amqp#rabbit#listener#LocallyTransactedTests.java +// if (revFiles.length >= 0) { +// for (File revFile : revFiles) { +// if (revFile.getName().endsWith(".java")) { +// String fileName = revFile.getName(); + File revFile = new File(gumTreeInput + "revFiles/"+fileName); + File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file + fileName = fileName.replace(".java", ".txt"); + File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file +// File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); + return msgFile; +// msgFile.setPositionFile(positionFile); +// msgFiles.add(msgFile); +// } +// } +// +// return msgFiles; +// } +// else{ +// return null; +// } + } + + public static void classifyByAlarmTypes() { + + final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE; + List alarmTypes = readStringList(alarmTypesFilePath); + //edit scripts, sizes of edit scripts, buggy tokens, patches. + classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPT_SIZES_FILE); + classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPTS_FILE); + classifyByAlarmTypes(alarmTypes, Configuration.BUGGY_CODE_TOKENS_FILE); + classifyByAlarmTypes2(alarmTypes, Configuration.PATCH_SOURCECODE_FILE); + } + + private static void classifyByAlarmTypes(List alarmTypes, String file) { + Map buildersMap = new HashMap<>(); + FileInputStream fis = null; + Scanner scanner = null; + try { + fis = new FileInputStream(file); + scanner = new Scanner(fis); + int counter = 0; + while (scanner.hasNextLine()) { + String alarmType = alarmTypes.get(counter); + StringBuilder builder = getBuilder(buildersMap, alarmType); + builder.append(scanner.nextLine() + "\n"); + counter ++; + if (counter % 1000 == 0) { + outputBuilders(buildersMap, file); + } + } + } catch (FileNotFoundException e) { + e.printStackTrace(); + } finally { + try { + scanner.close(); + fis.close(); + } catch (IOException e) { + e.printStackTrace(); + } + } + outputBuilders(buildersMap, file); + } + + private static void classifyByAlarmTypes2(List alarmTypes, String patchSourcecodeFile) { + Map buildersMap = new HashMap<>(); + FileInputStream fis = null; + Scanner scanner = null; + try { + fis = new FileInputStream(patchSourcecodeFile); + scanner = new Scanner(fis); + int counter = 0; + String singlePatch = ""; + while (scanner.hasNextLine()) { + String line = scanner.nextLine(); + if (Configuration.PATCH_SIGNAL.equals(line)) { + if (!"".equals(singlePatch)) { + String alarmType = alarmTypes.get(counter); + StringBuilder builder = getBuilder(buildersMap, alarmType); + builder.append(scanner.nextLine() + "\n"); + counter ++; + if (counter % 2000 == 0) { + outputBuilders(buildersMap, patchSourcecodeFile); + } + } + singlePatch = line + "\n"; + } + singlePatch += line + "\n"; + } + } catch (FileNotFoundException e) { + e.printStackTrace(); + } finally { + try { + scanner.close(); + fis.close(); + } catch (IOException e) { + e.printStackTrace(); + } + } + + outputBuilders(buildersMap, patchSourcecodeFile); + } + + private static void outputBuilders(Map map, String fileNameStr) { + File file = new File(fileNameStr); + String fileName = file.getName(); + String parentPath = file.getParent(); + for (Map.Entry entry : map.entrySet()) { + String alarmType = entry.getKey(); + StringBuilder builder = entry.getValue(); + + FileHelper.outputToFile(parentPath + "/" + alarmType + "/" + fileName, builder, true); + + builder.setLength(0); + entry.setValue(builder); + } + } + + public static List readStringList(String inputFile) { + List list = new ArrayList<>(); + FileInputStream fis = null; + Scanner scanner = null; + try { + fis = new FileInputStream(inputFile); + scanner = new Scanner(fis); + while(scanner.hasNextLine()) { + list.add(scanner.nextLine()); + } + } catch (FileNotFoundException e) { + e.printStackTrace(); + } finally { + try { + scanner.close(); + fis.close(); + } catch (IOException e) { + e.printStackTrace(); + } + } + return list; + } + + private static StringBuilder getBuilder(Map buildersMap, String alarmType) { + if (buildersMap.containsKey(alarmType)) { + return buildersMap.get(alarmType); + } else { + StringBuilder builder = new StringBuilder(); + buildersMap.put(alarmType, builder); + return builder; + } + } +} diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java new file mode 100644 index 0000000..f5bf52e --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -0,0 +1,60 @@ +package edu.lu.uni.serval; + +import edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader; +import edu.lu.uni.serval.FixPatternParser.cluster.CalculatePairs; +import edu.lu.uni.serval.FixPatternParser.cluster.ImportPairs2DB; +import edu.lu.uni.serval.FixPatternParser.cluster.StoreFile; + +/** + * Created by anilkoyuncu on 14/04/2018. + */ +public class Launcher { + + public static void main(String[] args) { + + String inputPath; + String portInner; + String serverWait; + String dbDir; + String chunkName; + String numOfWorkers; + String jobType; + String port; + String outputPath; + if (args.length > 0) { + jobType = args[0]; + inputPath = args[1]; + portInner = args[2]; + serverWait = args[3]; + chunkName = args[4]; + numOfWorkers = args[5]; + dbDir = args[6]; + port = args[6]; + outputPath = args[7]; + } else { + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; + portInner = "6380"; + serverWait = "10000"; + chunkName = "dumps.rdb"; + dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + numOfWorkers = "1"; + jobType = "AKKA"; + port = "6399"; + outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; + } + String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir); + + + switch (jobType){ + case "STORE": + StoreFile.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers); + case "CALCPAIRS": + CalculatePairs.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers,port,outputPath); + case "IMPORTPAIRS": + ImportPairs2DB.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers); + case "AKKA": + AkkaTreeLoader.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers,port); + } + } + +} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java index 6ccb32e..c00f09e 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java @@ -203,10 +203,12 @@ public class HierarchicalRegrouper { if (type != 83 && type != 77 && type != 78 && type != 79 && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 && type != 76 && type != 84 && type != 87 && type != 88 && type != 42) { - // ArrayType, PrimitiveType, SimpleType, ParameterizedType, + // ArrayType, PrimitiveType, SimpleType, ParameterizedType, // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName return null; } + + // } else if (parent.getType() == 31) { // method declaration // int type = action.getNode().getType(); // if (Checker.isStatement(type)) {// statements From ba977655fe1160d37d0f2685914b3cdd418bb495 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 14 Apr 2018 19:33:13 +0200 Subject: [PATCH 098/127] launcher --- .../cluster/AkkaTreeLoader.java | 24 +++++++++---------- src/main/java/edu/lu/uni/serval/Launcher.java | 6 ++--- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index b27459f..8e98ed9 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -93,7 +93,7 @@ public class AkkaTreeLoader { } // public static void main(String[] args) { - public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers,String port){ + public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port){ // String inputPath; //// String outputPath; @@ -134,7 +134,7 @@ public class AkkaTreeLoader { // numOfWorkers = "1"; // // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",portInner,serverWait,chunkName,dbDir); log.info(parameters); // if (option.equals("CALC")) { @@ -142,34 +142,34 @@ public class AkkaTreeLoader { // log.info("Calculate pairs done"); // }else { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); - loadRedis(cmd,serverWait); + String cmd1 = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); + loadRedis(cmd1,serverWait); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); - loadRedis(cmd,serverWait); + String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); + loadRedis(cmd2,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); - comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); + comparePairs(innerPool,outerPool); String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(portInner)); - loadRedis(stopServer,serverWait); + String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); + loadRedis(stopServer1,serverWait); stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(port)); - loadRedis(stopServer,serverWait); + String stopServer2 = String.format(stopServer,Integer.valueOf(port)); + loadRedis(stopServer2,serverWait); // } } - public static void comparePairs(String inputPath, JedisPool innerPool,JedisPool outerPool,String serverWait,String chunkName, String dbDir,String numOfWorkers){ + public static void comparePairs(JedisPool innerPool,JedisPool outerPool){ ScanResult scan; diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index f5bf52e..830b055 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -29,8 +29,8 @@ public class Launcher { chunkName = args[4]; numOfWorkers = args[5]; dbDir = args[6]; - port = args[6]; - outputPath = args[7]; + port = args[7]; + outputPath = args[8]; } else { inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; portInner = "6380"; @@ -53,7 +53,7 @@ public class Launcher { case "IMPORTPAIRS": ImportPairs2DB.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers); case "AKKA": - AkkaTreeLoader.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers,port); + AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port); } } From 90d6f986207b38e94b5a0a4b1d6eaa307dab7f59 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sun, 15 Apr 2018 13:36:01 +0200 Subject: [PATCH 099/127] level1db --- .../cluster/TreeLoaderClusterL1.java | 48 ++++++++++--------- src/main/java/edu/lu/uni/serval/Launcher.java | 11 +++-- 2 files changed, 32 insertions(+), 27 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java index dd82e21..2890e72 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -37,30 +37,34 @@ public class TreeLoaderClusterL1 { private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); - public static void main(String[] args){ +// public static void main(String[] args){ + public static void main(String portInner,String serverWait,String port,String inputPath){ - String inputPath; - String outputPath; - String port; - String portInner; - String serverWait; - if (args.length > 0) { - inputPath = args[0]; - outputPath = args[1]; - port = args[2]; - serverWait = args[3]; - portInner = args[4]; +// String inputPath; +// String outputPath; +// String port; +// String portInner; +// String serverWait; +// if (args.length > 0) { +// inputPath = args[0]; +// outputPath = args[1]; +// port = args[2]; +// serverWait = args[3]; +// portInner = args[4]; +// +// } else { +//// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/redis"; +// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; +// port = "6379"; +// portInner = "6380"; +// serverWait = "10000"; +// +// +// } - } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6379"; - portInner = "6380"; - serverWait = "10000"; - - - } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nport %s",inputPath,portInner,serverWait,port); + log.info(parameters); String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, inputPath,"level1.rdb",Integer.valueOf(port)); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 830b055..e00fcb5 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -1,9 +1,6 @@ package edu.lu.uni.serval; -import edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader; -import edu.lu.uni.serval.FixPatternParser.cluster.CalculatePairs; -import edu.lu.uni.serval.FixPatternParser.cluster.ImportPairs2DB; -import edu.lu.uni.serval.FixPatternParser.cluster.StoreFile; +import edu.lu.uni.serval.FixPatternParser.cluster.*; /** * Created by anilkoyuncu on 14/04/2018. @@ -38,7 +35,7 @@ public class Launcher { chunkName = "dumps.rdb"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "1"; - jobType = "AKKA"; + jobType = "LEVEL1DB"; port = "6399"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; } @@ -54,6 +51,10 @@ public class Launcher { ImportPairs2DB.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers); case "AKKA": AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port); + case "LEVEL1DB": + TreeLoaderClusterL1.main(portInner,serverWait,port,inputPath); + + } } From bbddbdfe59cd0811c52a61660fc119c24e85ec0f Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Mon, 16 Apr 2018 18:25:57 +0200 Subject: [PATCH 100/127] defects4j worked --- .../cluster/AkkaTreeLoader.java | 6 +- .../cluster/CalculatePairs.java | 10 +-- .../FixPatternParser/cluster/Compare.java | 11 ++-- .../cluster/ImportPairs2DB.java | 8 +-- .../FixPatternParser/cluster/StoreFile.java | 9 ++- .../cluster/TreeLoaderClusterL1.java | 10 +-- .../patch/CommitPatchParser.java | 2 +- .../violations/FixedViolationHunkParser.java | 7 +- .../MultiThreadTreeLoaderCluster.java | 51 ++++++++------- .../MultiThreadTreeLoaderCluster3.java | 58 ++++++++++++----- .../violations/TestHunkParser.java | 65 ++++++++----------- src/main/java/edu/lu/uni/serval/Launcher.java | 63 ++++++++++++++---- .../ParseFixPatternWorker.java | 2 + 13 files changed, 186 insertions(+), 116 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 8e98ed9..273c166 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -93,7 +93,7 @@ public class AkkaTreeLoader { } // public static void main(String[] args) { - public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port){ + public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port, String dumpsName){ // String inputPath; //// String outputPath; @@ -134,7 +134,7 @@ public class AkkaTreeLoader { // numOfWorkers = "1"; // // } - String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",portInner,serverWait,chunkName,dbDir); + String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,serverWait,chunkName,dbDir,dumpsName); log.info(parameters); // if (option.equals("CALC")) { @@ -142,7 +142,7 @@ public class AkkaTreeLoader { // log.info("Calculate pairs done"); // }else { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String cmd1 = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); + String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port)); loadRedis(cmd1,serverWait); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index ccc4e95..96b766c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -30,7 +30,7 @@ import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poo public class CalculatePairs { private static Logger log = LoggerFactory.getLogger(CalculatePairs.class); // public static void main(String[] args) { - public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers,String port,String outputPath){ + public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName){ // String inputPath; // String port; @@ -62,12 +62,12 @@ public class CalculatePairs { // // // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir); + String parameters = String.format("\nport %s \nserverWait %s \nchunkName %s \ndbDir %s",port,serverWait,chunkName,dbDir); log.info(parameters); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port)); + cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port)); loadRedis(cmd,serverWait); FileHelper.createDirectory(outputPath); @@ -99,7 +99,7 @@ public class CalculatePairs { String line = null; try { - FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +"textfile.txt", "rw").getChannel(); + FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +".txt", "rw").getChannel(); ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); int fileCounter = 0; @@ -116,7 +116,7 @@ public class CalculatePairs { }else{ log.info("Next pair dump"); fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java index 76350e0..1b3d5cb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java @@ -27,6 +27,8 @@ public class Compare { Map resultMap; Jedis jedis = null; + ITree oldTree = null; + ITree newTree = null; try { jedis = innerPool.getResource(); @@ -40,9 +42,9 @@ public class Compare { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); - ITree oldTree = getSimpliedTree(firstValue,outerPool); + oldTree = getSimpliedTree(firstValue,outerPool); - ITree newTree = getSimpliedTree(secondValue,outerPool); + newTree = getSimpliedTree(secondValue,outerPool); Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); m.match(); @@ -67,7 +69,7 @@ public class Compare { if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - log.info(matchKey); +// log.info(matchKey); jedis.select(1); jedis.set(matchKey, result); @@ -81,7 +83,8 @@ public class Compare { } catch (Exception e) { - log.error(e.toString() + " {}", (name)); + + log.error(e.toString() + " {}", name); }finally { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index a0fa800..1287814 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -21,7 +21,7 @@ public class ImportPairs2DB { private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); // public static void main(String[] args) { - public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers){ + public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String numOfWorkers){ // String inputPath; // String portInner; @@ -44,11 +44,11 @@ public class ImportPairs2DB { // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; // numOfWorkers = "1"; // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nnumOfWorks %s \ndbDir %s",csvInputPath,portInner,serverWait,numOfWorkers,dbDir); log.info(parameters); - File folder = new File(inputPath); + File folder = new File(csvInputPath); File[] subFolders = folder.listFiles(); Stream stream = Arrays.stream(subFolders); List pjs = stream @@ -63,7 +63,7 @@ public class ImportPairs2DB { log.info(cmd); loadRedisWait(cmd); - cmd = "bash "+dbDir + "redisImportSingle.sh" +" %s %s"; + cmd = "bash "+dbDir + "/redisImportSingle.sh" +" %s %s"; cmd = String.format(cmd, pj.getPath(), portInt); log.info(cmd); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java index c680d96..560975b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java @@ -26,7 +26,7 @@ public class StoreFile { private static Logger log = LoggerFactory.getLogger(StoreFile.class); // public static void main(String[] args) { - public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers){ + public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName){ // String inputPath; // String portInner; // String serverWait; @@ -48,7 +48,7 @@ public class StoreFile { // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; // numOfWorkers = "1"; // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir); + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir); log.info(parameters); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; @@ -84,6 +84,11 @@ public class StoreFile { .forEach(m -> storeCore(portInner, m.split(",")[1],m.split(",")[0])); log.info(parameters); + + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + String stopServer2 = String.format(stopServer,Integer.valueOf(portInner)); + loadRedis(stopServer2,serverWait); + } public static void storeCore(String portInner,String path,String key){ diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java index 2890e72..88454a9 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -38,7 +38,7 @@ public class TreeLoaderClusterL1 { private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); // public static void main(String[] args){ - public static void main(String portInner,String serverWait,String port,String inputPath){ + public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path){ // String inputPath; // String outputPath; @@ -67,13 +67,13 @@ public class TreeLoaderClusterL1 { log.info(parameters); String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, inputPath,"level1.rdb",Integer.valueOf(port)); + cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port)); loadRedis(cmd,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - String level1Path = inputPath + "/level1"; +// String level1Path = inputPath + "/level1"; File chunks = new File(level1Path); File[] listFiles = chunks.listFiles(); Stream stream = Arrays.stream(listFiles); @@ -81,8 +81,8 @@ public class TreeLoaderClusterL1 { .filter(x -> x.getName().endsWith(".rdb")) .collect(Collectors.toList()); for (File db : dbs) { - String cmdInner = "bash "+level1Path + "/" + "startServer.sh" +" %s %s %s"; - cmdInner = String.format(cmdInner, level1Path,db.getName(),Integer.valueOf(portInner)); + String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; + cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner)); loadRedis(cmdInner,serverWait); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java index c5db6b0..4c266e7 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java @@ -20,7 +20,7 @@ public class CommitPatchParser extends Parser{ @Override public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { } - + protected DiffEntryHunk matchHunk(int startLine, int endLine, int startLine2, int endLine2, String actionStr, List hunks) { for (DiffEntryHunk hunk : hunks) { int bugStartLine = hunk.getBugLineStartNum(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index eaa7a53..75057ed 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -49,10 +49,11 @@ public class FixedViolationHunkParser extends FixedViolationParser { FileOutputStream f = null; + try { - String pj = diffentryFile.getParent().split("GumTreeInputBug13April")[1]; - String root = diffentryFile.getParent().split("GumTreeInputBug13April")[0]; - String hunkTreeFileName = root+"GumTreeOutput13April/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + String pj = diffentryFile.getParent().split("Defects4J")[1]; + String root = diffentryFile.getParent().split("Defects4J")[0]; + String hunkTreeFileName = root+"GumTreeOutputDefects4J/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); f = new FileOutputStream(new File(hunkTreeFileName)); ObjectOutputStream o = new ObjectOutputStream(f); o.writeObject(actionSet); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index c4e73ba..bc0bd5d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -88,7 +88,7 @@ public class MultiThreadTreeLoaderCluster { cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"10000"); - calculatePairsOfClusters(inputPath, outputPath); +// calculatePairsOfClusters(inputPath, outputPath); // mainCompare(inputPath,port,pairsCSVPath,importScript); // calculatePairs(inputPath, outputPath); // processMessages(inputPath,outputPath); @@ -119,15 +119,25 @@ public class MultiThreadTreeLoaderCluster { log.info("Load done"); } - public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { + public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner) { - String cmd; - cmd = "bash " + importScript +" %s %s"; + String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf("6399"),20000000); + + String cmd3; + cmd3 = "bash " + importScript +" %s %s"; + + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); File folder = new File(pairsCSVPath); @@ -139,7 +149,7 @@ public class MultiThreadTreeLoaderCluster { for (File f:folders){ - if(f.getName().startsWith("cluster0")) { +// if(f.getName().startsWith("cluster0")) { try (Jedis jedis = jedisPool.getResource()) { @@ -153,7 +163,7 @@ public class MultiThreadTreeLoaderCluster { int size = scan.getResult().size(); if (size == 0) { - String comd = String.format(cmd,f.getPath(),port); + String comd = String.format(cmd3,f.getPath(),portInner); loadRedis(comd); scan = jedis.scan("0", sc); @@ -169,13 +179,13 @@ public class MultiThreadTreeLoaderCluster { //76 scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName,outerPool)); + .forEach(m -> coreCompare(m, jedisPool, clusterName,outerPool)); jedis.save(); } - } +// } } @@ -224,23 +234,18 @@ public class MultiThreadTreeLoaderCluster { Jedis inner = null; String[] split2 = firstValue.split("/"); String cluster = split2[1]; - - File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List folders = stream - .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) - .collect(Collectors.toList()); - - String[] split1 = folders.get(0).getName().split(".txt_"); - String s = split1[0]; - String[] splitPJ = split1[1].split("_"); + String fullFileName = split2[2]; + String[] split = fullFileName.split(".txt_"); + String pureFileName = split[0]; + String[] splitPJ = split[1].split("_"); String project = splitPJ[1]; String actionSetPosition = splitPJ[0]; + + try { inner = outerPool.getResource(); - String filename = project + "/ActionSetDumps/" + split2[2]; + String filename = project + "/ActionSetDumps/" + pureFileName + ".txt_" + actionSetPosition; String si= inner.get(filename); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); @@ -400,7 +405,7 @@ public class MultiThreadTreeLoaderCluster { - private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName,JedisPool outerPool) { + private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool) { try (Jedis jedis = jedisPool.getResource()) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 65d7f04..b8d499a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -99,7 +99,7 @@ public class MultiThreadTreeLoaderCluster3 { cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); - mainCompare(inputPath,port,pairsCSVPath,importScript); +// mainCompare(inputPath,port,pairsCSVPath,importScript); // calculatePairs(inputPath, outputPath); // processMessages(inputPath,outputPath); // evaluateResults(inputPath,outputPath); @@ -160,13 +160,27 @@ public class MultiThreadTreeLoaderCluster3 { log.info("Load done"); } - public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { +// public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { + public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner) { - String cmd; - cmd = "bash " + importScript +" %s %s"; + String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); + + + String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); + edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); + + + String cmd3; + cmd3 = "bash " + importScript +" %s %s"; + + + JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf("6399"),20000000); File folder = new File(pairsCSVPath); @@ -192,7 +206,7 @@ public class MultiThreadTreeLoaderCluster3 { int size = scan.getResult().size(); if (size == 0) { - String comd = String.format(cmd, f.getPath(), port); + String comd = String.format(cmd3, f.getPath(), portInner); edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster. loadRedis(comd); @@ -207,7 +221,7 @@ public class MultiThreadTreeLoaderCluster3 { scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName, outerPool)); + .forEach(m -> coreCompare(m, jedisPool, clusterName, outerPool)); jedis.save(); @@ -241,9 +255,9 @@ public class MultiThreadTreeLoaderCluster3 { String actionSetPosition = splitPJ[0]; Integer asp = Integer.valueOf(actionSetPosition); - if (asp > 1){ - return null; - } +// if (asp > 1){ +// return null; +// } ITree tree = null; @@ -464,6 +478,20 @@ public class MultiThreadTreeLoaderCluster3 { oldTokens.add(hours.trim()); } } + }else if(label.startsWith("MOV") && upd == false){ + String timeRegex = "@@(.*)@TO@(.*)"; + Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL); + java.util.regex.Matcher matcher = pattern.matcher(split[1]); + + if (matcher.matches()) { + String hours = matcher.group(1); + if (hours.startsWith("MethodName:")){ + String methodName = hours.split(":")[1]; + oldTokens.add(methodName); + }else { + oldTokens.add(hours.trim()); + } + } } boolean alreadyAddParentMethodName = false; for (String s : m) { @@ -536,13 +564,13 @@ public class MultiThreadTreeLoaderCluster3 { } } -// if (oldTokens.size() == 0 || oldTokens.size() > 3) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){ -// log.info("dur bakalim nereye!???"); -// } + if (oldTokens.size() == 0 ) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){ + log.info("dur bakalim nereye!???"); + } return oldTokens; } - private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName,JedisPool outerPool) { + private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool) { try (Jedis jedis = jedisPool.getResource()) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 61f3125..9b9ba0d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -1,54 +1,45 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import static java.lang.System.err; +import akka.actor.ActorRef; +import akka.actor.ActorSystem; +import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; +import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor; +import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; +import edu.lu.uni.serval.config.Configuration; +import edu.lu.uni.serval.utils.FileHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.IOException; import java.util.*; -import java.util.concurrent.ExecutionException; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.Future; -import java.util.concurrent.TimeUnit; -import java.util.concurrent.TimeoutException; import java.util.stream.Collectors; import java.util.stream.Stream; -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import edu.lu.uni.serval.FixPatternParser.RunnableParser; -import edu.lu.uni.serval.MultipleThreadsParser.AkkaParser; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor; -import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import org.eclipse.jgit.revwalk.RevCommit; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - public class TestHunkParser { private static Logger log = LoggerFactory.getLogger(TestHunkParser.class); - public static void main(String[] args) { +// public static void main(String[] args) { + public static void main(String inputPath, String outputPath,String numOfWorkers) { // input data -// String rootPath = "/Users/anilkoyuncu/bugStudy"; - String inputPath; - String outputPath; - if(args.length > 0){ - inputPath = args[1]; - outputPath = args[0]; - }else{ -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug13April"; -// outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput13April"; - } - +//// String rootPath = "/Users/anilkoyuncu/bugStudy"; +// String inputPath; +// String outputPath; +// if(args.length > 0){ +// inputPath = args[1]; +// outputPath = args[0]; +// }else{ +//// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug13April"; +//// outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; +// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput13April"; +// } + String parameters = String.format("\nInput path %s \nOutput path %s",inputPath,outputPath); + log.info(parameters); File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); @@ -74,7 +65,7 @@ public class TestHunkParser { // continue; // } - final List msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" + final List msgFiles = getMessageFiles(target.toString() + "/", outputPath); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" System.out.println(msgFiles.size()); if(msgFiles.size() == 0) continue; @@ -108,7 +99,7 @@ public class TestHunkParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(100, editScriptsFilePath, + parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), editScriptsFilePath, patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { @@ -178,7 +169,7 @@ public class TestHunkParser { } - private static List getMessageFiles(String gumTreeInput) { + private static List getMessageFiles(String gumTreeInput,String outputPath) { String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile File revFilesPath = new File(inputPath + "revFiles/"); File[] revFiles = revFilesPath.listFiles(); // project folders diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index e00fcb5..ec2dcf1 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -1,6 +1,9 @@ package edu.lu.uni.serval; import edu.lu.uni.serval.FixPatternParser.cluster.*; +import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster; +import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster3; +import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; /** * Created by anilkoyuncu on 14/04/2018. @@ -9,7 +12,7 @@ public class Launcher { public static void main(String[] args) { - String inputPath; +// String inputPath; String portInner; String serverWait; String dbDir; @@ -17,42 +20,74 @@ public class Launcher { String numOfWorkers; String jobType; String port; - String outputPath; + String pairsPath; + String csvInputPath; + String dumpsName; + String gumInput; + String gumOutput; if (args.length > 0) { jobType = args[0]; - inputPath = args[1]; + gumInput = args[1]; portInner = args[2]; serverWait = args[3]; chunkName = args[4]; numOfWorkers = args[5]; dbDir = args[6]; port = args[7]; - outputPath = args[8]; + pairsPath = args[8]; + csvInputPath = args[9]; + dumpsName = args[10]; + gumOutput =args[12]; } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; + gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; portInner = "6380"; serverWait = "10000"; - chunkName = "dumps.rdb"; + chunkName = "textfile.txt.csv.rdb"; dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "1"; - jobType = "LEVEL1DB"; + jobType = "L3PAIRDB"; port = "6399"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; + pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; + gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J"; + csvInputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J-CSV"; + dumpsName = "dumpsDefect4J.rdb"; } - String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir); +// String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir); switch (jobType){ + case "DUMPTREE": + TestHunkParser.main(gumInput,gumOutput,numOfWorkers); + break; case "STORE": - StoreFile.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers); + StoreFile.main(gumOutput,portInner,serverWait,dbDir,dumpsName); + break; case "CALCPAIRS": - CalculatePairs.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers,port,outputPath); + CalculatePairs.main(serverWait,dbDir,dumpsName,port,pairsPath,"DEFECT4J"); + break; case "IMPORTPAIRS": - ImportPairs2DB.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers); + ImportPairs2DB.main(csvInputPath,portInner,serverWait,dbDir,numOfWorkers); + break; case "AKKA": - AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port); + AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port,dumpsName); + break; case "LEVEL1DB": - TreeLoaderClusterL1.main(portInner,serverWait,port,inputPath); + TreeLoaderClusterL1.main(portInner,serverWait,port,dbDir,"level1-defect4j.rdb",dbDir+"/level1-defect4j/"); + break; + //CALC python abstractPatch.py to from cluster folder + case "L2CALCPAIRS": + MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/"); + break; + case "L2PAIRDB": + MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301"); + break; + case "L3CALCPAIRS": + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l","/Users/anilkoyuncu/bugStudy/dataset/"); + break; + case "L3PAIRDB": + MultiThreadTreeLoaderCluster3.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-2l-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl2-d4j.rdb",dumpsName,"6301"); + break; } diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index bc581c4..14a6844 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -85,6 +85,8 @@ public class ParseFixPatternWorker extends UntypedActor { File revFile = msgFile.getRevFile(); File prevFile = msgFile.getPrevFile(); File diffentryFile = msgFile.getDiffEntryFile(); + + // File positionFile = msgFile.getPositionFile(); /*if (revFile.getName().toLowerCase().contains("test")) { continue; From ec0b90a6b0082ce31a134b92d075d7c6cde7bfd8 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 18 Apr 2018 10:18:32 +0200 Subject: [PATCH 101/127] new without thread block --- FixPatternMiner.iml | 4 +- pom.xml | 7 +- .../cluster/AkkaTreeLoader.java | 32 ++-- .../cluster/CalculatePairs.java | 65 +++++--- .../cluster/ImportPairs2DB.java | 18 ++- .../FixPatternParser/cluster/StoreFile.java | 34 +++-- .../cluster/TreeLoaderClusterL1.java | 15 +- .../violations/CallShell.java | 41 +++++ .../violations/FixedViolationHunkParser.java | 70 ++++++--- .../MultiThreadTreeLoaderCluster.java | 6 +- .../MultiThreadTreeLoaderCluster3.java | 4 +- .../violations/TestHunkParser.java | 5 +- src/main/java/edu/lu/uni/serval/Launcher.java | 144 +++++++++++------- 13 files changed, 294 insertions(+), 151 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index 76bff5b..98bff37 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -52,8 +52,8 @@ - - + + diff --git a/pom.xml b/pom.xml index 393feb7..b62a4ff 100644 --- a/pom.xml +++ b/pom.xml @@ -79,9 +79,14 @@ amqp-client 4.0.0 + + junit + junit + 4.11 + - + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 273c166..3158884 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -4,6 +4,7 @@ import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.Tree; import com.github.gumtreediff.tree.TreeContext; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -15,6 +16,7 @@ import java.util.*; import java.util.concurrent.Executors; import java.util.function.Consumer; import java.util.stream.Collectors; +import org.junit.Assert; /** * Created by anilkoyuncu on 19/03/2018. @@ -53,9 +55,9 @@ public class AkkaTreeLoader { StreamGobbler streamGobbler = new StreamGobbler(process.getInputStream(), System.out::println); Executors.newSingleThreadExecutor().submit(streamGobbler); -// int exitCode = process.waitFor(); -// assert exitCode == 0; - Thread.sleep(Integer.valueOf(serverWait)); + int exitCode = process.waitFor(); + assert exitCode == 0; +// Thread.sleep(Integer.valueOf(serverWait)); } catch (IOException e) { e.printStackTrace(); @@ -66,6 +68,8 @@ public class AkkaTreeLoader { log.info("Load done"); } + private static Consumer consumer = Assert::assertNotNull; + public static void loadRedisWait(String cmd){ Process process; @@ -77,7 +81,7 @@ public class AkkaTreeLoader { StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); + new StreamGobbler(process.getInputStream(), consumer); Executors.newSingleThreadExecutor().submit(streamGobbler); int exitCode = process.waitFor(); assert exitCode == 0; @@ -93,7 +97,7 @@ public class AkkaTreeLoader { } // public static void main(String[] args) { - public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port, String dumpsName){ + public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port, String dumpsName) throws Exception { // String inputPath; //// String outputPath; @@ -141,14 +145,15 @@ public class AkkaTreeLoader { // calculatePairs(inputPath, port); // log.info("Calculate pairs done"); // }else { + CallShell cs = new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port)); - loadRedis(cmd1,serverWait); - +// loadRedis(cmd1,serverWait); + cs.runShell(cmd1,serverWait); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); - loadRedis(cmd2,serverWait); - +// loadRedis(cmd2,serverWait); + cs.runShell(cmd2,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); @@ -158,12 +163,13 @@ public class AkkaTreeLoader { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); - loadRedis(stopServer1,serverWait); - +// loadRedis(stopServer1,serverWait); + cs.runShell(stopServer1,serverWait); stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,Integer.valueOf(port)); - loadRedis(stopServer2,serverWait); +// loadRedis(stopServer2,serverWait); // } + cs.runShell(stopServer2,serverWait); } @@ -181,7 +187,7 @@ public class AkkaTreeLoader { ScanParams sc = new ScanParams(); //150000000 sc.count(150000000); - sc.match("pair_*"); + sc.match("pair_[0-9]*"); scan = inner.scan("0", sc); int size = scan.getResult().size(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index 96b766c..dccc9a6 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -1,6 +1,7 @@ package edu.lu.uni.serval.FixPatternParser.cluster; import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.utils.FileHelper; import org.javatuples.Pair; import org.slf4j.Logger; @@ -10,10 +11,7 @@ import redis.clients.jedis.JedisPool; import redis.clients.jedis.ScanParams; import redis.clients.jedis.ScanResult; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.RandomAccessFile; +import java.io.*; import java.nio.ByteBuffer; import java.nio.channels.FileChannel; import java.nio.file.Files; @@ -30,7 +28,7 @@ import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poo public class CalculatePairs { private static Logger log = LoggerFactory.getLogger(CalculatePairs.class); // public static void main(String[] args) { - public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName){ + public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName) throws Exception { // String inputPath; // String port; @@ -65,11 +63,11 @@ public class CalculatePairs { String parameters = String.format("\nport %s \nserverWait %s \nchunkName %s \ndbDir %s",port,serverWait,chunkName,dbDir); log.info(parameters); - + CallShell cs =new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port)); - loadRedis(cmd,serverWait); - +// loadRedis(cmd,serverWait); + cs.runShell(cmd,serverWait); FileHelper.createDirectory(outputPath); @@ -98,10 +96,9 @@ public class CalculatePairs { byte [] buf = new byte[0]; String line = null; try { + FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".txt"); + DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); - FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +".txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - int fileCounter = 0; for (int i = 0; i < result.size(); i++) { @@ -110,22 +107,38 @@ public class CalculatePairs { line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - } - - - + outStream.write(line.getBytes()); } } - rwChannel.close(); + outStream.close(); +// FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +".txt", "rw").getChannel(); +// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); +// int fileCounter = 0; +// +// +// for (int i = 0; i < result.size(); i++) { +// for (int j = i + 1; j < result.size(); j++) { +// +// +// +// line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; +// buf = line.getBytes(); +// if(wrBuf.remaining() > 500) { +// wrBuf.put(buf); +// }else{ +// log.info("Next pair dump"); +// fileCounter++; +// rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); +// wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); +// } +// +// +// +// +// } +// } +// rwChannel.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { @@ -136,6 +149,10 @@ public class CalculatePairs { e.printStackTrace(); } + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + String stopServer2 = String.format(stopServer,Integer.valueOf(port)); +// loadRedis(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait); log.info("Done pairs"); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 1287814..d4a5e1d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -1,5 +1,6 @@ package edu.lu.uni.serval.FixPatternParser.cluster; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -10,8 +11,8 @@ import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedisWait; +//import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; +//import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedisWait; /** @@ -21,7 +22,7 @@ public class ImportPairs2DB { private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); // public static void main(String[] args) { - public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String numOfWorkers){ + public static void main(String csvInputPath,String portInner,String serverWait,String dbDir) throws Exception { // String inputPath; // String portInner; @@ -44,7 +45,7 @@ public class ImportPairs2DB { // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; // numOfWorkers = "1"; // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nnumOfWorks %s \ndbDir %s",csvInputPath,portInner,serverWait,numOfWorkers,dbDir); + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \ndbDir %s",csvInputPath,portInner,serverWait,dbDir); log.info(parameters); @@ -61,18 +62,21 @@ public class ImportPairs2DB { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); log.info(cmd); - loadRedisWait(cmd); + CallShell cs = new CallShell(); + cs.runShell(cmd); cmd = "bash "+dbDir + "/redisImportSingle.sh" +" %s %s"; cmd = String.format(cmd, pj.getPath(), portInt); log.info(cmd); - loadRedisWait(cmd); + cs.runShell(cmd); portInt++; - //TODO missing kill server script + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + String stopServer2 = String.format(stopServer,Integer.valueOf(portInner)); + cs.runShell(stopServer2); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java index 560975b..d32bc63 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java @@ -1,5 +1,6 @@ package edu.lu.uni.serval.FixPatternParser.cluster; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -17,6 +18,7 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; +import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poolConfig; /** * Created by anilkoyuncu on 03/04/2018. @@ -26,7 +28,7 @@ public class StoreFile { private static Logger log = LoggerFactory.getLogger(StoreFile.class); // public static void main(String[] args) { - public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName){ + public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String operation) throws Exception { // String inputPath; // String portInner; // String serverWait; @@ -48,12 +50,13 @@ public class StoreFile { // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; // numOfWorkers = "1"; // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir); + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \noperation %s",inputPath,portInner,serverWait,chunkName,dbDir,operation); log.info(parameters); - + CallShell cs = new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner)); - loadRedis(cmd,serverWait); +// loadRedis(cmd,serverWait); + cs.runShell(cmd,serverWait); File folder = new File(inputPath); File[] subFolders = folder.listFiles(); @@ -67,40 +70,43 @@ public class StoreFile { File[] files = pj.listFiles(); Stream fileStream = Arrays.stream(files); List fs = fileStream - .filter(x -> x.getName().startsWith("ActionSetDumps")) + .filter(x -> x.getName().startsWith(operation)) .collect(Collectors.toList()); File[] dumps = fs.get(0).listFiles(); for (File f : dumps) { String name = f.getName(); - String key = pjName + "/"+ "ActionSetDumps/" + name; + String key = pjName + "/"+ operation+"/" + name; String result = key +","+f.getPath(); workList.add(result); } } + log.info(String.valueOf(workList.size())); + + JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + workList.stream().parallel() - .forEach(m -> storeCore(portInner, m.split(",")[1],m.split(",")[0])); + .forEach(m -> storeCore(innerPool, m.split(",")[1],m.split(",")[0])); log.info(parameters); String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,Integer.valueOf(portInner)); - loadRedis(stopServer2,serverWait); - +// loadRedis(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait); } - public static void storeCore(String portInner,String path,String key){ + public static void storeCore(JedisPool innerPool,String path,String key){ try { - JedisPool pool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(portInner), 20000000); - ScanResult scan; + HierarchicalActionSet actionSet = null; - HierarchicalActionSet NewactionSet = null; + try { FileInputStream fi = new FileInputStream(new File(path)); ObjectInputStream oi = new ObjectInputStream(fi); @@ -120,8 +126,8 @@ public class StoreFile { e.printStackTrace(); } + try (Jedis inner = innerPool.getResource()) { - try (Jedis inner = pool.getResource()) { inner.set(key,toString(actionSet)); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java index 88454a9..431dc84 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -5,6 +5,7 @@ import com.github.gumtreediff.actions.model.*; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; @@ -38,7 +39,7 @@ public class TreeLoaderClusterL1 { private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); // public static void main(String[] args){ - public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path){ + public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path) throws Exception { // String inputPath; // String outputPath; @@ -68,8 +69,9 @@ public class TreeLoaderClusterL1 { String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port)); - loadRedis(cmd,serverWait); - +// loadRedis(cmd,serverWait); + CallShell cs = new CallShell(); + cs.runShell(cmd,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); @@ -83,7 +85,8 @@ public class TreeLoaderClusterL1 { for (File db : dbs) { String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner)); - loadRedis(cmdInner,serverWait); +// loadRedis(cmdInner,serverWait); + cs.runShell(cmdInner,serverWait); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); Jedis inner = null; @@ -136,8 +139,8 @@ public class TreeLoaderClusterL1 { String stopServer = "bash "+level1Path + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(portInner)); - loadRedis(stopServer,serverWait); - +// loadRedis(stopServer,serverWait); + cs.runShell(stopServer,serverWait); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java new file mode 100644 index 0000000..07e0398 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java @@ -0,0 +1,41 @@ +package edu.lu.uni.serval.FixPatternParser.violations; + +/** + * Created by anilkoyuncu on 17/04/2018. + */ +import java.io.*; +public class CallShell { + + + + + public void runShell(String command) throws Exception { + + Process process = Runtime.getRuntime().exec(command); + BufferedReader reader = new BufferedReader(new InputStreamReader( + process.getInputStream())); + String s; + while ((s = reader.readLine()) != null) { + System.out.println("Script output: " + s); + } + + } + + public void runShell(String command,String serverWait) throws Exception { + + Process process = Runtime.getRuntime().exec(command); + BufferedReader reader = new BufferedReader(new InputStreamReader( + process.getInputStream())); + String s; + while ((s = reader.readLine()) != null) { + System.out.println("Script output: " + s); + } + Thread.sleep(Integer.valueOf(serverWait)); + + } + + + + +} + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 75057ed..0f51308 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -6,6 +6,9 @@ import java.util.HashMap; import java.util.List; import java.util.Map; +import com.github.gumtreediff.actions.model.Delete; +import com.github.gumtreediff.actions.model.Insert; +import com.github.gumtreediff.actions.model.Move; import com.github.gumtreediff.actions.model.Update; import com.github.gumtreediff.tree.ITree; @@ -40,35 +43,56 @@ public class FixedViolationHunkParser extends FixedViolationParser { @Override public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); - -// boolean isUpdate = -// actionSets.stream().allMatch(p -> p.getAction() instanceof Update); - int hunkSet = 0; -// if(isUpdate){ - for (HierarchicalActionSet actionSet : actionSets) { + if (actionSets.size() != 0) { + boolean isUpdate = + actionSets.stream().allMatch(p -> p.getAction() instanceof Update); + boolean isInsert = + actionSets.stream().allMatch(p -> p.getAction() instanceof Insert); + boolean isDelete = + actionSets.stream().allMatch(p -> p.getAction() instanceof Delete); + boolean isMove = + actionSets.stream().allMatch(p -> p.getAction() instanceof Move); + int hunkSet = 0; + if (isUpdate || isInsert || isDelete || isMove) { + for (HierarchicalActionSet actionSet : actionSets) { + String folder = null; + if (isUpdate) { + folder = "/UPD/"; + } else if (isDelete) { + folder = "/DEL/"; + } else if (isInsert) { + folder = "/INS/"; + } else if (isMove) { + folder = "/MOV/"; + } - FileOutputStream f = null; + FileOutputStream f = null; - try { - String pj = diffentryFile.getParent().split("Defects4J")[1]; - String root = diffentryFile.getParent().split("Defects4J")[0]; - String hunkTreeFileName = root+"GumTreeOutputDefects4J/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); - f = new FileOutputStream(new File(hunkTreeFileName)); - ObjectOutputStream o = new ObjectOutputStream(f); - o.writeObject(actionSet); + try { +// String pj = diffentryFile.getParent().split("Defects4J")[1]; + String datasetName = diffentryFile.getParent().split("dataset/")[1].split("/")[0]; + String[] split1 = diffentryFile.getParent().split(datasetName); + String root = split1[0]; + String pj = split1[1].split("/")[1]; - o.close(); - f.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); + String hunkTreeFileName = root + "GumTreeOutput" + datasetName + "/" + pj + folder + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + f = new FileOutputStream(new File(hunkTreeFileName)); + ObjectOutputStream o = new ObjectOutputStream(f); + o.writeObject(actionSet); + + o.close(); + f.close(); + } catch (FileNotFoundException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + hunkSet++; } - hunkSet++; - } -// } + } + } } // public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index bc0bd5d..a7734f3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -126,9 +126,9 @@ public class MultiThreadTreeLoaderCluster { edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); +// String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; +// cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); +// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); String cmd3; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index b8d499a..17c1639 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -779,7 +779,7 @@ orginal calculate pairs, from all dumps of the projects .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "pairs-2l/"); + FileHelper.createDirectory(outputPath + "/pairs-2l/"); for (File pj : pjs) { File[] files = pj.listFiles(); @@ -835,7 +835,7 @@ orginal calculate pairs, from all dumps of the projects // ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, 1000*treesFileNames.size()*treesFileNames.size()); // int fileCounter = 0; - FileOutputStream fos = new FileOutputStream(outputPath + "pairs-2l/" +filename+".txt"); + FileOutputStream fos = new FileOutputStream(outputPath + "/pairs-2l/" +filename+".txt"); DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 9b9ba0d..d13f7b4 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -78,7 +78,10 @@ public class TestHunkParser { final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; - FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ActionSetDumps"); + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/UPD"); + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/INS"); + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/DEL"); + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/MOV"); FileHelper.deleteDirectory(editScriptsFilePath); FileHelper.deleteDirectory(patchesSourceCodeFilePath); FileHelper.deleteDirectory(buggyTokensFilePath); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index ec2dcf1..976afd7 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -25,72 +25,106 @@ public class Launcher { String dumpsName; String gumInput; String gumOutput; + String datasetPath; + String pjName; if (args.length > 0) { jobType = args[0]; - gumInput = args[1]; - portInner = args[2]; - serverWait = args[3]; - chunkName = args[4]; - numOfWorkers = args[5]; - dbDir = args[6]; - port = args[7]; - pairsPath = args[8]; - csvInputPath = args[9]; - dumpsName = args[10]; - gumOutput =args[12]; + portInner = args[1]; + serverWait = args[2]; + numOfWorkers = args[3]; + port = args[4]; + dumpsName = args[5]; + datasetPath = args[6]; + pjName = args[7]; +// gumInput = args[1]; +// chunkName = args[4]; +// dbDir = args[6]; +// pairsPath = args[8]; +// csvInputPath = args[9]; +// gumOutput =args[12]; } else { // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; - gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; +// gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; portInner = "6380"; - serverWait = "10000"; - chunkName = "textfile.txt.csv.rdb"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "1"; - jobType = "L3PAIRDB"; + serverWait = "50000"; + chunkName = "Bug13April.txt.csv.rdb"; +// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; + numOfWorkers = "10"; + jobType = "AKKA"; port = "6399"; - pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; - gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J"; - csvInputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J-CSV"; - dumpsName = "dumpsDefect4J.rdb"; +// pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; +// gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J"; +// csvInputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J-CSV"; + dumpsName = "dumps-Bug13April.rdb"; + datasetPath = "/Users/anilkoyuncu/bugStudy/dataset"; + pjName = "Bug13April"; } + gumInput = datasetPath +"/"+pjName+"/"; + gumOutput = datasetPath + "/GumTreeOutput" + pjName; + dbDir = datasetPath + "/redis"; + pairsPath = datasetPath + "/pairsImport"+pjName; + csvInputPath = datasetPath + "/pairsImport"+pjName+"-CSV"; // String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir); + try { + switch (jobType) { + case "DUMPTREE": + TestHunkParser.main(gumInput, gumOutput, numOfWorkers); + break; + case "STORE": + StoreFile.main(gumOutput, portInner, serverWait, dbDir, "INS"+dumpsName,"INS"); + StoreFile.main(gumOutput, portInner, serverWait, dbDir, "DEL"+dumpsName,"DEL"); + StoreFile.main(gumOutput, portInner, serverWait, dbDir, "UPD"+dumpsName,"UPD"); + StoreFile.main(gumOutput, portInner, serverWait, dbDir, "MOV"+dumpsName,"MOV"); + break; + case "CALCPAIRS": + CalculatePairs.main(serverWait, dbDir, "INS"+dumpsName, portInner, pairsPath+"INS", pjName+"INS"); + CalculatePairs.main(serverWait, dbDir, "DEL"+dumpsName, portInner, pairsPath+"DEL", pjName+"DEL"); + CalculatePairs.main(serverWait, dbDir, "UPD"+dumpsName, portInner, pairsPath+"UPD", pjName+"UPD"); + CalculatePairs.main(serverWait, dbDir, "MOV"+dumpsName, portInner, pairsPath+"MOV", pjName+"MOV"); + break; + case "IMPORTPAIRS": + ImportPairs2DB.main(csvInputPath+"INS", portInner, serverWait, dbDir); + ImportPairs2DB.main(csvInputPath+"DEL", portInner, serverWait, dbDir); + ImportPairs2DB.main(csvInputPath+"MOV", portInner, serverWait, dbDir); + ImportPairs2DB.main(csvInputPath+"UPD", portInner, serverWait, dbDir); + break; + case "AKKA": + String chunk = pjName; + AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"INS"+".txt.csv.rdb" , port, "INS"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"DEL"+".txt.csv.rdb", port, "DEL"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"UPD"+".txt.csv.rdb", port, "UPD"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"MOV"+".txt.csv.rdb", port, "MOV"+dumpsName); + break; + case "LEVEL1DB": + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-BugsDotJar.rdb", dbDir + "/level1-BugsDotJar/"); + break; + //CALC python abstractPatch.py to from cluster folder + case "L2CALCPAIRS": + // MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/"); + MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/cluster", datasetPath); + break; + case "L2PAIRDB": + // MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301"); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath + "/pairs-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-13april.rdb", dumpsName, "6301"); + break; + case "L3CALCPAIRS": + // MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l",datasetPath); + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/cluster-2l", datasetPath); + break; + case "L3PAIRDB": + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath + "/pairs-2l-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-13april.rdb", dumpsName, "6301"); + break; + } + } catch (Exception e) { + e.printStackTrace(); + } + - switch (jobType){ - case "DUMPTREE": - TestHunkParser.main(gumInput,gumOutput,numOfWorkers); - break; - case "STORE": - StoreFile.main(gumOutput,portInner,serverWait,dbDir,dumpsName); - break; - case "CALCPAIRS": - CalculatePairs.main(serverWait,dbDir,dumpsName,port,pairsPath,"DEFECT4J"); - break; - case "IMPORTPAIRS": - ImportPairs2DB.main(csvInputPath,portInner,serverWait,dbDir,numOfWorkers); - break; - case "AKKA": - AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port,dumpsName); - break; - case "LEVEL1DB": - TreeLoaderClusterL1.main(portInner,serverWait,port,dbDir,"level1-defect4j.rdb",dbDir+"/level1-defect4j/"); - break; - //CALC python abstractPatch.py to from cluster folder - case "L2CALCPAIRS": - MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/"); - break; - case "L2PAIRDB": - MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301"); - break; - case "L3CALCPAIRS": - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l","/Users/anilkoyuncu/bugStudy/dataset/"); - break; - case "L3PAIRDB": - MultiThreadTreeLoaderCluster3.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-2l-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl2-d4j.rdb",dumpsName,"6301"); - break; } - } - +// System.exit(1); } + + From 30f33270c158df5dc45a90ab5e254edcf27665c2 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Wed, 18 Apr 2018 18:54:49 +0200 Subject: [PATCH 102/127] new dataset --- .../cluster/TreeLoaderClusterL1.java | 14 +-- .../violations/FixedViolationHunkParser.java | 2 + .../MultiThreadTreeLoaderCluster.java | 28 +++--- .../MultiThreadTreeLoaderCluster3.java | 92 +++++++++++++------ src/main/java/edu/lu/uni/serval/Launcher.java | 19 ++-- 5 files changed, 100 insertions(+), 55 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java index 431dc84..c81d8f2 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -21,13 +21,9 @@ import java.nio.ByteBuffer; import java.nio.channels.FileChannel; import java.time.Duration; import java.util.*; -import java.util.concurrent.Executors; -import java.util.function.Consumer; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; - /** * Created by anilkoyuncu on 19/03/2018. */ @@ -39,7 +35,7 @@ public class TreeLoaderClusterL1 { private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); // public static void main(String[] args){ - public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path) throws Exception { + public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path,String innerTypePrefix) throws Exception { // String inputPath; // String outputPath; @@ -81,6 +77,7 @@ public class TreeLoaderClusterL1 { Stream stream = Arrays.stream(listFiles); List dbs = stream .filter(x -> x.getName().endsWith(".rdb")) + .filter(x-> x.getName().startsWith(innerTypePrefix)) .collect(Collectors.toList()); for (File db : dbs) { String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; @@ -137,12 +134,17 @@ public class TreeLoaderClusterL1 { innerPool.close(); } - String stopServer = "bash "+level1Path + "/" + "stopServer.sh" +" %s"; + String stopServer = "bash "+inputPath + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(portInner)); // loadRedis(stopServer,serverWait); cs.runShell(stopServer,serverWait); } + String stopServer1 = "bash "+inputPath + "/" + "stopServer.sh" +" %s"; + stopServer1 = String.format(stopServer1,Integer.valueOf(port)); +// loadRedis(stopServer,serverWait); + cs.runShell(stopServer1,serverWait); + // calculatePairsOfClusters(inputPath, outputPath); // mainCompare(inputPath,port,pairsCSVPath,importScript); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 0f51308..4d6e156 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -95,6 +95,8 @@ public class FixedViolationHunkParser extends FixedViolationParser { } } + + // public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { // // GumTree results // List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index a7734f3..2c788b7 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -119,15 +119,18 @@ public class MultiThreadTreeLoaderCluster { log.info("Load done"); } - public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner) { + public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait,String type) throws Exception { + CallShell cs = new CallShell(); String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); +// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); + cs.runShell(cmd1,serverWait); -// String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; -// cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); + String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); + cs.runShell(cmd2,serverWait); // edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); @@ -164,7 +167,8 @@ public class MultiThreadTreeLoaderCluster { if (size == 0) { String comd = String.format(cmd3,f.getPath(),portInner); - loadRedis(comd); +// loadRedis(comd); + cs.runShell(comd); scan = jedis.scan("0", sc); size = scan.getResult().size(); @@ -179,7 +183,7 @@ public class MultiThreadTreeLoaderCluster { //76 scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, jedisPool, clusterName,outerPool)); + .forEach(m -> coreCompare(m, jedisPool, clusterName,outerPool,type)); jedis.save(); @@ -207,7 +211,7 @@ public class MultiThreadTreeLoaderCluster { } - public static Pair getTree(String firstValue, JedisPool outerPool){ + public static Pair getTree(String firstValue, JedisPool outerPool,String type){ // HierarchicalActionSet actionSet = null; @@ -245,7 +249,7 @@ public class MultiThreadTreeLoaderCluster { try { inner = outerPool.getResource(); - String filename = project + "/ActionSetDumps/" + pureFileName + ".txt_" + actionSetPosition; + String filename = project + "/"+type+"/" + pureFileName + ".txt_" + actionSetPosition; String si= inner.get(filename); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); @@ -405,7 +409,7 @@ public class MultiThreadTreeLoaderCluster { - private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool) { + private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool,String type) { try (Jedis jedis = jedisPool.getResource()) { @@ -459,8 +463,8 @@ public class MultiThreadTreeLoaderCluster { // } try { - Pair oldPair = getTree(firstValue, outerPool); - Pair newPair = getTree(secondValue, outerPool); + Pair oldPair = getTree(firstValue, outerPool,type); + Pair newPair = getTree(secondValue, outerPool,type); ITree oldTree = oldPair.getValue0(); ITree newTree = newPair.getValue0(); @@ -631,7 +635,7 @@ orginal calculate pairs, from all dumps of the projects String line = null; try { - FileOutputStream fos = new FileOutputStream(outputPath + "pairs/" +filename+".txt"); + FileOutputStream fos = new FileOutputStream(outputPath + "/pairs/" +filename+".txt"); DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 17c1639..2aa3097 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -161,17 +161,18 @@ public class MultiThreadTreeLoaderCluster3 { } // public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { - public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner) { + public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait, String type) throws Exception { + CallShell cs = new CallShell(); String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - +// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); + cs.runShell(cmd1,serverWait); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); - +// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); + cs.runShell(cmd2,serverWait); String cmd3; cmd3 = "bash " + importScript +" %s %s"; @@ -207,8 +208,9 @@ public class MultiThreadTreeLoaderCluster3 { if (size == 0) { String comd = String.format(cmd3, f.getPath(), portInner); - edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster. - loadRedis(comd); + cs.runShell(comd); +// edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster. +// loadRedis(comd); scan = jedis.scan("0", sc); size = scan.getResult().size(); @@ -221,7 +223,7 @@ public class MultiThreadTreeLoaderCluster3 { scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, jedisPool, clusterName, outerPool)); + .forEach(m -> coreCompare(m, jedisPool, clusterName, outerPool,type)); jedis.save(); @@ -242,7 +244,7 @@ public class MultiThreadTreeLoaderCluster3 { - public static ITree getTree(String firstValue, JedisPool outerPool){ + public static ITree getTree(String firstValue, JedisPool outerPool,String type){ // String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; String[] split2 = firstValue.split("/"); String cluster = split2[1]; @@ -268,7 +270,7 @@ public class MultiThreadTreeLoaderCluster3 { try { inner = outerPool.getResource(); - String fn = project + "/ActionSetDumps/" + s + ".txt_" + actionSetPosition; + String fn = project + "/"+type+"/" + s + ".txt_" + actionSetPosition; String si= inner.get(fn); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); @@ -443,6 +445,36 @@ public class MultiThreadTreeLoaderCluster3 { addToken = true; } + }else if(sType.equals("7")){//assignment + m.add(hours.trim().split("=")[0]); + m.add(to.trim().split("=")[0]); + addToken = true; + + }else if(sType.equals("43") && oldDescendant.getParent() != null && oldDescendant.getParent().getParent() != null){// catch clause + if(oldDescendant.getParent().getType() == 44 && oldDescendant.getParent().getParent().getType() == 12){ + m.add(hours.trim()); + m.add(to.trim()); + addToken = true; + } + }else if(sType.equals("59") && oldDescendant.getChildren().size()==1 && oldDescendant.getHeight()==1 ){ + if( oldDescendant.getChild(0).getType() == 34 || oldDescendant.getChild(0).getType() == 45) { + m.add(hours.trim().split("=")[0]); + m.add(to.trim().split("=")[0]); + addToken = true; + } + }else if(sType.equals("42") && oldDescendant.getParent() != null && oldDescendant.getParent().getType() == 27 ){//infix varuable change + + m.add(hours.trim()); + m.add(to.trim()); + addToken = true; + }else if(sType.equals("-1") && oldDescendant.getChildren().size()==0 && oldDescendant.getHeight()==0 ){//operator + m.add(hours.trim()); + m.add(to.trim()); + addToken = true; + }else if(sType.equals("83") && oldDescendant.getChildren().size()==0 && oldDescendant.getHeight()==0 ){//modifier + m.add(hours.trim()); + m.add(to.trim()); + addToken = true; }else{ m.add(hours.trim()); m.add(to.trim()); @@ -504,23 +536,23 @@ public class MultiThreadTreeLoaderCluster3 { oldTokens.add(methodName); }else if (s.startsWith("MethodName:")){ String methodName = s.split(":")[1]; -// ITree parent = oldDescendant.getParent(); -// -// if(parent!= null && parent.getType() == 32 && !alreadyAddParentMethodName){ //parent is method invocation statement -// String parentLabel = parent.getLabel(); -// String[] pns = parentLabel.split("\\." + methodName); -// if(pns.length > 1) { -// String parentName = pns[0]; -// String[] parentNameSplit = parentName.split("@@"); -// if (parentNameSplit.length > 1) { -// String parentMethodName = parentNameSplit[1]; -// String s1 = parentMethodName.split("@TO@")[0]; -// oldTokens.add(s1.trim()); -// alreadyAddParentMethodName = true; -// } -// } -// -// } + ITree parent = oldDescendant.getParent(); + + if(parent!= null && parent.getType() == 32 && !alreadyAddParentMethodName){ //parent is method invocation statement + String parentLabel = parent.getLabel(); + String[] pns = parentLabel.split("\\." + methodName); + if(pns.length > 1) { + String parentName = pns[0]; + String[] parentNameSplit = parentName.split("@@"); + if (parentNameSplit.length > 1) { + String parentMethodName = parentNameSplit[1]; + String s1 = parentMethodName.split("@TO@")[0]; + oldTokens.add(s1.trim()); + alreadyAddParentMethodName = true; + } + } + + } oldTokens.add(methodName); }else if( sType.equals("59") || sType.equals("43")|| sType.equals("53") || sType.equals("7") || sType.equals("27") || sType.equals("83") || sType.equals("44") ||sType.equals("78") || sType.equals("41") || addToken){ // if(sType.equals("27") || sType.equals("83") || sType.equals("44")){ @@ -570,7 +602,7 @@ public class MultiThreadTreeLoaderCluster3 { return oldTokens; } - private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool) { + private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool,String type) { try (Jedis jedis = jedisPool.getResource()) { @@ -621,8 +653,8 @@ public class MultiThreadTreeLoaderCluster3 { // } try { - ITree oldTree = getTree(firstValue,outerPool); - ITree newTree = getTree(secondValue,outerPool); + ITree oldTree = getTree(firstValue,outerPool,type); + ITree newTree = getTree(secondValue,outerPool,type); if(oldTree == null || newTree == null) { jedis.select(0); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 976afd7..ef6292a 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -46,11 +46,11 @@ public class Launcher { // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; // gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; portInner = "6380"; - serverWait = "50000"; + serverWait = "5000"; chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "AKKA"; + jobType = "LEVEL1DB"; port = "6399"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; // gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J"; @@ -97,23 +97,28 @@ public class Launcher { AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"MOV"+".txt.csv.rdb", port, "MOV"+dumpsName); break; case "LEVEL1DB": - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-BugsDotJar.rdb", dbDir + "/level1-BugsDotJar/"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir + "/level1-Bug13April/",pjName + "UPD"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir + "/level1-Bug13April/",pjName + "INS"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "DEL"+".rdb", dbDir + "/level1-Bug13April/",pjName + "DEL"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "MOV"+".rdb", dbDir + "/level1-Bug13April/",pjName + "MOV"); break; //CALC python abstractPatch.py to from cluster folder case "L2CALCPAIRS": // MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/"); - MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/cluster", datasetPath); + MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterBug13April", datasetPath); break; case "L2PAIRDB": // MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301"); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath + "/pairs-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-13april.rdb", dumpsName, "6301"); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath + "/pairs-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-13april.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); break; + + //CALC via python case "L3CALCPAIRS": // MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l",datasetPath); - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/cluster-2l", datasetPath); + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterBug13April-2l", datasetPath); break; case "L3PAIRDB": - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath + "/pairs-2l-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-13april.rdb", dumpsName, "6301"); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath + "/pairs-2l-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-13april.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); break; } } catch (Exception e) { From ec40c4e10dba5c12e95902a3422f1744e7bdc4a6 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 20 Apr 2018 11:49:25 +0200 Subject: [PATCH 103/127] new version --- .../cluster/ImportPairs2DB.java | 6 +- .../violations/TestHunkParser.java | 4 +- src/main/java/edu/lu/uni/serval/Launcher.java | 61 ++++++++++++++----- 3 files changed, 51 insertions(+), 20 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index d4a5e1d..98546e9 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -22,7 +22,7 @@ public class ImportPairs2DB { private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); // public static void main(String[] args) { - public static void main(String csvInputPath,String portInner,String serverWait,String dbDir) throws Exception { + public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String datasetPath) throws Exception { // String inputPath; // String portInner; @@ -63,9 +63,9 @@ public class ImportPairs2DB { cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); log.info(cmd); CallShell cs = new CallShell(); - cs.runShell(cmd); + cs.runShell(cmd,serverWait); - cmd = "bash "+dbDir + "/redisImportSingle.sh" +" %s %s"; + cmd = "bash "+datasetPath + "/redisImportSingle.sh" +" %s %s"; cmd = String.format(cmd, pj.getPath(), portInt); log.info(cmd); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index d13f7b4..3744196 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -184,9 +184,9 @@ public class TestHunkParser { File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file fileName = fileName.replace(".java", ".txt"); File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file +// File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); - msgFile.setPositionFile(positionFile); +// msgFile.setPositionFile(positionFile); msgFiles.add(msgFile); // } } diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index ef6292a..7a4184c 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -1,6 +1,7 @@ package edu.lu.uni.serval; import edu.lu.uni.serval.FixPatternParser.cluster.*; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster; import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster3; import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; @@ -27,13 +28,14 @@ public class Launcher { String gumOutput; String datasetPath; String pjName; + String pythonPath; if (args.length > 0) { jobType = args[0]; portInner = args[1]; serverWait = args[2]; numOfWorkers = args[3]; port = args[4]; - dumpsName = args[5]; + pythonPath = args[5]; datasetPath = args[6]; pjName = args[7]; // gumInput = args[1]; @@ -47,23 +49,25 @@ public class Launcher { // gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; portInner = "6380"; serverWait = "5000"; - chunkName = "Bug13April.txt.csv.rdb"; +// chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "LEVEL1DB"; + jobType = "IMPORTPAIRS"; port = "6399"; + pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; // gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J"; // csvInputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J-CSV"; - dumpsName = "dumps-Bug13April.rdb"; +// dumpsName = "dumps-Bug13April.rdb"; datasetPath = "/Users/anilkoyuncu/bugStudy/dataset"; - pjName = "Bug13April"; + pjName = "allDataset"; } gumInput = datasetPath +"/"+pjName+"/"; gumOutput = datasetPath + "/GumTreeOutput" + pjName; dbDir = datasetPath + "/redis"; pairsPath = datasetPath + "/pairsImport"+pjName; - csvInputPath = datasetPath + "/pairsImport"+pjName+"-CSV"; + dumpsName = "dumps-"+pjName+".rdb"; +// csvInputPath = datasetPath + "/pairsImport"+pjName+"-CSV"; // String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir); try { @@ -82,20 +86,47 @@ public class Launcher { CalculatePairs.main(serverWait, dbDir, "DEL"+dumpsName, portInner, pairsPath+"DEL", pjName+"DEL"); CalculatePairs.main(serverWait, dbDir, "UPD"+dumpsName, portInner, pairsPath+"UPD", pjName+"UPD"); CalculatePairs.main(serverWait, dbDir, "MOV"+dumpsName, portInner, pairsPath+"MOV", pjName+"MOV"); + break; + case "TRANSFORM": + CallShell cs =new CallShell(); + String cmd = "bash "+datasetPath + "/" + "transformCSV.sh" +" %s %s"; + String cmd1 = String.format(cmd, pairsPath+"INS",pairsPath+"INS"+"-CSV"); + cs.runShell(cmd1); + String cmd2 = String.format(cmd, pairsPath+"UPD",pairsPath+"UPD"+"-CSV"); + cs.runShell(cmd2); + String cmd3 = String.format(cmd, pairsPath+"DEL",pairsPath+"DEL"+"-CSV"); + cs.runShell(cmd3); + String cmd4 = String.format(cmd, pairsPath+"MOV",pairsPath+"MOV"+"-CSV"); + cs.runShell(cmd4); + break; case "IMPORTPAIRS": - ImportPairs2DB.main(csvInputPath+"INS", portInner, serverWait, dbDir); - ImportPairs2DB.main(csvInputPath+"DEL", portInner, serverWait, dbDir); - ImportPairs2DB.main(csvInputPath+"MOV", portInner, serverWait, dbDir); - ImportPairs2DB.main(csvInputPath+"UPD", portInner, serverWait, dbDir); + ImportPairs2DB.main(pairsPath+"INS"+"-CSV", portInner, serverWait, dbDir,datasetPath); + ImportPairs2DB.main(pairsPath+"UPD"+"-CSV", portInner, serverWait, dbDir,datasetPath); + ImportPairs2DB.main(pairsPath+"DEL"+"-CSV", portInner, serverWait, dbDir,datasetPath); + ImportPairs2DB.main(pairsPath+"MOV"+"-CSV", portInner, serverWait, dbDir,datasetPath); break; case "AKKA": - String chunk = pjName; - AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"INS"+".txt.csv.rdb" , port, "INS"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"DEL"+".txt.csv.rdb", port, "DEL"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"UPD"+".txt.csv.rdb", port, "UPD"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, chunk +"MOV"+".txt.csv.rdb", port, "MOV"+dumpsName); + + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"INS"+".txt.csv.rdb" , port, "INS"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"DEL"+".txt.csv.rdb", port, "DEL"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+".txt.csv.rdb", port, "UPD"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+".txt.csv.rdb", port, "MOV"+dumpsName); break; + case "L1DB": + CallShell cs1 =new CallShell(); + String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db11 = String.format(db1, dbDir,pjName +"INS"+".txt.csv.rdb" ,Integer.valueOf(port)); + cs1.runShell(db11,serverWait); + String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; + String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName, port, "matches" + pjName + "INS"); + + cs1.runShell(formatRunPy); + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(port)); + cs1.runShell(stopServer,serverWait); + break; + case "LEVEL1DB": TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir + "/level1-Bug13April/",pjName + "UPD"); TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir + "/level1-Bug13April/",pjName + "INS"); From 55a8ba947c2278b1ddd850d0da23f66bb935040a Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 20 Apr 2018 13:04:02 +0200 Subject: [PATCH 104/127] lach --- src/main/java/edu/lu/uni/serval/Launcher.java | 43 ++++++++++++++++++- 1 file changed, 41 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 7a4184c..04e4088 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -52,7 +52,7 @@ public class Launcher { // chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "IMPORTPAIRS"; + jobType = "AKKA"; port = "6399"; pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; @@ -119,12 +119,51 @@ public class Launcher { String db11 = String.format(db1, dbDir,pjName +"INS"+".txt.csv.rdb" ,Integer.valueOf(port)); cs1.runShell(db11,serverWait); String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; - String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName, port, "matches" + pjName + "INS"); + String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "INS", port, "matches" + pjName + "INS"); cs1.runShell(formatRunPy); String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(port)); cs1.runShell(stopServer,serverWait); + + + + String db2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db12 = String.format(db2, dbDir,pjName +"DEL"+".txt.csv.rdb" ,Integer.valueOf(port)); + cs1.runShell(db12,serverWait); + String formatRunPy1 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "DEL", port, "matches" + pjName + "DEL"); + + cs1.runShell(formatRunPy1); + String stopServer2 = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer2 = String.format(stopServer2,Integer.valueOf(port)); + cs1.runShell(stopServer2,serverWait); + + + + String db3 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db13 = String.format(db3, dbDir,pjName +"MOV"+".txt.csv.rdb" ,Integer.valueOf(port)); + cs1.runShell(db13,serverWait); + + String formatRunPy3 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "MOV", port, "matches" + pjName + "MOV"); + + cs1.runShell(formatRunPy3); + String stopServer3 = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer3 = String.format(stopServer3,Integer.valueOf(port)); + cs1.runShell(stopServer3,serverWait); + + + + String db4 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db14 = String.format(db4, dbDir,pjName +"UPD"+".txt.csv.rdb" ,Integer.valueOf(port)); + cs1.runShell(db14,serverWait); + + String formatRunPy4 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "UPD", port, "matches" + pjName + "UPD"); + + cs1.runShell(formatRunPy4); + String stopServer4 = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer4 = String.format(stopServer4,Integer.valueOf(port)); + cs1.runShell(stopServer4,serverWait); + break; case "LEVEL1DB": From b2c20113f2f27b18f46ee29a017b54d184d8b5f4 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 20 Apr 2018 14:42:05 +0200 Subject: [PATCH 105/127] split chunks --- .../cluster/CalculatePairs.java | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index dccc9a6..cfcacaf 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -96,25 +96,9 @@ public class CalculatePairs { byte [] buf = new byte[0]; String line = null; try { - FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".txt"); - DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); - - - - for (int i = 0; i < result.size(); i++) { - for (int j = i + 1; j < result.size(); j++) { - - - - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; - outStream.write(line.getBytes()); - - } - } - outStream.close(); -// FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +".txt", "rw").getChannel(); -// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); -// int fileCounter = 0; +// FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".txt"); +// DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); +// // // // for (int i = 0; i < result.size(); i++) { @@ -123,22 +107,38 @@ public class CalculatePairs { // // // line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; -// buf = line.getBytes(); -// if(wrBuf.remaining() > 500) { -// wrBuf.put(buf); -// }else{ -// log.info("Next pair dump"); -// fileCounter++; -// rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); -// wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); -// } -// -// -// +// outStream.write(line.getBytes()); // // } // } -// rwChannel.close(); +// outStream.close(); + int fileCounter = 0; + FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + + + for (int i = 0; i < result.size(); i++) { + for (int j = i + 1; j < result.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + } + + + + + } + } + rwChannel.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { From cb2855e1f3cf4968ae26ab24e3e6cb6dc2b6d4ed Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 20 Apr 2018 17:07:59 +0200 Subject: [PATCH 106/127] l --- .../FixPatternParser/cluster/CalculatePairs.java | 5 +++-- .../FixPatternParser/cluster/ImportPairs2DB.java | 8 +++++--- src/main/java/edu/lu/uni/serval/Launcher.java | 15 +++++++++------ 3 files changed, 17 insertions(+), 11 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index cfcacaf..3f46c8b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -114,7 +114,8 @@ public class CalculatePairs { // outStream.close(); int fileCounter = 0; FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + int maxSize = 500*500000; + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); for (int i = 0; i < result.size(); i++) { @@ -130,7 +131,7 @@ public class CalculatePairs { log.info("Next pair dump"); fileCounter++; rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 98546e9..6527ffb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -71,12 +71,14 @@ public class ImportPairs2DB { log.info(cmd); cs.runShell(cmd); + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + String stopServer2 = String.format(stopServer,portInt); + cs.runShell(stopServer2,serverWait); + portInt++; - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - String stopServer2 = String.format(stopServer,Integer.valueOf(portInner)); - cs.runShell(stopServer2); + } diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 04e4088..3bce337 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -29,6 +29,7 @@ public class Launcher { String datasetPath; String pjName; String pythonPath; + String dbNo; if (args.length > 0) { jobType = args[0]; portInner = args[1]; @@ -38,6 +39,7 @@ public class Launcher { pythonPath = args[5]; datasetPath = args[6]; pjName = args[7]; + dbNo = args[8]; // gumInput = args[1]; // chunkName = args[4]; // dbDir = args[6]; @@ -48,11 +50,11 @@ public class Launcher { // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; // gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; portInner = "6380"; - serverWait = "5000"; + serverWait = "50000"; // chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "AKKA"; + jobType = "IMPORTPAIRS"; port = "6399"; pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; @@ -61,6 +63,7 @@ public class Launcher { // dumpsName = "dumps-Bug13April.rdb"; datasetPath = "/Users/anilkoyuncu/bugStudy/dataset"; pjName = "allDataset"; + dbNo = "0"; } gumInput = datasetPath +"/"+pjName+"/"; gumOutput = datasetPath + "/GumTreeOutput" + pjName; @@ -108,10 +111,10 @@ public class Launcher { break; case "AKKA": - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"INS"+".txt.csv.rdb" , port, "INS"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"DEL"+".txt.csv.rdb", port, "DEL"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+".txt.csv.rdb", port, "UPD"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+".txt.csv.rdb", port, "MOV"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"INS"+dbNo+".txt.csv.rdb" , port, "INS"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"DEL"+dbNo+".txt.csv.rdb", port, "DEL"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+dbNo+".txt.csv.rdb", port, "UPD"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+dbNo+".txt.csv.rdb", port, "MOV"+dumpsName); break; case "L1DB": CallShell cs1 =new CallShell(); From 14818f2aedb52dcf3299f55b6839b73144b30f22 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 20 Apr 2018 17:23:58 +0200 Subject: [PATCH 107/127] l --- src/main/java/edu/lu/uni/serval/Launcher.java | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 3bce337..9256a29 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -30,6 +30,7 @@ public class Launcher { String pjName; String pythonPath; String dbNo; + String actionType; if (args.length > 0) { jobType = args[0]; portInner = args[1]; @@ -40,6 +41,7 @@ public class Launcher { datasetPath = args[6]; pjName = args[7]; dbNo = args[8]; + actionType = args[9]; // gumInput = args[1]; // chunkName = args[4]; // dbDir = args[6]; @@ -54,7 +56,7 @@ public class Launcher { // chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "IMPORTPAIRS"; + jobType = "AKKA"; port = "6399"; pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; @@ -64,6 +66,7 @@ public class Launcher { datasetPath = "/Users/anilkoyuncu/bugStudy/dataset"; pjName = "allDataset"; dbNo = "0"; + actionType ="DEL"; } gumInput = datasetPath +"/"+pjName+"/"; gumOutput = datasetPath + "/GumTreeOutput" + pjName; @@ -111,10 +114,10 @@ public class Launcher { break; case "AKKA": - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"INS"+dbNo+".txt.csv.rdb" , port, "INS"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"DEL"+dbNo+".txt.csv.rdb", port, "DEL"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+dbNo+".txt.csv.rdb", port, "UPD"+dumpsName); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+dbNo+".txt.csv.rdb", port, "MOV"+dumpsName); + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+dbNo+".txt.csv.rdb" , port, actionType+dumpsName); +// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"DEL"+dbNo+".txt.csv.rdb", port, "DEL"+dumpsName); +// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+dbNo+".txt.csv.rdb", port, "UPD"+dumpsName); +// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+dbNo+".txt.csv.rdb", port, "MOV"+dumpsName); break; case "L1DB": CallShell cs1 =new CallShell(); From 625eeffd7241e3a61ed44adbf5a64c9370e50996 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 20 Apr 2018 18:20:04 +0200 Subject: [PATCH 108/127] level1 --- .../FixPatternParser/cluster/TreeLoaderClusterL1.java | 2 +- src/main/java/edu/lu/uni/serval/Launcher.java | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java index c81d8f2..e29c9b9 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -95,7 +95,7 @@ public class TreeLoaderClusterL1 { ScanParams sc = new ScanParams(); //150000000 sc.count(150000000); - sc.match("match_*"); + sc.match("match_[0-9]*"); ScanResult scan; scan = inner.scan("0", sc); int size = scan.getResult().size(); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 9256a29..bb354cb 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -56,7 +56,7 @@ public class Launcher { // chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "AKKA"; + jobType = "LEVEL1DB"; port = "6399"; pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; @@ -173,10 +173,10 @@ public class Launcher { break; case "LEVEL1DB": - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir + "/level1-Bug13April/",pjName + "UPD"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir + "/level1-Bug13April/",pjName + "INS"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "DEL"+".rdb", dbDir + "/level1-Bug13April/",pjName + "DEL"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "MOV"+".rdb", dbDir + "/level1-Bug13April/",pjName + "MOV"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir ,pjName + "UPD"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir ,pjName + "INS"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "DEL"+".rdb", dbDir ,pjName + "DEL"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "MOV"+".rdb", dbDir ,pjName + "MOV"); break; //CALC python abstractPatch.py to from cluster folder case "L2CALCPAIRS": From e8df96a3984e5fe7c66ddc71c5a1f34426a48a65 Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Sat, 21 Apr 2018 22:03:41 +0200 Subject: [PATCH 109/127] changes last --- .../MultiThreadTreeLoaderCluster.java | 20 ++- .../MultiThreadTreeLoaderCluster3.java | 20 ++- src/main/java/edu/lu/uni/serval/Launcher.java | 148 ++++++++++++++++-- 3 files changed, 163 insertions(+), 25 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index 2c788b7..db61643 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -193,6 +193,14 @@ public class MultiThreadTreeLoaderCluster { } + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); +// loadRedis(stopServer2,serverWait); + cs.runShell(stopServer1,serverWait); + + String stopServer2 = String.format(stopServer,Integer.valueOf(port)); +// loadRedis(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait); @@ -586,20 +594,22 @@ orginal calculate pairs, from all dumps of the projects /* pairs of each cluster */ - public static void calculatePairsOfClusters(String inputPath, String outputPath) { + public static void calculatePairsOfClusters(String inputPath, String outputPath,String type) { File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List pjs = stream .filter(x -> !x.getName().startsWith(".")) + .filter(x-> x.isDirectory()) .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "pairs/"); + FileHelper.createDirectory(outputPath + "/pairs"+type); for (File pj : pjs) { + File[] files = pj.listFiles(); List fileList = Arrays.asList(files); - readMessageFilesCluster(fileList, outputPath,inputPath,pj.getName()); + readMessageFilesCluster(fileList, outputPath,inputPath,pj.getName(),type); } @@ -617,7 +627,7 @@ orginal calculate pairs, from all dumps of the projects .forEach(m -> coreLoop(m, outputPath,inputPath)); } - private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster) { + private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster,String type) { List treesFileNames = new ArrayList<>(); @@ -635,7 +645,7 @@ orginal calculate pairs, from all dumps of the projects String line = null; try { - FileOutputStream fos = new FileOutputStream(outputPath + "/pairs/" +filename+".txt"); + FileOutputStream fos = new FileOutputStream(outputPath + "/pairs"+type+"/" +filename+".txt"); DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 2aa3097..5f9a4a2 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -231,6 +231,15 @@ public class MultiThreadTreeLoaderCluster3 { } } + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); +// loadRedis(stopServer2,serverWait); + cs.runShell(stopServer1,serverWait); + + String stopServer2 = String.format(stopServer,Integer.valueOf(port)); +// loadRedis(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait); + @@ -803,15 +812,16 @@ orginal calculate pairs, from all dumps of the projects /* pairs of each cluster */ - public static void calculatePairsOfClusters(String inputPath, String outputPath) { + public static void calculatePairsOfClusters(String inputPath, String outputPath,String type) { File folder = new File(inputPath); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List pjs = stream .filter(x -> !x.getName().startsWith(".")) + .filter(x->x.isDirectory()) .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "/pairs-2l/"); + FileHelper.createDirectory(outputPath + "/pairs-2l"+type); for (File pj : pjs) { File[] files = pj.listFiles(); @@ -822,7 +832,7 @@ orginal calculate pairs, from all dumps of the projects } File[] clusterFiles = cluster.listFiles(); List clusterFilesL = Arrays.asList(clusterFiles); - readMessageFilesCluster(clusterFilesL, outputPath, inputPath, pj.getName(), cluster.getName()); + readMessageFilesCluster(clusterFilesL, outputPath, inputPath, pj.getName(), cluster.getName(),type); @@ -845,7 +855,7 @@ orginal calculate pairs, from all dumps of the projects .forEach(m -> coreLoop(m, outputPath,inputPath)); } - private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster, String subCluster) { + private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster, String subCluster,String type) { List treesFileNames = new ArrayList<>(); @@ -867,7 +877,7 @@ orginal calculate pairs, from all dumps of the projects // ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, 1000*treesFileNames.size()*treesFileNames.size()); // int fileCounter = 0; - FileOutputStream fos = new FileOutputStream(outputPath + "/pairs-2l/" +filename+".txt"); + FileOutputStream fos = new FileOutputStream(outputPath + "/pairs-2l"+type+"/" +filename+".txt"); DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index bb354cb..58bec66 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -56,7 +56,7 @@ public class Launcher { // chunkName = "Bug13April.txt.csv.rdb"; // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; numOfWorkers = "10"; - jobType = "LEVEL1DB"; + jobType = "L3DB"; port = "6399"; pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; // pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; @@ -119,10 +119,20 @@ public class Launcher { // AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+dbNo+".txt.csv.rdb", port, "UPD"+dumpsName); // AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+dbNo+".txt.csv.rdb", port, "MOV"+dumpsName); break; + + + case "LEVEL1DB": + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir ,pjName + "UPD"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir ,pjName + "INS"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "DEL"+".rdb", dbDir ,pjName + "DEL"); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "MOV"+".rdb", dbDir ,pjName + "MOV"); + break; + + case "L1DB": CallShell cs1 =new CallShell(); String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db11 = String.format(db1, dbDir,pjName +"INS"+".txt.csv.rdb" ,Integer.valueOf(port)); + String db11 = String.format(db1, dbDir,"level1-"+pjName+ "INS"+".rdb" ,Integer.valueOf(port)); cs1.runShell(db11,serverWait); String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "INS", port, "matches" + pjName + "INS"); @@ -135,7 +145,7 @@ public class Launcher { String db2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db12 = String.format(db2, dbDir,pjName +"DEL"+".txt.csv.rdb" ,Integer.valueOf(port)); + String db12 = String.format(db2, dbDir,"level1-"+pjName+ "DEL"+".rdb" ,Integer.valueOf(port)); cs1.runShell(db12,serverWait); String formatRunPy1 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "DEL", port, "matches" + pjName + "DEL"); @@ -147,7 +157,7 @@ public class Launcher { String db3 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db13 = String.format(db3, dbDir,pjName +"MOV"+".txt.csv.rdb" ,Integer.valueOf(port)); + String db13 = String.format(db3, dbDir,"level1-"+pjName+ "MOV"+".rdb" ,Integer.valueOf(port)); cs1.runShell(db13,serverWait); String formatRunPy3 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "MOV", port, "matches" + pjName + "MOV"); @@ -160,7 +170,7 @@ public class Launcher { String db4 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db14 = String.format(db4, dbDir,pjName +"UPD"+".txt.csv.rdb" ,Integer.valueOf(port)); + String db14 = String.format(db4, dbDir,"level1-"+pjName+ "UPD"+".rdb" ,Integer.valueOf(port)); cs1.runShell(db14,serverWait); String formatRunPy4 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "UPD", port, "matches" + pjName + "UPD"); @@ -172,30 +182,138 @@ public class Launcher { break; - case "LEVEL1DB": - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir ,pjName + "UPD"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir ,pjName + "INS"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "DEL"+".rdb", dbDir ,pjName + "DEL"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "MOV"+".rdb", dbDir ,pjName + "MOV"); - break; + //CALC python abstractPatch.py to from cluster folder case "L2CALCPAIRS": // MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/"); - MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterBug13April", datasetPath); + MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "MOV", datasetPath,"MOV"); + MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "INS", datasetPath,"INS"); + MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "DEL", datasetPath,"DEL"); + MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "UPD", datasetPath,"UPD"); + break; + + case "TRANSFORM2": + CallShell cs2 =new CallShell(); + String cmdL2 = "bash "+datasetPath + "/" + "transformCSV.sh" +" %s %s"; + String cmd1a = String.format(cmdL2, datasetPath+"/pairsINS",datasetPath+"/pairsINS"+"-CSV"); + cs2.runShell(cmd1a); + String cmd2a = String.format(cmdL2, datasetPath+"/pairsUPD",datasetPath+"/pairsUPD"+"-CSV"); + cs2.runShell(cmd2a); + String cmd3a = String.format(cmdL2, datasetPath+"/pairsDEL",datasetPath+"/pairsDEL"+"-CSV"); + cs2.runShell(cmd3a); + String cmd4a = String.format(cmdL2, datasetPath+"/pairsMOV",datasetPath+"/pairsMOV"+"-CSV"); + cs2.runShell(cmd4a); + break; case "L2PAIRDB": // MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301"); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath + "/pairs-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-13april.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsINS"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"INS.rdb", "INS"+dumpsName, "6301",serverWait,"INS"); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsUPD"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"UPD.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsDEL"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"DEL.rdb", "DEL"+dumpsName, "6301",serverWait,"DEL"); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsMOV"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"MOV.rdb", "MOV"+dumpsName, "6301",serverWait,"MOV"); break; + case "L2DB": + CallShell cs3 =new CallShell(); + String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+"INS.rdb",Integer.valueOf(port)); + cs3.runShell(db1b,serverWait); + String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; + String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "INS", port, datasetPath + "/cluster-2l"+pjName+ "INS"); + + cs3.runShell(formatRunPy1a); + String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer1a,Integer.valueOf(port)); + cs3.runShell(stopServer,serverWait); + + String db2b = String.format(db22, dbDir,"clusterl1-"+pjName+"UPD.rdb",Integer.valueOf(port)); + cs3.runShell(db2b,serverWait); + String formatRunPy2a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "UPD", port, datasetPath + "/cluster-2l"+pjName+ "UPD"); + cs3.runShell(formatRunPy2a); + stopServer = String.format(stopServer1a,Integer.valueOf(port)); + cs3.runShell(stopServer,serverWait); + + String db3b = String.format(db22, dbDir,"clusterl1-"+pjName+"DEL.rdb",Integer.valueOf(port)); + cs3.runShell(db3b,serverWait); + String formatRunPy3a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "DEL", port, datasetPath + "/cluster-2l"+pjName+ "DEL"); + cs3.runShell(formatRunPy3a); + stopServer = String.format(stopServer1a,Integer.valueOf(port)); + cs3.runShell(stopServer,serverWait); + + String db4b = String.format(db22, dbDir,"clusterl1-"+pjName+"MOV.rdb",Integer.valueOf(port)); + cs3.runShell(db4b,serverWait); + String formatRunPy4a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "MOV", port, datasetPath + "/cluster-2l"+pjName+ "MOV"); + cs3.runShell(formatRunPy4a); + stopServer = String.format(stopServer1a,Integer.valueOf(port)); + cs3.runShell(stopServer,serverWait); + + + break; //CALC via python case "L3CALCPAIRS": // MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l",datasetPath); - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterBug13April-2l", datasetPath); +// MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterBug13April-2l", datasetPath); + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "UPD", datasetPath,"UPD"); + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "INS", datasetPath,"INS"); + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "DEL", datasetPath,"DEL"); + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "MOV", datasetPath,"MOV"); + break; + + case "TRANSFORM3": + CallShell cs4 =new CallShell(); + String cmdL4 = "bash "+datasetPath + "/" + "transformCSV.sh" +" %s %s"; + String cmd5a = String.format(cmdL4, datasetPath+"/pairs-2lINS",datasetPath+"/pairs-2lINS"+"-CSV"); + cs4.runShell(cmd5a); + String cmd5b = String.format(cmdL4, datasetPath+"/pairs-2lUPD",datasetPath+"/pairs-2lUPD"+"-CSV"); + cs4.runShell(cmd5b); + String cmd5c = String.format(cmdL4, datasetPath+"/pairs-2lDEL",datasetPath+"/pairs-2lDEL"+"-CSV"); + cs4.runShell(cmd5c); + String cmd5d = String.format(cmdL4, datasetPath+"/pairs-2lMOV",datasetPath+"/pairs-2lMOV"+"-CSV"); + cs4.runShell(cmd5d); + break; case "L3PAIRDB": - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath + "/pairs-2l-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-13april.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); +// MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath + "/pairs-2l-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-13april.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lMOV"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"MOV.rdb", "MOV"+dumpsName, "6301",serverWait,"MOV"); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lDEL"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"DEL.rdb", "DEL"+dumpsName, "6301",serverWait,"DEL"); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lUPD"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"UPD.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lINS"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"INS.rdb", "INS"+dumpsName, "6301",serverWait,"INS"); + break; + + case "L3DB": + CallShell cs5 =new CallShell(); + String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+"INS.rdb",Integer.valueOf(port)); + cs5.runShell(dbaa,serverWait); + String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; + String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "INS", port, datasetPath + "/cluster-2l"+pjName+ "INS"); + + cs5.runShell(formatRunPya); + String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServera,Integer.valueOf(port)); + cs5.runShell(stopServer,serverWait); + + String dbb = String.format(dba, dbDir,"clusterl2-"+pjName+"UPD.rdb",Integer.valueOf(port)); + cs5.runShell(dbb,serverWait); + String formatRunPyb = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "UPD", port, datasetPath + "/cluster-2l"+pjName+ "UPD"); + cs5.runShell(formatRunPyb); + stopServer = String.format(stopServera,Integer.valueOf(port)); + cs5.runShell(stopServer,serverWait); + + String dbc = String.format(dba, dbDir,"clusterl2-"+pjName+"DEL.rdb",Integer.valueOf(port)); + cs5.runShell(dbc,serverWait); + String formatRunPyc = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "DEL", port, datasetPath + "/cluster-2l"+pjName+ "DEL"); + cs5.runShell(formatRunPyc); + stopServer = String.format(stopServera,Integer.valueOf(port)); + cs5.runShell(stopServer,serverWait); + + String dbd = String.format(dba, dbDir,"clusterl2-"+pjName+"MOV.rdb",Integer.valueOf(port)); + cs5.runShell(dbd,serverWait); + String formatRunPyd = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "MOV", port, datasetPath + "/cluster-2l"+pjName+ "MOV"); + cs5.runShell(formatRunPyd); + stopServer = String.format(stopServera,Integer.valueOf(port)); + cs5.runShell(stopServer,serverWait); } } catch (Exception e) { e.printStackTrace(); From 931ce5c04fa55ededec661f7c9612f1df8663abe Mon Sep 17 00:00:00 2001 From: Anil Koyuncu Date: Fri, 27 Apr 2018 15:25:28 +0200 Subject: [PATCH 110/127] ase submitted --- .../cluster/AkkaTreeLoader.java | 2 +- .../MultiThreadTreeLoaderCluster3.java | 47 ++++++++++++------- .../violations/TestHunkParserSingleFile.java | 6 +-- src/main/java/edu/lu/uni/serval/Launcher.java | 28 +++++------ 4 files changed, 48 insertions(+), 35 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 3158884..5315d0d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -253,7 +253,7 @@ public class AkkaTreeLoader { ITree children =null; TreeContext tc = new TreeContext(); tree = getASTTree(actionSet, parent, children,tc); - tree.setParent(null); +// tree.setParent(null); tc.validate(); } catch (IOException e) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 5f9a4a2..c0a221f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -396,7 +396,8 @@ public class MultiThreadTreeLoaderCluster3 { (sType.equals("43") && oldDescendant.getHeight() == 0 && oldDescendant.getChildren().size() == 0) || (sType.equals("53") )|| //&& oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || (sType.equals("7") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || - (sType.equals("41") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) + (sType.equals("41") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) || + (sType.equals("40") && oldDescendant.getHeight() == 1 && oldDescendant.getChildren().size() == 1) ){ // int depth = oldDescendant.getChildren().size(); @@ -476,6 +477,12 @@ public class MultiThreadTreeLoaderCluster3 { m.add(hours.trim()); m.add(to.trim()); addToken = true; + }else if(sType.equals("40") && oldDescendant.getChildren().size()==1 && oldDescendant.getHeight()==1 ){//qualified name + + m.add(hours.trim()); + m.add(to.trim()); + addToken = true; + }else if(sType.equals("-1") && oldDescendant.getChildren().size()==0 && oldDescendant.getHeight()==0 ){//operator m.add(hours.trim()); m.add(to.trim()); @@ -484,6 +491,10 @@ public class MultiThreadTreeLoaderCluster3 { m.add(hours.trim()); m.add(to.trim()); addToken = true; + }else if(sType.equals("39") && oldDescendant.getChildren().size()==0 && oldDescendant.getHeight()==0 ){//primitive type + m.add(hours.trim()); + m.add(to.trim()); + addToken = true; }else{ m.add(hours.trim()); m.add(to.trim()); @@ -497,9 +508,11 @@ public class MultiThreadTreeLoaderCluster3 { if (matcher.matches()) { String hours = matcher.group(1); - if (hours.startsWith("MethodName:")){ + if (hours.startsWith("MethodName:")) { String methodName = hours.split(":")[1]; oldTokens.add(methodName); +// }else if(sType.equals("34")){ +// oldTokens.add("NumberLiteral"); }else { oldTokens.add(hours.trim()); } @@ -547,21 +560,21 @@ public class MultiThreadTreeLoaderCluster3 { String methodName = s.split(":")[1]; ITree parent = oldDescendant.getParent(); - if(parent!= null && parent.getType() == 32 && !alreadyAddParentMethodName){ //parent is method invocation statement - String parentLabel = parent.getLabel(); - String[] pns = parentLabel.split("\\." + methodName); - if(pns.length > 1) { - String parentName = pns[0]; - String[] parentNameSplit = parentName.split("@@"); - if (parentNameSplit.length > 1) { - String parentMethodName = parentNameSplit[1]; - String s1 = parentMethodName.split("@TO@")[0]; - oldTokens.add(s1.trim()); - alreadyAddParentMethodName = true; - } - } - - } +// if(parent!= null && parent.getType() == 32 && !alreadyAddParentMethodName){ //parent is method invocation statement +// String parentLabel = parent.getLabel(); +// String[] pns = parentLabel.split("\\." + methodName); +// if(pns.length > 1) { +// String parentName = pns[0]; +// String[] parentNameSplit = parentName.split("@@"); +// if (parentNameSplit.length > 1) { +// String parentMethodName = parentNameSplit[1]; +// String s1 = parentMethodName.split("@TO@")[0]; +// oldTokens.add(s1.trim()); +// alreadyAddParentMethodName = true; +// } +// } +// +// } oldTokens.add(methodName); }else if( sType.equals("59") || sType.equals("43")|| sType.equals("53") || sType.equals("7") || sType.equals("27") || sType.equals("83") || sType.equals("44") ||sType.equals("78") || sType.equals("41") || addToken){ // if(sType.equals("27") || sType.equals("83") || sType.equals("44")){ diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java index 0266e2a..624eb85 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java @@ -32,7 +32,7 @@ public class TestHunkParserSingleFile { outputPath = args[0]; }else{ // inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; - inputPath = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4"; + inputPath = "/Users/anilkoyuncu/bugStudy/dataset/allDataset"; // outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputSingle"; } @@ -59,9 +59,9 @@ public class TestHunkParserSingleFile { // List pjList = Arrays.asList("DATAJPA","ZXing","PDE","SWS","SWT", "SWF", "COLLECTIONS", "JDT"); List files = new ArrayList(); // files.add("5d9d60_76f5be_components#camel-jaxb#src#test#java#org#apache#camel#jaxb#FallbackTypeConverterShouldNotThrowExceptionTest.java"); - files.add("49821e_3cc787_components#camel-infinispan#src#main#java#org#apache#camel#component#infinispan#InfinispanConstants.java"); + files.add("d6c5e5_9f96d9_hbase-server#src#main#java#org#apache#hadoop#hbase#master#RegionStates.java"); for(String f : files){ - String pjName = "CAMEL"; + String pjName = "HBASE"; // for (File target : folders) { // String pjName = target.getName(); // if (!pjList.contains(pjName)){ diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 58bec66..11069d4 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -66,7 +66,7 @@ public class Launcher { datasetPath = "/Users/anilkoyuncu/bugStudy/dataset"; pjName = "allDataset"; dbNo = "0"; - actionType ="DEL"; + actionType ="UPD"; } gumInput = datasetPath +"/"+pjName+"/"; gumOutput = datasetPath + "/GumTreeOutput" + pjName; @@ -301,19 +301,19 @@ public class Launcher { stopServer = String.format(stopServera,Integer.valueOf(port)); cs5.runShell(stopServer,serverWait); - String dbc = String.format(dba, dbDir,"clusterl2-"+pjName+"DEL.rdb",Integer.valueOf(port)); - cs5.runShell(dbc,serverWait); - String formatRunPyc = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "DEL", port, datasetPath + "/cluster-2l"+pjName+ "DEL"); - cs5.runShell(formatRunPyc); - stopServer = String.format(stopServera,Integer.valueOf(port)); - cs5.runShell(stopServer,serverWait); - - String dbd = String.format(dba, dbDir,"clusterl2-"+pjName+"MOV.rdb",Integer.valueOf(port)); - cs5.runShell(dbd,serverWait); - String formatRunPyd = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "MOV", port, datasetPath + "/cluster-2l"+pjName+ "MOV"); - cs5.runShell(formatRunPyd); - stopServer = String.format(stopServera,Integer.valueOf(port)); - cs5.runShell(stopServer,serverWait); +// String dbc = String.format(dba, dbDir,"clusterl2-"+pjName+"DEL.rdb",Integer.valueOf(port)); +// cs5.runShell(dbc,serverWait); +// String formatRunPyc = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "DEL", port, datasetPath + "/cluster-2l"+pjName+ "DEL"); +// cs5.runShell(formatRunPyc); +// stopServer = String.format(stopServera,Integer.valueOf(port)); +// cs5.runShell(stopServer,serverWait); +//// +// String dbd = String.format(dba, dbDir,"clusterl2-"+pjName+"MOV.rdb",Integer.valueOf(port)); +// cs5.runShell(dbd,serverWait); +// String formatRunPyd = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "MOV", port, datasetPath + "/cluster-2l"+pjName+ "MOV"); +// cs5.runShell(formatRunPyd); +// stopServer = String.format(stopServera,Integer.valueOf(port)); +// cs5.runShell(stopServer,serverWait); } } catch (Exception e) { e.printStackTrace(); From 3649e7476a9e604ad659a5b3a637d3e0f907b12a Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 3 May 2018 10:33:14 +0200 Subject: [PATCH 111/127] release version; --- FixPatternMiner.iml | 6 +- pom.xml | 21 + .../uni/serval/FixPatternParser/Parser.java | 2 +- .../FixPatternParser/RunnableParser.java | 11 +- .../cluster/AkkaTreeLoader.java | 155 +---- .../cluster/CalculatePairs.java | 186 +---- .../cluster/ImportPairs2DB.java | 25 +- .../cluster/TreeLoaderClusterL1.java | 650 +----------------- .../patch/CommitPatchParser.java | 4 + .../violations/FixedViolationHunkParser.java | 6 +- .../violations/FixedViolationParser.java | 9 +- .../violations/MultiThreadTreeLoader.java | 2 +- .../MultiThreadTreeLoaderCluster.java | 457 +----------- .../MultiThreadTreeLoaderCluster3.java | 403 +---------- .../FixPatternParser/violations/Producer.java | 4 - .../violations/TestHunkParser.java | 268 +------- .../violations/TestHunkParserSingleFile.java | 3 +- src/main/java/edu/lu/uni/serval/Launcher.java | 322 ++------- .../MultipleThreadsParser/AkkaParser.java | 4 +- .../MultipleThreadsParser/AkkaParser2.java | 4 +- .../ParseFixPatternActor.java | 12 +- .../ParseFixPatternWorker.java | 67 +- src/main/resource/app.properties | 15 + src/main/resource/logback.xml | 6 +- 24 files changed, 272 insertions(+), 2370 deletions(-) create mode 100644 src/main/resource/app.properties diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index 98bff37..2f4552f 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -19,9 +19,6 @@ - - - @@ -42,6 +39,9 @@ + + + diff --git a/pom.xml b/pom.xml index b62a4ff..f999f12 100644 --- a/pom.xml +++ b/pom.xml @@ -13,6 +13,8 @@ UTF-8 2.4.11 + 1.1.2 + 1.7.7 @@ -41,6 +43,25 @@ gen.jdt 2.0.0-SNAPSHOT + + + + org.slf4j + slf4j-api + ${slf4j-api.version} + + + + + ch.qos.logback + logback-classic + ${logback.version} + + + ch.qos.logback + logback-core + ${logback.version} + diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java index d7f7dfb..fe86e18 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java @@ -31,7 +31,7 @@ public abstract class Parser implements ParserInterface { protected String originalTree = ""; // Guide of generating patches. protected String actionSets = ""; // Guide of generating patches. - public abstract void parseFixPatterns(File prevFile, File revFile, File diffEntryFile); + public abstract void parseFixPatterns(File prevFile, File revFile, File diffEntryFile,String project); protected List parseChangedSourceCodeWithGumTree(File prevFile, File revFile) { List actionSets = new ArrayList<>(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/RunnableParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/RunnableParser.java index 850a5a2..891af4f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/RunnableParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/RunnableParser.java @@ -8,6 +8,7 @@ public class RunnableParser implements Runnable { private File revFile; private File diffentryFile; private Parser parser; + private String project; public RunnableParser(File prevFile, File revFile, File diffentryFile, Parser parser) { this.prevFile = prevFile; @@ -16,8 +17,16 @@ public class RunnableParser implements Runnable { this.parser = parser; } + public RunnableParser(File prevFile, File revFile, File diffentryFile, Parser parser,String project) { + this.prevFile = prevFile; + this.revFile = revFile; + this.diffentryFile = diffentryFile; + this.parser = parser; + this.project = project; + } + @Override public void run() { - parser.parseFixPatterns(prevFile, revFile, diffentryFile); + parser.parseFixPatterns(prevFile, revFile, diffentryFile,project); } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index 5315d0d..c03416a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -70,89 +70,22 @@ public class AkkaTreeLoader { private static Consumer consumer = Assert::assertNotNull; - public static void loadRedisWait(String cmd){ - Process process; - try { -// String comd = String.format(cmd, f.getAbsoluteFile()); - process = Runtime.getRuntime() - - .exec(cmd); - - - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), consumer); - Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; - - - } catch (IOException e) { - e.printStackTrace(); - } - catch (InterruptedException e) { - e.printStackTrace(); - } - log.info("Load done"); - } - -// public static void main(String[] args) { public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port, String dumpsName) throws Exception { -// String inputPath; -//// String outputPath; -// String port; -// String portInner; -//// String pairsCSVPath; -// String importScript; -//// String pairsCompletedPath; -// String serverWait; -//// String option; -// String dbDir; -// String chunkName; -// String numOfWorkers; -// if (args.length > 0) { -// inputPath = args[0]; -// portInner = args[1]; -// serverWait = args[2]; -//// option = args[4]; -// chunkName = args[3]; -// numOfWorkers = args[4]; -// dbDir = args[5]; -// port = args[6]; -//// pairsCSVPath = args[3]; -//// importScript = args[4]; -//// pairsCompletedPath = args[3]; -// } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; -//// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; -// port = "6399"; -// portInner = "6380"; -// serverWait = "10000"; -//// option = "COMP"; -//// pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; -//// importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; -//// pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; -// chunkName ="chunk3.rdb"; -// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; -// numOfWorkers = "1"; -// -// } + String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,serverWait,chunkName,dbDir,dumpsName); log.info(parameters); -// if (option.equals("CALC")) { -// calculatePairs(inputPath, port); -// log.info("Calculate pairs done"); -// }else { + CallShell cs = new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port)); -// loadRedis(cmd1,serverWait); + cs.runShell(cmd1,serverWait); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); -// loadRedis(cmd2,serverWait); + cs.runShell(cmd2,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); @@ -163,12 +96,11 @@ public class AkkaTreeLoader { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); -// loadRedis(stopServer1,serverWait); + cs.runShell(stopServer1,serverWait); stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,Integer.valueOf(port)); -// loadRedis(stopServer2,serverWait); -// } + cs.runShell(stopServer2,serverWait); @@ -196,20 +128,7 @@ public class AkkaTreeLoader { List result = scan.getResult(); -// ActorSystem system = null; -// ActorRef parsingActor = null; -// final WorkMessage msg = new WorkMessage(0, result,innerPort,inputPath,dbDir,serverWait); -// try { -// -// log.info("Akka begins..."); -// system = ActorSystem.create("Tree-System"); -// parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers),dbDir,innerPort,serverWait), "tree-actor"); -// parsingActor.tell(msg, ActorRef.noSender()); -// } catch (Exception e) { -// system.shutdown(); -// e.printStackTrace(); -// } -// greeter.tell(); + result .parallelStream() .forEach(m -> @@ -316,41 +235,6 @@ public class AkkaTreeLoader { return parent; } - public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ - - int newType = 0; - - String astNodeType = actionSet.getAstNodeType(); - List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); - - if(keysByValue.size() != 1){ - log.error("Birden cok astnodemapmapping"); - } - newType = keysByValue.get(0); - if(actionSet.getParent() == null){ - //root - - parent = new Tree(newType,""); - }else{ - children = new Tree(newType,""); - parent.addChild(children); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getASTTree(subAction,children,null); - - } - - - } - return parent; - } - static final JedisPoolConfig poolConfig = buildPoolConfig(); @@ -371,31 +255,6 @@ public class AkkaTreeLoader { return poolConfig; } - private static List getMessageFiles(String gumTreeInput) { - String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile - File revFilesPath = new File(inputPath + "revFiles/"); - File[] revFiles = revFilesPath.listFiles(); // project folders - List msgFiles = new ArrayList<>(); - if (revFiles.length >= 0) { - for (File revFile : revFiles) { -// if (revFile.getName().endsWith(".java")) { - String fileName = revFile.getName(); - File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file - fileName = fileName.replace(".java", ".txt"); - File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file - edu.lu.uni.serval.MultipleThreadsParser.MessageFile msgFile = new edu.lu.uni.serval.MultipleThreadsParser.MessageFile(revFile, prevFile, diffentryFile); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); -// } - } - - return msgFiles; - } - else{ - return null; - } - } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index 3f46c8b..e72be9e 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -1,9 +1,7 @@ package edu.lu.uni.serval.FixPatternParser.cluster; -import com.github.gumtreediff.tree.ITree; import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.utils.FileHelper; -import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.Jedis; @@ -12,14 +10,8 @@ import redis.clients.jedis.ScanParams; import redis.clients.jedis.ScanResult; import java.io.*; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; -import java.nio.file.Files; -import java.nio.file.StandardCopyOption; -import java.util.ArrayList; import java.util.List; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poolConfig; /** @@ -27,46 +19,17 @@ import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poo */ public class CalculatePairs { private static Logger log = LoggerFactory.getLogger(CalculatePairs.class); -// public static void main(String[] args) { + public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName) throws Exception { -// String inputPath; -// String port; -// String portInner; -// String serverWait; -// String dbDir; -// String chunkName; -// String outputPath; -// -// if (args.length > 0) { -// inputPath = args[0]; -// portInner = args[1]; -// serverWait = args[2]; -// chunkName = args[3]; -// -// dbDir = args[5]; -// port = args[6]; -// outputPath = args[7]; -// -// } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; -// -// port = "6399"; -// portInner = "6380"; -// serverWait = "10000"; -// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport"; -// chunkName ="chunk"; -// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; -// -// -// } + String parameters = String.format("\nport %s \nserverWait %s \nchunkName %s \ndbDir %s",port,serverWait,chunkName,dbDir); log.info(parameters); CallShell cs =new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port)); -// loadRedis(cmd,serverWait); + cs.runShell(cmd,serverWait); FileHelper.createDirectory(outputPath); @@ -96,9 +59,26 @@ public class CalculatePairs { byte [] buf = new byte[0]; String line = null; try { -// FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".txt"); -// DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); -// + FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".csv"); + DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); + + + + for (int i = 0; i < result.size(); i++) { + for (int j = i + 1; j < result.size(); j++) { + + + + line = String.valueOf(i) +"," + String.valueOf(j) + "," + result.get(i) + "," + result.get(j)+"\n"; + outStream.write(line.getBytes()); + + } + } + outStream.close(); +// int fileCounter = 0; +// FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); +// int maxSize = 500*500000; +// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); // // // for (int i = 0; i < result.size(); i++) { @@ -107,39 +87,22 @@ public class CalculatePairs { // // // line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; -// outStream.write(line.getBytes()); +// buf = line.getBytes(); +// if(wrBuf.remaining() > 500) { +// wrBuf.put(buf); +// }else{ +// log.info("Next pair dump"); +// fileCounter++; +// rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); +// wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); +// } +// +// +// // // } // } -// outStream.close(); - int fileCounter = 0; - FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); - int maxSize = 500*500000; - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); - - - for (int i = 0; i < result.size(); i++) { - for (int j = i + 1; j < result.size(); j++) { - - - - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); - } - - - - - } - } - rwChannel.close(); +// rwChannel.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { @@ -157,81 +120,4 @@ public class CalculatePairs { log.info("Done pairs"); } - - - - - -// comparePairs(inputPath, innerPool,outerPool, serverWait,chunkName,dbDir,numOfWorkers); - -// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; -// stopServer = String.format(stopServer,Integer.valueOf(portInner)); -// loadRedis(stopServer,serverWait); -// } - - - - - -// public static void corePairs(,ArrayList> list){ -// String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; -// cmd = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); -// loadRedis(cmd,serverWait); -// JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); -// -// -// -// Jedis jedis = null; -// for (Pair objects : list) { -// -// try { -// String key = objects.getValue0(); -// String value = objects.getValue1(); -// jedis = innerPool.getResource(); -// -// -// String[] split = value.split(","); -// -// -// jedis.hset(key, "0", split[0]); -// jedis.hset(key, "1", split[1]); -// -// -// //10000000 -// if (pairCounter % 10000000 == 0) { -// -// File dbPath = new File(dbDir + "/" + chunkName); -// File savePath = new File(dbDir + "/" + "chunk" + String.valueOf(fileCounter) + ".rdb"); -// try { -// jedis.save(); -// log.info("saving key {} chunk {}",key,fileCounter); -// while (jedis.ping() == "PONG") { -// log.info("wait"); -// } -// Thread.sleep(Integer.valueOf(serverWait)); -// -// Files.copy(dbPath.toPath(), savePath.toPath(), StandardCopyOption.REPLACE_EXISTING); -// fileCounter++; -// jedis.flushDB(); -// while (jedis.ping() == "PONG") { -// log.info("wait"); -// } -// Thread.sleep(Integer.valueOf(serverWait)); -// -// } catch (IOException e) { -// -// e.printStackTrace(); -// } -// -// -// } -// }catch (Exception e) { -// log.error(e.toString() + " {}", (key)); -// }finally { -// if (jedis != null) { -// jedis.close(); -// } -// } -// } -// } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index 6527ffb..a170fe6 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -20,31 +20,10 @@ import java.util.stream.Stream; */ public class ImportPairs2DB { private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); -// public static void main(String[] args) { public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String datasetPath) throws Exception { -// String inputPath; -// String portInner; -// String serverWait; -// String dbDir; -// String chunkName; -// String numOfWorkers; -// if (args.length > 0) { -// inputPath = args[0]; -// portInner = args[1]; -// serverWait = args[2]; -// chunkName = args[3]; -// numOfWorkers = args[4]; -// dbDir = args[5]; -// } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; -// portInner = "6380"; -// serverWait = "10000"; -// chunkName ="dumps.rdb"; -// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; -// numOfWorkers = "1"; -// } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \ndbDir %s",csvInputPath,portInner,serverWait,dbDir); log.info(parameters); @@ -65,7 +44,7 @@ public class ImportPairs2DB { CallShell cs = new CallShell(); cs.runShell(cmd,serverWait); - cmd = "bash "+datasetPath + "/redisImportSingle.sh" +" %s %s"; + cmd = "bash "+datasetPath + "/redisSingleImport.sh" +" %s %s"; cmd = String.format(cmd, pj.getPath(), portInt); log.info(cmd); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java index e29c9b9..07ca3af 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java @@ -1,26 +1,14 @@ package edu.lu.uni.serval.FixPatternParser.cluster; -import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.*; -import com.github.gumtreediff.matchers.Matcher; -import com.github.gumtreediff.matchers.Matchers; -import com.github.gumtreediff.tree.ITree; import edu.lu.uni.serval.FixPatternParser.violations.CallShell; -import edu.lu.uni.serval.gumtree.GumTreeComparer; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; -import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; -import java.io.*; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; +import java.io.File; import java.time.Duration; -import java.util.*; +import java.util.Arrays; +import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -29,49 +17,23 @@ import java.util.stream.Stream; */ public class TreeLoaderClusterL1 { - private static int resultType; - - private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); -// public static void main(String[] args){ public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path,String innerTypePrefix) throws Exception { -// String inputPath; -// String outputPath; -// String port; -// String portInner; -// String serverWait; -// if (args.length > 0) { -// inputPath = args[0]; -// outputPath = args[1]; -// port = args[2]; -// serverWait = args[3]; -// portInner = args[4]; -// -// } else { -//// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/redis"; -// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; -// port = "6379"; -// portInner = "6380"; -// serverWait = "10000"; -// -// -// } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nport %s",inputPath,portInner,serverWait,port); log.info(parameters); String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port)); -// loadRedis(cmd,serverWait); + CallShell cs = new CallShell(); cs.runShell(cmd,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); -// String level1Path = inputPath + "/level1"; File chunks = new File(level1Path); File[] listFiles = chunks.listFiles(); Stream stream = Arrays.stream(listFiles); @@ -82,7 +44,7 @@ public class TreeLoaderClusterL1 { for (File db : dbs) { String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner)); -// loadRedis(cmdInner,serverWait); + cs.runShell(cmdInner,serverWait); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); @@ -146,607 +108,9 @@ public class TreeLoaderClusterL1 { cs.runShell(stopServer1,serverWait); -// calculatePairsOfClusters(inputPath, outputPath); -// mainCompare(inputPath,port,pairsCSVPath,importScript); - // calculatePairs(inputPath, outputPath); -// processMessages(inputPath,outputPath); -// evaluateResults(inputPath,outputPath); - - } - - - public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { - - String cmd; - cmd = "bash " + importScript +" %s"; - - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - - - File folder = new File(pairsCSVPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List folders = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - for (File f:folders){ - - if(f.getName().startsWith("cluster76")) { - - - try (Jedis jedis = jedisPool.getResource()) { - // do operations with jedis resource - ScanParams sc = new ScanParams(); - sc.count(150000000); - sc.match("pair_[0-9]*"); - - log.info("Scanning"); - ScanResult scan = jedis.scan("0", sc); - int size = scan.getResult().size(); - - if (size == 0) { -// loadRedis(cmd, f); - - scan = jedis.scan("0", sc); - size = scan.getResult().size(); - - } - log.info("Scanned " + String.valueOf(size)); - - - String clusterName = f.getName().replaceAll("[^0-9]+", ""); - - - //76 - - scan.getResult().parallelStream() - .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName)); - - - jedis.save(); - - } - } - - - } - } - - - - - - public static Pair getTree(String firstValue){ - String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; - String[] split2 = firstValue.split("/"); - String cluster = split2[1]; - - - File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List folders = stream - .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2])) - .collect(Collectors.toList()); - - - - String[] split1 = folders.get(0).getName().split(".txt_"); - String s = split1[0]; - String[] splitPJ = split1[1].split("_"); - String project = splitPJ[1]; - String actionSetPosition = splitPJ[0]; - - File prevFile = new File(gumTreeInput + project+ "/" + "prevFiles/prev_" + s + ".java");// previous file - File revFile = new File(gumTreeInput + project+ "/" + "revFiles/" + s + ".java");//rev file - - List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); - - HierarchicalActionSet actionSet = actionSets.get(Integer.valueOf(actionSetPosition)); -// for (HierarchicalActionSet actionSet : actionSets) { - - - - ITree actionTree= null; - ITree test2 = null; - getActionTree(actionSet); - ITree node = actionSet.getNode(); - List descendants = node.getDescendants(); - for (ITree descendant : descendants) { - if(descendant.getType() <= 100){ - descendant.setType(104); - } - } - node.setParent(null); - - - // } -// } - - Pair pair = new Pair<>(node,project); - return pair; - } - - - public static void getActionTree(HierarchicalActionSet actionSet){ - - - int newType = 0; - - Action action = actionSet.getAction(); - if (action instanceof Update){ - newType = 101; - }else if(action instanceof Insert){ - newType =100; - }else if(action instanceof Move){ - newType = 102; - }else if(action instanceof Delete){ - newType=103; - }else{ - new Exception("unknow action"); - } - actionSet.getNode().setType(newType); -// actionSet.getNode().setLabel(""); - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - getActionTree(subAction); - } - - - } - - } -// public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ -// -// int newType = 0; -// -// Action action = actionSet.getAction(); -// if (action instanceof Update){ -// newType = 101; -// }else if(action instanceof Insert){ -// newType =100; -// }else if(action instanceof Move){ -// newType = 102; -// }else if(action instanceof Delete){ -// newType=103; -// }else{ -// new Exception("unknow action"); -// } -// if(actionSet.getParent() == null){ -// //root -// -// parent = new Tree(newType,""); -// }else{ -// children = new Tree(newType,""); -// parent.addChild(children); -// } -// List subActions = actionSet.getSubActions(); -// if (subActions.size() != 0){ -// for (HierarchicalActionSet subAction : subActions) { -// -// if(actionSet.getParent() == null){ -// children = parent; -// } -// getActionTree(subAction,children,null); -// -// } -// -// -// } -// return parent; -// } - - - - private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName) { - - - try (Jedis jedis = jedisPool.getResource()) { - - - Map resultMap = jedis.hgetAll(name); - - resultMap.get("0"); - - - String[] split = name.split("_"); - String i = null; - String j =null; - try { - i = split[1]; - j = split[2]; - } - catch (Exception e){ - e.printStackTrace(); - } - String firstValue = resultMap.get("0"); - String secondValue = resultMap.get("1"); - - - - - - -// firstValue = inputPath + firstValue; -// secondValue = inputPath + secondValue; - -// String[] firstValueSplit = firstValue.split("/"); -// String[] secondValueSplit = secondValue.split("/"); -// -// if (firstValueSplit.length == 1) { -// firstValue = inputPath + firstValueSplit[0]; -// } else { -// firstValue = inputPath + firstValueSplit[1]; -// } -// -// if (secondValueSplit.length == 1) { -// secondValue = inputPath + secondValueSplit[0]; -// } else { -// secondValue = inputPath + secondValueSplit[1]; -// } - - try { - Pair oldPair = getTree(firstValue); - Pair newPair = getTree(secondValue); - - ITree oldTree = oldPair.getValue0(); - ITree newTree = newPair.getValue0(); - - String oldProject = oldPair.getValue1(); - String newProject = newPair.getValue1(); - - - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - - String resultKey = "result_" + (String.valueOf(i)) + "_" + String.valueOf(j); - double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); - String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); - double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); - String diceSimilarity = String.format("%1.2f", diceSimilarity1); - double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); - String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - - String editDistance = String.valueOf(actions.size()); -// jedis.select(1); - String result = resultMap.get("0") + "," + oldProject +"," + resultMap.get("1") + "," +newProject+ "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; -// jedis.set(resultKey, result); - - if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) - || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { - String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); - jedis.select(1); - jedis.set(matchKey, result); - } - jedis.select(0); - String pairKey = "pair_" + (String.valueOf(i)) + "_" + String.valueOf(j); - jedis.del(pairKey); - -// log.info("Completed " + resultKey); - - }catch (Exception e){ - log.error(e.toString() + " {}",(name)); - - - } - - - - - } - } - - - - protected static List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { - List actionSets = new ArrayList<>(); - // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); - if (gumTreeResults == null) { - resultType = 1; - return null; - } else if (gumTreeResults.size() == 0){ - resultType = 2; - return actionSets; - } else { - // Regroup GumTre results. - List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); -// for (HierarchicalActionSet actionSet : allActionSets) { -// String astNodeType = actionSet.getAstNodeType(); -// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { -// actionSets.add(actionSet); -// } -// } - - // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. - // variable effects range, sub-actions are these kinds of modification? -// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); - - ListSorter sorter = new ListSorter<>(allActionSets); - actionSets = sorter.sortAscending(); - - if (actionSets.size() == 0) { - resultType = 3; - } - - return actionSets; - } - } - - -/* -orginal calculate pairs, from all dumps of the projects - */ - public static void calculatePairs(String inputPath, String outputPath) { - File folder = new File(inputPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - List fileToCompare = new ArrayList<>(); - for (File pj : pjs) { - File[] files = pj.listFiles(new FilenameFilter() { - public boolean accept(File dir, String name) { - return name.startsWith("ASTDumps"); - } - }); - Collections.addAll(fileToCompare, files[0].listFiles()); - - } - System.out.println("a"); -// compareAll(fileToCompare); - readMessageFiles(fileToCompare, outputPath); - } - - /* - pairs of each cluster - */ - public static void calculatePairsOfClusters(String inputPath, String outputPath) { - File folder = new File(inputPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - FileHelper.createDirectory(outputPath + "pairs/"); - for (File pj : pjs) { - File[] files = pj.listFiles(); - List fileList = Arrays.asList(files); - - readMessageFilesCluster(fileList, outputPath,inputPath,pj.getName()); - - } - - } - - public static void processMessages(String inputPath, String outputPath) { - File folder = new File(outputPath + "pairs_splitted/"); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "comparison_splitted/"); - pjs.parallelStream() - .forEach(m -> coreLoop(m, outputPath,inputPath)); - } - - private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster) { - - List treesFileNames = new ArrayList<>(); - - - for (File target : folders) { - - treesFileNames.add(target.toString()); - } - - log.info("Calculating pairs"); -// treesFileNames = treesFileNames.subList(0,100); - - String filename = "cluster" + cluster; - byte [] buf = new byte[0]; - String line = null; - try { - - FileOutputStream fos = new FileOutputStream(outputPath + "pairs/" +filename+".txt"); - DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); - - - - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - - - - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; - outStream.write(line.getBytes()); - - } - } - outStream.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - }catch (java.nio.BufferOverflowException e) { - log.error(line); - log.error(String.valueOf(buf.length)); - e.printStackTrace(); - } - - log.info("Done pairs"); - } - - - - public static ITree getSimpliedTree(String fn) { - ITree tree = null; - try { - FileInputStream fi = new FileInputStream(new File(fn)); - ObjectInputStream oi = new ObjectInputStream(fi); - tree = (ITree) oi.readObject(); - oi.close(); - fi.close(); - - - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - -// tree.setLabel(""); - tree.setParent(null); -// List descendants = tree.getDescendants(); -// for (ITree descendant : descendants) { -// descendant.setLabel(""); -// } - - return tree; - - } - - - private static void coreLoop(File mes, String outputPath,String inputPath) { - try { - - log.info("Starting in coreLoop"); - - BufferedReader br = null; - String sCurrentLine = null; - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); - - br = new BufferedReader( - new FileReader(mes)); - while ((sCurrentLine = br.readLine()) != null) { - String currentLine = sCurrentLine; - String[] split = currentLine.split("\t"); - String i = split[0]; - String j = split[1]; - String firstValue = split[2]; - String secondValue = split[3]; - - firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; - secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; - - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); - - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(firstValue); - writer.write("\t"); - writer.write(secondValue); - writer.write("\n"); - - - } - writer.close(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - - } - log.info("Completed output_" + mes.getName()); - } - - private static void readMessageFiles(List folders, String outputPath) { - - List treesFileNames = new ArrayList<>(); - - - for (File target : folders) { - - treesFileNames.add(target.toString()); - } - FileHelper.createDirectory(outputPath + "pairs/"); - log.info("Calculating pairs"); -// treesFileNames = treesFileNames.subList(0,100); - byte [] buf = new byte[0]; - String line = null; - try { - - FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - int fileCounter = 0; - - - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - - - - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - } - - - - - } - } - rwChannel.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - }catch (java.nio.BufferOverflowException e) { - log.error(line); - log.error(String.valueOf(buf.length)); - e.printStackTrace(); - } - - log.info("Done pairs"); - } - static final JedisPoolConfig poolConfig = buildPoolConfig(); @@ -767,8 +131,6 @@ orginal calculate pairs, from all dumps of the projects } - -// return msgFiles; } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java index 4c266e7..b1edcc3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java @@ -98,4 +98,8 @@ public class CommitPatchParser extends Parser{ return buggyStatements + fixedStatements; } + @Override + public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile, String project) { + + } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 4d6e156..485d0f0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -41,7 +41,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { public String unfixedViolations = ""; @Override - public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { + public void parseFixPatterns(File prevFile, File revFile, File diffentryFile,String project) { List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); if (actionSets.size() != 0) { boolean isUpdate = @@ -71,12 +71,12 @@ public class FixedViolationHunkParser extends FixedViolationParser { try { // String pj = diffentryFile.getParent().split("Defects4J")[1]; - String datasetName = diffentryFile.getParent().split("dataset/")[1].split("/")[0]; + String datasetName = project; String[] split1 = diffentryFile.getParent().split(datasetName); String root = split1[0]; String pj = split1[1].split("/")[1]; - String hunkTreeFileName = root + "GumTreeOutput" + datasetName + "/" + pj + folder + diffentryFile.getName() + "_" + String.valueOf(hunkSet); + String hunkTreeFileName = root + "EnhancedASTDiff" + datasetName + "/" + pj + folder + diffentryFile.getName() + "_" + String.valueOf(hunkSet); f = new FileOutputStream(new File(hunkTreeFileName)); ObjectOutputStream o = new ObjectOutputStream(f); o.writeObject(actionSet); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java index a94c1c0..264e854 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java @@ -37,7 +37,7 @@ public class FixedViolationParser extends Parser { protected String violationTypes = ""; @Override - public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { + public void parseFixPatterns(File prevFile, File revFile, File diffentryFile,String project) { } /** @@ -134,7 +134,12 @@ public class FixedViolationParser extends Parser { public String getAlarmTypes() { return violationTypes; } - + + @Override + public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { + + } + // public void setUselessViolations(List uselessViolations) { // this.uselessViolations = uselessViolations; // } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java index a30d3fc..197a573 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java @@ -259,7 +259,7 @@ public class MultiThreadTreeLoader { }catch (Exception e){ - log.error(e.toString() + " {}",(name)); + log.warn(e.toString() + " {}",(name)); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index db61643..3cbab7d 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -5,119 +5,27 @@ import com.github.gumtreediff.actions.model.*; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.Tree; import com.github.gumtreediff.tree.TreeContext; -import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; import java.io.*; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; import java.time.Duration; import java.util.*; -import java.util.concurrent.Executors; -import java.util.function.Consumer; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; - /** * Created by anilkoyuncu on 19/03/2018. */ public class MultiThreadTreeLoaderCluster { - private static int resultType; - - private static class StreamGobbler implements Runnable { - private InputStream inputStream; - private Consumer consumer; - - public StreamGobbler(InputStream inputStream, Consumer consumer) { - this.inputStream = inputStream; - this.consumer = consumer; - } - - @Override - public void run() { - new BufferedReader(new InputStreamReader(inputStream)).lines() - .forEach(consumer); - } - } - private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster.class); - public static void main(String[] args){ - - String inputPath; - String outputPath; - String port; - String pairsCSVPath; - String importScript; - String dbDir; - if (args.length > 0) { - inputPath = args[0]; - outputPath = args[1]; - port = args[2]; - pairsCSVPath = args[3]; - importScript = args[4]; - dbDir = args[5]; - } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; - inputPath = "/Users/anilkoyuncu/bugStudy/code/python/clusterDumps"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6381"; - pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs-csv/"; - importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - } - - String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"cluster1.rdb",Integer.valueOf(port)); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); - - - cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"10000"); - -// calculatePairsOfClusters(inputPath, outputPath); -// mainCompare(inputPath,port,pairsCSVPath,importScript); - // calculatePairs(inputPath, outputPath); -// processMessages(inputPath,outputPath); -// evaluateResults(inputPath,outputPath); - - } - - public static void loadRedis(String cmd){ - Process process; - - try { - - process = Runtime.getRuntime() - - .exec(cmd); - - - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); - Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; - } catch (IOException e) { - e.printStackTrace(); - } catch (InterruptedException e) { - e.printStackTrace(); - } - log.info("Load done"); - } public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait,String type) throws Exception { @@ -222,31 +130,11 @@ public class MultiThreadTreeLoaderCluster { public static Pair getTree(String firstValue, JedisPool outerPool,String type){ -// HierarchicalActionSet actionSet = null; -// try { -// FileInputStream fi = new FileInputStream(new File(dumps + firstValue)); -// ObjectInputStream oi = new ObjectInputStream(fi); -// actionSet = (HierarchicalActionSet) oi.readObject(); -// oi.close(); -// fi.close(); -// -// -// } catch (FileNotFoundException e) { -// log.error("File not found"); -// e.printStackTrace(); -// } catch (IOException e) { -// log.error("Error initializing stream"); -// e.printStackTrace(); -// } catch (ClassNotFoundException e) { -// // TODO Auto-generated catch block -// e.printStackTrace(); -// } - ITree tree = null; Jedis inner = null; String[] split2 = firstValue.split("/"); - String cluster = split2[1]; - String fullFileName = split2[2]; + + String fullFileName = split2[split2.length-1]; String[] split = fullFileName.split(".txt_"); String pureFileName = split[0]; String[] splitPJ = split[1].split("_"); @@ -269,17 +157,6 @@ public class MultiThreadTreeLoaderCluster { tree.setParent(null); tc.validate(); -// log.info(tc.toString()); - -// ITree newTree = ((Update)actionSet.getAction()).getNewNode(); -// ITree oldTree = ((Update)actionSet.getAction()).getNode(); -// -// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); -// m.match(); -// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); -// ag.generate(); -// List actions = ag.getActions(); -// log.info(actions.toString()); } catch (IOException e) { e.printStackTrace(); @@ -346,77 +223,7 @@ public class MultiThreadTreeLoaderCluster { return parent; } -// public static void getActionTree(HierarchicalActionSet actionSet){ -// -// -// int newType = 0; -// -// Action action = actionSet.getAction(); -// if (action instanceof Update){ -// newType = 101; -// }else if(action instanceof Insert){ -// newType =100; -// }else if(action instanceof Move){ -// newType = 102; -// }else if(action instanceof Delete){ -// newType=103; -// }else{ -// new Exception("unknow action"); -// } -// actionSet.getNode().setType(newType); -//// actionSet.getNode().setLabel(""); -// List subActions = actionSet.getSubActions(); -// if (subActions.size() != 0){ -// for (HierarchicalActionSet subAction : subActions) { -// getActionTree(subAction); -// } -// -// -// } -// -// } -// public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ -// -// int newType = 0; -// -// Action action = actionSet.getAction(); -// if (action instanceof Update){ -// newType = 101; -// }else if(action instanceof Insert){ -// newType =100; -// }else if(action instanceof Move){ -// newType = 102; -// }else if(action instanceof Delete){ -// newType=103; -// }else{ -// new Exception("unknow action"); -// } -// if(actionSet.getParent() == null){ -// //root -// -// parent = new Tree(newType,""); -// }else{ -// children = new Tree(newType,""); -// parent.addChild(children); -// } -// List subActions = actionSet.getSubActions(); -// if (subActions.size() != 0){ -// for (HierarchicalActionSet subAction : subActions) { -// -// if(actionSet.getParent() == null){ -// children = parent; -// } -// getActionTree(subAction,children,null); -// -// } -// -// -// } -// return parent; -// } - - private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool,String type) { @@ -441,34 +248,6 @@ public class MultiThreadTreeLoaderCluster { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); -// if (firstValue.equals("71d453_0b5934_hbase-server#src#main#java#org#apache#hadoop#hbase#regionserver#RSRpcServices.txt_0")){ -// //3f70d6_9ee9c5_camel-core#src#main#java#org#apache#camel#builder#NotifyBuilder.txt_0_CAMEL -// //29ea3e_71c614_spring-batch-core#src#test#java#org#springframework#batch#core#domain#JobExecutionTests.txt_0_BATCH -// log.info(firstValue); -// } - - - - - - -// firstValue = inputPath + firstValue; -// secondValue = inputPath + secondValue; - -// String[] firstValueSplit = firstValue.split("/"); -// String[] secondValueSplit = secondValue.split("/"); -// -// if (firstValueSplit.length == 1) { -// firstValue = inputPath + firstValueSplit[0]; -// } else { -// firstValue = inputPath + firstValueSplit[1]; -// } -// -// if (secondValueSplit.length == 1) { -// secondValue = inputPath + secondValueSplit[0]; -// } else { -// secondValue = inputPath + secondValueSplit[1]; -// } try { Pair oldPair = getTree(firstValue, outerPool,type); @@ -516,7 +295,7 @@ public class MultiThreadTreeLoaderCluster { // log.info("Completed " + resultKey); }catch (Exception e){ - log.error(e.toString() + " {}",(name)); + log.warn(e.toString() + " {}",(name)); } @@ -529,68 +308,6 @@ public class MultiThreadTreeLoaderCluster { - protected static List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { - List actionSets = new ArrayList<>(); - // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); - if (gumTreeResults == null) { - resultType = 1; - return null; - } else if (gumTreeResults.size() == 0){ - resultType = 2; - return actionSets; - } else { - // Regroup GumTre results. - List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); -// for (HierarchicalActionSet actionSet : allActionSets) { -// String astNodeType = actionSet.getAstNodeType(); -// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { -// actionSets.add(actionSet); -// } -// } - - // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. - // variable effects range, sub-actions are these kinds of modification? -// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); - - ListSorter sorter = new ListSorter<>(allActionSets); - actionSets = sorter.sortAscending(); - - if (actionSets.size() == 0) { - resultType = 3; - } - - return actionSets; - } - } - - -/* -orginal calculate pairs, from all dumps of the projects - */ - public static void calculatePairs(String inputPath, String outputPath) { - File folder = new File(inputPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - List fileToCompare = new ArrayList<>(); - for (File pj : pjs) { - File[] files = pj.listFiles(new FilenameFilter() { - public boolean accept(File dir, String name) { - return name.startsWith("ASTDumps"); - } - }); - Collections.addAll(fileToCompare, files[0].listFiles()); - - } - System.out.println("a"); -// compareAll(fileToCompare); - readMessageFiles(fileToCompare, outputPath); - } - /* pairs of each cluster */ @@ -615,17 +332,6 @@ orginal calculate pairs, from all dumps of the projects } - public static void processMessages(String inputPath, String outputPath) { - File folder = new File(outputPath + "pairs_splitted/"); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "comparison_splitted/"); - pjs.parallelStream() - .forEach(m -> coreLoop(m, outputPath,inputPath)); - } private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster,String type) { @@ -645,7 +351,7 @@ orginal calculate pairs, from all dumps of the projects String line = null; try { - FileOutputStream fos = new FileOutputStream(outputPath + "/pairs"+type+"/" +filename+".txt"); + FileOutputStream fos = new FileOutputStream(outputPath + "/pairs"+type+"/" +filename+".csv"); DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); @@ -655,7 +361,7 @@ orginal calculate pairs, from all dumps of the projects - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; + line = String.valueOf(i) +"," + String.valueOf(j) + "," + treesFileNames.get(i).replace(inputPath,"") + "," + treesFileNames.get(j).replace(inputPath,"")+"\n"; outStream.write(line.getBytes()); } @@ -676,159 +382,6 @@ orginal calculate pairs, from all dumps of the projects - public static ITree getSimpliedTree(String fn) { - ITree tree = null; - try { - FileInputStream fi = new FileInputStream(new File(fn)); - ObjectInputStream oi = new ObjectInputStream(fi); - tree = (ITree) oi.readObject(); - oi.close(); - fi.close(); - - - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - -// tree.setLabel(""); - tree.setParent(null); -// List descendants = tree.getDescendants(); -// for (ITree descendant : descendants) { -// descendant.setLabel(""); -// } - - return tree; - - } - - - private static void coreLoop(File mes, String outputPath,String inputPath) { - try { - - log.info("Starting in coreLoop"); - - BufferedReader br = null; - String sCurrentLine = null; - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); - - br = new BufferedReader( - new FileReader(mes)); - while ((sCurrentLine = br.readLine()) != null) { - String currentLine = sCurrentLine; - String[] split = currentLine.split("\t"); - String i = split[0]; - String j = split[1]; - String firstValue = split[2]; - String secondValue = split[3]; - - firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; - secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; - - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); - - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(firstValue); - writer.write("\t"); - writer.write(secondValue); - writer.write("\n"); - - - } - writer.close(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - - } - log.info("Completed output_" + mes.getName()); - } - - private static void readMessageFiles(List folders, String outputPath) { - - List treesFileNames = new ArrayList<>(); - - - for (File target : folders) { - - treesFileNames.add(target.toString()); - } - FileHelper.createDirectory(outputPath + "pairs/"); - log.info("Calculating pairs"); -// treesFileNames = treesFileNames.subList(0,100); - byte [] buf = new byte[0]; - String line = null; - try { - - FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - int fileCounter = 0; - - - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - - - - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - } - - - - - } - } - rwChannel.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - }catch (java.nio.BufferOverflowException e) { - log.error(line); - log.error(String.valueOf(buf.length)); - e.printStackTrace(); - } - - log.info("Done pairs"); - } - static final JedisPoolConfig poolConfig = buildPoolConfig(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index c0a221f..3ebca74 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -38,127 +38,9 @@ import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoade */ public class MultiThreadTreeLoaderCluster3 { - private static int resultType; - - private static class StreamGobbler implements Runnable { - private InputStream inputStream; - private Consumer consumer; - - public StreamGobbler(InputStream inputStream, Consumer consumer) { - this.inputStream = inputStream; - this.consumer = consumer; - } - - @Override - public void run() { - new BufferedReader(new InputStreamReader(inputStream)).lines() - .forEach(consumer); - } - } private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster3.class); - public static void main(String[] args){ - - String inputPath; - String outputPath; - String port; - String pairsCSVPath; - String importScript; - String csvScript; - String dbDir; - if (args.length > 0) { - inputPath = args[0]; - outputPath = args[1]; - port = args[2]; - pairsCSVPath = args[3]; - importScript = args[4]; - csvScript = args[5]; - dbDir = args[6]; - } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2/"; - inputPath = "/Users/anilkoyuncu/bugStudy/code/python/cluster2L"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6379"; - pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs-2l-csv/"; - importScript = "/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh"; - csvScript = "/Users/anilkoyuncu/bugStudy/dataset/transformCSV.sh"; - dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - } - -// calculatePairsOfClusters(inputPath, outputPath); - -// createCSV(csvScript,outputPath + "pairs-2l/",pairsCSVPath); - - //create csv file and move - String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"cluster2.rdb",Integer.valueOf(port)); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); - - cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399")); - edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000"); - -// mainCompare(inputPath,port,pairsCSVPath,importScript); - // calculatePairs(inputPath, outputPath); -// processMessages(inputPath,outputPath); -// evaluateResults(inputPath,outputPath); - - } - - public static void createCSV(String csvScript, String f1, String f2){ - String cmd; - cmd = "bash " + csvScript +" %s %s"; - Process process = null; - File source = new File(f1); - File dest = new File(f2); - log.info(source.getName()); - log.info(dest.getName()); - try { - String comd = String.format(cmd, source.getAbsoluteFile() ,dest.getAbsoluteFile()); - process = Runtime.getRuntime() - - .exec(comd); - - - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); - Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; - } catch (IOException e) { - e.printStackTrace(); - } catch (InterruptedException e) { - e.printStackTrace(); - }finally { - process.destroyForcibly(); - } - log.info("Load done"); - - } - - public static void loadRedis(String cmd, File f){ - Process process; - log.info(f.getName()); - try { - String comd = String.format(cmd, f.getAbsoluteFile()); - process = Runtime.getRuntime() - - .exec(comd); - - - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); - Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; - } catch (IOException e) { - e.printStackTrace(); - } catch (InterruptedException e) { - e.printStackTrace(); - } - log.info("Load done"); - } // public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait, String type) throws Exception { @@ -256,9 +138,9 @@ public class MultiThreadTreeLoaderCluster3 { public static ITree getTree(String firstValue, JedisPool outerPool,String type){ // String gumTreeInput = "/Volumes/data/bugStudy_backup/dataset/GumTreeInputBug4/"; String[] split2 = firstValue.split("/"); - String cluster = split2[1]; - String subCluster = split2[2]; - String filename = split2[3]; + + String filename = split2[split2.length-1]; +// String filename = split2[3]; String[] split1= filename.split(".txt_"); String s = split1[0]; String[] splitPJ = split1[1].split("_"); @@ -347,35 +229,6 @@ public class MultiThreadTreeLoaderCluster3 { return parent; } - public static ITree getActionTree(HierarchicalActionSet actionSet){ - - - int newType = 0; - - Action action = actionSet.getAction(); - if (action instanceof Update){ - newType = 101; - }else if(action instanceof Insert){ - newType =100; - }else if(action instanceof Move){ - newType = 102; - }else if(action instanceof Delete){ - newType=103; - }else{ - new Exception("unknow action"); - } - actionSet.getNode().setType(newType); -// actionSet.getNode().setLabel(""); - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - getActionTree(subAction); - } - - - } - return actionSet.getNode(); - } private static List getNames(ITree oldTree, List oldTokens){ @@ -618,9 +471,9 @@ public class MultiThreadTreeLoaderCluster3 { } } - if (oldTokens.size() == 0 ) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){ - log.info("dur bakalim nereye!???"); - } +// if (oldTokens.size() == 0 ) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){ +// log.info("dur bakalim nereye!???"); +// } return oldTokens; } @@ -704,9 +557,9 @@ public class MultiThreadTreeLoaderCluster3 { oldTokens = getNames(oldTree,oldTokens); newTokens = getNames(newTree,newTokens); - if(oldTokens.size() == 0 || newTokens.size() == 0){ - log.error("Cluster {} has no tokens on pair {}",clusterName , name); - } +// if(oldTokens.size() == 0 || newTokens.size() == 0){ +// log.error("Cluster {} has no tokens on pair {}",clusterName , name); +// } // Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); // m.match(); CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); @@ -732,9 +585,9 @@ public class MultiThreadTreeLoaderCluster3 { // log.info(firstValue); // log.info(secondValue); // log.info("************"); - if(!overallSimi.equals(1.0)){ - log.info(""); - } +// if(!overallSimi.equals(1.0)){ +// log.info(""); +// } String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); String result = firstValue + "," + secondValue + ","+String.join(",", oldTokens); jedis.select(1); @@ -747,7 +600,7 @@ public class MultiThreadTreeLoaderCluster3 { }catch (Exception e){ - log.error(e.toString() + " {}",(name)); + log.warn(e.toString() + " {}",(name)); } @@ -759,69 +612,6 @@ public class MultiThreadTreeLoaderCluster3 { } - - protected static List parseChangedSourceCodeWithGumTree2(File prevFile, File revFile) { - List actionSets = new ArrayList<>(); - // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); - if (gumTreeResults == null) { - resultType = 1; - return null; - } else if (gumTreeResults.size() == 0){ - resultType = 2; - return actionSets; - } else { - // Regroup GumTre results. - List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); -// for (HierarchicalActionSet actionSet : allActionSets) { -// String astNodeType = actionSet.getAstNodeType(); -// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { -// actionSets.add(actionSet); -// } -// } - - // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. - // variable effects range, sub-actions are these kinds of modification? -// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); - - ListSorter sorter = new ListSorter<>(allActionSets); - actionSets = sorter.sortAscending(); - - if (actionSets.size() == 0) { - resultType = 3; - } - - return actionSets; - } - } - - -/* -orginal calculate pairs, from all dumps of the projects - */ - public static void calculatePairs(String inputPath, String outputPath) { - File folder = new File(inputPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - List fileToCompare = new ArrayList<>(); - for (File pj : pjs) { - File[] files = pj.listFiles(new FilenameFilter() { - public boolean accept(File dir, String name) { - return name.startsWith("ASTDumps"); - } - }); - Collections.addAll(fileToCompare, files[0].listFiles()); - - } - System.out.println("a"); -// compareAll(fileToCompare); - readMessageFiles(fileToCompare, outputPath); - } - /* pairs of each cluster */ @@ -856,17 +646,7 @@ orginal calculate pairs, from all dumps of the projects } - public static void processMessages(String inputPath, String outputPath) { - File folder = new File(outputPath + "pairs_splitted/"); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "comparison_splitted/"); - pjs.parallelStream() - .forEach(m -> coreLoop(m, outputPath,inputPath)); - } + private static void readMessageFilesCluster(List folders, String outputPath,String inputPath,String cluster, String subCluster,String type) { @@ -890,7 +670,7 @@ orginal calculate pairs, from all dumps of the projects // ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, 1000*treesFileNames.size()*treesFileNames.size()); // int fileCounter = 0; - FileOutputStream fos = new FileOutputStream(outputPath + "/pairs-2l"+type+"/" +filename+".txt"); + FileOutputStream fos = new FileOutputStream(outputPath + "/pairs-2l"+type+"/" +filename+".csv"); DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); @@ -900,7 +680,7 @@ orginal calculate pairs, from all dumps of the projects - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace(inputPath,"") + "\t" + treesFileNames.get(j).replace(inputPath,"")+"\n"; + line = String.valueOf(i) +"," + String.valueOf(j) + "," + treesFileNames.get(i).replace(inputPath,"") + "," + treesFileNames.get(j).replace(inputPath,"")+"\n"; outStream.write(line.getBytes()); // buf = line.getBytes(); // if(wrBuf.remaining() > 500) { @@ -933,159 +713,8 @@ orginal calculate pairs, from all dumps of the projects - public static ITree getSimpliedTree(String fn) { - ITree tree = null; - try { - FileInputStream fi = new FileInputStream(new File(fn)); - ObjectInputStream oi = new ObjectInputStream(fi); - tree = (ITree) oi.readObject(); - oi.close(); - fi.close(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - -// tree.setLabel(""); - tree.setParent(null); -// List descendants = tree.getDescendants(); -// for (ITree descendant : descendants) { -// descendant.setLabel(""); -// } - - return tree; - - } - - - private static void coreLoop(File mes, String outputPath,String inputPath) { - try { - - log.info("Starting in coreLoop"); - - BufferedReader br = null; - String sCurrentLine = null; - BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath + "comparison_splitted/" + "output_" + mes.getName())); - - br = new BufferedReader( - new FileReader(mes)); - while ((sCurrentLine = br.readLine()) != null) { - String currentLine = sCurrentLine; - String[] split = currentLine.split("\t"); - String i = split[0]; - String j = split[1]; - String firstValue = split[2]; - String secondValue = split[3]; - - firstValue = inputPath + firstValue.split("GumTreeOutput2")[1]; - secondValue = inputPath + secondValue.split("GumTreeOutput2")[1]; - - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); - - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(firstValue); - writer.write("\t"); - writer.write(secondValue); - writer.write("\n"); - - - } - writer.close(); - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - - } - log.info("Completed output_" + mes.getName()); - } - - private static void readMessageFiles(List folders, String outputPath) { - - List treesFileNames = new ArrayList<>(); - - - for (File target : folders) { - - treesFileNames.add(target.toString()); - } - FileHelper.createDirectory(outputPath + "pairs/"); - log.info("Calculating pairs"); -// treesFileNames = treesFileNames.subList(0,100); - byte [] buf = new byte[0]; - String line = null; - try { - - FileChannel rwChannel = new RandomAccessFile(outputPath + "pairs/" +"textfile.txt", "rw").getChannel(); - ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - int fileCounter = 0; - - - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - - - - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + treesFileNames.get(i).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","") + "\t" + treesFileNames.get(j).replace("/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2","")+"\n"; - buf = line.getBytes(); - if(wrBuf.remaining() > 500) { - wrBuf.put(buf); - }else{ - log.info("Next pair dump"); - fileCounter++; - rwChannel = new RandomAccessFile(outputPath+"pairs/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel(); - wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE); - } - - - - - } - } - rwChannel.close(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - }catch (java.nio.BufferOverflowException e) { - log.error(line); - log.error(String.valueOf(buf.length)); - e.printStackTrace(); - } - - log.info("Done pairs"); - } - static final JedisPoolConfig poolConfig = buildPoolConfig(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java index 339f28b..53bd576 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java @@ -1,18 +1,14 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import com.oracle.tools.packager.Log; import com.rabbitmq.client.Channel; import com.rabbitmq.client.Connection; import com.rabbitmq.client.ConnectionFactory; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.Jedis; -import redis.clients.jedis.JedisPool; import java.io.File; import java.io.FilenameFilter; import java.io.IOException; -import java.nio.file.Files; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 3744196..7f2a019 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -5,16 +5,14 @@ import akka.actor.ActorSystem; import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor; import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; -import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.utils.FileHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -22,21 +20,8 @@ public class TestHunkParser { private static Logger log = LoggerFactory.getLogger(TestHunkParser.class); // public static void main(String[] args) { - public static void main(String inputPath, String outputPath,String numOfWorkers) { - // input data + public static void main(String inputPath, String outputPath,String numOfWorkers,String project) { -//// String rootPath = "/Users/anilkoyuncu/bugStudy"; -// String inputPath; -// String outputPath; -// if(args.length > 0){ -// inputPath = args[1]; -// outputPath = args[0]; -// }else{ -//// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4"; -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug13April"; -//// outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/"; -// outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput13April"; -// } String parameters = String.format("\nInput path %s \nOutput path %s",inputPath,outputPath); log.info(parameters); @@ -48,51 +33,39 @@ public class TestHunkParser { .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); -// List targetList = new ArrayList(); -// for (File f:folders){ -// for(File f1 :f.listFiles()){ -// if (!f1.getName().startsWith(".")){ -// targetList.add(f1); -// } -// } -// } - -// List pjList = Arrays.asList("DATAJPA","ZXing","PDE","SWS","SWT", "SWF", "COLLECTIONS", "JDT"); for (File target : folders) { String pjName = target.getName(); -// if (!pjList.contains(pjName)){ -// continue; -// } - final List msgFiles = getMessageFiles(target.toString() + "/", outputPath); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" + + final List msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" System.out.println(msgFiles.size()); if(msgFiles.size() == 0) continue; String GUM_TREE_OUTPUT = outputPath + "/"+ pjName + "/"; - final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; - final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; - final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; - final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; - final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; +// final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; +// final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; +// final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; +// final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; +// final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; FileHelper.createDirectory(GUM_TREE_OUTPUT + "/UPD"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/INS"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/DEL"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/MOV"); - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - FileHelper.deleteDirectory(alarmTypesFilePath); +// FileHelper.deleteDirectory(editScriptsFilePath); +// FileHelper.deleteDirectory(patchesSourceCodeFilePath); +// FileHelper.deleteDirectory(buggyTokensFilePath); +// FileHelper.deleteDirectory(editScriptSizesFilePath); +// FileHelper.deleteDirectory(alarmTypesFilePath); - StringBuilder astEditScripts = new StringBuilder(); - StringBuilder tokens = new StringBuilder(); - StringBuilder sizes = new StringBuilder(); - StringBuilder patches = new StringBuilder(); - StringBuilder alarmTypes = new StringBuilder(); +// StringBuilder astEditScripts = new StringBuilder(); +// StringBuilder tokens = new StringBuilder(); +// StringBuilder sizes = new StringBuilder(); +// StringBuilder patches = new StringBuilder(); +// StringBuilder alarmTypes = new StringBuilder(); int a = 0; @@ -102,77 +75,32 @@ public class TestHunkParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), project), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { system.shutdown(); e.printStackTrace(); } -// int counter = 0; -// for (MessageFile msgFile : msgFiles) { -// FixedViolationHunkParser parser = new FixedViolationHunkParser(); -// -// final ExecutorService executor = Executors.newSingleThreadExecutor(); -// // schedule the work -// final Future future = executor.submit(new RunnableParser(msgFile.getPrevFile(), -// msgFile.getRevFile(), msgFile.getDiffEntryFile(), parser)); -// try { -// // where we wait for task to complete -// future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); -// String editScripts = parser.getAstEditScripts(); -// if (!editScripts.equals("")) { -// astEditScripts.append(editScripts); -// tokens.append(parser.getTokensOfSourceCode()); -// sizes.append(parser.getSizes()); -// patches.append(parser.getPatchesSourceCode()); -// alarmTypes.append(parser.getAlarmTypes()); -// -// a++; -// if (a % 100 == 0) { -// FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); -// FileHelper.outputToFile(buggyTokensFilePath, tokens, true); -// FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); -// FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); -// FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); -// astEditScripts.setLength(0); -// tokens.setLength(0); -// sizes.setLength(0); -// patches.setLength(0); -// alarmTypes.setLength(0); -// System.out.println("Finish of parsing " + a + " files......"); -// } -// } -// } catch (TimeoutException e) { -// err.println("task timed out"); -// future.cancel(true /* mayInterruptIfRunning */); -// } catch (InterruptedException e) { -// err.println("task interrupted"); -// } catch (ExecutionException e) { -// err.println("task aborted"); -// } finally { -// executor.shutdownNow(); -// } -// } - FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); - FileHelper.outputToFile(buggyTokensFilePath, tokens, true); - FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); - FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); - FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); - astEditScripts.setLength(0); - tokens.setLength(0); - sizes.setLength(0); - patches.setLength(0); - alarmTypes.setLength(0); - System.out.println(a); + +// FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); +// FileHelper.outputToFile(buggyTokensFilePath, tokens, true); +// FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); +// FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); +// astEditScripts.setLength(0); +// tokens.setLength(0); +// sizes.setLength(0); +// patches.setLength(0); +// alarmTypes.setLength(0); +// System.out.println(a); // classifyByAlarmTypes(); } } - private static List getMessageFiles(String gumTreeInput,String outputPath) { + private static List getMessageFiles(String gumTreeInput) { String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile File revFilesPath = new File(inputPath + "revFiles/"); File[] revFiles = revFilesPath.listFiles(); // project folders @@ -197,132 +125,6 @@ public class TestHunkParser { return null; } } - - public static void classifyByAlarmTypes() { - final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE; - List alarmTypes = readStringList(alarmTypesFilePath); - //edit scripts, sizes of edit scripts, buggy tokens, patches. - classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPT_SIZES_FILE); - classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPTS_FILE); - classifyByAlarmTypes(alarmTypes, Configuration.BUGGY_CODE_TOKENS_FILE); - classifyByAlarmTypes2(alarmTypes, Configuration.PATCH_SOURCECODE_FILE); - } - private static void classifyByAlarmTypes(List alarmTypes, String file) { - Map buildersMap = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(file); - scanner = new Scanner(fis); - int counter = 0; - while (scanner.hasNextLine()) { - String alarmType = alarmTypes.get(counter); - StringBuilder builder = getBuilder(buildersMap, alarmType); - builder.append(scanner.nextLine() + "\n"); - counter ++; - if (counter % 1000 == 0) { - outputBuilders(buildersMap, file); - } - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - outputBuilders(buildersMap, file); - } - - private static void classifyByAlarmTypes2(List alarmTypes, String patchSourcecodeFile) { - Map buildersMap = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(patchSourcecodeFile); - scanner = new Scanner(fis); - int counter = 0; - String singlePatch = ""; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - if (Configuration.PATCH_SIGNAL.equals(line)) { - if (!"".equals(singlePatch)) { - String alarmType = alarmTypes.get(counter); - StringBuilder builder = getBuilder(buildersMap, alarmType); - builder.append(scanner.nextLine() + "\n"); - counter ++; - if (counter % 2000 == 0) { - outputBuilders(buildersMap, patchSourcecodeFile); - } - } - singlePatch = line + "\n"; - } - singlePatch += line + "\n"; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - outputBuilders(buildersMap, patchSourcecodeFile); - } - - private static void outputBuilders(Map map, String fileNameStr) { - File file = new File(fileNameStr); - String fileName = file.getName(); - String parentPath = file.getParent(); - for (Map.Entry entry : map.entrySet()) { - String alarmType = entry.getKey(); - StringBuilder builder = entry.getValue(); - - FileHelper.outputToFile(parentPath + "/" + alarmType + "/" + fileName, builder, true); - - builder.setLength(0); - entry.setValue(builder); - } - } - - public static List readStringList(String inputFile) { - List list = new ArrayList<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(inputFile); - scanner = new Scanner(fis); - while(scanner.hasNextLine()) { - list.add(scanner.nextLine()); - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return list; - } - - private static StringBuilder getBuilder(Map buildersMap, String alarmType) { - if (buildersMap.containsKey(alarmType)) { - return buildersMap.get(alarmType); - } else { - StringBuilder builder = new StringBuilder(); - buildersMap.put(alarmType, builder); - return builder; - } - } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java index 624eb85..58ad0dc 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java @@ -102,8 +102,7 @@ public class TestHunkParserSingleFile { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(1, editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); + parsingActor = system.actorOf(ParseFixPatternActor.props(1, "dataset"), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { system.shutdown(); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 11069d4..1c5d87f 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -5,315 +5,137 @@ import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster; import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster3; import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.FileInputStream; +import java.io.IOException; +import java.util.Properties; /** * Created by anilkoyuncu on 14/04/2018. */ public class Launcher { - public static void main(String[] args) { + private static Logger log = LoggerFactory.getLogger(Launcher.class); + + public static void main(String[] args) throws IOException { + + + Properties appProps = new Properties(); + + String appConfigPath = args[0]; +// String appConfigPath = "/Users/anilkoyuncu/bugStudy/release/code/app.properties"; + appProps.load(new FileInputStream(appConfigPath)); + + String portInner = appProps.getProperty("portInner","6380"); + String serverWait = appProps.getProperty("serverWait", "50000"); + String numOfWorkers = appProps.getProperty("numOfWorkers", "10"); + String jobType = appProps.getProperty("jobType","ALL"); + String port = appProps.getProperty("port","6399"); + String pythonPath = appProps.getProperty("pythonPath","/Users/anilkoyuncu/bugStudy/code/python"); + String datasetPath = appProps.getProperty("datasetPath","/Users/anilkoyuncu/bugStudy/dataset"); + String pjName = appProps.getProperty("pjName","allDataset"); + String dbNo = appProps.getProperty("dbNo","0"); + String actionType = appProps.getProperty("actionType","UPD"); + String threshold = appProps.getProperty("threshold","1"); + + String parameters = String.format("\nportInner %s " + + "\nserverWait %s \nnumOfWorkers %s " + + "\njobType %s \nport %s " + + "\npythonPath %s \ndatasetPath %s" + + "\npjName %s \ndbNo %s \nactionType %s \nthreshold %s" + , portInner, serverWait, numOfWorkers, jobType, port, pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + + log.info(parameters); + + mainLaunch(portInner, serverWait, numOfWorkers, jobType, port, pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + + + } + + public static void mainLaunch(String portInner,String serverWait, String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType,String threshold){ + -// String inputPath; - String portInner; - String serverWait; String dbDir; - String chunkName; - String numOfWorkers; - String jobType; - String port; String pairsPath; - String csvInputPath; String dumpsName; String gumInput; String gumOutput; - String datasetPath; - String pjName; - String pythonPath; - String dbNo; - String actionType; - if (args.length > 0) { - jobType = args[0]; - portInner = args[1]; - serverWait = args[2]; - numOfWorkers = args[3]; - port = args[4]; - pythonPath = args[5]; - datasetPath = args[6]; - pjName = args[7]; - dbNo = args[8]; - actionType = args[9]; -// gumInput = args[1]; -// chunkName = args[4]; -// dbDir = args[6]; -// pairsPath = args[8]; -// csvInputPath = args[9]; -// gumOutput =args[12]; - } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs"; -// gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/"; - portInner = "6380"; - serverWait = "50000"; -// chunkName = "Bug13April.txt.csv.rdb"; -// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; - numOfWorkers = "10"; - jobType = "L3DB"; - port = "6399"; - pythonPath = "/Users/anilkoyuncu/bugStudy/code/python"; -// pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J"; -// gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J"; -// csvInputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J-CSV"; -// dumpsName = "dumps-Bug13April.rdb"; - datasetPath = "/Users/anilkoyuncu/bugStudy/dataset"; - pjName = "allDataset"; - dbNo = "0"; - actionType ="UPD"; - } + gumInput = datasetPath +"/"+pjName+"/"; - gumOutput = datasetPath + "/GumTreeOutput" + pjName; + gumOutput = datasetPath + "/EnhancedASTDiff" + pjName; dbDir = datasetPath + "/redis"; pairsPath = datasetPath + "/pairsImport"+pjName; dumpsName = "dumps-"+pjName+".rdb"; -// csvInputPath = datasetPath + "/pairsImport"+pjName+"-CSV"; -// String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir); try { switch (jobType) { - case "DUMPTREE": - TestHunkParser.main(gumInput, gumOutput, numOfWorkers); + case "ENHANCEDASTDIFF": + TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); break; - case "STORE": - StoreFile.main(gumOutput, portInner, serverWait, dbDir, "INS"+dumpsName,"INS"); - StoreFile.main(gumOutput, portInner, serverWait, dbDir, "DEL"+dumpsName,"DEL"); - StoreFile.main(gumOutput, portInner, serverWait, dbDir, "UPD"+dumpsName,"UPD"); - StoreFile.main(gumOutput, portInner, serverWait, dbDir, "MOV"+dumpsName,"MOV"); + case "CACHE": + StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); break; - case "CALCPAIRS": - CalculatePairs.main(serverWait, dbDir, "INS"+dumpsName, portInner, pairsPath+"INS", pjName+"INS"); - CalculatePairs.main(serverWait, dbDir, "DEL"+dumpsName, portInner, pairsPath+"DEL", pjName+"DEL"); - CalculatePairs.main(serverWait, dbDir, "UPD"+dumpsName, portInner, pairsPath+"UPD", pjName+"UPD"); - CalculatePairs.main(serverWait, dbDir, "MOV"+dumpsName, portInner, pairsPath+"MOV", pjName+"MOV"); - break; - case "TRANSFORM": - CallShell cs =new CallShell(); - String cmd = "bash "+datasetPath + "/" + "transformCSV.sh" +" %s %s"; - String cmd1 = String.format(cmd, pairsPath+"INS",pairsPath+"INS"+"-CSV"); - cs.runShell(cmd1); - String cmd2 = String.format(cmd, pairsPath+"UPD",pairsPath+"UPD"+"-CSV"); - cs.runShell(cmd2); - String cmd3 = String.format(cmd, pairsPath+"DEL",pairsPath+"DEL"+"-CSV"); - cs.runShell(cmd3); - String cmd4 = String.format(cmd, pairsPath+"MOV",pairsPath+"MOV"+"-CSV"); - cs.runShell(cmd4); + case "LEVEL1": + CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); - break; - case "IMPORTPAIRS": - ImportPairs2DB.main(pairsPath+"INS"+"-CSV", portInner, serverWait, dbDir,datasetPath); - ImportPairs2DB.main(pairsPath+"UPD"+"-CSV", portInner, serverWait, dbDir,datasetPath); - ImportPairs2DB.main(pairsPath+"DEL"+"-CSV", portInner, serverWait, dbDir,datasetPath); - ImportPairs2DB.main(pairsPath+"MOV"+"-CSV", portInner, serverWait, dbDir,datasetPath); - break; - case "AKKA": + ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+dbNo+".txt.csv.rdb" , port, actionType+dumpsName); -// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"DEL"+dbNo+".txt.csv.rdb", port, "DEL"+dumpsName); -// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"UPD"+dbNo+".txt.csv.rdb", port, "UPD"+dumpsName); -// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +"MOV"+dbNo+".txt.csv.rdb", port, "MOV"+dumpsName); - break; + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); - case "LEVEL1DB": - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "UPD"+".rdb", dbDir ,pjName + "UPD"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "INS"+".rdb", dbDir ,pjName + "INS"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "DEL"+".rdb", dbDir ,pjName + "DEL"); - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ "MOV"+".rdb", dbDir ,pjName + "MOV"); - break; - - - case "L1DB": CallShell cs1 =new CallShell(); String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db11 = String.format(db1, dbDir,"level1-"+pjName+ "INS"+".rdb" ,Integer.valueOf(port)); + String db11 = String.format(db1, dbDir,"level1-"+pjName+ actionType+".rdb" ,Integer.valueOf(port)); cs1.runShell(db11,serverWait); - String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; - String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "INS", port, "matches" + pjName + "INS"); + String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; + String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, "matches" + pjName + actionType, threshold); cs1.runShell(formatRunPy); String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(port)); cs1.runShell(stopServer,serverWait); - - - - String db2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db12 = String.format(db2, dbDir,"level1-"+pjName+ "DEL"+".rdb" ,Integer.valueOf(port)); - cs1.runShell(db12,serverWait); - String formatRunPy1 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "DEL", port, "matches" + pjName + "DEL"); - - cs1.runShell(formatRunPy1); - String stopServer2 = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer2 = String.format(stopServer2,Integer.valueOf(port)); - cs1.runShell(stopServer2,serverWait); - - - - String db3 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db13 = String.format(db3, dbDir,"level1-"+pjName+ "MOV"+".rdb" ,Integer.valueOf(port)); - cs1.runShell(db13,serverWait); - - String formatRunPy3 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "MOV", port, "matches" + pjName + "MOV"); - - cs1.runShell(formatRunPy3); - String stopServer3 = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer3 = String.format(stopServer3,Integer.valueOf(port)); - cs1.runShell(stopServer3,serverWait); - - - - String db4 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db14 = String.format(db4, dbDir,"level1-"+pjName+ "UPD"+".rdb" ,Integer.valueOf(port)); - cs1.runShell(db14,serverWait); - - String formatRunPy4 = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ "UPD", port, "matches" + pjName + "UPD"); - - cs1.runShell(formatRunPy4); - String stopServer4 = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer4 = String.format(stopServer4,Integer.valueOf(port)); - cs1.runShell(stopServer4,serverWait); - break; - //CALC python abstractPatch.py to from cluster folder - case "L2CALCPAIRS": - // MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/"); - MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "MOV", datasetPath,"MOV"); - MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "INS", datasetPath,"INS"); - MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "DEL", datasetPath,"DEL"); - MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ "UPD", datasetPath,"UPD"); - break; + case "LEVEL2": + MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ actionType, datasetPath,actionType); - case "TRANSFORM2": - CallShell cs2 =new CallShell(); - String cmdL2 = "bash "+datasetPath + "/" + "transformCSV.sh" +" %s %s"; - String cmd1a = String.format(cmdL2, datasetPath+"/pairsINS",datasetPath+"/pairsINS"+"-CSV"); - cs2.runShell(cmd1a); - String cmd2a = String.format(cmdL2, datasetPath+"/pairsUPD",datasetPath+"/pairsUPD"+"-CSV"); - cs2.runShell(cmd2a); - String cmd3a = String.format(cmdL2, datasetPath+"/pairsDEL",datasetPath+"/pairsDEL"+"-CSV"); - cs2.runShell(cmd3a); - String cmd4a = String.format(cmdL2, datasetPath+"/pairsMOV",datasetPath+"/pairsMOV"+"-CSV"); - cs2.runShell(cmd4a); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); - break; - case "L2PAIRDB": - // MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301"); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsINS"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"INS.rdb", "INS"+dumpsName, "6301",serverWait,"INS"); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsUPD"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"UPD.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsDEL"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"DEL.rdb", "DEL"+dumpsName, "6301",serverWait,"DEL"); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairsMOV"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+"MOV.rdb", "MOV"+dumpsName, "6301",serverWait,"MOV"); - break; - - case "L2DB": CallShell cs3 =new CallShell(); String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+"INS.rdb",Integer.valueOf(port)); + String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+actionType+".rdb",Integer.valueOf(port)); cs3.runShell(db1b,serverWait); - String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; - String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "INS", port, datasetPath + "/cluster-2l"+pjName+ "INS"); + String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; + String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); cs3.runShell(formatRunPy1a); String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer1a,Integer.valueOf(port)); cs3.runShell(stopServer,serverWait); - - String db2b = String.format(db22, dbDir,"clusterl1-"+pjName+"UPD.rdb",Integer.valueOf(port)); - cs3.runShell(db2b,serverWait); - String formatRunPy2a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "UPD", port, datasetPath + "/cluster-2l"+pjName+ "UPD"); - cs3.runShell(formatRunPy2a); - stopServer = String.format(stopServer1a,Integer.valueOf(port)); - cs3.runShell(stopServer,serverWait); - - String db3b = String.format(db22, dbDir,"clusterl1-"+pjName+"DEL.rdb",Integer.valueOf(port)); - cs3.runShell(db3b,serverWait); - String formatRunPy3a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "DEL", port, datasetPath + "/cluster-2l"+pjName+ "DEL"); - cs3.runShell(formatRunPy3a); - stopServer = String.format(stopServer1a,Integer.valueOf(port)); - cs3.runShell(stopServer,serverWait); - - String db4b = String.format(db22, dbDir,"clusterl1-"+pjName+"MOV.rdb",Integer.valueOf(port)); - cs3.runShell(db4b,serverWait); - String formatRunPy4a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ "MOV", port, datasetPath + "/cluster-2l"+pjName+ "MOV"); - cs3.runShell(formatRunPy4a); - stopServer = String.format(stopServer1a,Integer.valueOf(port)); - cs3.runShell(stopServer,serverWait); - - break; //CALC via python - case "L3CALCPAIRS": - // MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l",datasetPath); -// MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterBug13April-2l", datasetPath); - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "UPD", datasetPath,"UPD"); - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "INS", datasetPath,"INS"); - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "DEL", datasetPath,"DEL"); - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ "MOV", datasetPath,"MOV"); - break; + case "LEVEL3": + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ actionType, datasetPath,actionType); - case "TRANSFORM3": - CallShell cs4 =new CallShell(); - String cmdL4 = "bash "+datasetPath + "/" + "transformCSV.sh" +" %s %s"; - String cmd5a = String.format(cmdL4, datasetPath+"/pairs-2lINS",datasetPath+"/pairs-2lINS"+"-CSV"); - cs4.runShell(cmd5a); - String cmd5b = String.format(cmdL4, datasetPath+"/pairs-2lUPD",datasetPath+"/pairs-2lUPD"+"-CSV"); - cs4.runShell(cmd5b); - String cmd5c = String.format(cmdL4, datasetPath+"/pairs-2lDEL",datasetPath+"/pairs-2lDEL"+"-CSV"); - cs4.runShell(cmd5c); - String cmd5d = String.format(cmdL4, datasetPath+"/pairs-2lMOV",datasetPath+"/pairs-2lMOV"+"-CSV"); - cs4.runShell(cmd5d); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); - break; - case "L3PAIRDB": -// MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath + "/pairs-2l-csv", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-13april.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lMOV"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"MOV.rdb", "MOV"+dumpsName, "6301",serverWait,"MOV"); - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lDEL"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"DEL.rdb", "DEL"+dumpsName, "6301",serverWait,"DEL"); - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lUPD"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"UPD.rdb", "UPD"+dumpsName, "6301",serverWait,"UPD"); - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2lINS"+"-CSV", datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+"INS.rdb", "INS"+dumpsName, "6301",serverWait,"INS"); - - break; - - case "L3DB": CallShell cs5 =new CallShell(); String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+"INS.rdb",Integer.valueOf(port)); + String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+actionType+".rdb",Integer.valueOf(port)); cs5.runShell(dbaa,serverWait); - String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s"; - String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "INS", port, datasetPath + "/cluster-2l"+pjName+ "INS"); + String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; + String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); cs5.runShell(formatRunPya); String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServera,Integer.valueOf(port)); cs5.runShell(stopServer,serverWait); + break; - String dbb = String.format(dba, dbDir,"clusterl2-"+pjName+"UPD.rdb",Integer.valueOf(port)); - cs5.runShell(dbb,serverWait); - String formatRunPyb = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "UPD", port, datasetPath + "/cluster-2l"+pjName+ "UPD"); - cs5.runShell(formatRunPyb); - stopServer = String.format(stopServera,Integer.valueOf(port)); - cs5.runShell(stopServer,serverWait); - -// String dbc = String.format(dba, dbDir,"clusterl2-"+pjName+"DEL.rdb",Integer.valueOf(port)); -// cs5.runShell(dbc,serverWait); -// String formatRunPyc = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "DEL", port, datasetPath + "/cluster-2l"+pjName+ "DEL"); -// cs5.runShell(formatRunPyc); -// stopServer = String.format(stopServera,Integer.valueOf(port)); -// cs5.runShell(stopServer,serverWait); -//// -// String dbd = String.format(dba, dbDir,"clusterl2-"+pjName+"MOV.rdb",Integer.valueOf(port)); -// cs5.runShell(dbd,serverWait); -// String formatRunPyd = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ "MOV", port, datasetPath + "/cluster-2l"+pjName+ "MOV"); -// cs5.runShell(formatRunPyd); -// stopServer = String.format(stopServera,Integer.valueOf(port)); -// cs5.runShell(stopServer,serverWait); } } catch (Exception e) { e.printStackTrace(); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java index d171fed..c1c1d7b 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java @@ -80,8 +80,8 @@ public class AkkaParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); +// parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, +// patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { system.shutdown(); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java index c6de0ca..b0057ae 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java @@ -99,8 +99,8 @@ public class AkkaParser2 { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, - patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); +// parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, +// patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { system.shutdown(); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java index 746db72..3e8fdf5 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java @@ -19,16 +19,13 @@ public class ParseFixPatternActor extends UntypedActor { private final int numberOfWorkers; private int counter = 0; - public ParseFixPatternActor(int numberOfWorkers, String editScriptsFilePath, String patchesSourceCodeFilePath, - String buggyTokensFilePath, String editScriptSizesFilePath) { + public ParseFixPatternActor(int numberOfWorkers, String project) { mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) - .props(ParseFixPatternWorker.props(editScriptsFilePath, patchesSourceCodeFilePath, - buggyTokensFilePath, editScriptSizesFilePath)), "mine-fix-pattern-router"); + .props(ParseFixPatternWorker.props(project)), "mine-fix-pattern-router"); this.numberOfWorkers = numberOfWorkers; } - public static Props props(final int numberOfWorkers, final String editScriptsFilePath, final String patchesSourceCodeFilePath, - final String buggyTokensFilePath, final String editScriptSizesFilePath) { + public static Props props(final int numberOfWorkers, final String project) { return Props.create(new Creator() { @@ -36,8 +33,7 @@ public class ParseFixPatternActor extends UntypedActor { @Override public ParseFixPatternActor create() throws Exception { - return new ParseFixPatternActor(numberOfWorkers, editScriptsFilePath, patchesSourceCodeFilePath, - buggyTokensFilePath, editScriptSizesFilePath); + return new ParseFixPatternActor(numberOfWorkers, project); } }); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index 14a6844..ae9cc74 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -27,29 +27,21 @@ import edu.lu.uni.serval.utils.FileHelper; public class ParseFixPatternWorker extends UntypedActor { private static Logger log = LoggerFactory.getLogger(ParseFixPatternActor.class); - private String editScriptsFilePath; - private String patchesSourceCodeFilePath; - private String editScriptSizesFilePath; - private String buggyTokensFilePath; + private String project; + - public ParseFixPatternWorker(String editScriptsFilePath, String patchesSourceCodeFilePath, - String buggyTokensFilePath, String editScriptSizesFilePath) { - this.editScriptsFilePath = editScriptsFilePath; - this.patchesSourceCodeFilePath = patchesSourceCodeFilePath; - this.editScriptSizesFilePath = editScriptSizesFilePath; - this.buggyTokensFilePath = buggyTokensFilePath; + public ParseFixPatternWorker(String project) { + this.project = project; } - public static Props props(final String editScriptsFile, final String patchesSourceCodeFile, final String buggyTokensFilePath, - final String editScriptSizesFilePath) { + public static Props props(final String project) { return Props.create(new Creator() { private static final long serialVersionUID = -7615153844097275009L; @Override public ParseFixPatternWorker create() throws Exception { - return new ParseFixPatternWorker(editScriptsFile, patchesSourceCodeFile, - buggyTokensFilePath, editScriptSizesFilePath); + return new ParseFixPatternWorker(project); } }); @@ -95,7 +87,7 @@ public class ParseFixPatternWorker extends UntypedActor { final ExecutorService executor = Executors.newSingleThreadExecutor(); // schedule the work - final Future future = executor.submit(new RunnableParser(prevFile, revFile, diffentryFile, parser)); + final Future future = executor.submit(new RunnableParser(prevFile, revFile, diffentryFile, parser,project)); try { // wait for task to complete future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); @@ -126,16 +118,16 @@ public class ParseFixPatternWorker extends UntypedActor { counter ++; if (counter % 100 == 0) { - FileHelper.outputToFile(editScriptsFilePath + "edistScripts_" + id + ".list", editScripts, true); - FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); - FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); - FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); +// FileHelper.outputToFile(editScriptsFilePath + "edistScripts_" + id + ".list", editScripts, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); +// FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); +// FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); editScripts.setLength(0); patchesSourceCode.setLength(0); sizes.setLength(0); tokens.setLength(0); log.info("Worker #" + id +" finialized parsing " + counter + " files..."); - FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); +// FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); testingInfo.setLength(0); } } @@ -157,10 +149,10 @@ public class ParseFixPatternWorker extends UntypedActor { } if (sizes.length() > 0) { - FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true); - FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); - FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); - FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); +// FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true); +// FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); +// FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); +// FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); editScripts.setLength(0); patchesSourceCode.setLength(0); sizes.setLength(0); @@ -184,31 +176,4 @@ public class ParseFixPatternWorker extends UntypedActor { } } - private int countAlarms(File positionFile, String type) {//, List uselessViolations) { - int counter = 0; - String content = FileHelper.readFile(positionFile); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - String[] elements = line.split(":"); - Violation v = new Violation(Integer.parseInt(elements[1]), Integer.parseInt(elements[2]), elements[0]); - String fileName = positionFile.getName().replace(".txt", ".java"); - v.setFileName(fileName); - counter ++; - if (!"".equals(type)) { - System.err.println(type + fileName + ":" + elements[1] + ":" + elements[2] + ":" + elements[0]); - } - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return counter; - } } diff --git a/src/main/resource/app.properties b/src/main/resource/app.properties new file mode 100644 index 0000000..5e48335 --- /dev/null +++ b/src/main/resource/app.properties @@ -0,0 +1,15 @@ +jobType = LEVEL2 +pjName = BugsDotJar +portInner = 6380 +dbNo = 0 +port = 6399 +serverWait = 10000 +numOfWorkers = 100 +pythonPath = /Users/anilkoyuncu/bugStudy/code/python +datasetPath = /Users/anilkoyuncu/bugStudy/release/code +actionType =UPD +threshold = 9 + +#ENHANCEDASTDIFF,CACHE,LEVEL1,LEVEL2,LEVEL3 + + diff --git a/src/main/resource/logback.xml b/src/main/resource/logback.xml index fd8e19f..58dd487 100644 --- a/src/main/resource/logback.xml +++ b/src/main/resource/logback.xml @@ -7,14 +7,14 @@ - %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{50} - %msg%n + %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{0} - %msg%n ${LOG_HOME}/myLog.log - %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{50} - %msg%n + %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{0} - %msg%n @@ -24,7 +24,7 @@ 30 - %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{50} - %msg%n + %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{0} - %msg%n 10MB From de05e901be1b2390dc2b3f6e523b70aa4494da67 Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 12 Jul 2018 13:39:19 +0200 Subject: [PATCH 112/127] launcher all --- src/main/java/edu/lu/uni/serval/Launcher.java | 121 ++++++++++-------- 1 file changed, 70 insertions(+), 51 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 1c5d87f..f6755cc 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -78,64 +78,22 @@ public class Launcher { StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); break; case "LEVEL1": - CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); - - ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); - - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); - - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); - - CallShell cs1 =new CallShell(); - String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db11 = String.format(db1, dbDir,"level1-"+pjName+ actionType+".rdb" ,Integer.valueOf(port)); - cs1.runShell(db11,serverWait); - String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; - String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, "matches" + pjName + actionType, threshold); - - cs1.runShell(formatRunPy); - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(port)); - cs1.runShell(stopServer,serverWait); + level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); break; - //CALC python abstractPatch.py to from cluster folder case "LEVEL2": - MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ actionType, datasetPath,actionType); - - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); - - CallShell cs3 =new CallShell(); - String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+actionType+".rdb",Integer.valueOf(port)); - cs3.runShell(db1b,serverWait); - String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; - String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); - - cs3.runShell(formatRunPy1a); - String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer1a,Integer.valueOf(port)); - cs3.runShell(stopServer,serverWait); + level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; //CALC via python case "LEVEL3": - MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ actionType, datasetPath,actionType); - - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); - - CallShell cs5 =new CallShell(); - String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; - String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+actionType+".rdb",Integer.valueOf(port)); - cs5.runShell(dbaa,serverWait); - String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; - String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); - - cs5.runShell(formatRunPya); - String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServera,Integer.valueOf(port)); - cs5.runShell(stopServer,serverWait); + level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; - + case "ALL": + TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); + StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); + level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); + level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); + level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); } } catch (Exception e) { e.printStackTrace(); @@ -145,6 +103,67 @@ public class Launcher { } + + private static void level1(String portInner, String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception { + CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); + + ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); + + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); + + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); + + CallShell cs1 =new CallShell(); + String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db11 = String.format(db1, dbDir,"level1-"+pjName+ actionType+".rdb" ,Integer.valueOf(port)); + cs1.runShell(db11,serverWait); + String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; + String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, "matches" + pjName + actionType, threshold); + + cs1.runShell(formatRunPy); + String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer,Integer.valueOf(port)); + cs1.runShell(stopServer,serverWait); + } + + private static void level2(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { + String stopServer; + MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ actionType, datasetPath,actionType); + + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); + + CallShell cs3 =new CallShell(); + String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+actionType+".rdb",Integer.valueOf(port)); + cs3.runShell(db1b,serverWait); + String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; + String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); + + cs3.runShell(formatRunPy1a); + String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServer1a,Integer.valueOf(port)); + cs3.runShell(stopServer,serverWait); + } + + private static void level3(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { + String stopServer; + MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ actionType, datasetPath,actionType); + + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); + + CallShell cs5 =new CallShell(); + String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; + String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+actionType+".rdb",Integer.valueOf(port)); + cs5.runShell(dbaa,serverWait); + String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; + String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); + + cs5.runShell(formatRunPya); + String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; + stopServer = String.format(stopServera,Integer.valueOf(port)); + cs5.runShell(stopServer,serverWait); + return; + } // System.exit(1); } From 7cc3dd46e77c352443c3028b708d703f9a3a4ebc Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 12 Jul 2018 16:16:51 +0200 Subject: [PATCH 113/127] all --- src/main/java/edu/lu/uni/serval/Launcher.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index f6755cc..5dea4a0 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -89,7 +89,7 @@ public class Launcher { level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; case "ALL": - TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); +// TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); From bbf90adb2054c0fe06ea83cda5769d7d8b1237e2 Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 2 Aug 2018 18:11:30 +0200 Subject: [PATCH 114/127] pattern extraction --- .../cluster/AkkaTreeLoader.java | 2 +- .../FixPatternParser/cluster/StoreFile.java | 24 +- src/main/java/edu/lu/uni/serval/Launcher.java | 9 +- .../ParseFixPatternWorker.java | 14 +- .../edu/lu/uni/serval/PatternExtractor.java | 294 ++++++++++++++++++ 5 files changed, 331 insertions(+), 12 deletions(-) create mode 100644 src/main/java/edu/lu/uni/serval/PatternExtractor.java diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java index c03416a..4119e3e 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java @@ -204,7 +204,7 @@ public class AkkaTreeLoader { List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); if(keysByValue.size() != 1){ - log.error("Birden cok astnodemapmapping"); + log.error("More than 1"); } newType = keysByValue.get(0); if(actionSet.getParent() == null){ diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java index d32bc63..b55731c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java @@ -2,6 +2,7 @@ package edu.lu.uni.serval.FixPatternParser.cluster; import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.apache.commons.lang3.ArrayUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.Jedis; @@ -65,15 +66,32 @@ public class StoreFile { .filter(x -> !x.getName().startsWith(".")) .collect(Collectors.toList()); List workList = new ArrayList(); + File[] dumps; for (File pj : pjs) { String pjName = pj.getName(); File[] files = pj.listFiles(); Stream fileStream = Arrays.stream(files); - List fs = fileStream - .filter(x -> x.getName().startsWith(operation)) + List fs; + if (operation.equals("ALL")){ + fs= fileStream + .filter(x -> x.getName().startsWith("UPD") || + x.getName().startsWith("INS") || + x.getName().startsWith("DEL") || + x.getName().startsWith("MOV")) .collect(Collectors.toList()); + File[] files1 = fs.get(0).listFiles(); + File[] files2 = fs.get(1).listFiles(); + File[] files3 = fs.get(2).listFiles(); + File[] files4 = fs.get(3).listFiles(); + dumps = Stream.of(files1, files2, files3,files4).flatMap(Stream::of).toArray(File[]::new); + }else{ + fs = fileStream + .filter(x -> x.getName().startsWith(operation)) + .collect(Collectors.toList()); + dumps = fs.get(0).listFiles(); + } + - File[] dumps = fs.get(0).listFiles(); for (File f : dumps) { String name = f.getName(); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 5dea4a0..c67cc19 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -37,7 +37,7 @@ public class Launcher { String datasetPath = appProps.getProperty("datasetPath","/Users/anilkoyuncu/bugStudy/dataset"); String pjName = appProps.getProperty("pjName","allDataset"); String dbNo = appProps.getProperty("dbNo","0"); - String actionType = appProps.getProperty("actionType","UPD"); + String actionType = appProps.getProperty("actionType","ALL"); String threshold = appProps.getProperty("threshold","1"); String parameters = String.format("\nportInner %s " + @@ -94,6 +94,13 @@ public class Launcher { level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); + break; + case "EXTRACTPATTERN": + PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,port,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + break; + case "GETPATTERN": + PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,port,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + break; } } catch (Exception e) { e.printStackTrace(); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index ae9cc74..8f88ce3 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -158,15 +158,15 @@ public class ParseFixPatternWorker extends UntypedActor { sizes.setLength(0); tokens.setLength(0); - FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); +// FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); testingInfo.setLength(0); } - String statistic = "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + - "\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults + - "\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + - "\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts; - FileHelper.outputToFile("OUTPUT/statistic_" + id + ".list", statistic, false); - FileHelper.outputToFile("OUTPUT/UnfixedV_" + id + ".list", builder, false); +// String statistic = "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + +// "\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults + +// "\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + +// "\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts; +// FileHelper.outputToFile("OUTPUT/statistic_" + id + ".list", statistic, false); +// FileHelper.outputToFile("OUTPUT/UnfixedV_" + id + ".list", builder, false); log.info("Worker #" + id +"finialized parsing " + counter + " files..."); log.info("Worker #" + id + " finialized the work..."); diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java new file mode 100644 index 0000000..4810bad --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -0,0 +1,294 @@ +package edu.lu.uni.serval; + +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.TreeContext; +import edu.lu.uni.serval.FixPatternParser.violations.CallShell; +import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; + +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.time.Duration; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.JedisPoolConfig; + +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getASTTree; +import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getSimpliedTree; +import static edu.lu.uni.serval.Launcher.mainLaunch; + +/** + * Created by anilkoyuncu on 02/08/2018. + */ +public class PatternExtractor { + private static Logger log = LoggerFactory.getLogger(PatternExtractor.class); + + + public static void mainLaunch(String portInner,String serverWait, String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType,String threshold) { + + + String dbDir; + String pairsPath; + String dumpsName; + String gumInput; + String gumOutput; + + gumInput = datasetPath + "/" + pjName + "/"; + gumOutput = datasetPath + "/EnhancedASTDiff" + pjName; + dbDir = datasetPath + "/redis"; + pairsPath = datasetPath + "/pairsImport" + pjName; + dumpsName = "dumps-" + pjName + ".rdb"; + + try { + + String rootPath = "/Users/anilkoyuncu/bugStudy/code/python"; + + String IDLIST_PATH =rootPath + "/defects4jpatterns.txt"; + + List fixes = readIdList(IDLIST_PATH); + + switch (jobType) { + case "EXTRACTPATTERN": + loadDB(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType,fixes); + break; + case "GETPATTERN": + getPattern(fixes,actionType); + } + } catch (Exception e) { + e.printStackTrace(); + } + + } + + + public static void loadDB(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String operation,List fixes) throws Exception { +// String inputPath; +// String portInner; +// String serverWait; +// String dbDir; +// String chunkName; +// String numOfWorkers; +// if (args.length > 0) { +// inputPath = args[0]; +// portInner = args[1]; +// serverWait = args[2]; +// chunkName = args[3]; +// numOfWorkers = args[4]; +// dbDir = args[5]; +// } else { +// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; +// portInner = "6399"; +// serverWait = "10000"; +// chunkName ="dumps.rdb"; +// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; +// numOfWorkers = "1"; +// } + String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \noperation %s", inputPath, portInner, serverWait, chunkName, dbDir, operation); + log.info(parameters); + CallShell cs = new CallShell(); + String cmd = "bash " + dbDir + "/" + "startServer.sh" + " %s %s %s"; + cmd = String.format(cmd, dbDir, chunkName, Integer.valueOf(portInner)); +// loadRedis(cmd,serverWait); + cs.runShell(cmd, serverWait); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + + String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; + String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; + for (String pattern:fixes) { + File folder = new File(clusterPath + pattern); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List patches = stream + .filter(x -> !x.getName().startsWith(".")) + .filter(x-> x.getName().endsWith(".git")) + .collect(Collectors.toList()); + + for (File patch : patches) { + String fn = patch.getName(); + String[] split = fn.split("_"); + String project = split[split.length -1]; + List list = new ArrayList(Arrays.asList(split)); + list.remove(list.size() - 1); + String joinFN = String.join("_", list); + fn = project + "/" + operation + "/" + joinFN; + String saveFN = pattern + "_"+ project + "_" + operation + "_" + joinFN; + Jedis inner = null; + String s = null; + try { + inner = outerPool.getResource(); + s = inner.get(fn); + if (s != null) { + + HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); + + + BufferedWriter writer = new BufferedWriter(new FileWriter(savePath+saveFN)); + writer.write(toString(actionSet)); + + writer.close(); + + + + + + } + + } catch (Exception e) { + e.printStackTrace(); + } finally { + if (inner != null) { + inner.close(); + } + } + + + + + + + } + + } + + + + + + } + + public static void getPattern(List fixes,String operation){ + String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; + String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; + for (String pattern:fixes) { + File folder = new File(clusterPath + pattern); + File[] listOfFiles = folder.listFiles(); + Stream stream = Arrays.stream(listOfFiles); + List patches = stream + .filter(x -> !x.getName().startsWith(".")) + .filter(x -> x.getName().endsWith(".git")) + .collect(Collectors.toList()); + + for (File patch : patches) { + String fn = patch.getName(); + String[] split = fn.split("_"); + String project = split[split.length - 1]; + List list = new ArrayList(Arrays.asList(split)); + list.remove(list.size() - 1); + String joinFN = String.join("_", list); + fn = project + "/" + operation + "/" + joinFN; + String saveFN = pattern + "_" + project + "_" + operation + "_" + joinFN; + try{ + String content = new String(Files.readAllBytes(Paths.get(savePath + saveFN))); + HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(content); + + + ITree simpliedTree = getSimpliedTree(actionSet); + simpliedTree.toString(); + }catch (Exception e){ + e.printStackTrace(); + } + } + } + } + + public static ITree getSimpliedTree(HierarchicalActionSet actionSet) { + + ITree tree = null; + Jedis inner = null; + try { + + ITree parent = null; + ITree children = null; + TreeContext tc = new TreeContext(); + tree = getASTTree(actionSet, parent, children, tc); +// tree.setParent(null); + tc.validate(); + + } catch (Exception e) { + e.printStackTrace(); + } + return tree; + } + + + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + private static String toString( Serializable o ) throws IOException { + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + ObjectOutputStream oos = new ObjectOutputStream( baos ); + oos.writeObject( o ); + oos.close(); + return Base64.getEncoder().encodeToString(baos.toByteArray()); + } + + /** Read the object from Base64 string. */ + private static Object fromString( String s ) throws IOException , + ClassNotFoundException { + byte[] data = Base64.getDecoder().decode(s); + ObjectInputStream ois = new ObjectInputStream( + new ByteArrayInputStream(data)); + Object o = ois.readObject(); + ois.close(); + return o; + } + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(false); + poolConfig.setTestOnReturn(false); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); +// poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } + + + public static List readIdList(String fileName) { + try { + BufferedReader reader = new BufferedReader(new FileReader(new File(fileName))); + + // n = Rownum ; m = Colnum + List fixCommits = new ArrayList(); + String line = reader.readLine(); + + int i = 0, j = 0; + while (line != null) { + String strArray[] = line.split("\t"); + + if (!line.trim().isEmpty()) { + + GitTravellerDefects4J.FixCommit test = new GitTravellerDefects4J.FixCommit(strArray[1],strArray[0]); + fixCommits.add(strArray[0]); +// for (String s : strArray) { +// if (!s.trim().isEmpty()) { +// FixCommit test = new FixCommit("",""); +// array[i][j++] = s; +// } +// } + line = reader.readLine(); +// i++; +// j = 0; + } + } + reader.close(); + return fixCommits; + } catch (IOException ex) { + System.out.println("Problems.."); + } + return null; + } +} From 863f8ce223f3d1421624a2c43a4a04a61753df02 Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 2 Aug 2018 18:23:50 +0200 Subject: [PATCH 115/127] pythonpath --- src/main/java/edu/lu/uni/serval/PatternExtractor.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index 4810bad..10a78f7 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -48,9 +48,9 @@ public class PatternExtractor { try { - String rootPath = "/Users/anilkoyuncu/bugStudy/code/python"; - String IDLIST_PATH =rootPath + "/defects4jpatterns.txt"; + + String IDLIST_PATH =pythonPath + "/defects4jpatterns.txt"; List fixes = readIdList(IDLIST_PATH); From 40c117e3d353efc2bf77905088aebe71fb271570 Mon Sep 17 00:00:00 2001 From: fixminer Date: Fri, 3 Aug 2018 13:36:11 +0200 Subject: [PATCH 116/127] removal of depenceny --- .../edu/lu/uni/serval/PatternExtractor.java | 33 ++++++++++--------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index 10a78f7..b5198bf 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -2,8 +2,7 @@ package edu.lu.uni.serval; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.TreeContext; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; -import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; + import java.io.*; import java.nio.file.Files; @@ -21,8 +20,6 @@ import redis.clients.jedis.JedisPool; import redis.clients.jedis.JedisPoolConfig; import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getASTTree; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getSimpliedTree; -import static edu.lu.uni.serval.Launcher.mainLaunch; /** * Created by anilkoyuncu on 02/08/2018. @@ -79,7 +76,7 @@ public class PatternExtractor { // inputPath = args[0]; // portInner = args[1]; // serverWait = args[2]; -// chunkName = args[3]; +g// chunkName = args[3]; // numOfWorkers = args[4]; // dbDir = args[5]; // } else { @@ -90,15 +87,17 @@ public class PatternExtractor { // dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; // numOfWorkers = "1"; // } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \noperation %s", inputPath, portInner, serverWait, chunkName, dbDir, operation); - log.info(parameters); - CallShell cs = new CallShell(); - String cmd = "bash " + dbDir + "/" + "startServer.sh" + " %s %s %s"; - cmd = String.format(cmd, dbDir, chunkName, Integer.valueOf(portInner)); -// loadRedis(cmd,serverWait); - cs.runShell(cmd, serverWait); +// String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \noperation %s", inputPath, portInner, serverWait, chunkName, dbDir, operation); +// log.info(parameters); +// CallShell cs = new CallShell(); +// String cmd = "bash " + dbDir + "/" + "startServer.sh" + " %s %s %s"; +// cmd = String.format(cmd, dbDir, chunkName, Integer.valueOf(portInner)); +//// loadRedis(cmd,serverWait); +// cs.runShell(cmd, serverWait); + + JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(6399),20000000); + - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; @@ -108,7 +107,7 @@ public class PatternExtractor { Stream stream = Arrays.stream(listOfFiles); List patches = stream .filter(x -> !x.getName().startsWith(".")) - .filter(x-> x.getName().endsWith(".git")) +// .filter(x-> x.getName().endsWith(".git")) .collect(Collectors.toList()); for (File patch : patches) { @@ -139,6 +138,8 @@ public class PatternExtractor { + }else{ + log.error(fn); } } catch (Exception e) { @@ -173,7 +174,7 @@ public class PatternExtractor { Stream stream = Arrays.stream(listOfFiles); List patches = stream .filter(x -> !x.getName().startsWith(".")) - .filter(x -> x.getName().endsWith(".git")) +// .filter(x -> x.getName().endsWith(".git")) .collect(Collectors.toList()); for (File patch : patches) { @@ -271,7 +272,7 @@ public class PatternExtractor { if (!line.trim().isEmpty()) { - GitTravellerDefects4J.FixCommit test = new GitTravellerDefects4J.FixCommit(strArray[1],strArray[0]); +// GitTravellerDefects4J.FixCommit test = new GitTravellerDefects4J.FixCommit(strArray[1],strArray[0]); fixCommits.add(strArray[0]); // for (String s : strArray) { // if (!s.trim().isEmpty()) { From b6d4c9a42e13b0295db7f9268ba20b9f37779ffc Mon Sep 17 00:00:00 2001 From: fixminer Date: Fri, 3 Aug 2018 13:40:19 +0200 Subject: [PATCH 117/127] removal of depenceny --- src/main/java/edu/lu/uni/serval/PatternExtractor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index b5198bf..3ccce6e 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -76,7 +76,7 @@ public class PatternExtractor { // inputPath = args[0]; // portInner = args[1]; // serverWait = args[2]; -g// chunkName = args[3]; +// chunkName = args[3]; // numOfWorkers = args[4]; // dbDir = args[5]; // } else { From 151a0a09a0cd06fa0cd0d39476801017741f2b7a Mon Sep 17 00:00:00 2001 From: fixminer Date: Mon, 6 Aug 2018 11:41:15 +0200 Subject: [PATCH 118/127] read all patterns --- .../edu/lu/uni/serval/PatternExtractor.java | 30 +++++++++++++++---- 1 file changed, 24 insertions(+), 6 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index 3ccce6e..f5e2459 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -101,8 +101,17 @@ public class PatternExtractor { String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; - for (String pattern:fixes) { - File folder = new File(clusterPath + pattern); + File patternsF = new File(clusterPath); + File[] listOfPatterns = patternsF.listFiles(); + Stream patterns = Arrays.stream(listOfPatterns); + List patternsL = patterns + .filter(x -> !x.getName().startsWith(".")) +// .filter(x-> x.getName().endsWith(".git")) + .collect(Collectors.toList()); + + + for (File pattern:patternsL) { + File folder = new File(clusterPath + pattern.getName()); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List patches = stream @@ -118,7 +127,7 @@ public class PatternExtractor { list.remove(list.size() - 1); String joinFN = String.join("_", list); fn = project + "/" + operation + "/" + joinFN; - String saveFN = pattern + "_"+ project + "_" + operation + "_" + joinFN; + String saveFN = pattern.getName() + "_"+ project + "_" + operation + "_" + joinFN; Jedis inner = null; String s = null; try { @@ -168,8 +177,17 @@ public class PatternExtractor { public static void getPattern(List fixes,String operation){ String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; - for (String pattern:fixes) { - File folder = new File(clusterPath + pattern); + + File patternsF = new File(clusterPath); + File[] listOfPatterns = patternsF.listFiles(); + Stream patterns = Arrays.stream(listOfPatterns); + List patternsL = patterns + .filter(x -> !x.getName().startsWith(".")) +// .filter(x-> x.getName().endsWith(".git")) + .collect(Collectors.toList()); + + for (File pattern:patternsL) { + File folder = new File(clusterPath + pattern.getName()); File[] listOfFiles = folder.listFiles(); Stream stream = Arrays.stream(listOfFiles); List patches = stream @@ -185,7 +203,7 @@ public class PatternExtractor { list.remove(list.size() - 1); String joinFN = String.join("_", list); fn = project + "/" + operation + "/" + joinFN; - String saveFN = pattern + "_" + project + "_" + operation + "_" + joinFN; + String saveFN = pattern.getName() + "_" + project + "_" + operation + "_" + joinFN; try{ String content = new String(Files.readAllBytes(Paths.get(savePath + saveFN))); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(content); From 10feafe43b2c67be94854579811518485a191b26 Mon Sep 17 00:00:00 2001 From: fixminer Date: Tue, 7 Aug 2018 18:47:51 +0200 Subject: [PATCH 119/127] reader --- .../edu/lu/uni/serval/PatternExtractor.java | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index f5e2459..db36733 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -20,6 +20,7 @@ import redis.clients.jedis.JedisPool; import redis.clients.jedis.JedisPoolConfig; import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getASTTree; +import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster3.getNames; /** * Created by anilkoyuncu on 02/08/2018. @@ -210,6 +211,21 @@ public class PatternExtractor { ITree simpliedTree = getSimpliedTree(actionSet); + + + List oldTokens = new ArrayList<>(); + List newTokens = new ArrayList<>(); + + +// if(secondValue.startsWith("/2/")){ +// log.info("newss"); +// } + + // 41 return statement + + oldTokens = getNames(actionSet.getNode(),oldTokens); + + simpliedTree.toString(); }catch (Exception e){ e.printStackTrace(); @@ -300,6 +316,101 @@ public class PatternExtractor { // } line = reader.readLine(); // i++; +// j = 0; + } + } + reader.close(); + return fixCommits; + } catch (IOException ex) { + System.out.println("Problems.."); + } + return null; + } + + + + public static class ProjectLiteral { + + + private String name; + private String file; + private String packageName; + private String className; + private String extend; + private String[] StringLit; + private String[] NumLit; + + + + + +// pj, file, p['packageName'], p['className'], +// p['extends'], p['StringLiteral'], p['NumberLiteral'] + ProjectLiteral(){} + + ProjectLiteral(String name, String file,String packageName, String className,String extend, String sLit, String nLit) { + this.name = name; + this.file = file; + this.packageName = packageName; + this.className = className; + this.extend = extend; + this.StringLit = sLit.split(";"); + this.NumLit = nLit.split(";"); + + + } +// projectLiterals.stream().filter(x->x.className.equals("XYTitleAnnotation")).collect(Collectors.toList()) + + + } + + + public static void main(String[] args) throws IOException { + List projectLiterals = readProjectCSV("/Users/anilkoyuncu/bugStudy/code/python/chart.csv"); + System.out.print(""); + } + + public static List readProjectCSV(String fileName) { + try { + BufferedReader reader = new BufferedReader(new FileReader(new File(fileName))); + + // n = Rownum ; m = Colnum + List fixCommits = new ArrayList(); + String line = reader.readLine(); + + int i = 0, j = 0; + while (line != null) { + String strArray[] = line.split("\t"); + + if (!line.trim().isEmpty()) { + log.info(String.valueOf(strArray.length)); + ProjectLiteral a = new ProjectLiteral(); + if (strArray.length == 8) { + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], strArray[7]); + }else if(strArray.length == 7){ + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], ""); + }else if(strArray.length == 6){ + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], "", ""); + + }else if(strArray.length == 5){ + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], "", "", ""); + }else if(strArray.length == 4){ + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], "", "", "", ""); + } + else{ + log.error("error"); + } + +// GitTravellerDefects4J.FixCommit test = new GitTravellerDefects4J.FixCommit(strArray[1],strArray[0]); + fixCommits.add(a); +// for (String s : strArray) { +// if (!s.trim().isEmpty()) { +// FixCommit test = new FixCommit("",""); +// array[i][j++] = s; +// } +// } + line = reader.readLine(); +// i++; // j = 0; } } From eddf8b0d3e878ea4fa2616d2c4430e43c16ce458 Mon Sep 17 00:00:00 2001 From: Kui Liu Date: Tue, 7 Aug 2018 19:47:01 +0200 Subject: [PATCH 120/127] Reading fix patterns. --- inputData/1.txt | 730 ++++++++++++++++++ pom.xml | 8 +- .../MultiThreadTreeLoaderCluster.java | 1 + .../MultiThreadTreeLoaderCluster3.java | 64 +- src/main/java/edu/lu/uni/serval/Launcher.java | 2 +- .../edu/lu/uni/serval/PatternExtractor.java | 27 +- .../java/edu/lu/uni/serval/TreeToString.java | 47 ++ .../regroup/HierarchicalRegrouperForC.java | 34 +- 8 files changed, 860 insertions(+), 53 deletions(-) create mode 100644 inputData/1.txt create mode 100644 src/main/java/edu/lu/uni/serval/TreeToString.java diff --git a/inputData/1.txt b/inputData/1.txt new file mode 100644 index 0000000..46e4275 --- /dev/null +++ b/inputData/1.txt @@ -0,0 +1,730 @@ 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+https://github.com/scifio/scifio.git +https://github.com/alibaba/RocketMQ.git +https://github.com/kuujo/copycat.git +https://github.com/jankotek/MapDB.git +https://github.com/droolsjbpm/kie-wb-distributions.git +https://github.com/buschmais/jqassistant.git +https://github.com/PLOS/ambra.git +https://github.com/spring-cloud/spring-cloud-netflix.git +https://github.com/apache/commons-math.git +https://github.com/OpenHFT/Chronicle-Network.git +https://github.com/chocoteam/choco3.git +https://github.com/apache/flume.git +https://github.com/rinde/RinSim.git +https://github.com/kotcrab/VisEditor.git +https://github.com/void256/nifty-gui.git +https://github.com/apache/uima-ducc.git +https://github.com/windup/windup.git +https://github.com/heuermh/dishevelled.git +https://github.com/salyh/javamailspec.git +https://github.com/SpoutDev/Spout.git +https://github.com/antlr/antlr4.git +https://github.com/Flipkart/quartz.git +https://github.com/rasto/lcmc.git +https://github.com/mafagafogigante/dungeon.git +https://github.com/PerfGeeks/pinpoint.git +https://github.com/opendaylight/openflowplugin.git +https://github.com/EngineHub/CommandHelper.git +https://github.com/tananaev/traccar.git +https://github.com/BroadleafCommerce/BroadleafCommerce.git +https://github.com/apache/hadoop-common.git +https://github.com/spring-projects/spring-boot.git +https://github.com/bcdev/beam.git +https://github.com/weld/core.git +https://github.com/elki-project/elki.git +https://github.com/belaban/JGroups.git +https://github.com/molgenis/molgenis.git +https://github.com/lennartj/jaxb2-maven-plugin.git +https://github.com/bugcy013/opennms-tmp-tools.git +https://github.com/Talend/tcommon-studio-se.git +https://github.com/netty/netty.git +https://github.com/openmicroscopy/bioformats.git +https://github.com/droolsjbpm/guvnor.git +https://github.com/jetty-project/codehaus-jetty6.git +https://github.com/apache/jackrabbit-oak.git +https://github.com/deegree/deegree3.git +https://github.com/apache/sling.git +https://github.com/EriclLee/ActiveMQ-On-Azure.git +https://github.com/amplab/tachyon.git +https://github.com/neo4j/neo4j.git +https://github.com/darranl/directory-server.git +https://github.com/hazelcast/hazelcast.git +https://github.com/infinispan/infinispan.git +https://github.com/DSpace/DSpace.git +https://github.com/mulesoft/mule.git +https://github.com/imCodePartnerAB/imcms.git +https://github.com/backslash47/webstart-maven-plugin.git +https://github.com/apache/hbase.git +https://github.com/languagetool-org/languagetool.git +https://github.com/droolsjbpm/drools.git +https://github.com/SpigotMC/Spigot-API.git +https://github.com/irstv/orbisgis.git +https://github.com/jgheerardyn/yields.git +https://github.com/ning/killbill.git +https://github.com/jline/jline2.git +https://github.com/altran/Whydah-UserIdentityBackend.git +https://github.com/encog/encog-java-core.git +https://github.com/highsource/jaxb2-basics.git +https://github.com/msoute/vertx-deploy-tools.git +https://github.com/apache/portals-pluto.git +https://github.com/antlr/stringtemplate4.git +https://github.com/kongchen/swagger-maven-plugin.git +https://github.com/gertvv/addis.git +https://github.com/ProjectCCNx/ccnx.git +https://github.com/mulesoft/mule-common.git +https://github.com/cismet/cismap-plugin.git +https://github.com/greese/dasein-cloud-azure.git +https://github.com/Requinard/TeamTab.git +https://github.com/SonarSource/jenkins-sonar-plugin.git +https://github.com/fbacchella/jrds.git +https://github.com/cdi-spec/cdi-tck.git +https://github.com/gwtbootstrap3/gwtbootstrap3.git +https://github.com/apache/commons-dbcp.git +https://github.com/timmolter/XChart.git +https://github.com/aranega/testgen.git +https://github.com/mysticfall/pivot4j.git +https://github.com/datasift/datasift-java.git +https://github.com/viktor-z/fb2pdf.git +https://github.com/Cas-B/Group17-BubbleBobble.git +https://github.com/TheCoder4eu/BootsFaces-OSP.git +https://github.com/UnifiedViews/Plugin-DevEnv.git +https://github.com/jidesoft/jide-oss.git +https://github.com/codescape/bitvunit.git +https://github.com/grandwazir/BanHammer.git +https://github.com/wildfly/wildfly-arquillian.git +https://github.com/Eluinhost/pluginframework.git +https://github.com/mtedone/podam.git +https://github.com/Mobicents/jss7.git +https://github.com/basis-technology-corp/rosette-common-java-api.git +https://github.com/webbit/webbit.git +https://github.com/GWASpi/GWASpi.git +https://github.com/jenkinsci/warnings-plugin.git +https://github.com/google/auto.git +https://github.com/TechnicPack/LauncherV3.git +https://github.com/ArtificerRepo/artificer.git +https://github.com/Jahia/external-provider.git +https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore.git +https://github.com/PEXPlugins/PermissionsEx.git \ No newline at end of file diff --git a/pom.xml b/pom.xml index f999f12..36579b2 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,13 @@ - + + + org.javatuples + javatuples + 1.2 + + edu.lu.uni simple-utils diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java index 3cbab7d..4282c0c 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java @@ -8,6 +8,7 @@ import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.TreeContext; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.utils.FileHelper; + import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 3ebca74..78ba333 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -1,38 +1,42 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.*; -import com.github.gumtreediff.matchers.Matcher; -import com.github.gumtreediff.matchers.Matchers; -import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.TreeContext; -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.gumtree.GumTreeComparer; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; -import org.apache.commons.lang3.StringUtils; -import org.javatuples.Pair; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import redis.clients.jedis.*; - -import java.io.*; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; -import java.time.Duration; -import java.util.*; -import java.util.concurrent.Executors; -import java.util.function.Consumer; -import java.util.regex.Pattern; -import java.util.stream.Collectors; -import java.util.stream.Stream; -import org.apache.commons.text.similarity.*; - import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getKeysByValue; import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster.fromString; +import java.io.BufferedOutputStream; +import java.io.DataOutputStream; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.IOException; +import java.time.Duration; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeSet; +import java.util.regex.Pattern; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.text.similarity.JaroWinklerDistance; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.TreeContext; + +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import edu.lu.uni.serval.utils.FileHelper; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.JedisPoolConfig; +import redis.clients.jedis.ScanParams; +import redis.clients.jedis.ScanResult; + /** * Created by anilkoyuncu on 19/03/2018. */ diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index c67cc19..35ac556 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -24,7 +24,7 @@ public class Launcher { Properties appProps = new Properties(); - String appConfigPath = args[0]; + String appConfigPath = "/Users/kui.liu/Downloads/app.properties";//args[0]; // String appConfigPath = "/Users/anilkoyuncu/bugStudy/release/code/app.properties"; appProps.load(new FileInputStream(appConfigPath)); diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index f5e2459..8b04ba8 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -12,6 +12,8 @@ import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; +import edu.lu.uni.serval.FixPattern.utils.Checker; +import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -175,15 +177,15 @@ public class PatternExtractor { } public static void getPattern(List fixes,String operation){ - String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; - String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; + String clusterPath = "/Users/kui.liu/Downloads/clusterallDatasetUPD/"; + String savePath = "/Users/kui.liu/Downloads/dumps/"; File patternsF = new File(clusterPath); File[] listOfPatterns = patternsF.listFiles(); Stream patterns = Arrays.stream(listOfPatterns); List patternsL = patterns .filter(x -> !x.getName().startsWith(".")) -// .filter(x-> x.getName().endsWith(".git")) +// .filter(x -> !x.getName().endsWith(".git")) .collect(Collectors.toList()); for (File pattern:patternsL) { @@ -192,7 +194,7 @@ public class PatternExtractor { Stream stream = Arrays.stream(listOfFiles); List patches = stream .filter(x -> !x.getName().startsWith(".")) -// .filter(x -> x.getName().endsWith(".git")) + .filter(x -> !x.getName().endsWith(".git")) .collect(Collectors.toList()); for (File patch : patches) { @@ -208,13 +210,26 @@ public class PatternExtractor { String content = new String(Files.readAllBytes(Paths.get(savePath + saveFN))); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(content); + int astType = actionSet.getNode().getType(); + if (Checker.isStatement(astType) || astType == 23 //FieldDeclaration + || astType == 31 //MethodDeclaration + || astType == 55) {//TypeDeclaration + System.out.println(actionSet); +// ITree actionTree = MultiThreadTreeLoader.getActionTree(actionSet, null, null); +// ITree simpliedTree = getSimpliedTree(actionSet); +// System.out.println(new TreeToString().toString(simpliedTree)); +// System.out.println(new TreeToString().toString(actionTree)); + System.out.println("======"); + } + - ITree simpliedTree = getSimpliedTree(actionSet); - simpliedTree.toString(); +// ITree simpliedTree = getSimpliedTree(actionSet); +// simpliedTree.toString(); }catch (Exception e){ e.printStackTrace(); } } + System.out.println("============"); } } diff --git a/src/main/java/edu/lu/uni/serval/TreeToString.java b/src/main/java/edu/lu/uni/serval/TreeToString.java new file mode 100644 index 0000000..e234b69 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/TreeToString.java @@ -0,0 +1,47 @@ +package edu.lu.uni.serval; + +import java.util.ArrayList; +import java.util.List; + +import com.github.gumtreediff.tree.ITree; + +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; + +public class TreeToString { + + private List strList = new ArrayList<>(); + + public String toString(ITree tree) { + List children = tree.getChildren(); + String str = ASTNodeMap.map.get(tree.getType()); + if (strList.size() == 0) { + strList.add(str); + for (ITree child : children) { + TreeToString t2s = new TreeToString(); + t2s.toString(child); + List strList1 = t2s.strList; + for (String str1 : strList1) { + strList.add("---" + str1); + } + } + } else { + strList.clear(); + strList.add(str); + for (ITree child : children) { + TreeToString t2s = new TreeToString(); + t2s.toString(child); + List strList1 = t2s.strList; + for (String str1 : strList1) { + strList.add("---" + str1); + } + } + } + + str = ""; + for (String str1 : strList) { + str += str1 + "\n"; + } + + return str; + } +} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java index d98ef8f..23df400 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java @@ -1,15 +1,19 @@ package edu.lu.uni.serval.gumtree.regroup; -import com.github.gumtreediff.actions.model.*; -import com.github.gumtreediff.tree.ITree; -import edu.lu.uni.serval.FixPattern.utils.CNodeMap; -import edu.lu.uni.serval.gumtree.GumTreeComparer; -import edu.lu.uni.serval.utils.ListSorter; - -import java.io.File; import java.util.ArrayList; import java.util.List; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.actions.model.Addition; +import com.github.gumtreediff.actions.model.Delete; +import com.github.gumtreediff.actions.model.Insert; +import com.github.gumtreediff.actions.model.Move; +import com.github.gumtreediff.actions.model.Update; +import com.github.gumtreediff.tree.ITree; + +import edu.lu.uni.serval.FixPattern.utils.CNodeMap; +import edu.lu.uni.serval.utils.ListSorter; + /** * Regroup GumTree results to a hierarchical construction. * @@ -18,14 +22,14 @@ import java.util.List; */ public class HierarchicalRegrouperForC { - public static void main(String[] args) { - GumTreeComparer com = new GumTreeComparer(); - File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c"); - File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c"); - List action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2); - List actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action); - System.out.println(actionSet); - } +// public static void main(String[] args) { +// GumTreeComparer com = new GumTreeComparer(); +// File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c"); +// File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c"); +// List action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2); +// List actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action); +// System.out.println(actionSet); +// } List actionSets = new ArrayList<>(); From 3d678eebb6a6c913152a7c7a86f63f01760759a2 Mon Sep 17 00:00:00 2001 From: fixminer Date: Wed, 8 Aug 2018 13:18:14 +0200 Subject: [PATCH 121/127] addition of memberReference and mI --- .../edu/lu/uni/serval/PatternExtractor.java | 22 +++++++++++++------ 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index db36733..5205cac 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -339,6 +339,8 @@ public class PatternExtractor { private String extend; private String[] StringLit; private String[] NumLit; + private String[] memberReference; + private String[] methodInvocation; @@ -348,7 +350,7 @@ public class PatternExtractor { // p['extends'], p['StringLiteral'], p['NumberLiteral'] ProjectLiteral(){} - ProjectLiteral(String name, String file,String packageName, String className,String extend, String sLit, String nLit) { + ProjectLiteral(String name, String file,String packageName, String className,String extend, String sLit, String nLit, String mr ,String mi) { this.name = name; this.file = file; this.packageName = packageName; @@ -356,6 +358,8 @@ public class PatternExtractor { this.extend = extend; this.StringLit = sLit.split(";"); this.NumLit = nLit.split(";"); + this.memberReference = mr.split(";"); + this.methodInvocation = nLit.split(";"); } @@ -385,17 +389,21 @@ public class PatternExtractor { if (!line.trim().isEmpty()) { log.info(String.valueOf(strArray.length)); ProjectLiteral a = new ProjectLiteral(); - if (strArray.length == 8) { - a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], strArray[7]); + if (strArray.length == 10) { + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], strArray[7],strArray[8],strArray[9]); + }else if (strArray.length == 9) { + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], strArray[7],strArray[8],""); + }else if (strArray.length == 8) { + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], strArray[7],"",""); }else if(strArray.length == 7){ - a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], ""); + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], strArray[6], "","",""); }else if(strArray.length == 6){ - a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], "", ""); + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], strArray[5], "", "","",""); }else if(strArray.length == 5){ - a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], "", "", ""); + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], strArray[4], "", "", "","",""); }else if(strArray.length == 4){ - a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], "", "", "", ""); + a = new ProjectLiteral(strArray[1], strArray[2], strArray[3], "", "", "", "","",""); } else{ log.error("error"); From bf19c4c02f090ceadf3761163bb7b4f2b15c9a94 Mon Sep 17 00:00:00 2001 From: fixminer Date: Sun, 9 Sep 2018 11:59:17 +0200 Subject: [PATCH 122/127] FIX: from pure action set to ALL --- .../violations/FixedViolationHunkParser.java | 40 +++++++++---------- .../MultiThreadTreeLoaderCluster3.java | 2 +- .../violations/TestHunkParser.java | 1 + src/main/java/edu/lu/uni/serval/Launcher.java | 14 +++---- .../edu/lu/uni/serval/PatternExtractor.java | 8 ++-- 5 files changed, 33 insertions(+), 32 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index 485d0f0..ccf4804 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -44,27 +44,27 @@ public class FixedViolationHunkParser extends FixedViolationParser { public void parseFixPatterns(File prevFile, File revFile, File diffentryFile,String project) { List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); if (actionSets.size() != 0) { - boolean isUpdate = - actionSets.stream().allMatch(p -> p.getAction() instanceof Update); - boolean isInsert = - actionSets.stream().allMatch(p -> p.getAction() instanceof Insert); - boolean isDelete = - actionSets.stream().allMatch(p -> p.getAction() instanceof Delete); - boolean isMove = - actionSets.stream().allMatch(p -> p.getAction() instanceof Move); +// boolean isUpdate = +// actionSets.stream().allMatch(p -> p.getAction() instanceof Update); +// boolean isInsert = +// actionSets.stream().allMatch(p -> p.getAction() instanceof Insert); +// boolean isDelete = +// actionSets.stream().allMatch(p -> p.getAction() instanceof Delete); +// boolean isMove = +// actionSets.stream().allMatch(p -> p.getAction() instanceof Move); int hunkSet = 0; - if (isUpdate || isInsert || isDelete || isMove) { +// if (isUpdate || isInsert || isDelete || isMove) { for (HierarchicalActionSet actionSet : actionSets) { - String folder = null; - if (isUpdate) { - folder = "/UPD/"; - } else if (isDelete) { - folder = "/DEL/"; - } else if (isInsert) { - folder = "/INS/"; - } else if (isMove) { - folder = "/MOV/"; - } + String folder = "/ALL/"; +// if (isUpdate) { +// folder = "/UPD/"; +// } else if (isDelete) { +// folder = "/DEL/"; +// } else if (isInsert) { +// folder = "/INS/"; +// } else if (isMove) { +// folder = "/MOV/"; +// } FileOutputStream f = null; @@ -91,7 +91,7 @@ public class FixedViolationHunkParser extends FixedViolationParser { hunkSet++; } - } +// } } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 3ebca74..445cd3a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -230,7 +230,7 @@ public class MultiThreadTreeLoaderCluster3 { } - private static List getNames(ITree oldTree, List oldTokens){ + public static List getNames(ITree oldTree, List oldTokens){ List descendants = oldTree.getDescendants(); descendants.add(0,oldTree); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index 7f2a019..d9bdd1f 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -75,6 +75,7 @@ public class TestHunkParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); + System.out.println(system.settings()); parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), project), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index c67cc19..9e167fc 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -112,13 +112,13 @@ public class Launcher { } private static void level1(String portInner, String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception { - CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); - - ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); - - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); - - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); +// CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); +// +// ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); +// +// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); +// +// TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); CallShell cs1 =new CallShell(); String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/PatternExtractor.java index 5205cac..5360b58 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/PatternExtractor.java @@ -100,8 +100,8 @@ public class PatternExtractor { - String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; - String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; + String clusterPath = "/Users/anilkoyuncu/bugStudy/release/code/clusterallDataset"+operation+"/"; + String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps"+operation+"/"; File patternsF = new File(clusterPath); File[] listOfPatterns = patternsF.listFiles(); Stream patterns = Arrays.stream(listOfPatterns); @@ -177,8 +177,8 @@ public class PatternExtractor { public static void getPattern(List fixes,String operation){ String clusterPath = "/Users/anilkoyuncu/bugStudy/release/dataset/output/clusterallDatasetUPD/"; - String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; - +// String savePath = "/Users/anilkoyuncu/bugStudy/release/dataset/dumps/"; + String savePath = "/Volumes/anil.koyuncu/dumps/"; File patternsF = new File(clusterPath); File[] listOfPatterns = patternsF.listFiles(); Stream patterns = Arrays.stream(listOfPatterns); From a8885c5eeaac8972689417fe12c198846bb06e18 Mon Sep 17 00:00:00 2001 From: fixminer Date: Mon, 10 Sep 2018 18:08:50 +0200 Subject: [PATCH 123/127] new change for big data --- .../cluster/CalculatePairs.java | 72 ++++++++++--------- .../cluster/ImportPairs2DB.java | 2 +- .../FixPatternParser/cluster/StoreFile.java | 2 +- .../MultiThreadTreeLoaderCluster3.java | 2 + .../violations/TestHunkParser.java | 1 + src/main/java/edu/lu/uni/serval/Launcher.java | 17 +++-- 6 files changed, 52 insertions(+), 44 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java index e72be9e..f906103 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java @@ -10,6 +10,8 @@ import redis.clients.jedis.ScanParams; import redis.clients.jedis.ScanResult; import java.io.*; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; import java.util.List; import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poolConfig; @@ -44,7 +46,7 @@ public class CalculatePairs { ScanParams sc = new ScanParams(); //150000000 - sc.count(150000000); + sc.count(1500000000); sc.match("*"); scan = outer.scan("0", sc); @@ -59,26 +61,9 @@ public class CalculatePairs { byte [] buf = new byte[0]; String line = null; try { - FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".csv"); - DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); - - - - for (int i = 0; i < result.size(); i++) { - for (int j = i + 1; j < result.size(); j++) { - - - - line = String.valueOf(i) +"," + String.valueOf(j) + "," + result.get(i) + "," + result.get(j)+"\n"; - outStream.write(line.getBytes()); - - } - } - outStream.close(); -// int fileCounter = 0; -// FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); -// int maxSize = 500*500000; -// ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); +// FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".csv"); +// DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); +// // // // for (int i = 0; i < result.size(); i++) { @@ -86,23 +71,40 @@ public class CalculatePairs { // // // -// line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; -// buf = line.getBytes(); -// if(wrBuf.remaining() > 500) { -// wrBuf.put(buf); -// }else{ -// log.info("Next pair dump"); -// fileCounter++; -// rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); -// wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); -// } -// -// -// +// line = String.valueOf(i) +"," + String.valueOf(j) + "," + result.get(i) + "," + result.get(j)+"\n"; +// outStream.write(line.getBytes()); // // } // } -// rwChannel.close(); +// outStream.close(); + int fileCounter = 0; + FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); + int maxSize = 500*500000; + ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); + + + for (int i = 0; i < result.size(); i++) { + for (int j = i + 1; j < result.size(); j++) { + + + + line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; + buf = line.getBytes(); + if(wrBuf.remaining() > 500) { + wrBuf.put(buf); + }else{ + log.info("Next pair dump"); + fileCounter++; + rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel(); + wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); + } + + + + + } + } + rwChannel.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java index a170fe6..3571263 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java @@ -32,7 +32,7 @@ public class ImportPairs2DB { File[] subFolders = folder.listFiles(); Stream stream = Arrays.stream(subFolders); List pjs = stream - .filter(x -> x.getName().endsWith(".csv")) + .filter(x -> x.getName().endsWith(".txt")) .collect(Collectors.toList()); Integer portInt = Integer.valueOf(portInner); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java index b55731c..d89e87b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java @@ -72,7 +72,7 @@ public class StoreFile { File[] files = pj.listFiles(); Stream fileStream = Arrays.stream(files); List fs; - if (operation.equals("ALL")){ + if (operation.equals("ALLOP")){ fs= fileStream .filter(x -> x.getName().startsWith("UPD") || x.getName().startsWith("INS") || diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java index 445cd3a..80a8802 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java @@ -565,6 +565,8 @@ public class MultiThreadTreeLoaderCluster3 { CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); CharSequence[] newSequences = newTokens.toArray(new CharSequence[newTokens.size()]); JaroWinklerDistance jwd = new JaroWinklerDistance(); + LevenshteinDistance ld = new LevenshteinDistance(); + Double overallSimi = Double.valueOf(1); if(oldSequences.length > 0 && (oldSequences.length == newSequences.length)){ for (int idx = 0; idx < newSequences.length; idx++) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java index d9bdd1f..3d8916e 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java @@ -55,6 +55,7 @@ public class TestHunkParser { FileHelper.createDirectory(GUM_TREE_OUTPUT + "/INS"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/DEL"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/MOV"); + FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ALL"); // FileHelper.deleteDirectory(editScriptsFilePath); // FileHelper.deleteDirectory(patchesSourceCodeFilePath); // FileHelper.deleteDirectory(buggyTokensFilePath); diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/Launcher.java index 9e167fc..4944628 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/Launcher.java @@ -77,6 +77,13 @@ public class Launcher { case "CACHE": StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); break; + case "COMP": + CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); + + ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); + + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); + case "LEVEL1": level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); break; @@ -112,13 +119,9 @@ public class Launcher { } private static void level1(String portInner, String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception { -// CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); -// -// ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); -// -// AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); -// -// TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); + + + TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); CallShell cs1 =new CallShell(); String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; From 0d391e1ab921dd30f626130b951f0232181e4837 Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 13 Sep 2018 16:18:06 +0200 Subject: [PATCH 124/127] akka version of tree comp --- pom.xml | 4 +- .../uni/serval/{ => fixminer}/Launcher.java | 50 +++--- .../{ => fixminer}/PatternExtractor.java | 26 +-- .../cluster/AkkaTreeLoader.java | 114 ++++++++++--- .../cluster/CalculatePairs.java | 22 ++- .../cluster}/CallShell.java | 6 +- .../cluster/Compare.java | 22 +-- .../cluster/ImportPairs2DB.java | 8 +- .../cluster}/MultiThreadTreeLoader.java | 6 +- .../MultiThreadTreeLoaderCluster.java | 6 +- .../MultiThreadTreeLoaderCluster3.java | 60 +++---- .../cluster}/RunnableCompare.java | 3 +- .../cluster/StoreFile.java | 9 +- .../cluster}/TreeActor.java | 41 ++--- .../cluster/TreeLoaderClusterL1.java | 3 +- .../cluster}/TreeWorker.java | 150 +++++++++++------- .../cluster}/WorkMessage.java | 4 +- .../fixminer/cluster/akka/AkkaTreeParser.java | 75 +++++++++ .../fixminer/cluster/akka/TreeMessage.java | 54 +++++++ 19 files changed, 432 insertions(+), 231 deletions(-) rename src/main/java/edu/lu/uni/serval/{ => fixminer}/Launcher.java (76%) rename src/main/java/edu/lu/uni/serval/{ => fixminer}/PatternExtractor.java (98%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser => fixminer}/cluster/AkkaTreeLoader.java (67%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser => fixminer}/cluster/CalculatePairs.java (82%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/CallShell.java (89%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser => fixminer}/cluster/Compare.java (78%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser => fixminer}/cluster/ImportPairs2DB.java (84%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/MultiThreadTreeLoader.java (99%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/MultiThreadTreeLoaderCluster.java (98%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/MultiThreadTreeLoaderCluster3.java (95%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/RunnableCompare.java (81%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser => fixminer}/cluster/StoreFile.java (93%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/TreeActor.java (56%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser => fixminer}/cluster/TreeLoaderClusterL1.java (97%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/TreeWorker.java (63%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer/cluster}/WorkMessage.java (87%) create mode 100644 src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/AkkaTreeParser.java create mode 100644 src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/TreeMessage.java diff --git a/pom.xml b/pom.xml index 36579b2..016c216 100644 --- a/pom.xml +++ b/pom.xml @@ -140,8 +140,8 @@ - edu.lu.uni.serval.Launcher - + edu.lu.uni.serval.fixminer.Launcher + diff --git a/src/main/java/edu/lu/uni/serval/Launcher.java b/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java similarity index 76% rename from src/main/java/edu/lu/uni/serval/Launcher.java rename to src/main/java/edu/lu/uni/serval/fixminer/Launcher.java index f1f170d..400f9a2 100644 --- a/src/main/java/edu/lu/uni/serval/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java @@ -1,10 +1,7 @@ -package edu.lu.uni.serval; +package edu.lu.uni.serval.fixminer; -import edu.lu.uni.serval.FixPatternParser.cluster.*; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; -import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster; -import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster3; import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; +import edu.lu.uni.serval.fixminer.cluster.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -24,37 +21,40 @@ public class Launcher { Properties appProps = new Properties(); - String appConfigPath = "/Users/kui.liu/Downloads/app.properties";//args[0]; +// String appConfigPath = "/Users/kui.liu/Downloads/app.properties";//args[0]; // String appConfigPath = "/Users/anilkoyuncu/bugStudy/release/code/app.properties"; + String appConfigPath = args[0]; appProps.load(new FileInputStream(appConfigPath)); String portInner = appProps.getProperty("portInner","6380"); String serverWait = appProps.getProperty("serverWait", "50000"); String numOfWorkers = appProps.getProperty("numOfWorkers", "10"); String jobType = appProps.getProperty("jobType","ALL"); - String port = appProps.getProperty("port","6399"); + String portDumps = appProps.getProperty("portDumps","6399"); String pythonPath = appProps.getProperty("pythonPath","/Users/anilkoyuncu/bugStudy/code/python"); String datasetPath = appProps.getProperty("datasetPath","/Users/anilkoyuncu/bugStudy/dataset"); String pjName = appProps.getProperty("pjName","allDataset"); String dbNo = appProps.getProperty("dbNo","0"); String actionType = appProps.getProperty("actionType","ALL"); String threshold = appProps.getProperty("threshold","1"); + String cursor = appProps.getProperty("cursor","10000000"); + String chunk = appProps.getProperty("chunk","1.txt"); String parameters = String.format("\nportInner %s " + "\nserverWait %s \nnumOfWorkers %s " + "\njobType %s \nport %s " + "\npythonPath %s \ndatasetPath %s" + - "\npjName %s \ndbNo %s \nactionType %s \nthreshold %s" - , portInner, serverWait, numOfWorkers, jobType, port, pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + "\npjName %s \ndbNo %s \nactionType %s \nthreshold %s \ncursor %s" + , portInner, serverWait, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,dbNo,actionType,threshold,cursor); log.info(parameters); - mainLaunch(portInner, serverWait, numOfWorkers, jobType, port, pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + mainLaunch(portInner, serverWait, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,dbNo,actionType,threshold,cursor,chunk); } - public static void mainLaunch(String portInner,String serverWait, String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType,String threshold){ + public static void mainLaunch(String portInner, String serverWait, String numOfWorkers, String jobType, String portDumps, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType, String threshold, String cursor, String chunk){ String dbDir; @@ -75,38 +75,40 @@ public class Launcher { TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); break; case "CACHE": - StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); + StoreFile.main(gumOutput, portDumps, serverWait, dbDir, actionType+dumpsName,actionType); break; case "COMP": - CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portInner, pairsPath+actionType, pjName+actionType); + CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portDumps, pairsPath+actionType, pjName+actionType); ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); - - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+".csv.rdb" , port, actionType+dumpsName); + break; + case "AKKA": + AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+chunk+".rdb" , portDumps, actionType+dumpsName,pairsPath+actionType,numOfWorkers,cursor); + break; case "LEVEL1": - level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); + level1(portInner, serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); break; //CALC python abstractPatch.py to from cluster folder case "LEVEL2": - level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); + level2(serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; //CALC via python case "LEVEL3": - level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); + level3(serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; case "ALL": // TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); - StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); - level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); - level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); - level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); +// StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); +// level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); +// level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); +// level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; case "EXTRACTPATTERN": - PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,port,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); break; case "GETPATTERN": - PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,port,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); break; } } catch (Exception e) { diff --git a/src/main/java/edu/lu/uni/serval/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java similarity index 98% rename from src/main/java/edu/lu/uni/serval/PatternExtractor.java rename to src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java index 99e8650..edd65c1 100644 --- a/src/main/java/edu/lu/uni/serval/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java @@ -1,19 +1,8 @@ -package edu.lu.uni.serval; +package edu.lu.uni.serval.fixminer; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.TreeContext; - - -import java.io.*; -import java.nio.file.Files; -import java.nio.file.Paths; -import java.time.Duration; -import java.util.*; -import java.util.stream.Collectors; -import java.util.stream.Stream; - import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -21,7 +10,18 @@ import redis.clients.jedis.Jedis; import redis.clients.jedis.JedisPool; import redis.clients.jedis.JedisPoolConfig; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getASTTree; +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.time.Duration; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Base64; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.getASTTree; /** * Created by anilkoyuncu on 02/08/2018. diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java similarity index 67% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java index 4119e3e..0c81786 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java @@ -1,11 +1,10 @@ -package edu.lu.uni.serval.FixPatternParser.cluster; +package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.Tree; import com.github.gumtreediff.tree.TreeContext; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.junit.Assert; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; @@ -16,7 +15,8 @@ import java.util.*; import java.util.concurrent.Executors; import java.util.function.Consumer; import java.util.stream.Collectors; -import org.junit.Assert; + +import static edu.lu.uni.serval.fixminer.cluster.akka.AkkaTreeParser.akkaCompare; /** * Created by anilkoyuncu on 19/03/2018. @@ -71,7 +71,7 @@ public class AkkaTreeLoader { private static Consumer consumer = Assert::assertNotNull; - public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port, String dumpsName) throws Exception { + public static void main(String portInner, String serverWait, String dbDir, String chunkName, String port, String dumpsName, String pairsPath, String numOfWorkers, String cursor) throws Exception { String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,serverWait,chunkName,dbDir,dumpsName); @@ -81,57 +81,115 @@ public class AkkaTreeLoader { CallShell cs = new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port)); - +// cs.runShell(cmd1,serverWait); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); - + log.info(cmd1); + log.info(cmd2); +// cs.runShell(cmd2,serverWait); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); +// Jedis jedis = new Jedis(new URI("redis://localhost:"+port)); +// while (!jedis.ping().equals("PONG")){ +// log.info("wait"); +// } +// +// jedis = new Jedis(new URI("redis://localhost:"+portInner)); +// while (!jedis.ping().equals("PONG")){ +// log.info("wait"); +// } - comparePairs(innerPool,outerPool); - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); +// String pairsIndexFile = pairsPath + "/"+ chunkName; +// pairsIndexFile = pairsIndexFile.replace("csv.rdb","index"); +// +// +// Pattern pattern = Pattern.compile(","); +// String csvFile = pairsIndexFile; +// try { +// try (BufferedReader in = new BufferedReader(new FileReader(csvFile));){ +// Map namefreq = in +// .lines() +// // .skip(1) +// .map(x -> pattern.split(x)) +// // .filter(x -> x[4].equals("CA") && x[3].equals("F")) +// .collect(HashMap::new, (map, x) -> +// map.put(x[0], x[1]), +// Map::putAll); +// // namefreq.forEach((k, v) -> System.out.println(k + " => " + v)); +// +// Jedis inner = null; +// try { +// inner = outerPool.getResource(); +// +// for (Map.Entry entry : namefreq.entrySet()) { +// String key = entry.getKey(); +// String value = entry.getValue(); +// inner.select(1); +// inner.set(key,value); +// // ... +// } +// +// +// }finally { +// if (inner != null) { +// inner.close(); +// } +// } +// +// +// } +// } catch (IOException e) { +// e.printStackTrace(); +// } - cs.runShell(stopServer1,serverWait); - stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - String stopServer2 = String.format(stopServer,Integer.valueOf(port)); - cs.runShell(stopServer2,serverWait); + +// comparePairs(innerPool,outerPool); + akkaCompare(innerPool,outerPool,numOfWorkers,cursor); + +// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; +// String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); +// +// cs.runShell(stopServer1,serverWait); +// stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; +// String stopServer2 = String.format(stopServer,Integer.valueOf(port)); +// +// cs.runShell(stopServer2,serverWait); } - public static void comparePairs(JedisPool innerPool,JedisPool outerPool){ ScanResult scan; + try (Jedis inner = innerPool.getResource()) { - while (inner.ping()== "PONG"){ + while (!inner.ping().equals("PONG")){ log.info("wait"); } ScanParams sc = new ScanParams(); //150000000 - sc.count(150000000); + log.info("Scanning "); + sc.count(250000000); + sc.match("pair_[0-9]*"); scan = inner.scan("0", sc); int size = scan.getResult().size(); - log.info("Scanning " + String.valueOf(size)); + log.info("Scanned " + String.valueOf(size)); } List result = scan.getResult(); - - - + log.info("Getting results"); result - .parallelStream() - .forEach(m -> + .parallelStream() + .forEach(m -> { Compare compare = new Compare(); compare.coreCompare(m, innerPool, outerPool); @@ -165,14 +223,20 @@ public class AkkaTreeLoader { Jedis inner = null; try { inner = outerPool.getResource(); - String s = inner.get(fn); + while (!inner.ping().equals("PONG")){ + log.info("wait"); + } + inner.select(1); + String dist2load = inner.get(fn); + inner.select(0); + String s = inner.get(dist2load); HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); ITree parent = null; ITree children =null; TreeContext tc = new TreeContext(); tree = getASTTree(actionSet, parent, children,tc); -// tree.setParent(null); + tree.setParent(null); tc.validate(); } catch (IOException e) { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java similarity index 82% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java index f906103..2e25b25 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java @@ -1,6 +1,5 @@ -package edu.lu.uni.serval.FixPatternParser.cluster; +package edu.lu.uni.serval.fixminer.cluster; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.utils.FileHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -14,7 +13,7 @@ import java.nio.ByteBuffer; import java.nio.channels.FileChannel; import java.util.List; -import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poolConfig; +import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig; /** * Created by anilkoyuncu on 05/04/2018. @@ -63,32 +62,42 @@ public class CalculatePairs { try { // FileOutputStream fos = new FileOutputStream(outputPath + "/" +pjName+".csv"); // DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(fos)); +// + FileOutputStream fosIndex = new FileOutputStream(outputPath + "/" +pjName+".index"); + DataOutputStream outStreamIndex = new DataOutputStream(new BufferedOutputStream(fosIndex)); +// // // // // for (int i = 0; i < result.size(); i++) { +// line = String.valueOf(i) +"," + result.get(i)+"\n"; +// outStreamIndex.write(line.getBytes()); +// // for (int j = i + 1; j < result.size(); j++) { // // // -// line = String.valueOf(i) +"," + String.valueOf(j) + "," + result.get(i) + "," + result.get(j)+"\n"; +// line = String.valueOf(i) +"," + String.valueOf(j)+"\n"; // + "," + result.get(i) + "," + result.get(j)+"\n"; // outStream.write(line.getBytes()); // // } // } // outStream.close(); +// outStreamIndex.close(); int fileCounter = 0; FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +String.valueOf(fileCounter)+".txt", "rw").getChannel(); - int maxSize = 500*500000; + int maxSize = 500*1000000; ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, maxSize); for (int i = 0; i < result.size(); i++) { + line = String.valueOf(i) +"," + result.get(i)+"\n"; + outStreamIndex.write(line.getBytes()); for (int j = i + 1; j < result.size(); j++) { - line = String.valueOf(i) +"\t" + String.valueOf(j) + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; + line = String.valueOf(i) +"\t" + String.valueOf(j)+"\n"; // + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; buf = line.getBytes(); if(wrBuf.remaining() > 500) { wrBuf.put(buf); @@ -104,6 +113,7 @@ public class CalculatePairs { } } + outStreamIndex.close(); rwChannel.close(); } catch (FileNotFoundException e) { e.printStackTrace(); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java similarity index 89% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java index 07e0398..d108dcf 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CallShell.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java @@ -1,9 +1,11 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer.cluster; /** * Created by anilkoyuncu on 17/04/2018. */ -import java.io.*; + +import java.io.BufferedReader; +import java.io.InputStreamReader; public class CallShell { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java similarity index 78% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java index 1b3d5cb..64900a3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java @@ -1,4 +1,4 @@ -package edu.lu.uni.serval.FixPatternParser.cluster; +package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.actions.ActionGenerator; import com.github.gumtreediff.actions.model.Action; @@ -13,7 +13,7 @@ import redis.clients.jedis.JedisPool; import java.util.List; import java.util.Map; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.getSimpliedTree; +import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.getSimpliedTree; /** * Created by anilkoyuncu on 03/04/2018. @@ -23,7 +23,7 @@ public class Compare { private Logger log = LoggerFactory.getLogger(Compare.class); - public void coreCompare(String name , JedisPool innerPool, JedisPool outerPool) { + public void coreCompare(String name, JedisPool innerPool, JedisPool outerPool) { Map resultMap; Jedis jedis = null; @@ -32,19 +32,21 @@ public class Compare { try { jedis = innerPool.getResource(); - resultMap = jedis.hgetAll(name); +// resultMap = jedis.hgetAll(name); String[] split = name.split("_"); String i = split[1]; String j = split[2]; - String firstValue = resultMap.get("0"); - String secondValue = resultMap.get("1"); - oldTree = getSimpliedTree(firstValue,outerPool); - newTree = getSimpliedTree(secondValue,outerPool); +// String firstValue = resultMap.get("0"); +// String secondValue = resultMap.get("1"); + + oldTree = getSimpliedTree(i,outerPool); + + newTree = getSimpliedTree(j,outerPool); Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); m.match(); @@ -63,7 +65,7 @@ public class Compare { String editDistance = String.valueOf(actions.size()); - String result = resultMap.get("0") + "," + resultMap.get("1") + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; + String result = i + "," + j + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) @@ -77,7 +79,7 @@ public class Compare { } - + jedis.select(0); jedis.del("pair_" + (String.valueOf(i)) + "_" + String.valueOf(j)); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java similarity index 84% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java index 3571263..fab81b6 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java @@ -1,18 +1,16 @@ -package edu.lu.uni.serval.FixPatternParser.cluster; +package edu.lu.uni.serval.fixminer.cluster; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.File; -import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -//import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; -//import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedisWait; +//import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis; +//import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedisWait; /** diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java similarity index 99% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java index 197a573..baa1c42 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java @@ -1,4 +1,4 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.actions.ActionGenerator; import com.github.gumtreediff.actions.model.*; @@ -14,11 +14,7 @@ import org.slf4j.LoggerFactory; import redis.clients.jedis.*; import java.io.*; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; import java.nio.file.Files; -import java.nio.file.StandardCopyOption; -import java.sql.Timestamp; import java.time.Duration; import java.util.*; import java.util.concurrent.Executors; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java similarity index 98% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java index 4282c0c..909b1b3 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java @@ -1,4 +1,4 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.actions.ActionGenerator; import com.github.gumtreediff.actions.model.*; @@ -33,14 +33,14 @@ public class MultiThreadTreeLoaderCluster { CallShell cs = new CallShell(); String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); -// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); +// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); cs.runShell(cmd1,serverWait); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); cs.runShell(cmd2,serverWait); -// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); +// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); String cmd3; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java similarity index 95% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java index c35d5f5..149ed53 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java @@ -1,41 +1,25 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoader.getKeysByValue; -import static edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster.fromString; - -import java.io.BufferedOutputStream; -import java.io.DataOutputStream; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileOutputStream; -import java.io.IOException; -import java.time.Duration; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.TreeSet; -import java.util.regex.Pattern; -import java.util.stream.Collectors; -import java.util.stream.Stream; +package edu.lu.uni.serval.fixminer.cluster; +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.TreeContext; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import edu.lu.uni.serval.utils.FileHelper; import org.apache.commons.lang3.StringUtils; import org.apache.commons.text.similarity.JaroWinklerDistance; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import redis.clients.jedis.*; -import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.TreeContext; +import java.io.*; +import java.time.Duration; +import java.util.*; +import java.util.regex.Pattern; +import java.util.stream.Collectors; +import java.util.stream.Stream; -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.utils.FileHelper; -import redis.clients.jedis.Jedis; -import redis.clients.jedis.JedisPool; -import redis.clients.jedis.JedisPoolConfig; -import redis.clients.jedis.ScanParams; -import redis.clients.jedis.ScanResult; +import static edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoader.getKeysByValue; +import static edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoaderCluster.fromString; /** * Created by anilkoyuncu on 19/03/2018. @@ -52,12 +36,12 @@ public class MultiThreadTreeLoaderCluster3 { CallShell cs = new CallShell(); String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); -// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); +// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); cs.runShell(cmd1,serverWait); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); -// edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); +// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); cs.runShell(cmd2,serverWait); String cmd3; @@ -95,7 +79,7 @@ public class MultiThreadTreeLoaderCluster3 { if (size == 0) { String comd = String.format(cmd3, f.getPath(), portInner); cs.runShell(comd); -// edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster. +// edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoaderCluster. // loadRedis(comd); scan = jedis.scan("0", sc); @@ -569,20 +553,22 @@ public class MultiThreadTreeLoaderCluster3 { CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); CharSequence[] newSequences = newTokens.toArray(new CharSequence[newTokens.size()]); JaroWinklerDistance jwd = new JaroWinklerDistance(); - LevenshteinDistance ld = new LevenshteinDistance(); +// LevenshteinDistance ld = new LevenshteinDistance(); - Double overallSimi = Double.valueOf(1); + Double overallSimi = Double.valueOf(0); if(oldSequences.length > 0 && (oldSequences.length == newSequences.length)){ for (int idx = 0; idx < newSequences.length; idx++) { Double simi = jwd.apply(newSequences[idx], oldSequences[idx]); - overallSimi = simi * overallSimi; + overallSimi = simi + overallSimi; } + overallSimi = overallSimi / oldSequences.length; }else{ overallSimi = Double.valueOf(0); // if(oldSequences.length != 0) { // log.info("ERROR"); // } } + int retval = Double.compare(overallSimi, Double.valueOf(0.8)); if(retval >= 0){ diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/RunnableCompare.java similarity index 81% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/RunnableCompare.java index 7f75eb5..f51ca09 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/RunnableCompare.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/RunnableCompare.java @@ -1,6 +1,5 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer.cluster; -import edu.lu.uni.serval.FixPatternParser.cluster.Compare; import redis.clients.jedis.JedisPool; public class RunnableCompare implements Runnable { diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java similarity index 93% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java index d89e87b..977b701 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java @@ -1,14 +1,10 @@ -package edu.lu.uni.serval.FixPatternParser.cluster; +package edu.lu.uni.serval.fixminer.cluster; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import org.apache.commons.lang3.ArrayUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.Jedis; import redis.clients.jedis.JedisPool; -import redis.clients.jedis.JedisPoolConfig; -import redis.clients.jedis.ScanResult; import java.io.*; import java.util.ArrayList; @@ -18,8 +14,7 @@ import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; -import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poolConfig; +import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig; /** * Created by anilkoyuncu on 03/04/2018. diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java similarity index 56% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java index 4b74489..443d889 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeActor.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java @@ -1,17 +1,19 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer.cluster; import akka.actor.ActorRef; import akka.actor.Props; import akka.actor.UntypedActor; import akka.japi.Creator; import akka.routing.RoundRobinPool; - +import edu.lu.uni.serval.fixminer.cluster.akka.TreeMessage; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; import java.util.List; -import static edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis; +import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis; public class TreeActor extends UntypedActor { @@ -21,20 +23,14 @@ public class TreeActor extends UntypedActor { private final int numberOfWorkers; private int counter = 0; - private String innerPort; - private String dbDir; - private String serverWait; - public TreeActor(int numberOfWorkers,String dbDir,String innerPort,String serverWait) { + public TreeActor(int numberOfWorkers) { mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) .props(TreeWorker.props()), "tree-router"); this.numberOfWorkers = numberOfWorkers; - this.innerPort = innerPort; - this.dbDir = dbDir; - this.serverWait = serverWait; } - public static Props props(final int numberOfWorkers, final String dbDir,final String innerPort, final String serverWait) { + public static Props props(final int numberOfWorkers) { return Props.create(new Creator() { @@ -42,7 +38,7 @@ public class TreeActor extends UntypedActor { @Override public TreeActor create() throws Exception { - return new TreeActor(numberOfWorkers,dbDir,innerPort,serverWait); + return new TreeActor(numberOfWorkers); } }); @@ -51,14 +47,13 @@ public class TreeActor extends UntypedActor { @SuppressWarnings("deprecation") @Override public void onReceive(Object message) throws Exception { - if (message instanceof WorkMessage) { - List files = ((WorkMessage) message).getMsgFiles(); - String innerPort = ((WorkMessage) message).getInnerPort(); - String inputPath = ((WorkMessage) message).getInputPath(); - String dbDir = ((WorkMessage) message).getDbDir(); - String serverWait = ((WorkMessage) message).getServerWait(); + if (message instanceof TreeMessage) { + List pairs = ((TreeMessage) message).getName(); + JedisPool innerPool = ((TreeMessage) message).getInnerPool(); + JedisPool outerPool = ((TreeMessage) message).getOuterPool(); - int size = files.size(); + + int size = pairs.size(); int average = size / numberOfWorkers; int reminder = size % numberOfWorkers; int counter = 0; @@ -68,8 +63,8 @@ public class TreeActor extends UntypedActor { if (counter < reminder) counter ++; int toIndex = (i + 1) * average + counter; - List filesOfWorkers = files.subList(fromIndex, toIndex); - final WorkMessage workMsg = new WorkMessage(i + 1, filesOfWorkers,innerPort,inputPath,dbDir,serverWait); + List pairsOfWorkers = pairs.subList(fromIndex, toIndex); + final TreeMessage workMsg = new TreeMessage(i + 1, pairsOfWorkers,innerPool,outerPool); mineRouter.tell(workMsg, getSelf()); logger.info("Assign a task to worker #" + (i + 1) + "..."); } @@ -81,9 +76,7 @@ public class TreeActor extends UntypedActor { this.getContext().stop(mineRouter); this.getContext().stop(getSelf()); this.getContext().system().shutdown(); - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - stopServer = String.format(stopServer,Integer.valueOf(innerPort)); - loadRedis(stopServer,serverWait); + } } else { unhandled(message); diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java similarity index 97% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java index 07ca3af..6435e58 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java @@ -1,6 +1,5 @@ -package edu.lu.uni.serval.FixPatternParser.cluster; +package edu.lu.uni.serval.fixminer.cluster; -import edu.lu.uni.serval.FixPatternParser.violations.CallShell; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java similarity index 63% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java index 37d5226..4c0e6a0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java @@ -1,24 +1,51 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer.cluster; import akka.actor.Props; import akka.actor.UntypedActor; import akka.japi.Creator; - -import edu.lu.uni.serval.FixPatternParser.cluster.Compare; +import edu.lu.uni.serval.config.Configuration; +import edu.lu.uni.serval.fixminer.cluster.akka.TreeMessage; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import redis.clients.jedis.JedisPool; import redis.clients.jedis.JedisPoolConfig; import java.time.Duration; import java.util.List; +import java.util.concurrent.*; + +import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.poolConfig; public class TreeWorker extends UntypedActor { private static Logger log = LoggerFactory.getLogger(TreeWorker.class); +// private JedisPool innerPool; +// private JedisPool outerPool; +// +// public TreeWorker(String innerPort,String outerPort) { +//// this.innerPool = innerPool; +//// this.outerPool = outerPool; +// this.outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(outerPort),20000000); +// this.innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(innerPort),20000000); +// +// +// } +// +// public static Props props(final String innerPort,final String outerPort) { +// return Props.create(new Creator() { +// +// private static final long serialVersionUID = -7615153844097275009L; +// +// @Override +// public TreeWorker create() throws Exception { +// return new TreeWorker(innerPort,outerPort); +// } +// +// }); +// } - public TreeWorker() { - + public TreeWorker() { } @@ -35,47 +62,48 @@ public class TreeWorker extends UntypedActor { }); } + + @Override public void onReceive(Object message) throws Exception { - if(message instanceof edu.lu.uni.serval.FixPatternParser.violations.WorkMessage) { + if(message instanceof TreeMessage) { // if (message instanceof edu.lu.uni.serval.MultipleThreadsParser.WorkMessage) { - edu.lu.uni.serval.FixPatternParser.violations.WorkMessage msg = (WorkMessage) message; - List files = msg.getMsgFiles(); - String innerPort = msg.getInnerPort(); - String inputPath = msg.getInputPath(); - String dbDir = msg.getDbDir(); - String serverWait = msg.getServerWait(); + TreeMessage msg = (TreeMessage) message; + List files = msg.getName(); + JedisPool innerPool = msg.getInnerPool(); + JedisPool outerPool = msg.getOuterPool(); + int id = msg.getId(); - int counter = new Object() { +// int counter = new Object() { int counter = 0; // -// for (String name : files) + for (String name : files) { - files.stream(). - parallel(). - peek(x -> counter++). - forEach(m -> - { - Compare compare = new Compare(); -// compare.coreCompare(m, inputPath, innerPort); - } - ); - } - }.counter; +// files.stream(). +// parallel(). +// peek(x -> counter++). +// forEach(m -> +// { +// Compare compare = new Compare(); +// compare.coreCompare(m, innerPool, outerPool); +// } +// ); +// } +// }.counter; // -// final ExecutorService executor = Executors.newFixedThreadPool(20); + final ExecutorService executor = Executors.newFixedThreadPool(20); // // schedule the work -// final Future future = executor.submit(new RunnableCompare(name, inputPath, innerPort, new Compare(poolConfig))); -// try { - // wait for task to complete -// future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); -// Compare compare = new Compare(poolConfig); -// compare.coreCompare(name, inputPath, innerPort); -// counter++; + final Future future = executor.submit(new RunnableCompare(name, innerPool, outerPool, new Compare())); + try { +// wait for task to complete + future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); + Compare compare = new Compare(); + compare.coreCompare(name, innerPool, outerPool); + counter++; // nullDiffEntry += parser.nullMatchedDiffEntry; // nullMappingGumTreeResults += parser.nullMappingGumTreeResult; // pureDeletion += parser.pureDeletions; @@ -115,22 +143,22 @@ public class TreeWorker extends UntypedActor { // testingInfo.setLength(0); // } // } -// } catch (TimeoutException e) { -// future.cancel(true); + } catch (TimeoutException e) { + future.cancel(true); ////// timeouts += countAlarms(positionFile, "#Timeout:"); // System.err.println("#Timeout: " + name); -// } catch (InterruptedException e) { + } catch (InterruptedException e) { ////// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); //// System.err.println("#TimeInterrupted: " + revFile.getName()); -// e.printStackTrace(); -// } catch (ExecutionException e) { + e.printStackTrace(); + } catch (ExecutionException e) { ////// timeouts += countAlarms(positionFile, "#TimeAborted:"); //// System.err.println("#TimeAborted: " + revFile.getName()); -// e.printStackTrace(); -// } finally { -// executor.shutdownNow(); -// } -// } + e.printStackTrace(); + } finally { + executor.shutdownNow(); + } + } log.info("bitti"); log.info("Worker #" + id +"finialized parsing " + counter + " files..."); @@ -169,24 +197,24 @@ public class TreeWorker extends UntypedActor { } } - static final JedisPoolConfig poolConfig = buildPoolConfig(); - - - private static JedisPoolConfig buildPoolConfig() { - final JedisPoolConfig poolConfig = new JedisPoolConfig(); - poolConfig.setMaxTotal(128); - poolConfig.setMaxIdle(128); - poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(true); - poolConfig.setTestOnReturn(true); - poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); - poolConfig.setNumTestsPerEvictionRun(3); - poolConfig.setBlockWhenExhausted(true); - - return poolConfig; - } +// static final JedisPoolConfig poolConfig = buildPoolConfig(); +// +// +// private static JedisPoolConfig buildPoolConfig() { +// final JedisPoolConfig poolConfig = new JedisPoolConfig(); +// poolConfig.setMaxTotal(128); +// poolConfig.setMaxIdle(128); +// poolConfig.setMinIdle(16); +// poolConfig.setTestOnBorrow(true); +// poolConfig.setTestOnReturn(true); +// poolConfig.setTestWhileIdle(true); +// poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); +// poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); +// poolConfig.setNumTestsPerEvictionRun(3); +// poolConfig.setBlockWhenExhausted(true); +// +// return poolConfig; +// } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/WorkMessage.java similarity index 87% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/WorkMessage.java index 6343c51..f009b25 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/WorkMessage.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/WorkMessage.java @@ -1,6 +1,4 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; +package edu.lu.uni.serval.fixminer.cluster; import java.util.List; diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/AkkaTreeParser.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/AkkaTreeParser.java new file mode 100644 index 0000000..d76b532 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/AkkaTreeParser.java @@ -0,0 +1,75 @@ +package edu.lu.uni.serval.fixminer.cluster.akka; + +import akka.actor.ActorRef; +import akka.actor.ActorSystem; +import edu.lu.uni.serval.fixminer.cluster.TreeActor; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.ScanParams; +import redis.clients.jedis.ScanResult; + +import java.util.List; + +/** + * Created by anilkoyuncu on 12/09/2018. + */ +public class AkkaTreeParser { + + private static Logger log = LoggerFactory.getLogger(AkkaTreeParser.class); + + + public static void akkaCompare(JedisPool innerPool, JedisPool outerPool, String numOfWorkers, String cursor){ + + final List listOfPairs = getMessages(innerPool,cursor); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/" + + + + + ActorSystem system = null; + ActorRef parsingActor = null; + final TreeMessage msg = new TreeMessage(0,listOfPairs, innerPool,outerPool); + try { + log.info("Akka begins..."); + system = ActorSystem.create("Compare-EnhancedDiff-System"); + + parsingActor = system.actorOf(TreeActor.props(Integer.valueOf(numOfWorkers)), "mine-fix-pattern-actor"); + parsingActor.tell(msg, ActorRef.noSender()); + } catch (Exception e) { + system.shutdown(); + e.printStackTrace(); + } + } + + public static List getMessages(JedisPool innerPool, String cursor){ + + + ScanResult scan; + + try (Jedis inner = innerPool.getResource()) { + while (!inner.ping().equals("PONG")){ + log.info("wait"); + } + + ScanParams sc = new ScanParams(); + //150000000 + log.info("Scanning "); + sc.count(Integer.valueOf(cursor)); + + sc.match("pair_[0-9]*"); + + scan = inner.scan("0", sc); + int size = scan.getResult().size(); + log.info("Scanned " + String.valueOf(size)); + } + List result = scan.getResult(); + log.info("Getting results"); + return result; + + + + + + } +} diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/TreeMessage.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/TreeMessage.java new file mode 100644 index 0000000..b23bfe8 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/akka/TreeMessage.java @@ -0,0 +1,54 @@ +package edu.lu.uni.serval.fixminer.cluster.akka; + +import redis.clients.jedis.JedisPool; + +import java.util.List; + +/** + * Created by anilkoyuncu on 12/09/2018. + */ +public class TreeMessage { + private int id; + private List name; + private JedisPool innerPool; + private JedisPool outerPool; + + public TreeMessage(int id, List name, JedisPool innerPool, JedisPool outerPool) { + this.id = id; + this.name = name; + this.innerPool = innerPool; + this.outerPool = outerPool; + } + + public int getId() { + return id; + } + + public void setId(int id) { + this.id = id; + } + + public List getName() { + return name; + } + + public void setName(List name) { + this.name = name; + } + + public JedisPool getInnerPool() { + return innerPool; + } + + public void setInnerPool(JedisPool innerPool) { + this.innerPool = innerPool; + } + + public JedisPool getOuterPool() { + return outerPool; + } + + public void setOuterPool(JedisPool outerPool) { + this.outerPool = outerPool; + } +} From 2408eb159ef3c7e1ba275692f6a4636a9876b07c Mon Sep 17 00:00:00 2001 From: fixminer Date: Thu, 13 Sep 2018 16:23:17 +0200 Subject: [PATCH 125/127] fix pair record problem in import --- .../uni/serval/fixminer/cluster/CalculatePairs.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java index 2e25b25..0c91b73 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java @@ -97,7 +97,8 @@ public class CalculatePairs { - line = String.valueOf(i) +"\t" + String.valueOf(j)+"\n"; // + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; +// line = String.valueOf(i) +"\t" + String.valueOf(j)+"\n"; // + "\t" + result.get(i) + "\t" + result.get(j)+"\n"; + line = String.valueOf(i) +"," + String.valueOf(j)+"\n"; // + "," + result.get(i) + "," + result.get(j)+"\n"; buf = line.getBytes(); if(wrBuf.remaining() > 500) { wrBuf.put(buf); @@ -125,10 +126,10 @@ public class CalculatePairs { e.printStackTrace(); } - String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; - String stopServer2 = String.format(stopServer,Integer.valueOf(port)); -// loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait); +// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; +// String stopServer2 = String.format(stopServer,Integer.valueOf(port)); +//// loadRedis(stopServer2,serverWait); +// cs.runShell(stopServer2,serverWait); log.info("Done pairs"); } From 4a9d87974eb7e342752495fdbef9ab7a04170bc8 Mon Sep 17 00:00:00 2001 From: fixminer Date: Mon, 17 Sep 2018 15:40:32 +0200 Subject: [PATCH 126/127] release candidate --- .../edu/lu/uni/serval/fixminer/Launcher.java | 12 ++-- .../fixminer/cluster/AkkaTreeLoader.java | 5 +- .../fixminer/cluster/CalculatePairs.java | 2 +- .../serval/fixminer/cluster/CallShell.java | 72 ++++++++++++++++++- .../uni/serval/fixminer/cluster/Compare.java | 1 + .../fixminer/cluster/ImportPairs2DB.java | 4 +- .../cluster/MultiThreadTreeLoaderCluster.java | 8 +-- .../MultiThreadTreeLoaderCluster3.java | 8 +-- .../serval/fixminer/cluster/StoreFile.java | 4 +- .../fixminer/cluster/TreeLoaderClusterL1.java | 8 +-- 10 files changed, 97 insertions(+), 27 deletions(-) diff --git a/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java b/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java index 400f9a2..6848d2c 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java @@ -128,14 +128,14 @@ public class Launcher { CallShell cs1 =new CallShell(); String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String db11 = String.format(db1, dbDir,"level1-"+pjName+ actionType+".rdb" ,Integer.valueOf(port)); - cs1.runShell(db11,serverWait); + cs1.runShell(db11,serverWait, port); String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, "matches" + pjName + actionType, threshold); cs1.runShell(formatRunPy); String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(port)); - cs1.runShell(stopServer,serverWait); + cs1.runShell(stopServer,serverWait, port); } private static void level2(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { @@ -147,14 +147,14 @@ public class Launcher { CallShell cs3 =new CallShell(); String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+actionType+".rdb",Integer.valueOf(port)); - cs3.runShell(db1b,serverWait); + cs3.runShell(db1b,serverWait, port); String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); cs3.runShell(formatRunPy1a); String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer1a,Integer.valueOf(port)); - cs3.runShell(stopServer,serverWait); + cs3.runShell(stopServer,serverWait, port); } private static void level3(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { @@ -166,14 +166,14 @@ public class Launcher { CallShell cs5 =new CallShell(); String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+actionType+".rdb",Integer.valueOf(port)); - cs5.runShell(dbaa,serverWait); + cs5.runShell(dbaa,serverWait, port); String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); cs5.runShell(formatRunPya); String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServera,Integer.valueOf(port)); - cs5.runShell(stopServer,serverWait); + cs5.runShell(stopServer,serverWait, port); return; } // System.exit(1); diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java index 0c81786..2e2c19b 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java @@ -82,13 +82,13 @@ public class AkkaTreeLoader { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port)); // - cs.runShell(cmd1,serverWait); + cs.runShell(cmd1,serverWait,port); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); log.info(cmd1); log.info(cmd2); // - cs.runShell(cmd2,serverWait); + cs.runShell(cmd2,serverWait, portInner); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); @@ -150,6 +150,7 @@ public class AkkaTreeLoader { // comparePairs(innerPool,outerPool); + Thread.sleep(Integer.valueOf(serverWait)); akkaCompare(innerPool,outerPool,numOfWorkers,cursor); // String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java index 0c91b73..5a80670 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java @@ -31,7 +31,7 @@ public class CalculatePairs { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port)); - cs.runShell(cmd,serverWait); + cs.runShell(cmd,serverWait, port); FileHelper.createDirectory(outputPath); diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java index d108dcf..3c32292 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java @@ -5,7 +5,10 @@ package edu.lu.uni.serval.fixminer.cluster; */ import java.io.BufferedReader; +import java.io.IOException; import java.io.InputStreamReader; +import java.util.concurrent.TimeUnit; + public class CallShell { @@ -23,7 +26,7 @@ public class CallShell { } - public void runShell(String command,String serverWait) throws Exception { + public static void runShell(String command, String serverWait, String port) throws Exception { Process process = Runtime.getRuntime().exec(command); BufferedReader reader = new BufferedReader(new InputStreamReader( @@ -32,8 +35,73 @@ public class CallShell { while ((s = reader.readLine()) != null) { System.out.println("Script output: " + s); } - Thread.sleep(Integer.valueOf(serverWait)); +// Thread.sleep(Integer.valueOf(serverWait)); + String cmd = "redis-cli -p %s ping"; + String cmd1 = String.format(cmd,Integer.valueOf(port)); + runPing(cmd1); + + + } + + public static void runPing(String command) throws Exception { +try{ + StringBuffer output = new StringBuffer(); + Process process = Runtime.getRuntime().exec(command); + BufferedReader reader = new BufferedReader(new InputStreamReader( + process.getInputStream())); + String s; + + BufferedReader stdError = new BufferedReader(new + InputStreamReader(process.getErrorStream())); + + + // read the output from the command +// System.out.println("Here is the standard output of the command:\n"); +// while ((s = reader.readLine()) != null && !s.equals("PONG")) { +// System.out.println(s); +// } + +// while(true){ + s = reader.readLine(); + + if(s !=null && s.equals("PONG")){ + System.out.println(s); + + }else{ + String e; + if((e = stdError.readLine()) == null) { + TimeUnit.MINUTES.sleep(1); + + runPing(command); + }else{ + System.out.println(e); + + } + } + +// System.out.println(s); +// } + // read any errors from the attempted command +// System.out.println("Here is the standard error of the command (if any):\n"); + while ((s = stdError.readLine()) != null) { + System.out.print(s); + } + +// System.exit(0); + } + catch (IOException e) { + System.out.println("exception happened - here's what I know: "); + e.printStackTrace(); + System.exit(-1); + } + + } + + public static void main(String[] args) throws Exception { + +// runPing("redis-cli -p 6380 ping"); + runShell("bash /Users/anilkoyuncu/bugStudy/release/code/redis/startServer.sh /Users/anilkoyuncu/bugStudy/release/code/redis Defects4JALL0.txt.rdb 6380","1","6380"); } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java index 64900a3..27ea1c1 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java @@ -87,6 +87,7 @@ public class Compare { } catch (Exception e) { log.error(e.toString() + " {}", name); +// e.printStackTrace(); }finally { diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java index fab81b6..b6a303f 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java @@ -40,7 +40,7 @@ public class ImportPairs2DB { cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); log.info(cmd); CallShell cs = new CallShell(); - cs.runShell(cmd,serverWait); + cs.runShell(cmd,serverWait, portInner); cmd = "bash "+datasetPath + "/redisSingleImport.sh" +" %s %s"; @@ -50,7 +50,7 @@ public class ImportPairs2DB { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,portInt); - cs.runShell(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait, portInner); portInt++; diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java index 909b1b3..09d0eb4 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java @@ -34,12 +34,12 @@ public class MultiThreadTreeLoaderCluster { String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); // edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - cs.runShell(cmd1,serverWait); + cs.runShell(cmd1,serverWait, port); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); - cs.runShell(cmd2,serverWait); + cs.runShell(cmd2,serverWait, port); // edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); @@ -105,11 +105,11 @@ public class MultiThreadTreeLoaderCluster { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); // loadRedis(stopServer2,serverWait); - cs.runShell(stopServer1,serverWait); + cs.runShell(stopServer1,serverWait, port); String stopServer2 = String.format(stopServer,Integer.valueOf(port)); // loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait, port); diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java index 149ed53..5cea1b4 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java @@ -37,12 +37,12 @@ public class MultiThreadTreeLoaderCluster3 { String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); // edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - cs.runShell(cmd1,serverWait); + cs.runShell(cmd1,serverWait, port); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); // edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); - cs.runShell(cmd2,serverWait); + cs.runShell(cmd2,serverWait, port); String cmd3; cmd3 = "bash " + importScript +" %s %s"; @@ -104,11 +104,11 @@ public class MultiThreadTreeLoaderCluster3 { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); // loadRedis(stopServer2,serverWait); - cs.runShell(stopServer1,serverWait); + cs.runShell(stopServer1,serverWait, port); String stopServer2 = String.format(stopServer,Integer.valueOf(port)); // loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait, port); diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java index 977b701..f6b9eb4 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java @@ -52,7 +52,7 @@ public class StoreFile { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner)); // loadRedis(cmd,serverWait); - cs.runShell(cmd,serverWait); + cs.runShell(cmd,serverWait, portInner); File folder = new File(inputPath); File[] subFolders = folder.listFiles(); @@ -108,7 +108,7 @@ public class StoreFile { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,Integer.valueOf(portInner)); // loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait); + cs.runShell(stopServer2,serverWait, portInner); } public static void storeCore(JedisPool innerPool,String path,String key){ diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java index 6435e58..e7e15b4 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java @@ -29,7 +29,7 @@ public class TreeLoaderClusterL1 { cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port)); CallShell cs = new CallShell(); - cs.runShell(cmd,serverWait); + cs.runShell(cmd,serverWait, port); JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); @@ -44,7 +44,7 @@ public class TreeLoaderClusterL1 { String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner)); - cs.runShell(cmdInner,serverWait); + cs.runShell(cmdInner,serverWait, port); JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); Jedis inner = null; @@ -98,13 +98,13 @@ public class TreeLoaderClusterL1 { String stopServer = "bash "+inputPath + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(portInner)); // loadRedis(stopServer,serverWait); - cs.runShell(stopServer,serverWait); + cs.runShell(stopServer,serverWait, port); } String stopServer1 = "bash "+inputPath + "/" + "stopServer.sh" +" %s"; stopServer1 = String.format(stopServer1,Integer.valueOf(port)); // loadRedis(stopServer,serverWait); - cs.runShell(stopServer1,serverWait); + cs.runShell(stopServer1,serverWait, port); From 2d12536b9378ae33d6e4d8020e95b84f017710c0 Mon Sep 17 00:00:00 2001 From: fixminer Date: Mon, 17 Sep 2018 18:29:33 +0200 Subject: [PATCH 127/127] release cand. 2 --- Dataset/LiveStudy/Patches | 119 - Dataset/Patterns/Fix-Patterns | 131 - .../Source-Code-Patterns-Unfixed-Violations | 107 - FixPatternMiner.iml | 28 +- inputData/1.txt | 730 - logs/FixedViolationCodeParseResults.log | 3521 - logs/HaveSourceCode.txt | 87622 ---------------- logs/MultiMethodsOrFieldOrInnerClasses.txt | 3867 - logs/MultiV.txt | 4327 - logs/Null.txt | 124 - logs/NullSourceCode.txt | 1305 - logs/NullV.txt | 3130 - logs/fixedTypes.txt | 339 - logs/myLog.log | 0 pom.xml | 19 +- .../uni/serval/FixPattern/utils/CNodeMap.java | 101 - .../lu/uni/serval/FixPattern/utils/EDiff.java | 98 + .../serval/FixPattern/utils/EDiffHelper.java | 88 + .../serval/FixPattern/utils/PoolBuilder.java | 33 + .../serval/FixPatternParser/CUCreator.java | 8 +- .../uni/serval/FixPatternParser/Parser.java | 467 +- .../FixPatternParser/ParserInterface.java | 10 +- .../serval/FixPatternParser/Tokenizer.java | 75 - .../patch/CommitPatchHunkParser.java | 113 - .../patch/CommitPatchParser.java | 105 - .../CommitPatchSingleStatementParser.java | 158 - .../FixPatternParser/violations/CSVUtils.java | 62 - .../FixPatternParser/violations/Consumer.java | 226 - .../violations/FieldViolation.java | 121 - .../violations/FixedViolationHunkParser.java | 251 +- .../violations/FixedViolationParser.java | 81 +- .../FixedViolationSingleStatementParser.java | 156 - .../FixPatternParser/violations/Message.java | 20 - .../FixPatternParser/violations/Producer.java | 150 - .../violations/Violation.java | 133 - .../MultipleThreadsParser/AkkaParser.java | 121 - .../MultipleThreadsParser/AkkaParser2.java | 146 - .../ParseFixPatternActor.java | 9 +- .../ParseFixPatternWorker.java | 54 +- .../SingleThreadParser.java | 190 - .../MultipleThreadsParser2/AkkaMatcher.java | 214 - .../DistanceCalculator.java | 68 - .../DistanceFunction.java | 5 - .../MatchFixPatternActor.java | 172 - .../MatchFixPatternWorker.java | 60 - .../MultipleThreadsParser2/ReturnMessage.java | 35 - .../MultipleThreadsParser2/WorkMessage.java | 39 - .../MultipleThreadsParser3/AkkaParser.java | 90 - .../MultipleThreadsParser3/AkkaParser2.java | 78 - .../ParseFixPatternActor.java | 80 - .../ParseFixPatternWorker.java | 122 - .../java/edu/lu/uni/serval/TreeToString.java | 47 - .../lu/uni/serval/config/Configuration.java | 84 - .../java/edu/lu/uni/serval/defects4j/Bug.java | 43 - .../lu/uni/serval/defects4j/BugParser.java | 206 - .../uni/serval/diffentry/DiffEntryHunk.java | 85 - .../uni/serval/diffentry/DiffEntryReader.java | 250 - .../edu/lu/uni/serval/diffentry/RegExp.java | 20 - .../EnhancedASTDiff.java} | 47 +- .../edu/lu/uni/serval/fixminer/Launcher.java | 73 +- .../uni/serval/fixminer/PatternExtractor.java | 45 +- .../TestHunkParserSingleFile.java | 133 +- .../TestTreeLoader.java | 191 +- .../fixminer/cluster/AkkaTreeLoader.java | 313 +- .../fixminer/cluster/CalculatePairs.java | 10 +- .../serval/fixminer/cluster/CallShell.java | 4 +- .../uni/serval/fixminer/cluster/Compare.java | 6 +- .../fixminer/cluster/ImportPairs2DB.java | 11 +- .../cluster/MultiThreadTreeLoader.java | 103 +- .../cluster/MultiThreadTreeLoaderCluster.java | 114 +- .../MultiThreadTreeLoaderCluster3.java | 156 +- ...{StoreFile.java => StoreEDiffInCache.java} | 68 +- .../serval/fixminer/cluster/TreeActor.java | 3 - .../fixminer/cluster/TreeLoaderClusterL1.java | 44 +- .../serval/fixminer/cluster/TreeWorker.java | 4 - .../serval/gumtree/regroup/ActionFilter.java | 254 - .../regroup/HierarchicalActionSet.java | 90 +- .../regroup/HierarchicalRegrouper.java | 24 +- .../regroup/HierarchicalRegrouperForC.java | 300 - .../gumtree/regroup/HunkActionFilter.java | 625 - .../gumtree/regroup/HunkFixPattern.java | 27 - .../serval/gumtree/regroup/SimpleTree.java | 68 - .../serval/gumtree/regroup/SimplifyTree.java | 902 - .../uni/serval/gumtree/regroup/Traveler.java | 140 - .../edu/lu/uni/serval/livestudy/Alarm.java | 33 - .../uni/serval/livestudy/ParseViolations.java | 212 - .../edu/lu/uni/serval/livestudy/Parser.java | 84 - .../edu/lu/uni/serval/livestudy/README.md | 6 - .../lu/uni/serval/livestudy/Violation.java | 25 - .../lu/uni/serval/parameters/ParseAlarms.java | 145 - .../lu/uni/serval/statistics/.Rapp.history | 0 .../lu/uni/serval/statistics/Categories.java | 75 - .../uni/serval/statistics/FixedProjects.java | 26 - .../uni/serval/statistics/FixedVilations.java | 47 - .../serval/statistics/HunkSizeComputer.java | 106 - .../statistics/NumberOfFilesAndCodeLines.java | 74 - .../statistics/ReadSpearmanResults.java | 104 - .../edu/lu/uni/serval/statistics/Spearman.R | 362 - .../statistics/SpearmanCodeGenerator.java | 81 - .../lu/uni/serval/statistics/Statistic.java | 947 - .../statistics/TenFoldPossibilities.java | 243 - .../statistics/TenFoldPossibilities2.java | 256 - .../statistics/TenFoldPossibilities3.java | 256 - .../uni/serval/statistics/TenFoldProjs.java | 121 - .../statistics/UnhappenedTypesLiveStudy.java | 73 - .../uni/serval/statistics/UnparsedFiles.java | 55 - .../edu/lu/uni/serval/violation/Alarm.java | 82 - .../lu/uni/serval/violation/Violation.java | 31 - .../serval/violation/code/parser/Test.java | 223 - .../code/parser/ViolatePositionReader.java | 138 - .../code/parser/ViolationCodeParser.java | 282 - .../code/parser/ViolationSourceCodeTree.java | 785 - .../serval/violation/parse/AlarmsReader.java | 197 - .../lu/uni/serval/violation/parse/Test.java | 83 - .../violation/parse/TestViolationParser.java | 94 - .../violation/parse/ViolationParser.java | 274 - 116 files changed, 650 insertions(+), 118668 deletions(-) delete mode 100644 Dataset/LiveStudy/Patches delete mode 100644 Dataset/Patterns/Fix-Patterns delete mode 100644 Dataset/Patterns/Source-Code-Patterns-Unfixed-Violations delete mode 100644 inputData/1.txt delete mode 100644 logs/FixedViolationCodeParseResults.log delete mode 100644 logs/HaveSourceCode.txt delete mode 100644 logs/MultiMethodsOrFieldOrInnerClasses.txt delete mode 100644 logs/MultiV.txt delete mode 100644 logs/Null.txt delete mode 100644 logs/NullSourceCode.txt delete mode 100644 logs/NullV.txt delete mode 100644 logs/fixedTypes.txt delete mode 100644 logs/myLog.log delete mode 100644 src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiff.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiffHelper.java create mode 100644 src/main/java/edu/lu/uni/serval/FixPattern/utils/PoolBuilder.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/Tokenizer.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchHunkParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchSingleStatementParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FieldViolation.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java delete mode 100644 src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Violation.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/AkkaMatcher.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceCalculator.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceFunction.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternActor.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternWorker.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/ReturnMessage.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/WorkMessage.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser2.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternActor.java delete mode 100644 src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternWorker.java delete mode 100644 src/main/java/edu/lu/uni/serval/TreeToString.java delete mode 100644 src/main/java/edu/lu/uni/serval/defects4j/Bug.java delete mode 100644 src/main/java/edu/lu/uni/serval/defects4j/BugParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java delete mode 100644 src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java delete mode 100644 src/main/java/edu/lu/uni/serval/diffentry/RegExp.java rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations/TestHunkParser.java => fixminer/EnhancedASTDiff.java} (59%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer}/TestHunkParserSingleFile.java (72%) rename src/main/java/edu/lu/uni/serval/{FixPatternParser/violations => fixminer}/TestTreeLoader.java (54%) rename src/main/java/edu/lu/uni/serval/fixminer/cluster/{StoreFile.java => StoreEDiffInCache.java} (64%) delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/ActionFilter.java delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkFixPattern.java delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/SimpleTree.java delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java delete mode 100644 src/main/java/edu/lu/uni/serval/gumtree/regroup/Traveler.java delete mode 100644 src/main/java/edu/lu/uni/serval/livestudy/Alarm.java delete mode 100644 src/main/java/edu/lu/uni/serval/livestudy/ParseViolations.java delete mode 100644 src/main/java/edu/lu/uni/serval/livestudy/Parser.java delete mode 100644 src/main/java/edu/lu/uni/serval/livestudy/README.md delete mode 100644 src/main/java/edu/lu/uni/serval/livestudy/Violation.java delete mode 100644 src/main/java/edu/lu/uni/serval/parameters/ParseAlarms.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/.Rapp.history delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/Categories.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/FixedProjects.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/FixedVilations.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/HunkSizeComputer.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/NumberOfFilesAndCodeLines.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/ReadSpearmanResults.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/Spearman.R delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/SpearmanCodeGenerator.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/Statistic.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities2.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities3.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/TenFoldProjs.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/UnhappenedTypesLiveStudy.java delete mode 100644 src/main/java/edu/lu/uni/serval/statistics/UnparsedFiles.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/Alarm.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/Violation.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/code/parser/Test.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/code/parser/ViolatePositionReader.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationCodeParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationSourceCodeTree.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/parse/AlarmsReader.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/parse/Test.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/parse/TestViolationParser.java delete mode 100644 src/main/java/edu/lu/uni/serval/violation/parse/ViolationParser.java diff --git a/Dataset/LiveStudy/Patches b/Dataset/LiveStudy/Patches deleted file mode 100644 index c94a805..0000000 --- a/Dataset/LiveStudy/Patches +++ /dev/null @@ -1,119 +0,0 @@ -BC_UNCONFIRMED_CAST -BC_UNCONFIRMED_CAST_OF_RETURN_VALUE Comments: no any useful common fix patterns. -EI_EXPOSE_REP -EI_EXPOSE_REP2 -IS2_INCONSISTENT_SYNC -NM_METHOD_NAMING_CONVENTION - -DE_MIGHT_IGNORE Compile failed. -DLS_DEAD_LOCAL_STORE Compile failed -NP_LOAD_OF_KNOWN_NULL_VALUE - -DM_CONVERT_CASE To be improved - -DM_BOXED_PRIMITIVE_FOR_PARSING -DM_DEFAULT_ENCODING -DM_FP_NUMBER_CTOR -DM_NUMBER_CTOR -ES_COMPARING_STRINGS_WITH_EQ Comments: ignored - -MS_PKGPROTECT -MS_SHOULD_BE_FINAL Comments: failed to checkstyle. - -NP_NONNULL_RETURN_VIOLATION -NP_NULL_ON_SOME_PATH -NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE -NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE -OBL_UNSATISFIED_OBLIGATION -OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE -ODR_OPEN_DATABASE_RESOURCE -OS_OPEN_STREAM -OS_OPEN_STREAM_EXCEPTION_PATH -PZLA_PREFER_ZERO_LENGTH_ARRAYS -RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE -REC_CATCH_EXCEPTION -RI_REDUNDANT_INTERFACES -RV_RETURN_VALUE_IGNORED_BAD_PRACTICE -RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT -SBSC_USE_STRINGBUFFER_CONCATENATION -SE_NO_SERIALVERSIONID -SF_SWITCH_NO_DEFAULT -SIC_INNER_SHOULD_BE_STATIC -SIC_INNER_SHOULD_BE_STATIC_ANON -SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING -ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD -UC_USELESS_CONDITION -UC_USELESS_OBJECT -UCF_USELESS_CONTROL_FLOW -UPM_UNCALLED_PRIVATE_METHOD -URF_UNREAD_FIELD -URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -UWF_UNWRITTEN_FIELD -VA_FORMAT_STRING_USES_NEWLINE -WMI_WRONG_MAP_ITERATOR - - -rejected 1 https://github.com/apache/commons-io/pull/47 -rejected 1 https://github.com/apache/commons-io/pull/45 - -rejected 1 https://github.com/apache/commons-lang/pull/298 - 5 https://github.com/apache/commons-lang/pull/297 -improved 1 https://github.com/apache/commons-lang/pull/297 Comments: some patches failed to pass test cases, some patches led to compile failed, some patches led to checkstyle failed. - - 2 https://github.com/apache/commons-math/pull/69 - 1 https://github.com/apache/commons-math/pull/68 Comments: inner static class, there is no need to fix the violations in this kind of class. - 2 https://github.com/apache/commons-math/pull/67 Comments: improve patches. - 1 https://github.com/apache/commons-math/pull/66 - -rejected 1 https://github.com/apache/ant/pull/47 -improved 1 https://github.com/apache/ant/pull/46 -merged 2 https://github.com/apache/ant/pull/46 - 2 https://github.com/apache/ant/pull/45 -rejected 3 https://github.com/apache/ant/pull/44 -merged 1 https://github.com/apache/ant/pull/43 -merged 5 https://github.com/apache/ant/pull/42 Comments: need to import new packages, unless the fixed patches will fail to compile. -merged 1 https://github.com/apache/ant/pull/41 - - 1 https://github.com/apache/aries/pull/80 - 1 https://github.com/apache/aries/pull/79 - 1 https://github.com/apache/aries/pull/78 - 1 https://github.com/apache/aries/pull/77 - 1 https://github.com/apache/aries/pull/76 - -rejected 1 https://github.com/apache/camel/pull/2031 ShouldBeFinal -rejected 6 https://github.com/apache/camel/pull/2029 master5 -merged 1 https://github.com/apache/camel/pull/2035 master7 -merged 2 https://github.com/apache/camel/pull/2032 Useless -merged 2 https://github.com/apache/camel/pull/2025 master6 -merged 1 https://github.com/apache/camel/pull/2024 master4 -merged 1 https://github.com/apache/camel/pull/2023 master2 -rejected 1 https://github.com/apache/camel/pull/2017 master3 Comments: compile failed, the return value of method invocation is not Boolean, it is a specific case. -merged 1 https://github.com/apache/camel/pull/2016 master -merged 6 https://github.com/apache/camel/pull/2038 boxedParsing - - - 3 https://github.com/apache/cassandra/pull/165 - 4 https://github.com/apache/cassandra/pull/164 - 2 https://github.com/apache/cassandra/pull/163 - -Fixed 1 https://github.com/fangyidong/json-simple/pull/126 Comments: fixed in another version. https://github.com/RalleYTN/SimpleJSON - 1 https://github.com/fangyidong/json-simple/pull/125 - -On hold 1 https://github.com/apache/mahout/pull/346 - 1 https://github.com/apache/mahout/pull/345 - 1 https://github.com/apache/mahout/pull/344 - -merged 2 https://github.com/apache/poi/pull/77 5 -merged 4 https://github.com/apache/poi/pull/78 6 -merged 2 https://github.com/apache/poi/pull/79 t -merged 1 https://github.com/apache/poi/pull/80 4 -merged 4 https://github.com/apache/poi/pull/76 2 -merged 30 https://github.com/apache/poi/pull/75 master -merged 1 https://github.com/apache/poi/pull/74 3 - - - -Some violations never happened in these projects: - diff --git a/Dataset/Patterns/Fix-Patterns b/Dataset/Patterns/Fix-Patterns deleted file mode 100644 index e14f13a..0000000 --- a/Dataset/Patterns/Fix-Patterns +++ /dev/null @@ -1,131 +0,0 @@ -===================================== -=========Useful Fix Patterns========= -===================================== -==============Detailed=============== -DM_CONVERT_CASE - (1) ADD a rule of Locale.ENGLISH into toLowerCase/toUpperCase. -RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE - (1) DEL Null-Check IfStatement, - (2) DEL Null-Check Conditional Expression. -REC_CATCH_EXCEPTION - (1) Change Exception to a specific exception class. -SE_NO_SERIALVERSIONID - (1) Insert a private static final field serialVersionUID. -VA_FORMAT_STRING_USES_NEWLINE - (1) DEL "$backslash$n", - (2) Replace "$backslash$n" with "n" -MS_SHOULD_BE_FINAL - (1) ADD a ``final'' modifier. -WMI_WRONG_MAP_ITERATOR - (1) Replace the KeySet iterating ForStatement with an EntrySet iterating ForStatement. -DM_NUMBER_CTOR - (1) Replace the NumberType ClassInstanceCreation with a NumberType.valueOf() method invocation. -SIC_INNER_SHOULD_BE_STATIC - (1) ADD a "static" modifier, - (2) DEL the buggy statements. -DE_MIGHT_IGNORE - (1) Change Exception to a specific exception class. -DM_BOXED_PRIMITIVE_FOR_PARSING - (1) Replace NumberType.valueOf() with NumberType.parseNumberType(). -DM_FP_NUMBER_CTOR - (1) DEL the buggy statement, - (2) Replace Double or Float ClassInstanceCreation with (Double or Float).valueOf(), - (3) Remove the Double or Float ClassInstanceCreation from the buggy expression. -MS_PKGPROTECT - (1) DEL the buggy statement, - (2) DEL the ``public'' or ``protected'' modifier - (3) Replace the ``public'' or ``protected'' modifier with the ``private'' modifier. - (4) DEL the initialization expression. -ES_COMPARING_STRINGS_WITH_EQ - (1) Replace the ``=='' InfixExpression with a stringVar.equals() method invocation. - - -===============Abstract============== -NP_NULL_ON_SOME_PATH - (1) ADD a Null-check statement or expression. -RI_REDUNDANT_INTERFACES - (1) DEL the implemented Interface type. -NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE - (1) ADD a Null-check statement or expression, - (2) DEL the buggy statement. -UCF_USELESS_CONTROL_FLOW - (1) DEL the buggy statement, - (2) DEL the useless ConditionalExpression. -UC_USELESS_CONDITION - (1) UPD the operator of a ConditionalExpersion, - (2) UPD an sub-expression of a ConditionExpression. -NP_LOAD_OF_KNOWN_NULL_VALUE - (1) DEL Null-check expression or statement, - (2) Replace the null-known variable with NULL. -SBSC_USE_STRINGBUFFER_CONCATENATION - (1) Replace String type with StringBuilder, and replace plus operator of StringVarialbe with the append method of StringBuilder. -UC_USELESS_OBJECT - (1) DEL the buggy statement. -UPM_UNCALLED_PRIVATE_METHOD - (1) DEL the buggy statements. -NM_METHOD_NAMING_CONVENTION - (1) Update Method Name of MethodDeclaration. -URF_UNREAD_FIELD - (1) DEL the buggy statement. -===================================== -NP_NONNULL_RETURN_VIOLATION - (1) DEL the null-returned ReturnStatement. - (2) Replace NullLiteral with an Expression which returns an empty list. -PZLA_PREFER_ZERO_LENGTH_ARRAYS - (1) DEL the buggy statement, - √ (2) Replace NullLiteral with an empty array. -SIC_INNER_SHOULD_BE_STATIC_ANON - (1) DEL a parameter of a ClassInstanceCreation in an AnonymousClassDeclaration, - (2) DEL the statement contains an AnonymousClassDeclaration, - √ (3) Replace the AnonymousClassDeclaration with an defined Static Object of this class. -DLS_DEAD_LOCAL_STORE - (1) DEL the buggy statement. -DM_DEFAULT_ENCODING - √ (1) ADD a parameter (i.e., "UTF-8") into the ClassInstanceCreation of a Stream object. - (2) Replace ClassInstanceCreation with a MethodInvocation. - (3) DEL the buggy statement. -BC_UNCONFIRMED_CAST - (1) DEL the buggy statement, - (2) DEL the Cast Type, - (3) Replace CastExpression with NullLiteral. -URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD - (1) ADD a ``final'' modifier, - √ (2) DEL the buggy statement. -RV_RETURN_VALUE_IGNORED_BAD_PRACTICE - (1) Replace boolean-returned statement with a a new MethodInvocation. - √ (2) ADD an IfStatement. -EI_EXPOSE_REP - (1) DEL the buggy statement, - * (2) Replace the being assigned Expression with a ConditionalExpression. - √ (3) Replace the Expression being assigned with other Expression -EI_EXPOSE_REP2 - (1) DEL the buggy statement, - * (2) Replace the being assigned Expression with a ConditionalExpression. - √ (3) Replace the being assigned Expression with other Expression. - -===================================== -==========Null Fix Patterns========== -===================================== -UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR null. -OBL_UNSATISFIED_OBLIGATION null. -OS_OPEN_STREAM_EXCEPTION_PATH null. -SF_SWITCH_NO_DEFAULT null. -UWF_UNWRITTEN_FIELD null. -IS2_INCONSISTENT_SYNC null. -ODR_OPEN_DATABASE_RESOURCE null. -SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING null. -OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE null. -OS_OPEN_STREAM null. -NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE null. - -===================================== -========Useless Fix Patterns========= -===================================== -BC_UNCONFIRMED_CAST_OF_RETURN_VALUE - (1) UPD T1 v1 = (T1) method_invocation() with T2 v1 = method_invocation(), - (2) DEL the buggy statement, - (3) Replace the buggy CastExpresion with a MethodInvocation. -ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD - (1) DEL the buggy statement. -RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE - (1) ADD a Null-check statement or expression. diff --git a/Dataset/Patterns/Source-Code-Patterns-Unfixed-Violations b/Dataset/Patterns/Source-Code-Patterns-Unfixed-Violations deleted file mode 100644 index a748015..0000000 --- a/Dataset/Patterns/Source-Code-Patterns-Unfixed-Violations +++ /dev/null @@ -1,107 +0,0 @@ -================================ -=========Single Pattern========= -================================ -SIC_INNER_SHOULD_BE_STATIC_ANON: new Type() { override some methods(...){...} }. Anonymous inner class declaration. 100% -DE_MIGHT_IGNORE: try{...} catch (Exception e) {...}, Exception is not any specified. -VA_FORMAT_STRING_USES_NEWLINE: "\n", this new line symbol is in a StringLiteral of a format method. -UCF_USELESS_CONTROL_FLOW: if (conditional expression) {empty statements.}. -UC_USELESS_CONDITION: if (conditional expressions) {...}. -UC_USELESS_OBJECT: T1 v1 = new T1(). -PZLA_PREFER_ZERO_LENGTH_ARRAYS: return null. -EI_EXPOSE_REP: return variable; -REC_CATCH_EXCEPTION: try{...} catch (Exception e) {...}, Exception is not any specific exception. -SF_SWITCH_NO_DEFAULT: switch(exp) {case1:...case2:...}, without default statement. -UWF_UNWRITTEN_FIELD: return exp / variable. -SBSC_USE_STRINGBUFFER_CONCATENATION: stringVariable += stringExp, -RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT: return method_invocation_exp. Method invocation statement returns a value, but does not assign the value to any variable. (High false positives.) -NP_NONNULL_RETURN_VIOLATION: return null. (High false positives.) -================================ -========Multiple Patterns======= -================================ -NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE: (1) for (File file : filesArray) {...} (2) for (int i =0; i < filesArray.length; i ++) {...} -DM_CONVERT_CASE: (1) stringExp.toLowerCase(), 24,897 - (2)stringExp.toUpperCase(). 10,406 -MS_PKGPROTECT: (1) public static final T1 v1 = initializationExp, 2442 - (2) protected static final T1 v1 = initializationExp. 175 - (3) protected static T1 v1 = initializationExp. 158 - (4) public static T1 v1 = initializationExp. 262, other 46 -SIC_INNER_SHOULD_BE_STATIC: (1) this.v1 = v2; 590 - (2) v1 = v2; 170 - (3) super(...). 213 -BC_UNCONFIRMED_CAST: (1) T1 v1 = (T(1) v2/exp, (2) v1 = (T(1) v2/exp, (3) ((T(1) v2).exp. -ES_COMPARING_STRINGS_WITH_EQ: (1) stringExp1 == stringExp2 IfStatement, ReturnStatement, WhileStatement. - (2) stringExp1 != stringExp2 -RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE: (1) if (exp == null ...) {...}, - (2) if (exp != null ...) {...}, - (3) exp == null ? exp1 : exp2, - (4) exp != null ? exp1 : exp2. -DM_NUMBER_CTOR: (1) new Long(...), (2)new Integer(...), (3)new Short(...), (4)new Byte(...), (5)new Char(...). -DM_FP_NUMBER_CTOR: (1) new Double(exp), (2)new Float(exp). -DM_BOXED_PRIMITIVE_FOR_PARSING: (1) Integer.valueOf(str), (2)Long.valueOf(str). Comments: it contains fewer patterns than findbugs. -EI_EXPOSE_REP2: (1) this.v1 = v2, - (2) v1 = v2. 3700 -BC_UNCONFIRMED_CAST_OF_RETURN_VALUE: (1) T1 v1 = (T) method_invocation(), - (2) v1 = (T) method_invocation(), - (3) ((T) method_invocation()).exp. -ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD: (1) static_v1 = instance_exp1.method_invocation(), - (2) v1 = instance_exp1.method_invocation(), - (3) v1 = exp1, other variable assignment statement. -RV_RETURN_VALUE_IGNORED_BAD_PRACTICE: (1) File.mkdirs(), - (2) File.mkdir(), - (3) File.delete(), - (4) File.createNewFile(), - (5) other exp.method_invoation() returns a value. -SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING: (1) sqlExecutionStatement = StringLiteral1 + stringV1 + ... + StringLiteral2 + stringV2. - (2) sqlRelatedVariable = sqlRelatedMethodInvocation(); -OS_OPEN_STREAM: (1) StreamType v = new StreamType(...), 2) streamVariable = new StreamType(new StreamType2(...)), e.g., 1. FileOutputStream fos = new FileOutputStream(outFile); -DM_DEFAULT_ENCODING: (1) new BufferedReader(new InputStreamReader(input)), 99+ - (2) new StreamWriter(output); - (3) stringExp.getBytes(), - (4) new String(byteExp), - (5) byteExp.toString(). -ODR_OPEN_DATABASE_RESOURCE: (1) conn.createStatement(), - (2) conn.createStatement.execute(...), - (3) PreparedStatement st = conn.prepareStatement(), - (4) DataBaseConnection conn = exp.getConnection(...). -NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE: (1) return method_invocation(...), 2) return class_instance_creation(...). -======================================== -==========Inefficient Patterns========== -======================================== -OBL_UNSATISFIED_OBLIGATION: (1) StreamType v = new StreamType(...), - (2) streamVariable = new StreamType(new StreamType2(...)), - (3) sqlStatementExp.executeMethod(). e.g., 1. FileOutputStream fos = new FileOutputStream(outFile); 2. ResultSet rs = sqlStmt.executeQuery(). -OS_OPEN_STREAM_EXCEPTION_PATH: (1) StreamType v = new StreamType(...), - (2) streamVariable = new StreamType(...). -IS2_INCONSISTENT_SYNC: (1) return v1, - (2) if(conditionalExp) {...}, - (3) sqlStmt = stringLiteral1 + stringExp + stringLiteral2. not very consistent. -OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE: (1) StreamType v = new StreamType(...), - (2) streamVariable = new StreamType(new StreamType2(...)), - (3) sqlStatementExp.executeMethod(). e.g., 1. FileOutputStream fos = new FileOutputStream(outFile); 2. ResultSet rs = sqlStmt.executeQuery(). -WMI_WRONG_MAP_ITERATOR: for statement { ... MapVariable.get(keyExp) ... }. or NULL. Lack of enough information. -======================================== -=====Redundant Inconsistent Pattern===== -======================================== -MS_SHOULD_BE_FINAL: (1) public (28,302) static T1 v1 = exp. e.g., public static int maxStringLength = 65535. - (2) protected (6,719) static T1 v1 = exp. -URF_UNREAD_FIELD: (1) this.v1 = v2, (2)this.v1 = new T(), (3)private Type v = exp. Comments: it contains more patterns than findbugs. only pattern 3 is consistent. -URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD: (1) this.v1 = v2, - (2) public/protected (static) T1 v1 = exp; Comments: only 2 is consistent. - (3) v1 = exp1. -======================================== -=========Inconsistent Patterns========= -======================================== -RI_REDUNDANT_INTERFACES: super(...). Comments: not very consistent. Locate on the position of super classes. -======================================== -==============Null Pattern============== -======================================== -===========Inaccurate Position========== -NM_METHOD_NAMING_CONVENTION: null. Comments: violate on title, but position locates on body. -SE_NO_SERIALVERSIONID: null. -UPM_UNCALLED_PRIVATE_METHOD: null. (method body) -UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR: null. inaccurate positions. -==========Specific Source Code========== -DLS_DEAD_LOCAL_STORE: null. Variable assignment statements. Comments: specific source code. -NP_NULL_ON_SOME_PATH: null. -NP_LOAD_OF_KNOWN_NULL_VALUE: null. -RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE: null. diff --git a/FixPatternMiner.iml b/FixPatternMiner.iml index 262312b..a7d8955 100644 --- a/FixPatternMiner.iml +++ b/FixPatternMiner.iml @@ -11,15 +11,6 @@ - - - - - - - - - @@ -27,9 +18,18 @@ + + + + + + + + + @@ -43,20 +43,12 @@ - - - - - - - - - + \ No newline at end of file diff --git a/inputData/1.txt b/inputData/1.txt deleted file mode 100644 index 46e4275..0000000 --- a/inputData/1.txt +++ /dev/null @@ -1,730 +0,0 @@ -https://github.com/IDPF/epubcheck.git -https://github.com/treasure-data/td-import-java.git -https://github.com/Atmosphere/atmosphere-extensions.git -https://github.com/astefanutti/camel-cdi.git -https://github.com/imagej/imagej-ui-swing.git -https://github.com/komoot/photon.git -https://github.com/FIWARE-Middleware/KIARA.git -https://github.com/mbosecke/pebble.git -https://github.com/metamx/java-util.git 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-#Illegal_Line_Position:Activiti-Activiti_0ea44a_749e0fmodules/activiti-engine/src/main/java/org/activiti/engine/impl/cmd/SubmitTaskFormCmd.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_0ea44a_749e0fmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_11bc1d_6c37a5modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:390:390:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_1347b3_a161aamodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_16e877_a6698bmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_16e877_a6698bmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_16e877_a6698bmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_16e877_a6698bmodules/activiti-engine/src/main/java/org/activiti/engine/impl/cmd/SubmitTaskFormCmd.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_16e877_a6698bmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-bpmn-converter/src/main/java/org/activiti/bpmn/converter/CallActivityXMLConverter.java:108:131:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-bpmn-converter/src/main/java/org/activiti/bpmn/converter/CallActivityXMLConverter.java:134:157:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:254:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:60:266:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/listener/DelegateExpressionExecutionListener.java:37:68:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/listener/DelegateExpressionTaskListener.java:36:66:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/listener/ExpressionTaskListener.java:28:41:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/el/JuelExpression.java:39:84:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/el/UelExpressionCondition.java:32:45:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/form/FormPropertyImpl.java:34:72:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/impl/scripting/JuelScriptEngine.java:306:323:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_205a58_aef8c4modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:661:661:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_21a8cc_7ca9b3modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_2744c6_dcc190modules/activiti-engine/src/main/java/org/activiti/engine/impl/test/PluggableActivitiTestCase.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:Activiti-Activiti_301028_ad3bf6modules/activiti-engine/src/main/java/org/activiti/engine/impl/test/PluggableActivitiTestCase.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:Activiti-Activiti_321b33_1851a5modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:702:702:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_4bb2be_a8e456modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/parser/EventSubscriptionDeclaration.java:38:90:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_542d1e_88f123modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/parser/BpmnParse.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:Activiti-Activiti_649746_dbff76modules/activiti-engine/src/main/java/org/activiti/engine/impl/ExecutionQueryImpl.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:Activiti-Activiti_649746_dbff76modules/activiti-engine/src/main/java/org/activiti/engine/impl/ProcessInstanceQueryImpl.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:Activiti-Activiti_649746_dbff76modules/activiti-engine/src/main/java/org/activiti/engine/impl/ProcessInstanceQueryImpl.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:Activiti-Activiti_724655_206c08modules/activiti-engine/src/main/java/org/activiti/engine/impl/AbstractQuery.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_724655_206c08modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_724655_206c08modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_724655_206c08modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_7dce14_94b753modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_7dce14_94b753modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_7dce14_94b753modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_7dce14_94b753modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/MessageThrowingEventListener.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_7dce14_94b753modules/activiti-engine/src/main/java/org/activiti/engine/impl/calendar/DurationBusinessCalendar.java:22:22:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:Activiti-Activiti_7dce14_94b753modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_8646b1_b13e7cmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:507:507:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_90446c_2d592dmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_90446c_2d592dmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_90446c_2d592dmodules/activiti-engine/src/main/java/org/activiti/engine/impl/calendar/DurationBusinessCalendar.java:22:22:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:Activiti-Activiti_90446c_2d592dmodules/activiti-engine/src/main/java/org/activiti/engine/impl/cmd/SubmitTaskFormCmd.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_90446c_2d592dmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-bpmn-converter/src/main/java/org/activiti/bpmn/converter/CallActivityXMLConverter.java:108:131:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-bpmn-converter/src/main/java/org/activiti/bpmn/converter/CallActivityXMLConverter.java:134:157:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-bpmn-converter/src/main/java/org/activiti/bpmn/converter/UserTaskXMLConverter.java:200:214:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/listener/DelegateExpressionExecutionListener.java:37:68:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/listener/DelegateExpressionTaskListener.java:36:66:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/listener/ExpressionTaskListener.java:28:41:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/el/JuelExpression.java:39:84:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/el/UelExpressionCondition.java:32:45:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/form/FormPropertyImpl.java:34:72:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/impl/scripting/JuelScriptEngine.java:306:323:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Activiti-Activiti_915ceb_d4b1f8modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:Activiti-Activiti_92f723_3e6b34modules/activiti-engine/src/main/java/org/activiti/engine/impl/persistence/entity/ProcessDefinitionEntity.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:Activiti-Activiti_ad0c9e_36f30cmodules/activiti-engine/src/main/java/org/activiti/engine/impl/AbstractQuery.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_ad0c9e_36f30cmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_ad0c9e_36f30cmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_ad0c9e_36f30cmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:Activiti-Activiti_b41f55_209872modules/activiti-engine/src/main/java/org/activiti/engine/impl/ProcessInstanceQueryImpl.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:Activiti-Activiti_b78775_c1a1d7modules/activiti-engine/src/main/java/org/activiti/engine/impl/db/DbSqlSessionFactory.java:217:217:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_ba49f7_d6278fmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_cac168_19fad0modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/IntermediateThrowNoneEventActivityBehavior.java:15:15:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_cac168_19fad0modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/ManualTaskActivityBehavior.java:23:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_cac168_19fad0modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/NoneStartEventActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_cac168_19fad0modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TaskActivityBehavior.java:22:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_d3b514_31807dmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:19:19:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_d3b514_31807dmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:62:273:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_d626cc_0014d1modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_d626cc_0014d1modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_d626cc_0014d1modules/activiti-engine/src/main/java/org/activiti/engine/impl/cmd/SubmitTaskFormCmd.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_d626cc_0014d1modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_dd5a65_8f8f09modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:729:729:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_e10fb4_f9dfe0modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_e57bd9_bc87a6modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_e57bd9_bc87a6modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_e57bd9_bc87a6modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_e57bd9_bc87a6modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/MessageThrowingEventListener.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_e57bd9_bc87a6modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_e612fe_d18e50modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:453:453:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_ed0ee2_470eb0modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_edec53_33ff3fmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_edec53_33ff3fmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_edec53_33ff3fmodules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_edec53_33ff3fmodules/activiti-engine/src/main/java/org/activiti/engine/impl/persistence/entity/ProcessDefinitionEntity.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_edec53_33ff3fmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_f18be5_7a781dmodules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:587:587:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_f6c242_fc85e3modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_f6c242_fc85e3modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_f6c242_fc85e3modules/activiti-engine/src/main/java/org/activiti/engine/impl/calendar/DurationBusinessCalendar.java:22:22:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:Activiti-Activiti_f6c242_fc85e3modules/activiti-engine/src/main/java/org/activiti/engine/impl/cmd/SubmitTaskFormCmd.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_f6c242_fc85e3modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_fce83e_08c2b8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/TransactionActivityBehavior.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_fce83e_08c2b8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/behavior/UserTaskActivityBehavior.java:47:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Activiti-Activiti_fce83e_08c2b8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/ClassDelegate.java:63:281:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Activiti-Activiti_fce83e_08c2b8modules/activiti-engine/src/main/java/org/activiti/engine/impl/bpmn/helper/MessageThrowingEventListener.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Activiti-Activiti_fce83e_08c2b8modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:658:658:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:Activiti-Activiti_ff016c_c16bc1modules/activiti-engine/src/main/java/org/activiti/engine/ProcessEngineConfiguration.java:502:502:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:adangel-pmd_21750b_f0049cpmd/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java:95:105:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:adangel-pmd_36224a_4d9b7bpmd/src/main/java/net/sourceforge/pmd/lang/rule/xpath/AbstractXPathRuleQuery.java:71:71:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:adangel-pmd_3aa04a_ddacf7pmd/src/main/java/net/sourceforge/pmd/util/datasource/ReaderDataSource.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:adangel-pmd_4aee86_d52db3pmd/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java:95:105:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:adangel-pmd_4f50ec_4a49e6pmd/src/main/java/net/sourceforge/pmd/lang/plsql/rule/codesize/TooManyFieldsRule.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:adangel-pmd_5f0280_dc945fpmd/src/main/java/net/sourceforge/pmd/lang/rule/xpath/AbstractXPathRuleQuery.java:71:71:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:adangel-pmd_782135_cb5feapmd/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:adangel-pmd_a7e4a1_28a663pmd/src/main/java/net/sourceforge/pmd/cpd/CPDConfiguration.java:66:72:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:adangel-pmd_a7e4a1_28a663pmd/src/main/java/net/sourceforge/pmd/cpd/CPDConfiguration.java:56:62:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:adangel-pmd_f0049c_6e1927pmd/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java:96:107:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:aeshell-aesh_1780ee_938c76src/test/java/org/jboss/aesh/console/aesh/AeshCommandDynamicTest.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:aeshell-aesh_70b25e_cc0bbdsrc/test/java/org/jboss/aesh/console/edit/ViEditingTest.java:59:66:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_73ca4c_d391f5src/main/java/org/jboss/aesh/graphics/Rectangle.java:48:111:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:aeshell-aesh_74793a_6d976csrc/test/java/org/jboss/aesh/console/edit/ViEditingTest.java:59:66:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_8d5337_88718dsrc/test/java/org/jboss/aesh/cl/TestPopulator5.java:84:94:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_8d5337_88718dsrc/test/java/org/jboss/aesh/console/aesh/AeshConsoleTest.java:152:162:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_b8034e_c7a895src/main/java/org/jboss/aesh/util/FileLister.java:440:458:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:aeshell-aesh_d165ef_6af253src/test/java/org/jboss/aesh/cl/CommandLineParserTest.java:269:269:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_d165ef_6af253src/test/java/org/jboss/aesh/cl/CommandLineParserTest.java:248:248:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_d165ef_6af253src/test/java/org/jboss/aesh/cl/ParseCompleteObjectTest.java:333:333:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_d165ef_6af253src/test/java/org/jboss/aesh/cl/ParseCompleteObjectTest.java:341:341:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_d165ef_6af253src/test/java/org/jboss/aesh/cl/ParserGeneratorTest.java:82:82:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_d165ef_6af253src/test/java/org/jboss/aesh/cl/ParserGeneratorTest.java:69:69:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aeshell-aesh_e75ac3_c4be23src/test/java/org/jboss/aesh/console/redirect/ConsoleRedirectionTest.java:35:35:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:aherbert-GDSC-SMLM_ac101f_3b4baasrc/main/java/gdsc/smlm/function/gaussian/CircularGaussian2DFunction.java:59:59:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:aherbert-GDSC-SMLM_ac101f_3b4baasrc/main/java/gdsc/smlm/function/gaussian/FixedGaussian2DFunction.java:59:59:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:aherbert-GDSC-SMLM_b5a526_c39c98src/main/java/gdsc/smlm/ij/plugins/GaussianFit.java:1323:1333:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:aherbert-GDSC-SMLM_b6538a_2db8f3src/main/java/gdsc/smlm/ij/utils/Utils.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:aherbert-GDSC-SMLM_c72492_d54f5asrc/main/java/gdsc/smlm/ij/plugins/BenchmarkSpotFilter.java:98:129:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:aherbert-GDSC-SMLM_e23773_c6e912src/main/java/gdsc/smlm/fitting/function/gaussian/CircularGaussian2DFunction.java:59:59:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:aherbert-GDSC-SMLM_e23773_c6e912src/main/java/gdsc/smlm/fitting/function/gaussian/FreeCircularGaussian2DFunction.java:59:59:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:aherbert-GDSC-SMLM_f32d6c_47ab63src/main/java/gdsc/smlm/fitting/function/PoissonGammaGaussianLikelihoodWrapper.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:aherbert-GDSC-SMLM_f32d6c_47ab63src/main/java/gdsc/smlm/fitting/function/PoissonGaussianLikelihoodWrapper.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:aherbert-GDSC-SMLM_fcfa17_5e8ac0src/main/java/gdsc/smlm/ga/ChromosomeComparator.java:21:35:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:aht-group-ofx_0e06e8_180211core/src/main/java/org/openfuxml/renderer/latex/AbstractOfxLatexRenderer.java:113:113:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:airlift-airlift_dd0c0a_a06897src/main/java/com/facebook/presto/Cursor.java:-1:-1:EQ_ABSTRACT_SELF -#Null_Violation_Hunk:albfan-jmeld_4ef974_ce89fcsrc/main/java/org/jmeld/ui/FolderDiffPanel.java:675:697:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:albfan-jmeld_b4f98d_c6c0ecsrc/main/java/org/jmeld/ui/action/Actions.java:51:64:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:albfan-jmeld_b4f98d_c6c0ecsrc/main/java/org/jmeld/ui/FolderDiffPanel.java:670:692:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:alibaba-druid_3eb0b6_aaf1f2src/main/java/com/alibaba/druid/sql/ast/statement/SQLJoinTableSource.java:73:73:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:alibaba-druid_b0f87d_8e7af7src/main/java/com/alibaba/druid/support/http/WebStatFilter.java:460:543:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:alibaba-druid_f9b615_79672fsrc/main/java/com/alibaba/druid/support/http/WebStatFilter.java:460:543:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:allanbank-mongodb-async-driver_222a77_541915src/main/java/com/allanbank/mongodb/Credential.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:allanbank-mongodb-async-driver_2df4f3_405b07src/main/java/com/allanbank/mongodb/MongoClientConfiguration.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:allanbank-mongodb-async-driver_4481cc_2bbf92src/main/java/com/allanbank/mongodb/bson/impl/RootDocument.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:allanbank-mongodb-async-driver_5ca324_112eb3src/main/java/com/allanbank/mongodb/bson/builder/impl/AbstractBuilder.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:allanbank-mongodb-async-driver_8cb7a0_7186dbsrc/test/java/com/allanbank/mongodb/client/callback/ReplyHandlerTest.java:316:326:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:allanbank-mongodb-async-driver_8cb7a0_7186dbsrc/test/java/com/allanbank/mongodb/client/state/ClusterPingerTest.java:1147:1158:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:allanbank-mongodb-async-driver_8cb7a0_7186dbsrc/test/java/com/allanbank/mongodb/client/state/ClusterPingerTest.java:1173:1184:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:allanbank-mongodb-async-driver_8cb7a0_7186dbsrc/test/java/com/allanbank/mongodb/client/state/ClusterPingerTest.java:1173:1184:SE_BAD_FIELD_INNER_CLASS -#Illegal_Line_Position:allanbank-mongodb-async-driver_98a1be_348fccsrc/main/java/com/allanbank/mongodb/connection/FutureCallback.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_98a1be_348fccsrc/main/java/com/allanbank/mongodb/connection/FutureCallback.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_98a901_e8cac9src/main/java/com/allanbank/mongodb/builder/AggregationGeoNear.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_98a901_e8cac9src/main/java/com/allanbank/mongodb/builder/GeoJson.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:allanbank-mongodb-async-driver_98a901_e8cac9src/main/java/com/allanbank/mongodb/connection/auth/MongoDbAuthenticator.java:165:197:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Illegal_Line_Position:allanbank-mongodb-async-driver_98a901_e8cac9src/main/java/com/allanbank/mongodb/Credential.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:allanbank-mongodb-async-driver_98a901_e8cac9src/main/java/com/allanbank/mongodb/error/MongoClientClosedException.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:allanbank-mongodb-async-driver_a264bd_c87300src/main/java/com/allanbank/mongodb/builder/AggregationGeoNear.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_a264bd_c87300src/main/java/com/allanbank/mongodb/builder/GeoJson.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:allanbank-mongodb-async-driver_a264bd_c87300src/main/java/com/allanbank/mongodb/connection/auth/MongoDbAuthenticator.java:165:197:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Illegal_Line_Position:allanbank-mongodb-async-driver_a264bd_c87300src/main/java/com/allanbank/mongodb/Credential.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:allanbank-mongodb-async-driver_a264bd_c87300src/main/java/com/allanbank/mongodb/error/MongoClientClosedException.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/bson/io/SizeOfVisitor.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/commands/Distinct.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/commands/Find.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/commands/FindAndModify.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/commands/GroupBy.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/commands/MapReduce.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/connection/socket/SocketConnection.java:589:610:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/error/ReplyException.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/MongoDbConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:allanbank-mongodb-async-driver_c760f4_8c7984src/main/java/com/allanbank/mongodb/util/IOUtils.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:allanbank-mongodb-async-driver_cfb78d_436794src/main/java/com/allanbank/mongodb/client/message/AggregateCommand.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:allanbank-mongodb-async-driver_e9d4ca_c3ef67src/main/java/com/allanbank/mongodb/error/ServerVersionException.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_168d1b_3dfe39src/main/java/de/fau/osr/gui/Viewer.java:164:164:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_2a2a86_935ef6src/main/java/de/fau/osr/gui/GuiView.java:37:51:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_3b5c4b_34223csrc/main/java/de/fau/osr/bl/RequirementsRelation.java:68:68:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_3b5c4b_34223csrc/main/java/de/fau/osr/gui/GuiView.java:39:53:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_3b5c4b_34223csrc/main/java/de/fau/osr/gui/GuiView.java:57:82:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_3dedae_4b3055src/main/java/de/fau/osr/gui/GuiView.java:57:82:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_3dedae_4b3055src/main/java/de/fau/osr/gui/GuiView.java:39:53:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_7dae98_d2f9fasrc/main/java/de/fau/osr/gui/GuiView.java:58:83:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_9c4d0f_5ed822src/main/java/de/fau/osr/gui/GuiView.java:37:51:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:AMOSTeam3-amos-ss15-proj3_bd327f_b4b69fsrc/main/java/de/fau/osr/gui/GuiView.java:329:352:SIC_INNER_SHOULD_BE_STATIC_ANON -#Illegal_Line_Position:anba-es6draft_2c2cc7_74ade4src/main/java/com/github/anba/es6draft/repl/Repl.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:anba-es6draft_328b5c_efa31bsrc/main/java/com/github/anba/es6draft/compiler/Types.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:anba-es6draft_3bcb8e_1717ebsrc/main/java/com/github/anba/es6draft/runtime/objects/GlobalObject.java:43:587:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_3bcb8e_1717ebsrc/main/java/com/github/anba/es6draft/runtime/objects/RegExpPrototype.java:49:560:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_4a2d1f_d77e5bsrc/main/java/com/github/anba/es6draft/runtime/objects/promise/PromiseConstructor.java:382:382:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:anba-es6draft_5a6b04_bf947fsrc/main/java/com/github/anba/es6draft/runtime/objects/ErrorConstructor.java:41:98:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_9e8242_988f13src/main/java/com/github/anba/es6draft/runtime/objects/binary/ArrayBufferConstructor.java:49:277:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_9e8242_988f13src/main/java/com/github/anba/es6draft/runtime/objects/ObjectConstructor.java:45:541:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_9e8242_988f13src/main/java/com/github/anba/es6draft/runtime/objects/RegExpConstructor.java:54:272:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_a4b45d_630e29src/main/java/com/github/anba/es6draft/runtime/types/builtins/BuiltinFunction.java:22:33:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:anba-es6draft_eb1062_0795d0src/main/java/com/github/anba/es6draft/runtime/internal/ScriptRuntime.java:2858:2858:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:anba-es6draft_ee6725_3d5774src/main/java/com/github/anba/es6draft/compiler/Types.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:ansell-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/profiles/OWL2QLProfile.java:351:387:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/profiles/OWL2RLProfile.java:288:345:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/profiles/OWL2RLProfile.java:356:415:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/util/HornAxiomVisitorEx.java:244:285:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/util/HornAxiomVisitorEx.java:187:240:SE_INNER_CLASS -#Illegal_Line_Position:ansell-owlapi_0b2270_b20fe9oboformat/src/main/java/org/obolibrary/oboformat/writer/OBOFormatWriter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:ansell-owlapi_0b8d35_8e556coboformat/src/main/java/org/obolibrary/oboformat/parser/OBOFormatParser.java:44:162:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ansell-owlapi_0b8d35_8e556coboformat/src/main/java/org/obolibrary/owl/LabelFunctionalFormat.java:13:13:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_101e91_621073parsers/src/main/java/org/coode/owlapi/latex/LatexAxiomsListOntologyFormat.java:49:53:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_112983_d13ce3tools/src/main/java/uk/ac/manchester/cs/owl/explanation/ordering/ExplanationOrdererImpl.java:373:385:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/BinaryRdfOntologyFormatFactory.java:12:28:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/N3OntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/NQuadsOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/NTriplesOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/RdfJsonOntologyFormatFactory.java:12:20:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/RDFXMLOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/TrigOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/TrixOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/TurtleOntologyFormatFactory.java:11:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioBinaryRdfOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioBinaryRdfParserFactory.java:46:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioJsonOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioJsonParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioN3OntologyStorerFactory.java:48:63:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioN3ParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNQuadsOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNQuadsParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNTriplesOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNTriplesParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioRDFXMLOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioRDFXMLParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrigOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrigParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrixOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrixParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTurtleOntologyStorerFactory.java:50:67:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTurtleParserFactory.java:47:52:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:ansell-owlapi_3221dd_f67b95oboformat/src/main/java/org/obolibrary/oboformat/writer/OBOFormatWriter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:ansell-owlapi_3ce0c8_72a28fparsers/src/main/java/de/uulm/ecs/ai/owlapi/krssparser/KRSS2OWLParserFactory.java:48:51:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:ansell-owlapi_3ce0c8_72a28fparsers/src/main/java/org/coode/owlapi/functionalparser/OWLFunctionalSyntaxParser.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebapi/src/main/java/org/semanticweb/owlapi/io/OWLParserFactoryImpl.java:14:31:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebapi/src/main/java/org/semanticweb/owlapi/util/OWLOntologyStorerFactoryImpl.java:33:52:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioBinaryRdfOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioJsonOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioN3OntologyStorerFactory.java:49:58:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioNQuadsOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioNTriplesOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioRDFXMLOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioTrigOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioTrixOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioTurtleOntologyStorerFactory.java:51:61:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_570cfa_93df9fimpl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLOntologyBuilderImpl.java:50:54:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_621073_07de69parsers/src/main/java/org/coode/owl/krssparser/KRSSOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_621073_07de69parsers/src/main/java/org/coode/owlapi/latex/LatexOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_621073_07de69parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxHTMLOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_621073_07de69parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_70efa7_d41db2tools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:878:878:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ansell-owlapi_70efa7_d41db2tools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:1258:1258:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ansell-owlapi_743e4c_8a6a56impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:1657:1691:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_743e4c_8a6a56impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:103:137:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_743e4c_8a6a56parsers/src/main/java/org/semanticweb/owlapi/rdf/rdfxml/parser/OWLRDFConsumer.java:1372:1372:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ansell-owlapi_777b3e_7b036eimpl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:94:128:SE_INNER_CLASS -#Illegal_Line_Position:ansell-owlapi_9c42ae_2fab17parsers/src/main/java/org/coode/owlapi/functionalparser/OWLFunctionalSyntaxParser.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/io/RDFParserMetaData.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/DefaultPrefixManager.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:ansell-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/HasPriorityComparator.java:29:45:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/HornAxiomVisitorEx.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/OWLEntityComparator.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:ansell-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:132:162:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ansell-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:132:162:SE_INNER_CLASS -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/MapPointer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLOntologyManagerImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/SWRLRuleImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4rio/src/main/java/org/semanticweb/owlapi/formats/RioRDFOntologyFormat.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4rio/src/main/java/org/semanticweb/owlapi/rio/RioOntologyStorer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ansell-owlapi_b4ba8c_e696d4rio/src/main/java/org/semanticweb/owlapi/rio/RioParserImpl.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:ansell-owlapi_b4ba8c_e696d4tools/src/main/java/uk/ac/manchester/cs/owl/explanation/ordering/ExplanationOrdererImpl.java:358:371:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ansell-owlapi_b5388d_2898c6impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/SWRLRuleImpl.java:254:317:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ansell-owlapi_e14abb_cc74b3parsers/src/main/java/org/semanticweb/owlapi/rdf/RDFRendererBase.java:568:581:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Illegal_Line_Position:ansell-owlapi_e15cc9_4cd590oboformat/src/main/java/org/coode/owlapi/oboformat/OBOFormatRenderer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:ansell-owlapi_e16e3b_b4ba8cimpl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:1353:1387:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_e3c497_ce87baimpl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:94:128:SE_INNER_CLASS -#Null_Violation_Hunk:ansell-owlapi_e3c497_ce87batools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:1258:1258:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ansell-owlapi_e3c497_ce87batools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:878:878:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ansell-owlapi_e7634e_edbdc7parsers/src/main/java/org/coode/owl/krssparser/KRSSOntologyFormat.java:51:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_e7634e_edbdc7parsers/src/main/java/org/coode/owlapi/latex/LatexAxiomsListOntologyFormat.java:52:58:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_e7634e_edbdc7parsers/src/main/java/org/coode/owlapi/latex/LatexOntologyFormat.java:51:56:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_e7634e_edbdc7parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxHTMLOntologyFormat.java:51:56:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:ansell-owlapi_e7634e_edbdc7parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxOntologyFormat.java:51:56:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:antoine-tran-Hedera_4363df_8b88eajava/experiments/org/hedera/io/RevisionConcatText.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:antoine-tran-Hedera_4363df_8b88eajava/experiments/org/hedera/mapreduce/WikiRevisionSolrIndexer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:antoine-tran-Hedera_d2b63f_f829aejava/main/org/hedera/mapreduce/io/wikipedia/WikiRevisionSamplePairReader.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:apache-archiva_31515d_fdc941maven-repository-indexer/src/main/java/org/apache/maven/repository/indexing/ArtifactRepositoryIndexSearcher.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:apache-archiva_5e6fb5_398db2maven-repository-indexer/src/main/java/org/apache/maven/repository/indexing/AbstractRepositoryIndexer.java:118:118:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:apache-archiva_70bbe7_911feemaven-repository-reports-standard/src/main/java/org/apache/maven/repository/reporting/CachedRepositoryQueryLayer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:apache-archiva_70bbe7_911feemaven-repository-reports-standard/src/main/java/org/apache/maven/repository/reporting/CachedRepositoryQueryLayer.java:107:107:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:apache-archiva_80fd20_2df87cmaven-repository-indexer/src/main/java/org/apache/maven/repository/indexing/AbstractRepositoryIndex.java:139:139:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:apache-archiva_f5fd46_58d71dmaven-repository-indexer/src/main/java/org/apache/maven/repository/indexing/AbstractRepositoryIndexer.java:91:91:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:apache-archiva_f5fd46_58d71dmaven-repository-indexer/src/main/java/org/apache/maven/repository/indexing/AbstractRepositoryIndexer.java:104:104:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:apache-commons-codec_d911dd_3400e5src/test/org/apache/commons/codec/binary/HexCharTest.java:122:122:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:apache-commons-codec_fee232_ae537csrc/java/org/apache/commons/codec/language/bm/PhoneticEngine.java:298:344:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:apache-commons-compress_697216_34e939src/main/java/org/apache/commons/compress/archivers/dump/DumpArchiveEntry.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:apache-commons-configuration_3696f4_894af8src/main/java/org/apache/commons/configuration/interpol/ExprLookup.java:204:220:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/BaseHierarchicalConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/CombinedConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/DataConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/DynamicCombinedConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/plist/XMLPropertyListConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/SubnodeConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_439052_a24375src/main/java/org/apache/commons/configuration/XMLConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-commons-configuration_6cb034_374421src/main/java/org/apache/commons/configuration2/plist/PropertyListParser.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:apache-commons-configuration_8c42aa_8b26e6src/java/org/apache/commons/configuration/plist/XMLPropertyListConfiguration.java:199:203:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:apache-commons-dbcp_37c3dd_5d4ab5src/java/org/apache/commons/dbcp2/BasicDataSource.java:196:196:IS2_INCONSISTENT_SYNC -#Null_Violation_Hunk:apache-commons-dbcp_37c3dd_5d4ab5src/java/org/apache/commons/dbcp2/BasicDataSource.java:197:197:IS2_INCONSISTENT_SYNC -#Illegal_Line_Position:apache-commons-fileupload_0ddfcd_4a1e17src/main/java/org/apache/commons/fileupload/util/mime/QuotedPrintableDecoder.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:apache-commons-fileupload_364a50_be46easrc/main/java/org/apache/commons/fileupload/util/mime/QuotedPrintableDecoder.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:apache-commons-lang_4975b8_618361src/test/java/org/apache/commons/lang3/concurrent/AtomicSafeInitializerTest.java:241:272:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:apache-commons-lang_66e42d_249788src/main/java/org/apache/commons/lang3/text/ExtendedMessageFormat.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:apache-commons-lang_6e4a19_a926c7src/java/org/apache/commons/lang3/Range.java:331:356:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:apache-commons-lang_7fac28_7b6c2csrc/test/java/org/apache/commons/lang3/builder/ToStringStyleTest.java:30:30:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:apache-commons-lang_c21e66_509e3dsrc/java/org/apache/commons/lang/text/ExtendedMessageFormat.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:apache-commons-lang_ef07c7_2842fdsrc/main/java/org/apache/commons/lang/text/ExtendedMessageFormat.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:apache-commons-math_389aa0_d868dbsrc/main/java/org/apache/commons/math3/optimization/GoalType.java:28:34:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:apache-commons-math_b7555d_166cfcsrc/main/java/org/apache/commons/math3/stat/descriptive/DescriptiveStatistics.java:770:813:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-ddlutils_ec20f7_e73adesrc/java/org/apache/ddlutils/util/StringUtilsExt.java:27:40:NM_SAME_SIMPLE_NAME_AS_SUPERCLASS -#Null_Violation_Hunk:apache-directory-fortress-core_2ae412_08ea40src/main/java/org/apache/directory/fortress/core/rbac/PwPolicy.java:331:777:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-directory-fortress-core_2ae412_08ea40src/main/java/org/apache/directory/fortress/core/rbac/Relationship.java:42:131:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-directory-fortress-core_2ae412_08ea40src/main/java/org/apache/directory/fortress/core/rbac/UserRole.java:101:616:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-directory-fortress-core_9bb82e_a4c5e2src/main/java/org/apache/directory/fortress/core/rbac/OrgUnit.java:185:414:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-directory-fortress-core_a6c5f7_ea2a82src/main/java/us/jts/fortress/rbac/UserRole.java:74:503:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-directory-shared_2b06ed_2fb0d2ldap/src/main/java/org/apache/directory/shared/ldap/aci/UserClass.java:211:211:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:apache-directory-shared_2b06ed_2fb0d2ldap/src/main/java/org/apache/directory/shared/ldap/aci/UserClass.java:240:240:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:apache-directory-shared_7e36ad_3db7f6ldap/src/main/java/org/apache/directory/shared/ldap/aci/ProtectedItem.java:342:342:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:apache-directory-shared_7e36ad_3db7f6ldap/src/main/java/org/apache/directory/shared/ldap/aci/ProtectedItem.java:311:311:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:apache-directory-shared_7e36ad_3db7f6ldap/src/main/java/org/apache/directory/shared/ldap/aci/ProtectedItem.java:285:285:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:apache-hadoop-common_1cb793_96e371src/main/java/org/apache/hadoop/hbase/regionserver/CoprocessorHost.java:64:71:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:apache-hadoop-common_6ceadd_221e8asrc/main/java/org/apache/hadoop/hbase/avro/generated/AIllegalArgument.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-hadoop-common_6ceadd_221e8asrc/main/java/org/apache/hadoop/hbase/avro/generated/AIOError.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:apache-hadoop-common_6ceadd_221e8asrc/main/java/org/apache/hadoop/hbase/avro/generated/AMasterNotRunning.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:apache-hadoop-common_c8529f_9b0a00src/main/java/org/apache/hadoop/hbase/regionserver/MemStoreFlusher.java:341:341:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:apache-hadoop-common_d1966a_122939src/test/java/org/apache/hadoop/hbase/master/TestCatalogJanitor.java:122:151:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:apache-httpclient_137da8_4f6599module-client/src/main/java/org/apache/http/conn/ssl/X509HostnameVerifier.java:-1:-1:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Null_Violation_Hunk:apache-httpclient_18e1a1_20680fhttpclient/src/main/java/org/apache/http/impl/client/DefaultRequestDirector.java:162:162:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:apache-httpclient_3dde3c_137da8module-client/src/main/java/org/apache/http/cookie/CookieIdentityComparator.java:46:62:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:apache-httpclient_3dde3c_137da8module-client/src/main/java/org/apache/http/cookie/CookiePathComparator.java:50:74:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:apache-httpclient_b1134f_e2da28httpclient-cache/src/main/java/org/apache/http/impl/client/cache/FileResource.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:apache-mahout_0853c0_b988c4mr/src/main/java/org/apache/mahout/cf/taste/impl/common/FixedRunningAverage.java:34:80:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-mahout_0853c0_b988c4mr/src/main/java/org/apache/mahout/cf/taste/impl/model/BooleanPreference.java:34:61:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-mahout_0853c0_b988c4mr/src/main/java/org/apache/mahout/cf/taste/impl/model/GenericPreference.java:37:67:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:apache-mina-sshd_231556_304d84src/main/java/org/apache/sshd/client/kex/AbstractDHGClient.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:apache-pdfbox_10f72d_83b29apdfbox/src/main/java/org/apache/pdfbox/pdmodel/font/FileSystemFontProvider.java:63:175:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:apache-pdfbox_3ff6e6_d20b9epdfbox/src/main/java/org/apache/pdfbox/rendering/PageDrawer.java:868:872:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:apache-pdfbox_4d4e29_e9e653preflight/src/main/java/org/apache/pdfbox/preflight/font/descriptor/FontDescriptorHelper.java:55:55:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:apache-pdfbox_571fa0_b31040tools/src/main/java/org/apache/pdfbox/tools/pdfdebugger/flagbitspane/FlagBitsPane.java:172:172:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:apache-pdfbox_7389bb_90c4b7pdfbox/src/main/java/org/apache/pdfbox/pdmodel/interactive/form/FieldUtils.java:81:86:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:apache-pdfbox_7389bb_90c4b7pdfbox/src/main/java/org/apache/pdfbox/pdmodel/interactive/form/FieldUtils.java:69:74:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:apache-pdfbox_b910b0_89dff6fontbox/src/main/java/org/apache/fontbox/util/BoundingBox.java:226:226:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:apache-pdfbox_f11a53_2b9c5atools/src/main/java/org/apache/pdfbox/tools/pdfdebugger/fontencodingpane/FontEncodingView.java:122:140:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:apache-pdfbox_fa9321_0269fftools/src/main/java/org/apache/pdfbox/tools/pdfdebugger/hexviewer/HexEditor.java:106:110:SIC_INNER_SHOULD_BE_STATIC_ANON -#Illegal_Line_Position:apache-wss4j_afb2b1_63f1bfsrc/org/apache/ws/security/components/crypto/CryptoBase.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:aranega-testgen_173978_518412src/main/java/simple/mypackage/z.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:ArcBees-gwtquery_1094cf_e163e1gwtquery-core/src/main/java/com/google/gwt/query/client/plugins/effects/ClipAnimation.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4b3e9b_65b737gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:106:106:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4b3e9b_65b737gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:108:108:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4b3e9b_65b737gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:105:105:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4b3e9b_65b737gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:34:34:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4b3e9b_65b737gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:44:44:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:72:72:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:32:32:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:30:30:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:58:58:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:28:28:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:73:73:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:35:35:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:69:69:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:40:40:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:66:66:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:83:83:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:62:62:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:67:67:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:74:74:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:45:45:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:43:43:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:59:59:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:76:76:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:65:65:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:60:60:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:71:71:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:38:38:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:33:33:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:42:42:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:37:37:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:79:79:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:78:78:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:64:64:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:81:81:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4be89b_8a4528gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:84:84:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_4d28be_693bebgwtquery-core/src/main/java/com/google/gwt/query/client/Function.java:221:221:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ArcBees-gwtquery_4d28be_693bebgwtquery-core/src/main/java/com/google/gwt/query/client/Function.java:213:213:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:ArcBees-gwtquery_7955d1_2b45e3gwtquery-core/src/main/java/com/google/gwt/query/client/impl/ConsoleBrowser.java:-1:-1:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ArcBees-gwtquery_8a4528_ee7b59gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:107:107:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ArcBees-gwtquery_8a4528_ee7b59gwtquery-core/src/main/java/com/google/gwt/query/client/css/CSS.java:104:104:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:ArcBees-gwtquery_8fa8fa_ac3521gwtquery-core/src/main/java/com/google/gwt/query/client/GQuery.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:ArcBees-gwtquery_9b5ecd_5485f3gwtquery-core/src/main/java/com/google/gwt/query/client/plugins/Effects.java:121:121:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ArcBees-gwtquery_a82893_aca58cgwtquery-core/src/main/super/com/google/gwt/query/super/com/google/gwt/query/client/GQ.java:46:47:LI_LAZY_INIT_STATIC -#Null_Violation_Hunk:ArcBees-gwtquery_bb71ac_5ae898gwtquery-core/src/main/java/com/google/gwt/query/client/Function.java:89:89:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ArcBees-gwtquery_bb71ac_5ae898gwtquery-core/src/main/java/com/google/gwt/query/client/Function.java:85:85:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ArcBees-gwtquery_c05283_678d43gwtquery-core/src/main/super/com/google/gwt/query/super/com/google/gwt/query/client/GQ.java:29:29:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:ArcBees-gwtquery_fd07d4_c5eadegwtquery-core/src/main/java/com/google/gwt/query/client/plugins/effects/ClipAnimation.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_1743d6_8863cacore/src/main/java/sem/group15/bubblebobble/core/objects/BubbleObject.java:67:67:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_59671b_4c1e10core/src/main/java/sem/group15/bubblebobble/core/LogicController.java:71:71:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_5d8bd5_595483core/src/main/java/sem/group15/bubblebobble/core/objects/FilledBubbleObject.java:46:46:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_886026_e02d08core/src/main/java/sem/group15/bubblebobble/core/objects/BubbleObject.java:72:72:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_a5318e_e7546bcore/src/main/java/sem/group15/bubblebobble/core/objects/FilledBubbleObject.java:46:46:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_c7ed48_9b5b95core/src/main/java/sem/group15/bubblebobble/core/objects/BubbleObject.java:72:72:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_cddb27_da5020core/src/main/java/sem/group15/bubblebobble/core/objects/BubbleObject.java:69:69:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_cfe14b_7fcbb4core/src/main/java/sem/group15/bubblebobble/core/objects/BubbleObject.java:67:67:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:arjovanramshorst-bubble-bobble-sem_e7546b_aaa245core/src/main/java/sem/group15/bubblebobble/core/BubbleBobble.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_ede5e2_7d86ddcore/src/main/java/sem/group15/bubblebobble/core/objects/FilledBubbleObject.java:46:46:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:arjovanramshorst-bubble-bobble-sem_f10739_886026core/src/main/java/sem/group15/bubblebobble/core/objects/FilledBubbleObject.java:47:47:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ATLauncher-ATLauncher_ae88a5_bf63absrc/main/java/com/atlauncher/workers/InstanceInstaller.java:348:348:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:AugGroup-hr-db_411aa8_ad1a58src/main/java/com/aug/hrdb/interceptor/AuditInterceptor.java:26:26:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:AugGroup-hr-db_d3b9d5_ea245dsrc/main/java/com/aug/hrdb/interceptor/AuditInterceptor.java:26:26:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:basho-riak-java-client_04ac47_673538src/main/java/com/basho/riak/client/mapreduce/MapReduceBuilder.java:256:256:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:basho-riak-java-client_1bb688_fd4c6dsrc/main/java/com/basho/riak/client/query/RiakObject.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:basho-riak-java-client_3c9bca_95c964src/main/java/com/basho/riak/pbc/RiakConnection.java:-1:-1:VO_VOLATILE_REFERENCE_TO_ARRAY -#Null_Violation_Hunk:basho-riak-java-client_4d59c2_cb2a5csrc/main/java/com/basho/riak/client/operations/StoreObject.java:41:41:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:basho-riak-java-client_734fb7_9a398bsrc/main/java/com/basho/riak/client/DefaultRiakObject.java:-1:-1:VO_VOLATILE_REFERENCE_TO_ARRAY -#Illegal_Line_Position:basho-riak-java-client_75f021_79a975src/main/java/com/basho/riak/client/core/ConnectionPool.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:basho-riak-java-client_c2dabe_b862e7src/main/java/com/basho/riak/client/util/BranchableInputStream.java:-1:-1:VO_VOLATILE_REFERENCE_TO_ARRAY 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-#Illegal_Line_Position:BattleNight-BattleNight-Core_3a4356_666d6csrc/main/java/me/limebyte/battlenight/core/BattleNight.java:-1:-1:MS_CANNOT_BE_FINAL -#Illegal_Line_Position:BattleNight-BattleNight-Core_53ed8e_b6dbd1src/main/java/me/limebyte/battlenight/core/BattleNight.java:-1:-1:MS_CANNOT_BE_FINAL -#Illegal_Line_Position:BattleNight-BattleNight-Core_e9231a_a63af4src/main/java/me/limebyte/battlenight/core/BattleNight.java:-1:-1:MS_CANNOT_BE_FINAL -#Illegal_Line_Position:BattleNight-BattleNight-Core_e9231a_a63af4src/main/java/me/limebyte/battlenight/core/util/Configuration.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:BattleNight-BattleNight-Core_e9231a_a63af4src/main/java/me/limebyte/battlenight/core/util/Configuration.java:-1:-1:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:bcdev-ceres_aa498c_c8f4c1ceres-binding/src/main/java/com/bc/ceres/binding/swing/internal/BindingImpl.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:belaban-JGroups_09ee63_c9a699src/org/jgroups/protocols/TP.java:153:153:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_09ee63_c9a699src/org/jgroups/protocols/TP.java:136:136:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_09ee63_c9a699src/org/jgroups/protocols/TP.java:278:278:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_3d6cda_0add49src/org/jgroups/protocols/TP.java:278:278:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_3d6cda_0add49src/org/jgroups/protocols/TP.java:136:136:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_4a4c98_7d3303src/org/jgroups/protocols/TP.java:153:153:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_4a4c98_7d3303src/org/jgroups/protocols/TP.java:278:278:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_4a4c98_7d3303src/org/jgroups/protocols/TP.java:136:136:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_6c80eb_1f6473src/org/jgroups/util/ProxyAddress.java:12:12:EQ_COMPARETO_USE_OBJECT_EQUALS -#Illegal_Line_Position:belaban-JGroups_8797b1_db28afsrc/org/jgroups/auth/X509Token.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:belaban-JGroups_8bad26_000902src/org/jgroups/protocols/TP.java:153:153:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_8bad26_000902src/org/jgroups/protocols/TP.java:136:136:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_8bad26_000902src/org/jgroups/protocols/TP.java:278:278:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_a47814_f79552src/org/jgroups/util/MutableDigest.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:belaban-JGroups_b7528c_f43e3bsrc/org/jgroups/blocks/executor/ExecutionService.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:belaban-JGroups_e1ca60_6bc167src/org/jgroups/protocols/TP.java:153:153:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_e1ca60_6bc167src/org/jgroups/protocols/TP.java:136:136:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:belaban-JGroups_e1ca60_6bc167src/org/jgroups/protocols/TP.java:278:278:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:bguerout-jongo_554fe7_88660esrc/main/java/org/jongo/marshall/jackson/JongoAnnotationIntrospector.java:25:30:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:bguerout-jongo_678169_b987dfsrc/main/java/org/jongo/marshall/jackson/JongoAnnotationIntrospector.java:25:30:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:bigdataops-bgpcep_1dca38_71f45fframework/src/main/java/org/opendaylight/protocol/framework/DispatcherImpl.java:104:112:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:biojava-biojava_2b3cd0_8eda39biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:2877:2963:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:biojava-biojava_37c190_836b26biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java:36:36:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:biojava-biojava_478a2f_33b355biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:biojava-biojava_478a2f_33b355biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java:36:36:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:biojava-biojava_4c225f_c673dbbiojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java:36:36:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:biojava-biojava_7f98fc_60643ebiojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/ExpressionFigure.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:biojava-biojava_8f86c4_b3c663biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:2097:2097:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:biojava-biojava_a591c7_d6ff9fbiojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:2881:2986:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:biojava-biojava_bbad75_8cd0a2biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java:36:36:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:biojava-biojava_c01faa_1fd8e7biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:biojava-biojava_d9b9e0_20b4eebiojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java:158:158:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:biojava-biojava_de5422_69b1edbiojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java:36:36:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:bitcoinj-bitcoinj_3caa41_a95518src/com/google/bitcoin/core/InventoryMessage.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:bitcoinj-bitcoinj_48fce9_ddb167src/com/google/bitcoin/core/Peer.java:261:310:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:bitcoinj-bitcoinj_48fce9_ddb167src/com/google/bitcoin/store/BoundedOverheadBlockStore.java:76:138:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:bitcoinj-bitcoinj_a5fc1c_0a4dbbsrc/com/google/bitcoin/core/Wallet.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:bitcoinj-bitcoinj_a86ca7_216debexamples/com/google/bitcoin/examples/toywallet/ToyWallet.java:238:267:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:bitcoinj-bitcoinj_dff3b2_3a463esrc/com/google/bitcoin/core/Transaction.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:bitcoinj-bitcoinj_dff3b2_3a463esrc/com/google/bitcoin/core/TransactionOutput.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:bitcoinj-bitcoinj_dff3b2_3a463esrc/com/google/bitcoin/core/VersionAck.java:24:36:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Bombe-Sone_0797df_a80191src/main/java/net/pterodactylus/sone/data/impl/IdOnlySone.java:27:27:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:Bombe-Sone_0cefad_cb0161src/main/java/net/pterodactylus/sone/data/impl/IdOnlySone.java:27:27:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:Bombe-Sone_7a858f_4804cfsrc/main/java/net/pterodactylus/sone/data/impl/IdOnlySone.java:27:27:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:Bombe-Sone_cf563e_ee05a6src/main/java/net/pterodactylus/sone/freenet/wot/DefaultOwnIdentity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:bpiwowar-experimaestro_5cb120_c00d92src/main/java/sf/net/experimaestro/manager/js/JSBaseObject.java:249:256:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:bpiwowar-experimaestro_5fbcd0_2839f8src/main/java/sf/net/experimaestro/server/JsonRPCServlet.java:80:165:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:BroadleafCommerce-BroadleafCommerce_413685_612fe8common/src/main/java/org/broadleafcommerce/common/resource/GeneratedResource.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:BroadleafCommerce-BroadleafCommerce_413685_612fe8common/src/main/java/org/broadleafcommerce/common/web/BroadleafRequestFilter.java:49:49:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:BroadleafCommerce-BroadleafCommerce_413685_612fe8core/broadleaf-framework/src/main/java/org/broadleafcommerce/core/search/service/solr/SolrIndexServiceImpl.java:59:59:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:brooklyncentral-clocker_6a2ab7_0badcbdist/src/main/java/brooklyn/clocker/example/MicroServiceDockerfileImpl.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:brooklyncentral-clocker_80c8d8_d2873ddist/src/main/java/brooklyn/clocker/example/MicroServiceDockerfileImpl.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:brooklyncentral-clocker_dae8d9_b4e125dist/src/main/java/brooklyn/clocker/example/MicroServiceDockerfileImpl.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:buddycloud-buddycloud-server-java_16c170_750817src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/pubsub/PubSubElementProcessorAbstract.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/channel/node/configuration/field/AccessModel.java:13:20:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/channel/node/configuration/field/ChannelType.java:13:20:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/channel/node/configuration/field/Field.java:17:17:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/channel/node/configuration/field/Field.java:16:16:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/db/jdbc/JDBCNodeStore.java:1763:1834:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/AbstractNamespace.java:99:99:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/discoitems/DiscoItemsGet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/discoitems/DiscoResult.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/pubsub/get/RepliesGet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:buddycloud-buddycloud-server-java_4263c5_b1f9a5src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/pubsub/get/ThreadGet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:buddycloud-buddycloud-server-java_581f6a_9b0628src/main/java/org/buddycloud/channelserver/packetprocessor/iq/namespace/pubsub/get/NodeConfigureGet.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:Bukkit-Bukkit_0b3a14_184d57src/main/java/org/bukkit/fillr/Fillr.java:9:9:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:Bukkit-Bukkit_105925_8e142esrc/main/java/org/bukkit/fillr/Fillr.java:9:9:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockBreakEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockDamageEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockDispenseEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockFormEvent.java:-1:-1:SE_BAD_FIELD 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-#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityCombustByBlockEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityCombustByEntityEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityDamageByBlockEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityDamageByEntityEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityDeathEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityTameEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityTargetEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/ItemSpawnEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/entity/PigZapEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/inventory/FurnaceSmeltEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/painting/PaintingPlaceEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerBedLeaveEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerChatEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerFishEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerInteractEntityEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerInteractEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerMoveEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerPortalEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerPortalEvent.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerRespawnEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleBlockCollisionEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleDestroyEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleEnterEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleEntityCollisionEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/weather/LightningStrikeEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/world/PortalCreateEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_219d00_ca71besrc/main/java/org/bukkit/event/world/StructureGrowEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_380b5c_0b03f7src/main/java/org/bukkit/event/player/PlayerBlockItemEvent.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_5c8bc6_e35037src/main/java/org/bukkit/event/player/PlayerChatEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Bukkit-Bukkit_5c8bc6_e35037src/main/java/org/bukkit/event/vehicle/VehicleEntityCollisionEvent.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:caprica-vlcj_28772f_ba633esrc/main/java/uk/co/caprica/vlcj/player/MediaPlayerEventAdapter.java:246:246:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:caprica-vlcj_292c85_d49055src/main/java/uk/co/caprica/vlcj/player/MediaPlayerEventAdapter.java:246:246:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:caprica-vlcj_322287_1ed4efsrc/main/java/uk/co/caprica/vlcj/binding/internal/libvlc_title_description_t.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Carboni-zebedee_5bb4a5_4a49efsrc/main/java/com/github/onsdigital/zebedee/Permissions.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:Carboni-zebedee_c4ab4d_0cac53src/main/java/com/github/onsdigital/zebedee/model/Collections.java:9:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Carboni-zebedee_eab3c5_9df926src/main/java/com/github/onsdigital/zebedee/model/Collections.java:9:83:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:carrotsearch-randomizedtesting_f3e2ca_a37013ant-junit4/src/main/java/com/carrotsearch/ant/tasks/junit4/events/mirrors/SerializableMirror.java:14:47:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_0aaabc_8afdc5src/main/java/org/group17/bubblebobble/Game.java:57:57:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_1d9be7_3811d5src/main/java/org/group17/bubblebobble/GUI.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_1d9be7_3811d5src/main/java/org/group17/bubblebobble/Main.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_3b682e_66a57csrc/main/java/org/group17/Gui/GUI.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_5de69a_26e8aasrc/main/java/org/group17/bubblebobble/GUI.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_5de69a_26e8aasrc/main/java/org/group17/bubblebobble/Main.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_706477_014038src/main/java/org/group17/bubblebobble/Game.java:36:36:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_9179cb_c7f330src/main/java/org/group17/bubblebobble/Game.java:36:36:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_9c6eb3_d307c4src/main/java/org/group17/bubblebobble/GUI.java:376:376:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_9c6eb3_d307c4src/main/java/org/group17/bubblebobble/GUI.java:351:394:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_9c6eb3_d307c4src/main/java/org/group17/bubblebobble/GUI.java:387:387:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_aa7fec_f2b089src/main/java/org/group17/Gui/GUI.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_e1fec5_c04b35src/main/java/org/group17/bubblebobble/GUI.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_e1fec5_c04b35src/main/java/org/group17/bubblebobble/GUI.java:386:386:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_e1fec5_c04b35src/main/java/org/group17/bubblebobble/Main.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_ee94f4_c2127fsrc/main/java/org/group17/bubblebobble/GUI.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Cas-B-Group17-BubbleBobble_ee94f4_c2127fsrc/main/java/org/group17/bubblebobble/Main.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:Cas-B-Group17-BubbleBobble_fd478a_9bc3bbsrc/main/java/org/group17/bubblebobble/Game.java:51:51:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:cdi-spec-cdi-tck_08b25b_73b89cimpl/src/main/java/org/jboss/jsr299/tck/tests/event/observer/enterprise/IndirectStockWatcher.java:21:21:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:cdi-spec-cdi-tck_08b25b_73b89cimpl/src/main/java/org/jboss/jsr299/tck/tests/event/observer/enterprise/LazyFarmer.java:21:21:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:cdi-spec-cdi-tck_1f4449_5c4cecimpl/src/main/java/org/jboss/jsr299/tck/tests/context/passivating/broken/decoratorWithNonPassivatingBeanConstructor/UnderwaterCity.java:21:27:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cdi-spec-cdi-tck_1f4449_5c4cecimpl/src/main/java/org/jboss/jsr299/tck/tests/context/passivating/broken/decoratorWithNonPassivatingInitializerMethod/UnderwaterCity.java:24:30:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cdi-spec-cdi-tck_1f4449_5c4cecimpl/src/main/java/org/jboss/jsr299/tck/tests/context/passivating/broken/decoratorWithNonPassivatingInjectedField/UnderwaterCity.java:21:27:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cdi-spec-cdi-tck_663aa2_3089a2impl/src/main/java/org/jboss/jsr299/tck/tests/event/resolve/binding/BindingTypeABinding.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cdi-spec-cdi-tck_663aa2_3089a2impl/src/main/java/org/jboss/jsr299/tck/tests/extensions/bean/bytype/TameLiteral.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cdi-spec-cdi-tck_663aa2_3089a2impl/src/main/java/org/jboss/jsr299/tck/tests/interceptors/definition/InterceptorDefinitionTest.java:177:177:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:cdi-spec-cdi-tck_663aa2_3089a2impl/src/main/java/org/jboss/jsr299/tck/tests/interceptors/definition/InterceptorDefinitionTest.java:305:305:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:cdi-spec-cdi-tck_663aa2_3089a2impl/src/main/java/org/jboss/jsr299/tck/tests/interceptors/definition/InterceptorDefinitionTest.java:152:152:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:cdi-spec-cdi-tck_83a7e7_07365fimpl/src/main/java/org/jboss/cdi/tck/tests/definition/qualifier/TameLiteral.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cdi-spec-cdi-tck_a08b80_fe2cf9impl/src/main/java/org/jboss/jsr299/tck/tests/context/passivating/broken/enterpriseBeanWithNonPassivatingConstructorFieldInDecorator/BrokenDecorator.java:31:31:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:cdi-spec-cdi-tck_a08b80_fe2cf9impl/src/main/java/org/jboss/jsr299/tck/tests/context/passivating/broken/enterpriseBeanWithNonPassivatingInjectedFieldInDecorator/BrokenDecorator.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:cdi-spec-cdi-tck_a08b80_fe2cf9impl/src/main/java/org/jboss/jsr299/tck/tests/context/passivating/broken/enterpriseBeanWithNonPassivatingInjectedFieldInDecorator/BrokenDecorator.java:26:26:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:chapmajs-shiro_087bbe_539f76src/org/jsecurity/authc/SimpleAccount.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:chapmajs-shiro_087bbe_539f76src/org/jsecurity/web/tags/PrincipalTag.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:chapmajs-shiro_087bbe_539f76src/org/jsecurity/web/tags/PrincipalTag.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:chapmajs-shiro_667ebd_a8c4a4src/org/jsecurity/web/attr/AbstractWebAttribute.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:charite-jannovar_39e5cb_77a4f3src/main/java/jannovar/reference/Chromosome.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:charite-jannovar_c2fc03_53ea99src/main/java/jannovar/impl/interval/Node.java:48:48:URF_UNREAD_FIELD -#Null_Violation_Hunk:charite-jannovar_c2fc03_53ea99src/main/java/jannovar/impl/interval/Node.java:42:42:URF_UNREAD_FIELD -#Null_Violation_Hunk:checkstyle-checkstyle_9470bb_12fc9asrc/test/resources/com/puppycrawl/tools/checkstyle/coding/InputVariableDeclarationUsageDistanceCheck.java:817:822:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:checkstyle-checkstyle_b6aabf_febbc9src/it/resources/com/google/checkstyle/test/chapter4formatting/rule4822variabledistance/InputVariableDeclarationUsageDistanceCheck.java:780:785:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:checkstyle-checkstyle_e7547b_d220d7src/test/resources/com/puppycrawl/tools/checkstyle/javadoc/InputTestNumberFormatException.java:4:4:NM_CLASS_NOT_EXCEPTION -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/ExistentialRuleformPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/JobPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/MetaProtocolPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/ProtocolPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/RelationshipPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/SequencingPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_0fc0fb_9e52b8swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/WorkspaceBackedView.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/ExistentialRuleformPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/JobPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/MetaProtocolPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/ProtocolPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/RelationshipPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/SequencingPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ChiralBehaviors-Ultrastructure_2c7537_5b5546swing-ui/src/main/java/com/chiralbehaviors/CoRE/workspace/swing/WorkspaceBackedView.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:chocoteam-choco3_245dc3_d92c1fchoco-solver/src/main/java/solver/constraints/nary/alldifferent/PropAllDiffBC.java:468:468:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:chocoteam-choco3_245dc3_d92c1fchoco-solver/src/main/java/solver/constraints/nary/automata/structure/regular/StoredDirectedMultiGraph.java:62:62:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:chocoteam-choco3_245dc3_d92c1fchoco-solver/src/main/java/solver/constraints/nary/automata/structure/regular/StoredDirectedMultiGraph.java:70:70:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:chocoteam-choco3_5bbaf9_4a3415choco-solver/src/main/java/org/chocosolver/solver/constraints/nary/cnf/LogicTreeToolBox.java:246:255:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:cismet-cismet-gui-commons_03b9eb_7c65a1src/main/java/de/cismet/security/handler/HTTPBasedAccessHandler.java:-1:-1:DMI_COLLECTION_OF_URLS -#Illegal_Line_Position:cjdev-versions-maven-plugin_05818d_53f370src/main/java/org/codehaus/mojo/versions/LockSnapshotsMojo.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:cjdev-versions-maven-plugin_05818d_53f370src/main/java/org/codehaus/mojo/versions/ResolveRangesMojo.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:cjdev-versions-maven-plugin_05818d_53f370src/main/java/org/codehaus/mojo/versions/UnlockSnapshotsMojo.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:cjdev-versions-maven-plugin_05818d_53f370src/main/java/org/codehaus/mojo/versions/UseReleasesMojo.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:cjdev-versions-maven-plugin_55dc5a_96b262src/main/java/org/codehaus/mojo/versions/DisplayDependencyUpdatesMojo.java:161:197:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:cjdev-versions-maven-plugin_5f8c44_04af5dsrc/main/java/org/codehaus/mojo/versions/UpdateChildModulesMojo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:cjdev-versions-maven-plugin_876b64_e596f1src/main/java/org/codehaus/mojo/versions/AbstractVersionsUpdaterMojo.java:448:552:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:cjdev-versions-maven-plugin_876b64_e596f1src/main/java/org/codehaus/mojo/versions/AbstractVersionsUpdaterMojo.java:562:571:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:cjdev-versions-maven-plugin_876b64_e596f1src/main/java/org/codehaus/mojo/versions/AbstractVersionsUpdaterMojo.java:581:590:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:cjdev-versions-maven-plugin_a67ece_51ee9bsrc/main/java/org/codehaus/mojo/versions/UpdateChildModulesMojo.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:cjdev-versions-maven-plugin_da1db8_b08982src/main/java/org/codehaus/mojo/versions/DisplayPluginUpdatesMojo.java:1374:1407:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:cjdev-versions-maven-plugin_e60b49_5c6476src/main/java/org/codehaus/mojo/versions/CompareDependenciesMojo.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_06a731_c2709bsrc/main/java/edu/clemson/cs/r2jt/typeandpopulate/Populator.java:2704:2717:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_0d5705_40468bsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyCTranslationInfo.java:110:110:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_115357_d1623dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslationInfo.java:108:108:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_11815c_f29377src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/InstantiatedTheoremPrioritizer.java:48:97:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_19f744_a8b76csrc/main/java/edu/clemson/cs/r2jt/proving2/AlgebraicProver.java:513:517:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_19f744_a8b76csrc/main/java/edu/clemson/cs/r2jt/proving2/AutomatedProver.java:463:491:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_1b3745_8decd1src/main/java/edu/clemson/cs/r2jt/population/Populator.java:1583:1596:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_1c12dd_37e24csrc/main/java/edu/clemson/cs/r2jt/proving/absyn/PExp.java:534:534:HE_HASHCODE_USE_OBJECT_EQUALS -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_2145b3_329519src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1180:1180:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_2145b3_329519src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1290:1301:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_35d9f9_56ce4bsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyCTranslationInfo.java:110:110:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_40b735_5270f8src/main/java/edu/clemson/cs/r2jt/proving/absyn/PExp.java:534:534:HE_HASHCODE_USE_OBJECT_EQUALS -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_460138_792ecfsrc/main/java/edu/clemson/cs/r2jt/proving2/model/PerVCProverModel.java:1062:1073:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_4c94b0_0a304dsrc/main/java/edu/clemson/cs/r2jt/archiving/Archiver.java:546:551:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_4c94b0_0a304dsrc/main/java/edu/clemson/cs/r2jt/archiving/Archiver.java:524:524:EI_EXPOSE_REP -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_4c94b0_0a304dsrc/main/java/edu/clemson/cs/r2jt/archiving/Archiver.java:325:325:REC_CATCH_EXCEPTION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_535e0a_c14ab7src/main/java/edu/clemson/cs/r2jt/typereasoning/TypeGraph.java:1087:1091:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_546b3f_c91dbesrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/SMTProver.java:302:302:SBSC_USE_STRINGBUFFER_CONCATENATION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_5c21e8_6157bcsrc/main/java/edu/clemson/cs/r2jt/vcgeneration/VCGenerator.java:1883:1883:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_5c21e8_6157bcsrc/main/java/edu/clemson/cs/r2jt/vcgeneration/VCGenerator.java:2903:2903:NP_NULL_ON_SOME_PATH -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_5c8848_955d44src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1219:1230:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_622cf6_7f72a5src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1708:1719:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_622cf6_7f72a5src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1598:1598:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_62e445_6a59d3src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/NormalizedAtomicExpressionMapImpl.java:172:172:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_64c586_d41ac9src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:499:499:DM_DEFAULT_ENCODING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_64c586_d41ac9src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:499:499:OS_OPEN_STREAM_EXCEPTION_PATH -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_64c586_d41ac9src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:499:499:OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_678acc_b7a8fesrc/main/java/edu/clemson/cs/r2jt/vcgeneration/VCGenerator.java:3168:3168:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6a59d3_f2823esrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/NormalizedAtomicExpressionMapImpl.java:178:178:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6a59d3_f2823esrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/Registry.java:62:62:WMI_WRONG_MAP_ITERATOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6a59d3_f2823esrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1819:1819:DE_MIGHT_IGNORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6a59d3_f2823esrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1859:1859:DE_MIGHT_IGNORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6a59d3_f2823esrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1758:1758:REC_CATCH_EXCEPTION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6ac4c9_da9566src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/TheoremCongruenceClosureImpl.java:38:38:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_6adf7f_573169src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:400:400:DM_DEFAULT_ENCODING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_7029e2_622cf6src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1572:1583:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_7564a0_d671d7src/main/java/edu/clemson/cs/r2jt/vcgeneration/VCGenerator.java:806:806:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_765a7d_b84720src/main/java/edu/clemson/cs/r2jt/proving2/JProverStateDisplay.java:217:280:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_792ecf_aa4f78src/main/java/edu/clemson/cs/r2jt/proving2/model/PerVCProverModel.java:1058:1069:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_7f2c5f_d40c02src/main/java/edu/clemson/cs/r2jt/proving2/proofsteps/StrengthenConsequentStep.java:57:61:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_84220c_70e2basrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/ConjunctionOfNormalizedAtomicExpressions.java:549:549:WMI_WRONG_MAP_ITERATOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_84220c_70e2basrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/NormalizedAtomicExpressionMapImpl.java:225:225:HE_HASHCODE_USE_OBJECT_EQUALS -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_86f012_cdeb70src/main/java/edu/clemson/cs/r2jt/proving2/transformations/ExpandAntecedentByImplication.java:165:215:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_997a8d_6a1c83src/main/java/edu/clemson/cs/r2jt/population/Populator.java:1583:1596:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9c34c9_2ae73dsrc/main/java/edu/clemson/cs/r2jt/population/Populator.java:2146:2159:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/AssumeStmt.java:129:129:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/BetweenExp.java:114:127:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/CharExp.java:91:91:DM_NUMBER_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/ConfirmStmt.java:125:125:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/Dec.java:43:43:DM_STRING_VOID_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/DoubleExp.java:134:134:FE_FLOATING_POINT_EQUALITY -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/EqualsExp.java:330:335:SF_SWITCH_NO_DEFAULT -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/Exp.java:401:401:NP_NULL_ON_SOME_PATH_MIGHT_BE_INFEASIBLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/Exp.java:422:422:NP_NULL_ON_SOME_PATH_MIGHT_BE_INFEASIBLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/FunctionArgList.java:100:109:CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/FunctionExp.java:213:213:NM_VERY_CONFUSING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/IfExp.java:261:269:SF_SWITCH_NO_DEFAULT -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/InitItem.java:119:119:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/InitItem.java:75:75:SA_FIELD_DOUBLE_ASSIGNMENT -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/MathVarDec.java:129:129:DM_STRING_VOID_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/ParameterVarDec.java:133:137:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/PrefixExp.java:177:177:DM_STRING_TOSTRING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/ProgramFunctionExp.java:177:177:DM_STRING_TOSTRING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/ProgramParamExp.java:183:183:DM_STRING_TOSTRING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/QuantExp.java:266:282:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/ResolveConceptualElement.java:90:90:DP_DO_INSIDE_DO_PRIVILEGED -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/Statement.java:39:39:DM_STRING_VOID_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/VarDec.java:113:116:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/VarExp.java:314:324:CN_IDIOM_NO_SUPER_CALL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/absyn/VariableDotExp.java:197:197:BC_UNCONFIRMED_CAST -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1394:1394:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1420:1420:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1374:1374:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1446:1446:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1352:1352:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:997:1005:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1201:1201:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1363:1363:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1291:1291:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1533:1539:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1384:1384:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1404:1404:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1432:1432:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1442:1442:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1333:1333:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1218:1218:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1223:1223:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1558:1566:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1322:1322:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1480:1480:SBSC_USE_STRINGBUFFER_CONCATENATION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1138:1138:UCF_USELESS_CONTROL_FLOW -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:983:991:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1184:1184:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/analysis/Analyzer.java:1582:1590:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/archiving/Archiver.java:105:105:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Location.java:89:89:OS_OPEN_STREAM -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Location.java:88:88:DM_DEFAULT_ENCODING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Location.java:145:147:CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Pos.java:68:68:EQ_SELF_USE_OBJECT -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Pos.java:68:68:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Symbol.java:59:59:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Symbol.java:59:59:EQ_SELF_USE_OBJECT -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/data/Symbol.java:92:92:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/entry/TypeEntry.java:52:52:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/errors/ErrorHandler.java:58:58:DM_DEFAULT_ENCODING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/errors/ErrorHandler.java:320:320:BC_IMPOSSIBLE_CAST -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/errors/ErrorHandler.java:66:66:DM_STRING_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1731:1731:DM_DEFAULT_ENCODING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1732:1732:OS_OPEN_STREAM_EXCEPTION_PATH -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1854:1854:DE_MIGHT_IGNORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/init/FileLocator.java:110:110:NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/location/DefinitionLocator.java:54:54:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/location/ProofLocator.java:59:59:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/location/TheoremLocator.java:59:59:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/parsing/ColsToken.java:54:54:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/population/OldPopulator.java:1732:1735:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/population/OldPopulator.java:1360:1361:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/population/OldPopulator.java:1750:1750:SIO_SUPERFLUOUS_INSTANCEOF -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/population/OldPopulator.java:1750:1750:BC_VACUOUS_INSTANCEOF -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/population/OldPopulator.java:1023:1023:RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/proving2/model/PerVCProverModel.java:1098:1107:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/proving2/proofsteps/LabelStep.java:36:36:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/proving2/proofsteps/StrengthenConsequentStep.java:96:96:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/proving2/utilities/InductiveSiteIterator.java:104:134:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/scope/Binding.java:212:212:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/scope/OldSymbolTable.java:836:836:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/scope/OldSymbolTable.java:768:769:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/scope/ScopeID.java:68:68:UCF_USELESS_CONTROL_FLOW -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyCTranslation.java:69:69:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyCTranslation.java:70:70:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyCTranslation.java:73:73:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslation.java:67:67:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslation.java:68:68:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:1858:1858:UCF_USELESS_CONTROL_FLOW -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:4022:4022:RV_RETURN_VALUE_IGNORED_BAD_PRACTICE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:2451:2451:UCF_USELESS_CONTROL_FLOW -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:4108:4108:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:3723:3733:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:2059:2059:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyJavaTranslator.java:4101:4104:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/Translator.java:2286:2286:SIO_SUPERFLUOUS_INSTANCEOF -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/Translator.java:4238:4241:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/Translator.java:990:990:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/Translator.java:3957:3957:DM_DEFAULT_ENCODING -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/Translator.java:3955:3955:RV_RETURN_VALUE_IGNORED_BAD_PRACTICE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/translation/Translator.java:2286:2286:BC_VACUOUS_INSTANCEOF -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/type/VoidType.java:67:67:DM_STRING_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/type/VoidType.java:63:63:DM_STRING_CTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/typeandpopulate/MTPowertypeApplication.java:68:68:BC_UNCONFIRMED_CAST -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/PrintAssertions.java:57:57:URF_UNREAD_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/PrintAssertions.java:321:321:UC_USELESS_CONDITION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/PrintAssertions.java:1118:1127:DB_DUPLICATE_BRANCHES -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:331:331:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:4701:4701:DB_DUPLICATE_BRANCHES -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:6306:6306:UCF_USELESS_CONTROL_FLOW -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:3808:3811:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:5789:5789:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:6108:6108:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:1036:1036:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:4316:4316:NP_NULL_ON_SOME_PATH -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:2581:2581:RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:689:689:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_9ee405_202d6dsrc/main/java/edu/clemson/cs/r2jt/verification/Verifier.java:8209:8209:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_b501a9_e13e1asrc/main/java/edu/clemson/cs/r2jt/proving2/transformations/ExpandAntecedentByImplication.java:165:215:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_bfca0d_bccfdfsrc/main/java/edu/clemson/cs/r2jt/translation/PrettyCTranslationInfo.java:110:110:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c13206_b73b4asrc/main/java/edu/clemson/cs/r2jt/vcgeneration/VCGenerator.java:1152:1152:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c13206_b73b4asrc/main/java/edu/clemson/cs/r2jt/vcgeneration/VCGenerator.java:676:676:RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c15b01_cd708asrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:47:47:SS_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c15b01_cd708asrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1813:1847:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c15b01_cd708asrc/main/java/edu/clemson/cs/r2jt/init/Controller.java:1742:1742:REC_CATCH_EXCEPTION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c3f27c_d06bf9src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/InstantiatedTheoremPrioritizer.java:49:98:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c6ddb8_267016src/main/java/edu/clemson/cs/r2jt/population/Populator.java:1587:1600:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_c6ecec_77ee2dsrc/main/java/edu/clemson/cs/r2jt/population/Populator.java:2142:2155:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_cd708a_b8f789src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:196:196:OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE -#Illegal_Line_Position:ClemsonRSRG-RESOLVE_cdeb70_e13e1asrc/main/java/edu/clemson/cs/r2jt/ResolveCompiler.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_ce7244_2145b3src/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:1267:1278:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:ClemsonRSRG-RESOLVE_d40c02_a996acsrc/main/java/edu/clemson/cs/r2jt/ResolveCompiler.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_d41ac9_a7cb0bsrc/main/java/edu/clemson/cs/r2jt/congruenceclassprover/ConjunctionOfNormalizedAtomicExpressions.java:820:820:WMI_WRONG_MAP_ITERATOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/CongruenceClassProver.java:83:83:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/ConjunctionOfNormalizedAtomicExpressions.java:115:115:SBSC_USE_STRINGBUFFER_CONCATENATION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/ConjunctionOfNormalizedAtomicExpressions.java:111:121:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/SearchBox.java:34:34:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/TheoremCongruenceClosureImpl.java:122:122:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/TheoremCongruenceClosureImpl.java:53:53:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_da9566_62e445src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/TheoremCongruenceClosureImpl.java:82:82:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_ddd63b_460138src/main/java/edu/clemson/cs/r2jt/proving2/proofsteps/StrengthenConsequentStep.java:85:89:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_e3b92d_e2c02asrc/main/java/edu/clemson/cs/r2jt/typeandpopulate2/PopulatingVisitor.java:975:986:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_f2823e_c15b01src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/NormalizedAtomicExpressionMapImpl.java:179:179:DLS_DEAD_LOCAL_STORE -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_f2823e_c15b01src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/NormalizedAtomicExpressionMapImpl.java:232:232:SBSC_USE_STRINGBUFFER_CONCATENATION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_f2823e_c15b01src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/NormalizedAtomicExpressionMapImpl.java:174:174:WMI_WRONG_MAP_ITERATOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_f2823e_c15b01src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/TheoremCongruenceClosureImpl.java:124:124:WMI_WRONG_MAP_ITERATOR -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_f2823e_c15b01src/main/java/edu/clemson/cs/r2jt/congruenceclassprover/TheoremCongruenceClosureImpl.java:114:114:SBSC_USE_STRINGBUFFER_CONCATENATION -#Null_Violation_Hunk:ClemsonRSRG-RESOLVE_f5361a_c3f27csrc/main/java/edu/clemson/cs/r2jt/population/Populator.java:2718:2731:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:clojure-clojure_1d5237_bd6e90src/jvm/clojure/lang/ASeq.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:118:143:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:437:501:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:192:258:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:262:311:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:374:433:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:315:369:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_494ab1_838302src/jvm/clojure/lang/Tuple.java:148:187:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_bfe14a_ae7acfsrc/jvm/clojure/lang/MapEntry.java:19:37:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:clojure-clojure_ed7419_b8607dsrc/jvm/clojure/lang/Tuple.java:266:299:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:cloudera-cdk_531a3a_95fb35src/main/java/com/cloudera/data/hdfs/HDFSDataset.java:14:14:URF_UNREAD_FIELD -#Null_Violation_Hunk:cloudera-cdk_b9e00a_97027csrc/main/java/com/cloudera/data/hdfs/HDFSDataset.java:14:14:URF_UNREAD_FIELD -#Null_Violation_Hunk:cloudera-cdk_e16e06_c53778src/main/java/com/cloudera/data/hdfs/HDFSDataset.java:13:13:URF_UNREAD_FIELD -#Null_Violation_Hunk:cloudera-cdk_ff00ea_81d4a8src/main/java/com/cloudera/data/hdfs/HDFSDataset.java:14:14:URF_UNREAD_FIELD -#Null_Violation_Hunk:cojen-Tupl_03e83e_271729src/main/java/org/cojen/tupl/Node.java:3093:3093:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:cojen-Tupl_29df95_605ba8src/main/java/org/cojen/tupl/FragmentCache.java:138:494:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:cojen-Tupl_4f8449_e4bf69src/main/java/org/cojen/tupl/BufferPool.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:cojen-Tupl_4f8449_e4bf69src/main/java/org/cojen/tupl/DirectPageCache.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:cojen-Tupl_4f8449_e4bf69src/main/java/org/cojen/tupl/Node.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:cojen-Tupl_682d54_4f8449src/main/java/org/cojen/tupl/FragmentCache.java:138:494:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:cojen-Tupl_746892_9c3f03src/main/java/org/cojen/tupl/BufferPool.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:cojen-Tupl_746892_9c3f03src/main/java/org/cojen/tupl/LockManager.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:cojen-Tupl_746892_9c3f03src/main/java/org/cojen/tupl/Node.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:cojen-Tupl_8ac1ee_67da42src/main/java/org/cojen/tupl/PageQueue.java:416:423:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:cojen-Tupl_a201e9_1940ddsrc/main/java/org/cojen/tupl/PageQueue.java:410:417:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:cojen-Tupl_ef756b_b06f57src/main/java/org/cojen/tupl/PageQueue.java:410:417:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_3ad13a_e6eb70src/main/java/edu/mines/acmX/exhibit/module_management/ModuleManager.java:272:274:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_697179_338283src/main/java/edu/mines/acmX/exhibit/module_management/ModuleManager.java:272:274:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_6c7aee_ebaa0dsrc/main/java/edu/mines/acmX/exhibit/input_services/hardware/drivers/KinectOpenNIDriver.java:120:126:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_6c7aee_ebaa0dsrc/main/java/edu/mines/acmX/exhibit/input_services/hardware/drivers/KinectOpenNIDriver.java:97:107:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_6c7aee_ebaa0dsrc/main/java/edu/mines/acmX/exhibit/input_services/hardware/drivers/KinectOpenNIDriver.java:110:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_6c7aee_ebaa0dsrc/main/java/edu/mines/acmX/exhibit/input_services/hardware/drivers/KinectOpenNIDriver.java:129:135:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_747a1d_feb35csrc/main/java/edu/mines/acmX/exhibit/stdlib/scoring/ScoreSaver.java:194:197:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_988fc7_37ce7esrc/main/java/edu/mines/acmX/exhibit/module_management/ModuleManager.java:295:297:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:ColoradoSchoolOfMines-interface_sdk_ac22b3_85056fsrc/main/java/edu/mines/acmX/exhibit/stdlib/scoring/ScoreSaver.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_ad0c00_a6d5f6src/main/java/edu/mines/acmX/exhibit/stdlib/scoring/ScoreSaver.java:208:211:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:ColoradoSchoolOfMines-interface_sdk_adc45d_85365dsrc/main/java/edu/mines/acmX/exhibit/module_manager/AWTModule.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ColoradoSchoolOfMines-interface_sdk_b90487_66d817src/main/java/edu/mines/acmX/exhibit/stdlib/scoring/ScoreSaver.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_b90487_ac22b3src/main/java/edu/mines/acmX/exhibit/stdlib/scoring/ScoreSaverPanel.java:137:137:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_c61769_496f26src/main/java/edu/mines/acmX/exhibit/module_management/ModuleManager.java:216:218:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ColoradoSchoolOfMines-interface_sdk_d3438e_f3545asrc/main/java/edu/mines/acmX/exhibit/module_management/ModuleManager.java:272:274:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:contextproject-discover_4af3b2_8196deapp/models/database/Processor/FeatureProcessor.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:contextproject-discover_4af3b2_8196deapp/models/seeker/RandomSeeker.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:contextproject-discover_590f01_0cbac4app/models/database/Processor/FeatureProcessor.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:contextproject-discover_8eea36_876decapp/models/profile/SoundcloudProfile.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:contextproject-discover_b1a48d_0775c2app/models/profile/SoundcloudProfile.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:contextproject-discover_e37d81_bc92e5app/models/database/Processor/FeatureProcessor.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:contextproject-discover_e37d81_bc92e5app/models/seeker/RandomSeeker.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:cylong1016-NJULily_8edee3_9e19adsrc/main/java/po/SalesPO.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:cylong1016-NJULily_8edee3_9e19adsrc/main/java/vo/SalesVO.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:cylong1016-NJULily_d39d82_68dd33src/main/java/businesslogic/userbl/UserBLService_Stub.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:dakusui-jcunit_189900_5ffbc5src/main/java/com/github/dakusui/jcunit/core/RuleSet.java:56:87:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:dakusui-jcunit_2e61d5_5247afsrc/main/java/com/github/dakusui/jcunit/core/Tuple.java:7:26:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:dakusui-jcunit_4e1efe_c7751esrc/main/java/com/github/dakusui/jcunit/fsm/StateRouter.java:43:43:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:dakusui-jcunit_50af45_45b23dsrc/main/java/com/github/dakusui/jcunit/constraints/constraintmanagers/ccs/CCSConstraintManager.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:dakusui-jcunit_50af45_45b23dsrc/main/java/com/github/dakusui/jcunit/core/Tuple.java:6:13:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:dakusui-jcunit_50af45_45b23dsrc/main/java/com/github/dakusui/jcunit/core/Tuple.java:6:13:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:dakusui-jcunit_71abf2_4c15dbsrc/main/java/com/github/dakusui/jcunit/core/tuples/TupleImpl.java:8:28:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:dakusui-jcunit_728933_961a58src/main/java/com/github/dakusui/lisj/FormResult.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:dakusui-jcunit_7ba222_d44767src/main/java/com/github/dakusui/jcunit/core/FrameworkMethodUtils.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:dakusui-jcunit_949b28_d14535src/main/java/com/github/dakusui/jcunit/core/Utils.java:404:404:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:dakusui-jcunit_949b28_d14535src/main/java/com/github/dakusui/jcunit/core/Utils.java:428:441:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:dakusui-jcunit_ac9a42_64bac3src/main/java/com/github/dakusui/jcunit/fsm/ScenarioSequence.java:205:261:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:dakusui-jcunit_bdd3d9_8f673fsrc/main/java/com/github/dakusui/jcunit/fsm/ScenarioSequence.java:205:261:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:dakusui-jcunit_c0a46a_9d5fadsrc/main/java/com/github/dakusui/jcunit/generators/TupleGeneratorFactory.java:107:107:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:dakusui-jcunit_e53674_9c96ffsrc/main/java/com/github/dakusui/jcunit/core/factor/FactorLoader.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:dankurka-mgwt_371cde_db6723src/main/java/com/googlecode/mgwt/ui/client/widget/MRadioButton.java:109:109:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:dankurka-mgwt_4e4cb4_dc6706src/main/java/com/googlecode/mgwt/ui/client/widget/impl/ScrollPanelNewPort.java:249:249:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:dankurka-mgwt_521c03_e1a6f7src/main/java/com/googlecode/mgwt/dom/client/event/animation/AnimationEndEvent.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:dankurka-mgwt_521c03_e1a6f7src/main/java/com/googlecode/mgwt/dom/client/event/animation/TransitionEndEvent.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:dankurka-mgwt_56d3d4_ade771src/main/java/com/googlecode/mgwt/ui/client/widget/impl/ScrollPanelNewPort.java:314:314:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:dankurka-mgwt_56d3d4_ade771src/main/java/com/googlecode/mgwt/ui/client/widget/impl/ScrollPanelNewPort.java:357:357:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:dankurka-mgwt_73abe0_b266aasrc/main/java/com/googlecode/mgwt/ui/client/util/impl/BaseOrientationHandler.java:85:85:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:dankurka-mgwt_73abe0_b266aasrc/main/java/com/googlecode/mgwt/ui/client/util/impl/MobileOrientationHandler.java:6:16:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:dankurka-mgwt_844eb2_4a2c84src/main/java/com/googlecode/mgwt/ui/client/util/impl/BaseOrientationHandler.java:51:51:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:dankurka-mgwt_8577c4_8db3e8src/main/java/com/googlecode/mgwt/ui/client/util/impl/BaseOrientationHandler.java:85:85:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:dankurka-mgwt_95deaf_9ceef3src/main/java/com/googlecode/mgwt/linker/server/propertyprovider/UserAgentPropertyProvider.java:5:30:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:dankurka-mgwt_95deaf_9ceef3src/main/java/com/googlecode/mgwt/ui/client/dialog/AnimatableDialogBase.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:dankurka-mgwt_c5552f_82ac48src/main/java/com/googlecode/mgwt/linker/server/Html5ManifestServlet.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:dankurka-mgwt_d0bb76_550527src/main/java/com/googlecode/mgwt/ui/client/widget/MRadioButton.java:109:109:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:datanucleus-datanucleus-core_368c44_4e090dsrc/java/org/datanucleus/store/schema/table/CompleteClassTable.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:datanucleus-datanucleus-core_5f1d15_1fdc5bsrc/java/org/datanucleus/enhancer/EnhanceUtils.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:datanucleus-datanucleus-core_883d2a_5e718esrc/java/org/datanucleus/metadata/MetaDataManager.java:1957:1982:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_883d2a_5e718esrc/java/org/datanucleus/metadata/MetaDataManager.java:188:207:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:datanucleus-datanucleus-core_8e256b_2c96d8src/main/java/org/datanucleus/store/types/wrappers/backed/Hashtable.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:datanucleus-datanucleus-core_8e256b_2c96d8src/main/java/org/datanucleus/store/types/wrappers/backed/LinkedHashMap.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:datanucleus-datanucleus-core_8e256b_2c96d8src/main/java/org/datanucleus/store/types/wrappers/backed/LinkedHashSet.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED 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-#Null_Violation_Hunk:datanucleus-datanucleus-core_b81254_b06e6dsrc/main/java/org/datanucleus/store/types/converters/UUIDStringConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/cache/CachedPC.java:167:210:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/identity/XcaliaIdentityStringTranslator.java:40:98:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/metadata/MetaDataManagerImpl.java:1870:1895:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/plugin/NonManagedPluginRegistry.java:273:292:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/plugin/OSGiPluginRegistry.java:152:168:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BigDecimalArrayByteBufferConverter.java:29:47:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BigDecimalDoubleConverter.java:28:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BigDecimalStringConverter.java:28:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BigIntegerArrayByteBufferConverter.java:29:47:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BigIntegerLongConverter.java:28:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BigIntegerStringConverter.java:28:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BitSetStringConverter.java:29:58:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BooleanArrayByteBufferConverter.java:28:46:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BooleanIntegerConverter.java:26:47:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/BooleanYNConverter.java:26:47:SE_NO_SERIALVERSIONID 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-#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/CharacterStringConverter.java:23:37:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/CharArrayByteBufferConverter.java:28:46:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/ColorComponentsConverter.java:25:48:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/ColorStringConverter.java:25:57:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/CurrencyStringConverter.java:25:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/DateLongConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/DoubleArrayByteBufferConverter.java:28:46:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/FloatArrayByteBufferConverter.java:28:46:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/IntArrayByteBufferConverter.java:28:46:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/IntegerStringConverter.java:23:48:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/LocaleStringConverter.java:36:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/LongArrayByteBufferConverter.java:28:46:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/LongStringConverter.java:23:48:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SerializableByteArrayConverter.java:33:109:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SerializableByteBufferConverter.java:34:112:SE_NO_SERIALVERSIONID 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-#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SqlTimeDateConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SqlTimeLongConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SqlTimestampDateConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SqlTimestampLongConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SqlTimestampStringConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/SqlTimeStringConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/StringBufferStringConverter.java:23:37:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/StringBuilderStringConverter.java:23:37:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/TimeZoneStringConverter.java:25:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/URIStringConverter.java:25:39:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/URLStringConverter.java:29:52:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:datanucleus-datanucleus-core_ff6ba4_d84b25src/main/java/org/datanucleus/store/types/converters/UUIDStringConverter.java:25:49:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:datasift-datasift-java_06ec00_0e6f0asrc/de/roderick/weberknecht/WebSocketHandshake.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:datasift-datasift-java_27ae5e_cd68a4src/org/datasift/tests/DataForTests.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:datasift-datasift-java_725ef4_8554dcsrc/de/roderick/weberknecht/WebSocketHandshake.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:datasift-datasift-java_bab64e_4c2226src/de/roderick/weberknecht/WebSocketHandshake.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:datasift-datasift-java_f527bc_7b9ba8src/de/roderick/weberknecht/WebSocketHandshake.java:-1:-1:UWF_NULL_FIELD 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-#Null_Violation_Hunk:digipost-digipost-api-client-java_939e59_8e8474src/main/java/no/digipost/api/client/representations/Invoice.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:DigitalPebble-storm-crawler_6e2f62_e3b66asrc/main/java/com/digitalpebble/storm/crawler/parse/filter/XPathFilter.java:57:65:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:DigitalPebble-storm-crawler_9d25b5_8d23b0src/main/java/com/digitalpebble/storm/crawler/parse/filter/XPathFilter.java:79:143:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:diirt-graphene_520955_c10e59graphene-profile/src/main/java/org/epics/graphene/profile/VisualProfiler.java:103:177:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:diirt-graphene_e76b36_4bd9e3graphene-profile/src/main/java/org/epics/graphene/profile/VisualProfiler.java:103:177:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:doanduyhai-Achilles_282b45_cd7e60src/main/java/fr/doan/achilles/entity/metadata/JoinWideMapMeta.java:-1:-1:UUF_UNUSED_FIELD 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-#Null_Violation_Hunk:droolsjbpm-guvnor_311325_194419guvnor-m2repo-editor/guvnor-m2repo-editor-backend/src/test/java/org/guvnor/m2repo/backend/server/M2RepositoryTest.java:208:227:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:droolsjbpm-optaplanner_09dc24_7df62fdrools-planner-examples/src/main/java/org/drools/planner/examples/nurserostering/domain/solver/EmployeeStrengthComparator.java:24:33:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:droolsjbpm-optaplanner_09dc24_7df62fdrools-planner-examples/src/main/java/org/drools/planner/examples/nurserostering/domain/solver/ShiftAssignmentDifficultyComparator.java:25:34:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:droolsjbpm-optaplanner_15f1a4_4def4cdrools-planner-core/src/main/java/org/drools/planner/core/move/generic/GenericChainedChangeMove.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS 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-#Null_Violation_Hunk:droolsjbpm-optaplanner_97637b_bfba74drools-planner-examples/src/main/java/org/drools/planner/examples/tsp/swingui/TspWorldPanel.java:77:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:droolsjbpm-optaplanner_98615c_fc8eefdrools-planner-examples/src/main/java/org/drools/planner/examples/common/business/SolutionBusiness.java:234:240:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:droolsjbpm-optaplanner_c7ea58_e01c7ddrools-planner-examples/src/main/java/org/drools/planner/examples/examination/solver/solution/initializer/ExaminationStartingSolutionInitializer.java:292:342:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:droolsjbpm-optaplanner_c8808e_cfabf4drools-planner-examples/src/main/java/org/drools/planner/examples/nurserostering/solver/solution/initializer/NurseRosteringStartingSolutionInitializer.java:111:124:SIC_INNER_SHOULD_BE_STATIC 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-#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREFormatException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREIllegalArgumentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREIncludeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREIndexOverflowException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientArgumentsException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientPermissionException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidPluginException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidProcedureException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidWorldException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREIOException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CRELengthException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CRENotFoundException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CRENullPointerException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREPlayerOfflineException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginChannelException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginInternalException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CRERangeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREReadOnlyException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREScoreboardException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CRESecurityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREShellException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CRESQLException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREUnageableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/exceptions/CRE/CREUntameableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:750:766:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2100ea_92a989src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:1101:1117:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_29e0b4_e1308fsrc/main/java/com/laytonsmith/abstraction/AbstractConvertor.java:147:213:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:EngineHub-CommandHelper_29e0b4_e1308fsrc/main/java/com/laytonsmith/core/functions/PlayerManagement.java:1066:1082:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_29e0b4_e1308fsrc/main/java/com/laytonsmith/core/functions/PlayerManagement.java:726:742:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_29e0b4_e1308fsrc/main/java/com/laytonsmith/core/functions/StringHandling.java:59:141:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_29e0b4_e1308fsrc/main/java/com/laytonsmith/core/functions/StringHandling.java:1074:1470:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_2ae44f_212764src/main/java/com/laytonsmith/core/functions/StringHandling.java:1074:1470:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:EngineHub-CommandHelper_2ed314_af92d8src/main/java/com/laytonsmith/core/exceptions/CRE/AbstractCREException.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:EngineHub-CommandHelper_306053_6dda0csrc/main/java/com/laytonsmith/core/functions/Recipes.java:32:46:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_3ae4af_38572fsrc/main/java/com/laytonsmith/core/functions/Recipes.java:32:46:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCAgeable.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCArmorStand.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCEntity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCFireball.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCHanging.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCHumanEntity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCLivingEntity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCPainting.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCPig.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCProjectile.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_4958cd_46c453src/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCVehicle.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_5932e4_073901src/main/java/com/laytonsmith/core/functions/StringHandling.java:1100:1496:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_59eed6_5be285src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:1113:1129:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_59eed6_5be285src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:762:778:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREBadEntityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREBadEntityTypeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREBindException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRECastException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREEnchantmentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREFormatException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREIllegalArgumentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREIncludeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREIndexOverflowException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientArgumentsException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientPermissionException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidPluginException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidProcedureException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidWorldException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREIOException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRELengthException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRENotFoundException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRENullPointerException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREPlayerOfflineException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginChannelException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginInternalException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRERangeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREReadOnlyException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREScoreboardException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRESecurityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREShellException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CRESQLException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREUnageableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/exceptions/CRE/CREUntameableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:750:766:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_6a2223_33e658src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:1101:1117:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_705090_3fe2f0src/main/java/com/laytonsmith/core/functions/StringHandling.java:1100:1496:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:EngineHub-CommandHelper_834b23_ccd7d2src/main/java/com/laytonsmith/aliasengine/Constructs/Construct.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:EngineHub-CommandHelper_85080f_6235ebsrc/main/java/com/laytonsmith/aliasengine/Constructs/Construct.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:EngineHub-CommandHelper_98b2d0_6e5733src/main/java/com/laytonsmith/abstraction/AbstractConvertor.java:147:213:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:EngineHub-CommandHelper_98c749_c9814bsrc/main/java/com/laytonsmith/abstraction/AbstractConvertor.java:147:213:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:EngineHub-CommandHelper_98fb8d_b80351src/main/java/com/laytonsmith/abstraction/AbstractConvertor.java:147:213:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:EngineHub-CommandHelper_9e66bf_36836dsrc/main/java/com/laytonsmith/abstraction/AbstractConvertor.java:147:213:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:EngineHub-CommandHelper_9e66bf_36836dsrc/main/java/com/laytonsmith/core/functions/PlayerManagement.java:749:765:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_9e66bf_36836dsrc/main/java/com/laytonsmith/core/functions/PlayerManagement.java:1100:1116:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_9e66bf_36836dsrc/main/java/com/laytonsmith/core/functions/Recipes.java:30:44:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_9e66bf_36836dsrc/main/java/com/laytonsmith/core/functions/StringHandling.java:62:158:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a1c615_845ee8src/main/java/com/laytonsmith/core/functions/StringHandling.java:62:158:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREBadEntityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREBadEntityTypeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREBindException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRECastException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREEnchantmentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREFormatException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREIllegalArgumentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREIncludeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREIndexOverflowException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientArgumentsException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientPermissionException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidPluginException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidProcedureException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidWorldException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREIOException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRELengthException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRENotFoundException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRENullPointerException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREPlayerOfflineException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginChannelException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginInternalException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRERangeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREReadOnlyException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREScoreboardException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRESecurityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREShellException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CRESQLException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREUnageableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/exceptions/CRE/CREUntameableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:1101:1117:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_a97663_773f13src/main/java/com/laytonsmith/core/functions/PlayerManagement.java:750:766:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_b4b41a_e6ca12src/main/java/com/laytonsmith/core/functions/StringHandling.java:1101:1497:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCAgeable.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCArmorStand.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCEntity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCFireball.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCHanging.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCHumanEntity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCLivingEntity.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCPainting.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCPig.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCProjectile.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_b78141_eb3dbbsrc/main/java/com/laytonsmith/abstraction/bukkit/entities/BukkitMCVehicle.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:EngineHub-CommandHelper_c4d85c_e2f954src/main/java/com/laytonsmith/core/functions/StringHandling.java:62:158:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREBadEntityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREBadEntityTypeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREBindException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRECastException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREEnchantmentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREFormatException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREIllegalArgumentException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREIncludeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREIndexOverflowException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientArgumentsException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREInsufficientPermissionException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidPluginException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidProcedureException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREInvalidWorldException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREIOException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRELengthException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRENotFoundException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRENullPointerException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREPlayerOfflineException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginChannelException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREPluginInternalException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRERangeException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREReadOnlyException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREScoreboardException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRESecurityException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREShellException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CRESQLException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREUnageableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_cd7172_ab76f4src/main/java/com/laytonsmith/core/exceptions/CRE/CREUntameableMobException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:EngineHub-CommandHelper_dedc17_ee3adcsrc/main/java/com/laytonsmith/core/functions/StringHandling.java:1100:1496:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:EngineHub-CommandHelper_ea5042_c0aadbsrc/main/java/com/laytonsmith/abstraction/AbstractConvertor.java:147:213:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:EngineHub-CommandHelper_f51d03_d8507bsrc/main/java/com/laytonsmith/core/functions/StringHandling.java:1100:1496:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ESAPI-esapi-java-legacy_456c1c_75e54esrc/main/java/org/owasp/esapi/Encoder.java:117:117:MS_MUTABLE_ARRAY -#Null_Violation_Hunk:ESAPI-esapi-java-legacy_456c1c_75e54esrc/main/java/org/owasp/esapi/Encoder.java:116:116:MS_MUTABLE_ARRAY -#Illegal_Line_Position:ESAPI-esapi-java-legacy_4941f5_5d38d1src/main/java/org/owasp/esapi/crypto/CipherSpec.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:ESAPI-esapi-java-legacy_533a22_f30905src/main/java/org/owasp/esapi/SafeFile.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:ESAPI-esapi-java-legacy_7bfb08_7c10dcsrc/main/java/org/owasp/esapi/SafeFile.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:ESAPI-esapi-java-legacy_bb1f83_3b3a45src/main/java/org/owasp/esapi/reference/FileBasedAuthenticator.java:224:236:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:eXistence-TeeTime_088233_0b650csrc/main/java/teetime/framework/pipe/PipeFactoryRegistry.java:12:12:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:eXistence-TeeTime_5516cb_03e71dsrc/main/java/teetime/framework/Analysis.java:44:44:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:eXistence-TeeTime_8b598c_b1d8f7src/main/java/teetime/framework/exceptionHandling/TerminateException.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:eXistence-TeeTime_9dd3d3_f15d28src/main/java/teetime/framework/Analysis.java:44:44:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:eXistence-TeeTime_b12b6f_6a869fsrc/main/java/teetime/stage/basic/merger/Merger.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:eXistence-TeeTime_c583f8_49c92fsrc/main/java/teetime/framework/pipe/PipeFactoryRegistry.java:10:10:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:eXistence-TeeTime_ed3c63_7b8894src/main/java/teetime/framework/Analysis.java:44:44:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:eXistence-TeeTime_f9ab1a_948956src/main/java/teetime/variant/explicitScheduling/stage/stringBuffer/handler/AbstractDataTypeHandler.java:32:32:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:FallenMoonNetwork-CanaryLib_3a257f_b60e32src/main/java/net/canarymod/user/Group.java:114:114:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:FallenMoonNetwork-CanaryLib_a73a2a_fde527src/main/java/net/canarymod/plugin/PluginLoader.java:695:728:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:FallenMoonNetwork-CanaryLib_e6ac81_74f4d5src/main/java/net/canarymod/backbone/GroupAccess.java:48:48:URF_UNREAD_FIELD -#Illegal_Line_Position:FasterXML-jackson-core_4646ed_a8bc72src/main/java/com/fasterxml/jackson/core/io/IOContext.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:FasterXML-jackson-core_594a75_e574b3src/main/java/com/fasterxml/jackson/core/json/UTF8StreamJsonParser.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:FasterXML-jackson-databind_034f3c_ef0022src/main/java/com/fasterxml/jackson/databind/PropertyNamingStrategy.java:282:306:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_034f3c_ef0022src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:220:229:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_034f3c_ef0022src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:232:241:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_034f3c_ef0022src/main/java/com/fasterxml/jackson/databind/ser/std/StdSerializer.java:45:298:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:FasterXML-jackson-databind_1875fc_5fda49src/main/java/com/fasterxml/jackson/databind/ext/DOMDeserializer.java:57:62:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_1875fc_5fda49src/main/java/com/fasterxml/jackson/databind/ext/DOMDeserializer.java:48:53:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_2e364b_6c6173src/main/java/com/fasterxml/jackson/databind/ser/std/StdJdkSerializers.java:139:159:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_2e364b_6c6173src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:81:89:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_2e364b_6c6173src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:103:111:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_2e364b_6c6173src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:71:78:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_308ed4_44f35asrc/main/java/com/fasterxml/jackson/databind/PropertyNamingStrategy.java:282:306:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_308ed4_44f35asrc/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:232:241:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_308ed4_44f35asrc/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:220:229:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_308ed4_44f35asrc/main/java/com/fasterxml/jackson/databind/ser/std/StdSerializer.java:45:298:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:FasterXML-jackson-databind_386e9f_df0408src/main/java/com/fasterxml/jackson/databind/PropertyNamingStrategy.java:282:306:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_386e9f_df0408src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:232:241:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_386e9f_df0408src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:220:229:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_386e9f_df0408src/main/java/com/fasterxml/jackson/databind/ser/std/StdSerializer.java:45:298:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:FasterXML-jackson-databind_3aee59_a49ab9src/main/java/com/fasterxml/jackson/databind/PropertyNamingStrategy.java:282:306:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_3aee59_a49ab9src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:220:229:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_3aee59_a49ab9src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:232:241:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_3aee59_a49ab9src/main/java/com/fasterxml/jackson/databind/ser/std/StdSerializer.java:45:298:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:FasterXML-jackson-databind_4312a2_5d2b25src/main/java/com/fasterxml/jackson/databind/deser/DeserializerCache.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:FasterXML-jackson-databind_4312a2_5d2b25src/main/java/com/fasterxml/jackson/databind/ser/std/StdJdkSerializers.java:139:159:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_4312a2_5d2b25src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:71:78:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_4312a2_5d2b25src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:81:89:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_4312a2_5d2b25src/main/java/com/fasterxml/jackson/databind/ser/std/StdKeySerializers.java:103:111:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:FasterXML-jackson-databind_5f0932_384e64src/main/java/com/fasterxml/jackson/databind/ser/std/StdJdkSerializers.java:139:159:SE_NO_SERIALVERSIONID 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-#Null_Violation_Hunk:forcedotcom-phoenix_ef2f81_f1e79asrc/main/java/com/salesforce/phoenix/filter/RowKeyComparisonFilter.java:92:130:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:FoxDev-FoxBot_066f03_7650besrc/main/java/uk/co/revthefox/foxbot/config/BotConfig.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:FoxDev-FoxBot_066f03_7650besrc/main/java/uk/co/revthefox/foxbot/config/BotConfig.java:34:34:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:FoxDev-FoxBot_619970_7de647src/main/java/uk/co/revthefox/foxbot/config/BotConfig.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:FoxDev-FoxBot_7650be_8a59edsrc/main/java/uk/co/revthefox/foxbot/config/BotConfig.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:FoxDev-FoxBot_f29721_602175src/main/java/uk/co/revthefox/foxbot/config/BotConfig.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:galenframework-galen_59002b_73f9dfsrc/main/java/net/mindengine/galen/reports/HtmlReportingListener.java:66:72:SIC_INNER_SHOULD_BE_STATIC 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-#Null_Violation_Hunk:GenomicParisCentre-eoulsan_0cd9ac_786ab4src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:604:770:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:GenomicParisCentre-eoulsan_1f4a24_9bac55src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/hadoop/HTSeqCountReducer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_237a78_4a4f27src/main/java/fr/ens/transcriptome/eoulsan/steps/mgmt/upload/DataFileDistCp.java:89:89:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_23e678_52b496src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:604:770:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_23e678_52b496src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:65:271:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_2fd750_6801cbsrc/main/java/fr/ens/transcriptome/eoulsan/core/Workflow.java:157:164:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_3483ae_e279b2src/main/java/fr/ens/transcriptome/eoulsan/core/Workflow.java:157:164:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:GenomicParisCentre-eoulsan_46cfa3_b0c06dsrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/hadoop/HTSeqCountReducer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_49f993_5d4b1esrc/main/java/fr/ens/transcriptome/eoulsan/core/Workflow.java:157:164:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:GenomicParisCentre-eoulsan_5687bd_ed8a34src/main/java/fr/ens/transcriptome/eoulsan/core/workflow/CommandWorkflowModel.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:GenomicParisCentre-eoulsan_68e564_4ecf5esrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/hadoop/HTSeqCountReducer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_6da22c_68e564src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:65:271:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_6da22c_68e564src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:604:770:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_775802_31c4bcsrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:65:271:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_775802_31c4bcsrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:604:770:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:GenomicParisCentre-eoulsan_8a9034_94b156src/main/java/fr/ens/transcriptome/eoulsan/core/SimpleContext.java:-1:-1:CI_CONFUSED_INHERITANCE 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-#Illegal_Line_Position:GenomicParisCentre-eoulsan_c4d21d_6b476esrc/main/java/fr/ens/transcriptome/eoulsan/core/workflow/DataList.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:GenomicParisCentre-eoulsan_c4d21d_6b476esrc/main/java/fr/ens/transcriptome/eoulsan/core/workflow/TaskContext.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_c917c6_081f87src/main/java/fr/ens/transcriptome/eoulsan/core/Workflow.java:157:164:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:GenomicParisCentre-eoulsan_d54204_191f98src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/hadoop/HTSeqCountReducer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:GenomicParisCentre-eoulsan_d5f5bd_66bdfbsrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/hadoop/HTSeqCountReducer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_d9695e_b0c06dsrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:604:770:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_d9695e_b0c06dsrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:65:271:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:GenomicParisCentre-eoulsan_def15a_7905e7src/main/java/fr/ens/transcriptome/eoulsan/steps/expression/hadoop/HTSeqCountReducer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:GenomicParisCentre-eoulsan_defb0f_23785bsrc/main/java/fr/ens/transcriptome/eoulsan/core/workflow/WorkflowContext.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:GenomicParisCentre-eoulsan_e25f80_407ba1src/main/java/fr/ens/transcriptome/eoulsan/core/workflow/WorkflowContext.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_e67e26_c04d2asrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:604:770:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_e67e26_c04d2asrc/main/java/fr/ens/transcriptome/eoulsan/steps/expression/TranscriptAndExonFinder.java:65:271:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GenomicParisCentre-eoulsan_ea2ea0_d4b5e6src/main/java/fr/ens/transcriptome/eoulsan/bio/SAMComparator.java:36:132:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:gertvv-addis_112427_e45403src/main/java/org/drugis/addis/entities/metaanalysis/AbstractMetaAnalysis.java:22:22:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:gertvv-addis_112427_e45403src/main/java/org/drugis/addis/entities/metaanalysis/AbstractMetaAnalysis.java:166:166:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:gertvv-addis_401d57_334499src/main/java/org/drugis/addis/gui/StudyGraph.java:108:116:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:gertvv-addis_401d57_334499src/main/java/org/drugis/addis/gui/StudyGraph.java:108:116:SE_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_43a299_fafb4csrc/main/java/org/drugis/addis/presentation/StudyGraphPresentation.java:22:36:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:gertvv-addis_52896d_72686csrc/main/java/org/drugis/addis/presentation/RandomEffectsMetaAnalysisPresentation.java:57:66:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:gertvv-addis_52896d_72686csrc/main/java/org/drugis/addis/presentation/RandomEffectsMetaAnalysisPresentation.java:57:66:SE_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_a3c2ed_dbfd2dsrc/main/java/org/drugis/addis/entities/metaanalysis/NetworkMetaAnalysis.java:9:9:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:gertvv-addis_a7ceac_2bafc1src/main/java/org/drugis/addis/entities/metaanalysis/RandomEffectsMetaAnalysis.java:275:338:SE_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:28:38:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:73:83:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:28:38:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:73:83:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:73:83:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:58:67:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:87:91:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:87:91:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:gertvv-addis_b5bc27_f5f432src/main/java/org/drugis/addis/presentation/wizard/MetaAnalysisWizardPresentation.java:58:67:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:gertvv-addis_bd9215_a3c2edsrc/main/java/org/drugis/addis/entities/metaanalysis/RandomEffectsMetaAnalysis.java:28:28:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:ghedlund-phon_22a2fc_4174deapp/src/main/java/ca/phon/app/session/editor/view/common/SegmentTierComponent.java:119:132:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ghedlund-phon_61c7ec_d30d79app/src/main/java/ca/phon/app/session/editor/view/common/SegmentTierComponent.java:119:132:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ghedlund-phon_af6f76_013f52app/src/main/java/ca/phon/app/project/NewSessionDialog.java:301:301:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ghedlund-phon_d3398d_3fea2eapp/src/main/java/ca/phon/app/session/editor/DefaultEditorViewModel.java:490:498:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:Gigaspaces-mongo-datasource_bcdba8_712d22src/main/java/com/gigaspaces/persistency/metadata/MongoMetadataInspector.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:google-closure-templates_3fd54b_200420java/src/com/google/template/soy/jssrc/internal/HelperFunctions.java:234:234:URF_UNREAD_FIELD -#Null_Violation_Hunk:google-guava_dd6db4_b16c75src/com/google/common/collect/ImmutableCollection.java:189:217:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:google-guava_dd6db4_b16c75src/com/google/common/collect/ImmutableCollection.java:221:238:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:google-guava_dd6db4_b16c75src/com/google/common/collect/RegularImmutableMap.java:197:221:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:google-guava_dd6db4_b16c75src/com/google/common/collect/RegularImmutableMap.java:171:186:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:google-guava_dd6db4_b16c75src/com/google/common/collect/SingletonImmutableMap.java:98:119:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GoogleCloudPlatform-gcloud-java_0265e0_110ab8src/main/java/com/google/gcloud/storage/StorageServiceImpl.java:471:583:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GoogleCloudPlatform-gcloud-java_0265e0_110ab8src/main/java/com/google/gcloud/storage/StorageServiceImpl.java:362:461:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GoogleCloudPlatform-gcloud-java_339696_c08181src/main/java/com/google/gcloud/storage/StorageServiceImpl.java:362:461:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:GoogleCloudPlatform-gcloud-java_339696_c08181src/main/java/com/google/gcloud/storage/StorageServiceImpl.java:471:583:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:GoogleCloudPlatform-gcloud-java_41422a_761fd0src/main/java/com/google/gcloud/datastore/StructuredQuery.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:GoogleCloudPlatform-gcloud-java_98b239_86201csrc/main/java/com/google/gcloud/datastore/Value.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:GoogleCloudPlatform-gcloud-java_a43992_f04010gcloud-java-datastore/src/main/java/com/google/gcloud/datastore/GqlQuery.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:GoogleCloudPlatform-gcloud-java_a43992_f04010gcloud-java-datastore/src/main/java/com/google/gcloud/datastore/StructuredQuery.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED 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-#Null_Violation_Hunk:graphaware-neo4j-framework_180558_1d9780src/test/java/com/graphaware/tx/event/improved/FilteredLazyTransactionDataIntegrationTest.java:1555:1574:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:graphaware-neo4j-framework_de11b5_98ff5fsrc/test/java/com/graphaware/framework/BaseGraphAwareFrameworkTest.java:105:109:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:graphaware-neo4j-framework_de11b5_98ff5fsrc/test/java/com/graphaware/framework/BaseGraphAwareFrameworkTest.java:105:109:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:graphhopper-graphhopper_24c1e6_f40e31src/main/java/com/graphhopper/coll/GHBitSetImpl.java:28:76:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:graphhopper-graphhopper_3200cb_a2090csrc/main/java/com/graphhopper/ui/MiniGraphUI.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:graphhopper-graphhopper_3200cb_a2090csrc/main/java/com/graphhopper/ui/MiniGraphUI.java:54:54:UWF_UNWRITTEN_FIELD 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-#Null_Violation_Hunk:instance01-MinigamesAPI_5f3d72_a4f312API/src/main/java/com/comze_instancelabs/minigamesapi/util/IconMenu.java:111:149:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:instance01-MinigamesAPI_7909ad_a7d507API/src/main/java/com/comze_instancelabs/minigamesapi/util/ArenaBlock.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:instance01-MinigamesAPI_924750_1cbc56API/src/com/comze_instancelabs/minigamesapi/sql/MySQL.java:51:51:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:instance01-MinigamesAPI_924750_1cbc56API/src/com/comze_instancelabs/minigamesapi/sql/SQLite.java:47:47:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:instance01-MinigamesAPI_c07f68_3b23f0API/src/main/java/com/comze_instancelabs/minigamesapi/sql/MySQL.java:51:51:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:instance01-MinigamesAPI_e2920f_991e47API/src/main/java/com/comze_instancelabs/minigamesapi/PluginInstance.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:irstv-orbisgis_d93325_4239eabundles/table-editor/src/main/java/org/orbisgis/tablegui/impl/ActionAddRow.java:80:80:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:jahlborn-jackcess_01c8f3_1c3fffsrc/java/com/healthmarketscience/jackcess/Cursor.java:478:478:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jahlborn-jackcess_01c8f3_1c3fffsrc/java/com/healthmarketscience/jackcess/Cursor.java:472:472:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jahlborn-jackcess_181185_a384c7src/java/com/healthmarketscience/jackcess/IndexPageCache.java:131:131:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:jahlborn-jackcess_324f49_2e5d00src/main/java/com/healthmarketscience/jackcess/impl/RowImpl.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:jahlborn-jackcess_5d47ae_3bbc8asrc/java/com/healthmarketscience/jackcess/Index.java:1222:1222:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_5d47ae_3bbc8asrc/java/com/healthmarketscience/jackcess/Index.java:1159:1159:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_5d47ae_3bbc8asrc/java/com/healthmarketscience/jackcess/Index.java:1321:1321:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_651986_eaccccsrc/java/com/healthmarketscience/jackcess/complex/AttachmentColumnInfo.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_651986_eaccccsrc/java/com/healthmarketscience/jackcess/complex/MultiValueColumnInfo.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_651986_eaccccsrc/java/com/healthmarketscience/jackcess/complex/UnsupportedColumnInfo.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_651986_eaccccsrc/java/com/healthmarketscience/jackcess/complex/VersionHistoryColumnInfo.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_a92600_c3ca22src/java/com/healthmarketscience/jackcess/Index.java:972:972:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_a92600_c3ca22src/java/com/healthmarketscience/jackcess/Index.java:1034:1034:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_a92600_c3ca22src/java/com/healthmarketscience/jackcess/Index.java:1140:1140:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_b6276a_a4aaebsrc/java/com/healthmarketscience/jackcess/Index.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:jahlborn-jackcess_cf6233_012405src/java/com/healthmarketscience/jackcess/complex/ComplexValueForeignKey.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:jahlborn-jackcess_d40e7e_d14cd3src/java/com/healthmarketscience/jackcess/Index.java:901:901:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jahlborn-jackcess_d40e7e_d14cd3src/java/com/healthmarketscience/jackcess/Index.java:1007:1007:EQ_COMPARETO_USE_OBJECT_EQUALS -#Illegal_Line_Position:jamesagnew-hapi-fhir_5296e8_d09755hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeChildResourceDefinition.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:jamesagnew-hapi-fhir_69461e_ad05d8hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/ListResource.java:231:809:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:jankotek-MapDB_05f432_1c9bf3src/main/java/org/mapdb/ByteBuffer2.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:jankotek-MapDB_0a513e_24bd04src/main/java/org/mapdb/CacheHashTable.java:40:47:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jankotek-MapDB_10648b_65abcesrc/main/java/org/mapdb/CacheHashTable.java:17:24:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jankotek-MapDB_15dd22_fb0d3fsrc/main/java/org/mapdb/SerializerPojo.java:703:737:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jankotek-MapDB_2c21b0_e89ed0src/main/java/org/mapdb/Volume.java:1989:1989:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:jankotek-MapDB_2d128e_894532src/main/java/org/mapdb/SerializerPojo.java:634:660:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jankotek-MapDB_2e5587_636544src/main/java/org/mapdb/CompressLZF.java:355:372:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_2f0ab9_130881src/main/java/org/mapdb/Serializer.java:202:220:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_352db1_7e1055src/main/java/org/mapdb/SerializerBase.java:1227:1297:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:jankotek-MapDB_59881f_0dbc5esrc/main/java/org/mapdb20/SerializerPojo.java:703:737:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jankotek-MapDB_5cbae4_ab1c6esrc/main/java/org/mapdb/Volume.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:jankotek-MapDB_669534_fa6141src/main/java/org/mapdb/Atomic.java:248:408:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_669534_fa6141src/main/java/org/mapdb/Atomic.java:428:589:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_669534_fa6141src/main/java/org/mapdb/Fun.java:63:107:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_669534_fa6141src/main/java/org/mapdb/Fun.java:116:175:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_669534_fa6141src/main/java/org/mapdb/Fun.java:185:256:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:jankotek-MapDB_669534_fa6141src/main/java/org/mapdb/SerializerPojo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:jankotek-MapDB_69c85c_f748cdsrc/main/java/org/mapdb/SerializerBase.java:34:35:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_716dbc_64f801src/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:jankotek-MapDB_7b86b1_435c83src/main/java/org/mapdb/CacheHashTable.java:40:47:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/BTreeKeySerializer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/BTreeMap.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/BTreeMap.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/Fun.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jankotek-MapDB_8dee37_dacbbfsrc/main/java/org/mapdb/Fun.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:jankotek-MapDB_99b619_bde4a9src/main/java/org/mapdb/DB.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:jankotek-MapDB_9a227f_16ad38src/main/java/org/mapdb/BTreeKeySerializer.java:56:79:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_a15a7a_4a0f83src/main/java/org/mapdb/BTreeKeySerializer.java:66:94:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_a15a7a_4a0f83src/main/java/org/mapdb/Fun.java:560:618:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_a15a7a_4a0f83src/main/java/org/mapdb/Fun.java:415:455:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_a15a7a_4a0f83src/main/java/org/mapdb/Fun.java:622:686:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_a15a7a_4a0f83src/main/java/org/mapdb/Fun.java:506:555:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_a15a7a_4a0f83src/main/java/org/mapdb/Fun.java:459:502:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:jankotek-MapDB_a302a8_dbe4fesrc/main/java/org/mapdb/StoreDirect.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:jankotek-MapDB_a302a8_dbe4fesrc/main/java/org/mapdb/StoreWAL.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:jankotek-MapDB_b3b8b4_6563f5src/main/java/org/mapdb20/Volume.java:1576:1576:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:jankotek-MapDB_c71a2a_461ee2src/main/java/org/mapdb/Fun.java:236:251:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_c71a2a_461ee2src/main/java/org/mapdb/Fun.java:277:299:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_c8c6e8_b08c06src/main/java/org/mapdb/Serializer.java:1440:1510:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jankotek-MapDB_cb1f65_be0f1asrc/main/java/org/mapdb/SerializerPojo.java:628:654:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jankotek-MapDB_f4c4a0_e7bc8bsrc/main/java/org/mapdb/AsyncWriteEngine.java:-1:-1:HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS -#Null_Violation_Hunk:jankotek-MapDB_feb207_6f28fbsrc/main/java/org/mapdb/SerializerPojo.java:628:654:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jboss-javassist-javassist_962a75_b66787src/main/javassist/bytecode/stackmap/TypeData.java:392:392:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:jboss-javassist-javassist_962a75_b66787src/main/javassist/bytecode/stackmap/TypeData.java:323:323:HE_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:jbossas-jboss-ejb-client_0facc1_a87bffsrc/main/java/org/jboss/ejb/client/remoting/GeneralInvocationFailureResponseHandler.java:97:109:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jbossas-jboss-ejb-client_119bc7_f59701src/main/java/org/jboss/ejb/client/EJBInvocationHandler.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:jbossas-jboss-ejb-client_2f4178_c8fa49src/main/java/org/jboss/ejb/client/remoting/ClusterNode.java:155:166:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jbossas-jboss-ejb-client_39af42_0398b3src/main/java/org/jboss/ejb/client/EJBClient.java:161:161:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:jbossas-jboss-ejb-client_39af42_0398b3src/test/java/org/jboss/ejb/client/test/proxy/EchoBean.java:32:37:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Null_Violation_Hunk:jbossas-jboss-ejb-client_a60c5a_d339a2src/main/java/org/jboss/ejb/client/remoting/ModuleAvailabilityMessageHandler.java:110:143:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jbossas-jboss-ejb-client_a6666e_543515src/main/java/org/jboss/ejb/client/remoting/ModuleAvailabilityMessageHandler.java:110:143:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jbossas-jboss-ejb-client_c43392_b1b8d4src/main/java/org/jboss/ejb/client/remoting/ClusterNode.java:155:166:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jbossas-jboss-ejb-client_c9d67f_e4fd05src/main/java/org/jboss/ejb/client/remoting/GeneralInvocationFailureResponseHandler.java:97:109:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jbossas-jboss-ejb-client_e4e2f5_35504csrc/main/java/org/jboss/ejb/client/RecoveryOnlySerializedEJBXAResource.java:42:137:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jbossas-jboss-ejb-client_f754b5_4e276csrc/main/java/org/jboss/ejb/client/SessionInterceptor.java:43:43:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:jcabi-jcabi-github_1cfc4d_a7d703src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_47050c_1dcb5fsrc/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_55d31d_8f76d5src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_75d449_c4724dsrc/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_7721b1_be9f87src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_8707c4_be49edsrc/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_91a5ed_dd6b62src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_af0de5_07aa91src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_b6a619_733132src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_b6e0ea_8e1b84src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_cc75c4_e85dffsrc/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_dd0d77_4563a6src/main/java/com/jcabi/github/RtStatuses.java:47:47:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_de398c_ee340csrc/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jcabi-jcabi-github_fdf5d6_258801src/main/java/com/jcabi/github/RtOrganization.java:48:48:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jenkinsci-acceptance-test-harness_a1fafd_edd3a9src/main/java/org/jenkinsci/test/acceptance/po/WorkflowJob.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:jenkinsci-git-client-plugin_00d987_890c85src/main/java/org/jenkinsci/plugins/gitclient/JGitProgressMonitor.java:15:34:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Null_Violation_Hunk:jenkinsci-git-client-plugin_12d541_d6945fsrc/main/java/org/jenkinsci/plugins/gitclient/JGitProgressMonitor.java:15:34:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Illegal_Line_Position:jenkinsci-git-client-plugin_1770d8_8bf0f4src/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jenkinsci-git-client-plugin_177334_eee5b5src/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jenkinsci-git-client-plugin_41c401_c0647esrc/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jenkinsci-git-client-plugin_4ba836_f5f1fesrc/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jenkinsci-git-client-plugin_5e816b_f759bcsrc/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jenkinsci-git-client-plugin_5e816b_f759bcsrc/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jenkinsci-git-client-plugin_7fd8d1_8ffb0esrc/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:jenkinsci-git-client-plugin_a34d1a_38d33bsrc/main/java/org/jenkinsci/plugins/gitclient/RemoteGitImpl.java:105:160:SE_INNER_CLASS -#Null_Violation_Hunk:jenkinsci-git-client-plugin_ab79be_6ae1cesrc/main/java/org/jenkinsci/plugins/gitclient/JGitProgressMonitor.java:15:34:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Illegal_Line_Position:jenkinsci-git-client-plugin_c1c0e5_2d41edsrc/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:jenkinsci-git-client-plugin_e7797a_fdcac5src/main/java/org/jenkinsci/plugins/gitclient/JGitProgressMonitor.java:15:34:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Null_Violation_Hunk:jenkinsci-git-client-plugin_fe7f56_41c401src/main/java/org/jenkinsci/plugins/gitclient/JGitTool.java:16:29:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jenkinsci-junit-plugin_520cba_905451src/main/java/hudson/tasks/junit/TestResultAction.java:56:56:UG_SYNC_SET_UNSYNC_GET -#Null_Violation_Hunk:jenkinsci-matrix-project-plugin_eb81a1_79ff52src/main/java/hudson/matrix/NoopMatrixConfigurationSorter.java:12:23:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:jenkinsci-remoting_846b3e_94ce96src/main/java/hudson/remoting/JarLoaderImpl.java:86:97:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-remoting_ba844a_075098src/main/java/hudson/remoting/JarLoaderImpl.java:86:97:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-remoting_c6432e_845151src/main/java/hudson/remoting/ResourceImageDirect.java:22:37:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:jenkinsci-remoting_d9c57f_0e4d75src/main/java/hudson/remoting/JarLoaderImpl.java:86:97:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-sauce-ondemand-plugin_b4c29e_c2f5f2src/main/java/hudson/plugins/sauce_ondemand/SauceOnDemandReport.java:99:108:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-sauce-ondemand-plugin_b8fb33_c5ad3bsrc/main/java/hudson/plugins/sauce_ondemand/AbstractAction.java:65:77:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-sauce-ondemand-plugin_c66742_c7c09esrc/main/java/hudson/plugins/sauce_ondemand/SauceOnDemandBuildAction.java:201:225:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-xunit-plugin_955eef_3634ffsrc/main/java/org/jenkinsci/plugins/xunit/XUnitPublisher.java:204:204:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jenkinsci-xunit-plugin_9a7e11_ab2562src/main/java/org/jenkinsci/plugins/xunit/XUnitProcessor.java:142:142:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jenkinsci-xunit-plugin_cfcbac_382868src/main/java/org/jenkinsci/plugins/xunit/XUnitPublisher.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/index/TestIndexDataProvider.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/index/TestIndexDataProvider.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/index/TestIndexDataProvider.java:851:1052:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/DefaultClarityScore.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/ImprovedClarityScore.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/ImprovedClarityScore.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/SimplifiedClarityScore.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/SimplifiedClarityScore.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/SimplifiedClarityScore.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:JensBee-QueryClarity_053a02_3a4f33src/main/java/de/unihildesheim/iw/Persistence.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:JensBee-QueryClarity_2f8a49_bab509src/main/java/de/unihildesheim/iw/lucene/scoring/clarity/AbstractClarityScoreCalculationBuilder.java:159:159:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:JensBee-QueryClarity_4d5d7f_75ff0dsrc/main/java/de/unihildesheim/lucene/index/DirectIndexDataProvider.java:867:867:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:JensBee-QueryClarity_529a32_a067bdsrc/main/java/de/unihildesheim/lucene/index/TestIndexDataProvider.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:JensBee-QueryClarity_529a32_a067bdsrc/main/java/de/unihildesheim/Persistence.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:JensBee-QueryClarity_61a243_053a02src/main/java/de/unihildesheim/iw/lucene/index/TestIndexDataProvider.java:642:824:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:JensBee-QueryClarity_a067bd_1a4521src/test/java/de/unihildesheim/lucene/index/IndexTestUtil.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:JensBee-QueryClarity_dc5848_c1bd49src/main/java/de/unihildesheim/iw/lucene/index/DirectIndexDataProvider.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:jensnerche-plantuml_15ff58_5e4772src/net/sourceforge/plantuml/cucadiagram/dot/DotMaker.java:772:782:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jensnerche-plantuml_15ff58_5e4772src/net/sourceforge/plantuml/cucadiagram/EntityMutable.java:45:45:EQ_COMPARETO_USE_OBJECT_EQUALS -#Illegal_Line_Position:jensnerche-plantuml_ba0d28_22372bsrc/net/sourceforge/plantuml/skin/BiColor.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:jensnerche-plantuml_d0f090_aebe49src/net/sourceforge/plantuml/graph2/RectanglesCollection.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:jensnerche-plantuml_e38ce0_983a63src/net/sourceforge/plantuml/ugraphic/svg/UGraphicSvg.java:177:185:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jeremylong-DependencyCheck_00a35c_d6e387src/main/java/org/owasp/dependencycheck/data/lucene/VersionTokenizingFilter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:jeremylong-DependencyCheck_0ad97d_dba1e0src/main/java/org/owasp/dependencycheck/analyzer/FalsePositiveAnalyzer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:jeremylong-DependencyCheck_13eb2b_772b0csrc/main/java/org/owasp/dependencycheck/data/lucene/VersionTokenizingFilter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:jeremylong-DependencyCheck_6f1936_0cf6cfsrc/main/java/org/codesecure/dependencycheck/utils/Settings.java:39:39:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jeremylong-DependencyCheck_768999_9e489csrc/main/java/org/codesecure/dependencycheck/utils/Settings.java:39:39:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jeremylong-DependencyCheck_7d9fa7_ff4e40src/main/java/org/codesecure/dependencycheck/dependency/VulnerableSoftware.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:jeremylong-DependencyCheck_b078d8_d7af14src/main/java/org/owasp/dependencycheck/analyzer/FalsePositiveAnalyzer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:jeremylong-DependencyCheck_f6cdf3_30ea51src/main/java/org/codesecure/dependencycheck/dependency/VulnerableSoftware.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:jgheerardyn-yields_05c880_c2aeb3foundations/src/main/java/io/yields/math/framework/impl/VariableDefinitionImpl.java:12:12:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:jgheerardyn-yields_f93107_03463ffoundations/src/main/java/io/yields/math/framework/impl/DoubleVariableDefinition.java:12:12:EQ_COMPARETO_USE_OBJECT_EQUALS -#Illegal_Line_Position:jline-jline2_6fcb72_5c0e40src/test/java/jline/internal/TerminalLineSettingsTest.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:jline-jline2_768328_677269src/main/java/jline/UnixTerminal.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:jline-jline2_7e4e78_f4b58dsrc/main/java/jline/console/completer/AggregateCompleter.java:91:106:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:jline-jline2_c02a57_078fc5src/main/java/jline/console/completer/AggregateCompleter.java:117:132:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:jline-jline2_dad3b5_1d493fsrc/test/java/jline/internal/TerminalLineSettingsTest.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:jmxtrans-jmxtrans_4b927e_f5e3desrc/com/googlecode/jmxtrans/model/output/BaseOutputWriter.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:johan-martenson-settlers_001a4e_f37eefsrc/main/java/org/appland/settlers/model/GameMap.java:174:272:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:johan-martenson-settlers_3b7007_0a7e77src/main/java/org/appland/settlers/model/Size.java:3:28:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:johan-martenson-settlers_5f8e28_64f70esrc/main/java/org/appland/settlers/model/Player.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:johan-martenson-settlers_8358bc_78003bsrc/main/java/org/appland/settlers/model/MapPoint.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:johan-martenson-settlers_971126_0a8acasrc/main/java/org/appland/settlers/model/GameUtils.java:169:185:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:johan-martenson-settlers_fe8ea9_76503esrc/main/java/org/appland/settlers/model/GameMap.java:140:220:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:JolantaWojcik-biojavaOwn_2b3cd0_8eda39biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:2877:2963:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:JolantaWojcik-biojavaOwn_8f86c4_b3c663biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:2097:2097:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:JolantaWojcik-biojavaOwn_a591c7_d6ff9fbiojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java:2881:2986:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:JolantaWojcik-biojavaOwn_a9e64c_be1e86biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/KaplanMeierFigure.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:JolantaWojcik-biojavaOwn_c01faa_1fd8e7biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:JolantaWojcik-biojavaOwn_d9b9e0_20b4eebiojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java:158:158:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:julianhyde-optiq_150c97_13136fsrc/main/java/net/hydromatic/optiq/jdbc/OptiqStatement.java:406:420:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:julianhyde-optiq_21e889_da2c64src/main/java/net/hydromatic/optiq/runtime/SortedMultiMap.java:28:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:julianhyde-optiq_da2c64_6ea494src/main/java/net/hydromatic/optiq/runtime/SortedMultiMap.java:26:41:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:71:71:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:69:69:MS_MUTABLE_ARRAY -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:77:77:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:61:61:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:51:51:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:53:53:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:73:73:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:88:88:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:75:75:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e60ee3_f4b648src/main/java/org/eigenbase/sql/type/SqlTypeName.java:49:49:MS_PKGPROTECT -#Null_Violation_Hunk:julianhyde-optiq_e8a52f_0da431src/main/java/net/hydromatic/optiq/jdbc/OptiqStatement.java:416:430:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:julianhyde-optiq_f62f1d_68a788src/main/java/net/hydromatic/optiq/jdbc/OptiqStatement.java:416:436:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junit-team-junit_15c604_74cab2src/main/java/org/junit/experimental/categories/CategoryFilterFactory.java:43:48:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:junit-team-junit_1d6914_c099a9src/main/java/org/junit/runner/notification/RunNotifier.java:-1:-1:VO_VOLATILE_REFERENCE_TO_ARRAY -#Null_Violation_Hunk:junit-team-junit_45f226_bcbf43src/main/java/org/junit/internal/runners/JUnit38ClassRunner.java:22:66:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junit-team-junit_51f22b_eaa279src/main/java/org/junit/internal/runners/JUnit38ClassRunner.java:24:68:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junit-team-junit_74cab2_582017src/main/java/org/junit/experimental/categories/CategoryFilterFactory.java:46:51:SIC_INNER_SHOULD_BE_STATIC 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-#Illegal_Line_Position:junkdog-artemis-odb_bf4978_5b068eartemis-weaver/src/main/java/com/artemis/meta/ClassMetadata.java:-1:-1:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:junkdog-artemis-odb_ca2dba_6a93b9artemis-matrix/src/main/java/com/artemis/model/ComponentDependencyMatrix.java:209:212:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:junkdog-artemis-odb_d5fb74_c7fec9artemis/src/main/java/com/artemis/EntityEditPool.java:114:114:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:junkdog-artemis-odb_dce69d_6ca4e4src/main/java/com/artemis/World.java:435:440:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junkdog-artemis-odb_dce69d_6ca4e4src/main/java/com/artemis/World.java:425:430:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junkdog-artemis-odb_dce69d_6ca4e4src/main/java/com/artemis/World.java:405:410:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junkdog-artemis-odb_dce69d_6ca4e4src/main/java/com/artemis/World.java:415:420:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:junkdog-artemis-odb_dce69d_6ca4e4src/main/java/com/artemis/World.java:395:400:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:junkdog-artemis-odb_e43739_8c5a4bartemis-test/src/main/java/com/artemis/component/TransPackedFloatReferencel.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:junkdog-artemis-odb_e9b4a7_bf4978artemis-weaver/src/main/java/com/artemis/meta/ClassMetadata.java:-1:-1:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:junkdog-artemis-odb_fbba4c_f86220artemis/src/main/java/com/artemis/EntitySystem.java:68:68:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:junkdog-artemis-odb_fbba4c_f86220artemis/src/main/java/com/artemis/EntitySystem.java:58:58:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:junkdog-artemis-odb_fbba4c_f86220artemis/src/main/java/com/artemis/EntitySystem.java:53:53:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:juzu-juzu_eddf91_97ba92src/main/java/org/juzu/impl/classloading/FileSystemClassLoader.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:juzu-juzu_eddf91_97ba92src/main/java/org/juzu/impl/spi/fs/ram/RAMDir.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:kaazing-gateway_48083b_f4cbe4src/main/java/org/kaazing/gateway/server/windowsservice/ExtendedAdvapi32.java:37:37:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:kaazing-gateway_48083b_f4cbe4src/main/java/org/kaazing/gateway/server/windowsservice/ExtendedAdvapi32.java:36:36:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:KittehOrg-KittehIRCClientLib_0acf82_645858src/main/java/org/kitteh/irc/IRCBot.java:149:212:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Illegal_Line_Position:KittehOrg-KittehIRCClientLib_1e140b_c0eb7csrc/main/java/org/kitteh/irc/IRCBot.java:-1:-1:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:KittehOrg-KittehIRCClientLib_ccf40d_ec63bfsrc/main/java/org/kitteh/irc/IRCBot.java:45:94:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/DeleteToken.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHAuthorization.java:88:88:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHBranch.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHCommit.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHCommit.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHCommitComment.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHEventInfo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHEventInfo.java:30:30:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHPersonSet.java:13:39:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHPullRequestCommitDetail.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHRepository.java:-1:-1:DMI_COLLECTION_OF_URLS -#Null_Violation_Hunk:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHRepository.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/GHThread.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/SearchResult.java:27:27:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:kohsuke-github-api_2d45ac_ec450bsrc/main/java/org/kohsuke/github/SearchResult.java:32:32:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:kohsuke-github-api_340fb3_202cffsrc/main/java/org/kohsuke/github/GHIssueComment.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_5159a2_e66536src/main/java/org/kohsuke/github/GHOrganization.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_5a418d_340fb3src/main/java/org/kohsuke/github/GHAuthorization.java:99:99:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:kohsuke-github-api_aad20d_b736e2src/main/java/org/kohsuke/github/GHObject.java:52:52:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_b736e2_d070f9src/main/java/org/kohsuke/github/GHAuthorization.java:91:91:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:kohsuke-github-api_e239ef_4660c6src/main/java/org/kohsuke/github/GHIssueComment.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/DeleteToken.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHAuthorization.java:88:88:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHBranch.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHCommit.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHCommit.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHCommitComment.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHEventInfo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHEventInfo.java:30:30:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHPersonSet.java:13:39:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHPullRequestCommitDetail.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHRepository.java:-1:-1:DMI_COLLECTION_OF_URLS -#Null_Violation_Hunk:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHRepository.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/GHThread.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/SearchResult.java:27:27:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:kohsuke-github-api_ebc97f_79c5b2src/main/java/org/kohsuke/github/SearchResult.java:32:32:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:korpling-ANNIS_1ae44a_de792bannis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:141:161:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:korpling-ANNIS_275edb_dde724annis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:141:161:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:korpling-ANNIS_43e0d0_5ed60aannis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:141:161:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:korpling-ANNIS_4ed705_100fd9annis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:141:161:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:korpling-ANNIS_6933c5_241796annis-libgui/src/main/java/annis/libgui/AnnisBaseUI.java:496:505:SE_INNER_CLASS -#Null_Violation_Hunk:korpling-ANNIS_73c890_0f56bfannis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:140:160:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:korpling-ANNIS_a16b70_16327dannis-libgui/src/main/java/annis/libgui/AnnisBaseUI.java:462:471:SE_INNER_CLASS -#Null_Violation_Hunk:korpling-ANNIS_d7c374_701d43annis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:141:161:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:korpling-ANNIS_fb1c6c_0f56bfannis-libgui/src/main/java/annis/libgui/ResolverProviderImpl.java:141:161:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:kotcrab-VisEditor_38fd11_2c6ed3src/pl/kotcrab/vis/sceneeditor/EditorState.java:69:69:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:kotcrab-VisEditor_38fd11_2c6ed3src/pl/kotcrab/vis/sceneeditor/SceneEditorConfig.java:-1:-1:MS_PKGPROTECT 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-#Null_Violation_Hunk:kuujo-vertigo_aafc57_6432e1src/main/java/net/kuujo/vertigo/cluster/AbstractCluster.java:33:33:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:599:615:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:699:715:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:639:655:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:659:675:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:619:635:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:579:595:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_0dcf0c_6a396esrc/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:679:695:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_26a25f_ec8b7dsrc/main/java/com/ldbc/driver/util/MapUtils.java:36:42:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:ldbc-ldbc_driver_26a25f_ec8b7dsrc/main/java/com/ldbc/driver/workloads/ldbc/snb/bi/LdbcSnbBiWorkload.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:ldbc-ldbc_driver_2c1146_825735src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:253:263:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_2c1146_825735src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:226:249:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_35c2ab_0cd4b4src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:253:263:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_35c2ab_0cd4b4src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:226:249:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_544b44_60eeb5src/main/java/com/ldbc/driver/util/MapUtils.java:38:44:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ldbc-ldbc_driver_60eeb5_fbe28fsrc/main/java/com/ldbc/driver/runtime/metrics/ThreadedQueuedMetricsService.java:261:261:UG_SYNC_SET_UNSYNC_GET -#Null_Violation_Hunk:ldbc-ldbc_driver_60eeb5_fbe28fsrc/main/java/com/ldbc/driver/runtime/metrics/ThreadedQueuedMetricsService.java:209:209:UG_SYNC_SET_UNSYNC_GET -#Null_Violation_Hunk:ldbc-ldbc_driver_60eeb5_fbe28fsrc/main/java/com/ldbc/driver/runtime/WorkloadStatusThread.java:142:159:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_617a9b_0c9a62src/main/java/com/ldbc/driver/runtime/executor/PreciseIndividualAsyncOperationStreamExecutorServiceThread.java:140:150:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_648f85_56c5f7src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:253:263:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_648f85_56c5f7src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:226:249:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:ldbc-ldbc_driver_920ee2_56b0d6src/main/java/com/ldbc/driver/runtime/executor/InitiatedTimeSubmittingOperationRetriever_NEW.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:ldbc-ldbc_driver_95c1f6_4a1f2esrc/main/java/com/ldbc/driver/util/MapUtils.java:38:44:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:ldbc-ldbc_driver_9a4058_81feb7src/main/java/com/ldbc/driver/runtime/WorkloadStatusThread.java:133:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:259:262:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:294:297:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:266:269:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:273:276:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:280:283:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:252:255:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_9a6d4f_04dbf2src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/LdbcSnbShortReadGenerator.java:287:290:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_a0add3_f8dc48src/main/java/com/ldbc/driver/runtime/WorkloadStatusThread.java:134:148:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_c7e12d_2d1711src/main/java/com/ldbc/driver/workloads/ldbc/snb/interactive/db/DummyLdbcSnbInteractiveDb.java:137:142:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:ldbc-ldbc_driver_cfebf3_b21851src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:253:263:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_cfebf3_b21851src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:226:249:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_e735a9_a0cfe6src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:226:249:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_e735a9_a0cfe6src/main/java/com/ldbc/driver/runtime/executor/UniformWindowedOperationStreamExecutorServiceThread.java:253:263:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:ldbc-ldbc_driver_ec8b7d_79f318src/main/java/com/ldbc/driver/runtime/coordination/ThreadedQueuedCompletionTimeService.java:234:234:UG_SYNC_SET_UNSYNC_GET -#Null_Violation_Hunk:ldbc-ldbc_driver_ec8b7d_79f318src/main/java/com/ldbc/driver/runtime/coordination/ThreadedQueuedCompletionTimeService.java:181:181:UG_SYNC_SET_UNSYNC_GET -#Null_Violation_Hunk:ldbc-ldbc_driver_ec8b7d_79f318src/main/java/com/ldbc/driver/validation/DbValidationResult.java:214:220:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:LEDS-sincap-entities_2a3fbd_3024f8src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/relatorios/TotalDoacaoInstituicao.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:LEDS-sincap-entities_2a3fbd_3024f8src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cgt/AplRelatorio.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_477e17_b18244src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/DTO/ProcessoNotificacaoDTO.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:LEDS-sincap-entities_4eb004_cd7ee4src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/util/dataFactory/PacienteData.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_4eb004_cd7ee4src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/util/dataFactory/ResponsavelData.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:LEDS-sincap-entities_6190c0_bed22csrc/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/relatorios/TotalDoacaoInstituicao.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:LEDS-sincap-entities_687bf5_6fc7c2src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/util/dataFactory/CaptacaoData.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_687bf5_6fc7c2src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/util/dataFactory/ProcessoNotificacaoData.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:LEDS-sincap-entities_69e43e_8b9a01src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_69e43e_8b9a01src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_69e43e_8b9a01src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_69e43e_8b9a01src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_6adc1b_8dfb6csrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:16:16:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_6adc1b_8dfb6csrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:16:16:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_706d25_4570aasrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_706d25_4570aasrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_706d25_4570aasrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_706d25_4570aasrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_83a062_9977e8src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_83a062_9977e8src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:21:21:HE_INHERITS_EQUALS_USE_HASHCODE -#Illegal_Line_Position:LEDS-sincap-entities_8ba099_59fbbbsrc/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/relatorios/ObitoCardio.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_9eb393_fe8f4esrc/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/util/dataFactory/CaptacaoData.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_9eb393_fe8f4esrc/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/util/dataFactory/ProcessoNotificacaoData.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_a282f1_f7d8e4src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/relatorios/RelEntrevistaFamiliar.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:LEDS-sincap-entities_acb6ca_de9889src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:21:21:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_acb6ca_de9889src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:21:21:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_c27272_01b57bsrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_c27272_01b57bsrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_c27272_01b57bsrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_c27272_01b57bsrc/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:HE_INHERITS_EQUALS_USE_HASHCODE -#Illegal_Line_Position:LEDS-sincap-entities_e19d06_a843c9src/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/DTO/EntrevistaDTO.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:LEDS-sincap-entities_e69070_59fbbbsrc/main/java/br/ifes/leds/sincap/gerenciaNotificacao/cln/cdp/relatorios/RelEntrevistaFamiliar.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:LEDS-sincap-entities_e711e4_232617src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:LEDS-sincap-entities_e711e4_232617src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:22:22:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_e711e4_232617src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/InstituicaoNotificadora.java:10:10:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_f15599_4f19f6src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:21:21:HE_INHERITS_EQUALS_USE_HASHCODE -#Null_Violation_Hunk:LEDS-sincap-entities_f15599_4f19f6src/main/java/br/ifes/leds/sincap/controleInterno/cln/cdp/AnalistaCNCDO.java:21:21:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lemire-RoaringBitmap_f3ac3c_9bbdb6src/main/java/me/lemire/roaringbitmap/experiments/StarSchemaBenchmark.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:lennartj-jaxb2-maven-plugin_0bd1fe_a07f14src/main/java/org/codehaus/mojo/jaxb2/XjcMojo.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:lennartj-jaxb2-maven-plugin_0d0e31_981dd3src/main/java/org/codehaus/mojo/jaxb2/XjcMojo.java:631:641:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:lennartj-jaxb2-maven-plugin_0d0e31_981dd3src/main/java/org/codehaus/mojo/jaxb2/XjcMojo.java:649:659:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:lexicalscope-svm_7458b3_196a46src/main/java/com/lexicalscope/symb/vm/StackFrame.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:libetl-soundtransform_cb8748_3f4bb5src/main/java/org/toilelibre/libe/soundtransform/infrastructure/service/audioformat/WavAudioFormatParser.java:13:43:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Illegal_Line_Position:liferay-liferay-maven-support_857591_e4a1adplugins/liferay-maven-plugin/src/main/java/com/liferay/maven/plugins/AbstractLiferayMojo.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:lightblue-platform-lightblue-core_021e10_1160e7util/src/main/java/com/redhat/lightblue/util/Path.java:67:172:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_1160e7_458c9ametadata/src/main/java/com/redhat/lightblue/metadata/parser/ParserRegistry.java:27:27:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lightblue-platform-lightblue-core_1becc2_1d9d53config/src/main/java/com/redhat/lightblue/config/DataSourcesConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:lightblue-platform-lightblue-core_1becc2_1d9d53config/src/main/java/com/redhat/lightblue/config/LightblueFactory.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:lightblue-platform-lightblue-core_356331_69ac15query-api/src/main/java/com/redhat/lightblue/query/ArrayMatchExpression.java:41:101:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_356331_69ac15query-api/src/main/java/com/redhat/lightblue/query/FieldComparisonExpression.java:43:103:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_356331_69ac15query-api/src/main/java/com/redhat/lightblue/query/UnaryLogicalExpression.java:37:95:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_356331_69ac15query-api/src/main/java/com/redhat/lightblue/query/ValueComparisonExpression.java:47:108:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lightblue-platform-lightblue-core_3eccdb_954742config/src/main/java/com/redhat/lightblue/config/DataSourcesConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:lightblue-platform-lightblue-core_3eccdb_954742crud/src/main/java/com/redhat/lightblue/crud/Factory.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:lightblue-platform-lightblue-core_3eccdb_954742crud/src/main/java/com/redhat/lightblue/interceptor/InterceptorManager.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:lightblue-platform-lightblue-core_69ac15_67cbfbquery-api/src/main/java/com/redhat/lightblue/query/ArrayQueryMatchProjection.java:30:52:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_69ac15_67cbfbquery-api/src/main/java/com/redhat/lightblue/query/ArrayRangeProjection.java:32:65:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_69ac15_67cbfbquery-api/src/main/java/com/redhat/lightblue/query/ProjectionList.java:40:86:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_75f478_4b9f6dquery-api/src/main/java/com/redhat/lightblue/query/CompositeSortKey.java:40:92:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_75f478_4b9f6dquery-api/src/main/java/com/redhat/lightblue/query/SortKey.java:37:99:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:lightblue-platform-lightblue-core_75f478_4b9f6dquery-api/src/main/java/com/redhat/lightblue/query/Value.java:41:118:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lightblue-platform-lightblue-core_7f462f_015fc1util/src/main/java/com/redhat/lightblue/util/Path.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:lightblue-platform-lightblue-core_8c6551_c68710lightblue-rdbms/crud/src/main/java/com/redhat/lightblue/crud/rdbms/OracleTranslator.java:55:55:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:lightblue-platform-lightblue-core_9f4372_1d7871metadata/src/main/java/com/redhat/lightblue/metadata/SimpleArrayElement.java:28:49:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lightblue-platform-lightblue-core_ad50da_b911d4config/src/main/java/com/redhat/lightblue/config/DataSourcesConfiguration.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:lightblue-platform-lightblue-core_ad50da_b911d4config/src/main/java/com/redhat/lightblue/config/LightblueFactory.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:lightblue-platform-lightblue-core_c95ac8_40f0c1lightblue-rdbms/crud/src/main/java/com/redhat/lightblue/crud/rdbms/RDBMSContext.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:lkroesen-BubbleBobble_248bb7_0ddc9csrc/main/java/website/frontrow/Board/Unit.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:lkroesen-BubbleBobble_9c4f06_845786src/main/java/website/frontrow/board/Unit.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:lkroesen-BubbleBobble_9c4f06_845786src/main/java/website/frontrow/board/Unit.java:88:88:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:lkroesen-BubbleBobble_9d17cb_7da454src/main/java/website/frontrow/board/Unit.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:lkroesen-BubbleBobble_9d17cb_7da454src/main/java/website/frontrow/board/Unit.java:22:22:NM_METHOD_NAMING_CONVENTION -#Illegal_Line_Position:lkroesen-BubbleBobble_be1350_05fedfsrc/main/java/website/frontrow/Game.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:lkroesen-BubbleBobble_cacac9_9656d4src/main/java/website/frontrow/board/Unit.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:lkroesen-BubbleBobble_cacac9_9656d4src/main/java/website/frontrow/board/Unit.java:88:88:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:locationtech-spatial4j_fe24dc_433adfsrc/main/java/com/spatial4j/core/io/WKTShapeParser.java:300:435:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:lrozenblyum-chess_526c4d_14ab03src/main/java/com/leokom/chess/gui/winboard/WinboardPlayer.java:14:14:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:lviggiano-owner_2e1390_2f4caesrc/main/java/org/aeonbits/owner/ConfigURLFactory.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:lviggiano-owner_2e1390_2f4caesrc/main/java/org/aeonbits/owner/ConfigURLFactory.java:23:47:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lviggiano-owner_99f038_85ad36owner/src/main/java/org/aeonbits/owner/loaders/XMLLoader.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:lviggiano-owner_bb8d83_472770owner/src/main/java/org/aeonbits/owner/loaders/PropertiesLoader.java:22:33:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:lviggiano-owner_d99778_a0a724src/main/java/org/aeonbits/owner/event/TransactionalPropertyChangeListener.java:-1:-1:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Illegal_Line_Position:maartentbm-ContextPL1_5ebc69_aee5c1src/main/java/nl/tudelft/ti2806/pl1/DGraph/BasicDNode.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:maartentbm-ContextPL1_6a09bb_ac18e1src/main/java/nl/tudelft/ti2806/pl1/gui/contentpane/GraphPanel.java:462:495:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:maartentbm-ContextPL1_7779ae_cecb83src/main/java/nl/tudelft/ti2806/pl1/gui/contentpane/Content.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:maartentbm-ContextPL1_9141b0_457ec1src/main/java/nl/tudelft/ti2806/pl1/gui/contentpane/GraphPanel.java:627:644:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:maartentbm-ContextPL1_98619c_7b1c1fsrc/main/java/nl/tudelft/ti2806/pl1/gui/contentpane/GraphPanel.java:626:643:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:maartentbm-ContextPL1_a14b22_5843b2src/main/java/nl/tudelft/ti2806/pl1/geneAnnotation/RefGeneCompare.java:14:21:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:maartentbm-ContextPL1_f2f13b_45e554src/main/java/nl/tudelft/ti2806/pl1/gui/contentpane/GraphPanel.java:626:643:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mafagafogigante-dungeon_0e1336_7d4a76src/main/java/org/dungeon/util/Percentage.java:36:54:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mafagafogigante-dungeon_1377cf_441001src/main/java/org/dungeon/entity/Visibility.java:31:36:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mafagafogigante-dungeon_41abd6_a4be99src/main/java/org/dungeon/io/FileLastModifiedComparator.java:31:35:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:mafagafogigante-dungeon_624972_0324d4src/main/java/org/dungeon/stats/ExplorationStatistics.java:37:128:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mafagafogigante-dungeon_6832e1_5b165asrc/main/java/org/dungeon/game/GameState.java:51:222:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mafagafogigante-dungeon_6b8078_6d0558src/main/java/org/dungeon/game/GameState.java:51:217:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mafagafogigante-dungeon_99e46c_3a1b22src/main/java/org/dungeon/entity/Visibility.java:31:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mafagafogigante-dungeon_9e06b3_7e685esrc/main/java/org/mafagafogigante/dungeon/stats/ExplorationStatisticsEntry.java:33:66:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:mafagafogigante-dungeon_a38a92_b2fe78src/main/java/org/dungeon/game/GameData.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:mafagafogigante-dungeon_af643b_c60ff8src/main/java/org/dungeon/game/GameData.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:mafagafogigante-dungeon_b2e6c6_5c0396src/main/java/org/dungeon/io/FileLastModifiedComparator.java:31:40:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:mafagafogigante-dungeon_b9a1c6_66e9e8src/main/java/org/dungeon/game/GameState.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:mafagafogigante-dungeon_e20f68_7c2d68src/main/java/org/dungeon/game/GameData.java:-1:-1:MS_CANNOT_BE_FINAL -#Illegal_Line_Position:mafagafogigante-dungeon_e40e2a_169c11src/main/java/org/dungeon/game/GameData.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:mafagafogigante-dungeon_e7efde_b32ab0src/main/java/org/dungeon/game/GameData.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:mafagafogigante-dungeon_e9ac18_c367f7src/main/java/org/dungeon/game/GameData.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:mafagafogigante-dungeon_eff3b5_69508fsrc/main/java/org/dungeon/entity/creatures/AttackAlgorithmId.java:25:27:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:mafagafogigante-dungeon_fd83df_eff3b5src/main/java/org/dungeon/entity/creatures/AttackAlgorithmId.java:25:27:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:mafagafogigante-dungeon_fdedc4_d53821src/main/java/org/dungeon/util/Constants.java:-1:-1:STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE -#Null_Violation_Hunk:marklogic-java-client-api_0d733f_b44c7csrc/main/java/com/marklogic/client/query/StructuredQueryBuilder.java:1738:1786:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:marklogic-java-client-api_51f056_93ff22src/main/java/com/marklogic/client/impl/GraphManagerImpl.java:405:409:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:marklogic-java-client-api_51f056_93ff22src/main/java/com/marklogic/client/impl/GraphManagerImpl.java:405:409:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:marklogic-java-client-api_565b38_2c1dc7src/main/java/com/marklogic/client/impl/QueryManagerImpl.java:342:412:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:marklogic-java-client-api_a96ff0_6dad85src/main/java/com/marklogic/client/io/DocumentMetadataHandle.java:134:240:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:marklogic-java-client-api_a96ff0_6dad85src/main/java/com/marklogic/client/io/DocumentMetadataHandle.java:134:240:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:marklogic-java-client-api_a96ff0_6dad85src/main/java/com/marklogic/client/io/DocumentMetadataHandle.java:134:240:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:marklogic-java-client-api_aae966_797ec5src/main/java/com/marklogic/client/query/StructuredQueryBuilder.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:marklogic-java-client-api_b84b38_4e35d5src/main/java/com/marklogic/client/io/SearchHandle.java:469:481:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:marklogic-java-client-api_e41113_117b4csrc/main/java/com/marklogic/client/io/SearchHandle.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:marklogic-java-client-api_e41113_117b4csrc/main/java/com/marklogic/client/io/TuplesHandle.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:marklogic-java-client-api_f41a0e_0de5d3src/main/java/com/marklogic/client/config/QueryOptions.java:2451:2451:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:marklogic-java-client-api_f41a0e_0de5d3src/main/java/com/marklogic/client/config/QueryOptions.java:2848:2848:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:marklogic-java-client-api_f41a0e_0de5d3src/main/java/com/marklogic/client/config/QueryOptions.java:1768:1769:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:marklogic-java-client-api_f41a0e_0de5d3src/main/java/com/marklogic/client/config/QueryOptions.java:2465:2465:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:marklogic-java-client-api_f41a0e_0de5d3src/main/java/com/marklogic/client/config/QueryOptions.java:2978:2978:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:marklogic-java-client-api_fb4400_c99c71src/main/java/com/marklogic/client/config/search/impl/ConstraintImpl.java:18:54:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:marschraner-svm_2e18c6_4d9f9bsrc/main/java/ch/metzenthin/svm/domain/commands/ValidateSchuelerCommand.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:marschraner-svm_89f00e_e99c78src/main/java/ch/metzenthin/svm/ui/control/AngehoerigerController.java:91:91:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:marschraner-svm_89f00e_e99c78src/main/java/ch/metzenthin/svm/ui/control/SchuelerController.java:212:212:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:marschraner-svm_b9e085_357b23src/main/java/ch/metzenthin/svm/ui/control/AngehoerigerController.java:91:91:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:marschraner-svm_b9e085_357b23src/main/java/ch/metzenthin/svm/ui/control/SchuelerController.java:212:212:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:marschraner-svm_c702f6_cc2d29src/main/java/ch/metzenthin/svm/common/utils/StringNumberComparator.java:8:53:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:marschraner-svm_ca5485_a97be6src/main/java/ch/metzenthin/svm/ui/components/SchuelerBereitsInDatenbankDialog.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:martiner-gooddata-java_4576bc_3acd35src/main/java/com/gooddata/AbstractService.java:119:166:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:martiner-gooddata-java_f39f14_0d65fasrc/main/java/com/gooddata/AbstractService.java:119:166:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:marylinh-ESAPI_JAVA_ALL_02f6e0_5a39f0src/main/java/org/owasp/esapi/Encoder.java:116:116:MS_MUTABLE_ARRAY -#Null_Violation_Hunk:marylinh-ESAPI_JAVA_ALL_02f6e0_5a39f0src/main/java/org/owasp/esapi/Encoder.java:117:117:MS_MUTABLE_ARRAY -#Null_Violation_Hunk:marylinh-ESAPI_JAVA_ALL_0b94bc_d6915fsrc/main/java/org/owasp/esapi/SafeFile.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:marylinh-ESAPI_JAVA_ALL_318c83_ce7767src/main/java/org/owasp/esapi/reference/DefaultUser.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:marylinh-ESAPI_JAVA_ALL_692c16_3c6e1bsrc/main/java/org/owasp/esapi/crypto/CipherSpec.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:marylinh-ESAPI_JAVA_ALL_ab1fa1_c505a1src/main/java/org/owasp/esapi/reference/FileBasedAuthenticator.java:224:236:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:marylinh-ESAPI_JAVA_ALL_fb3cde_2ba17fsrc/main/java/org/owasp/esapi/SafeFile.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:marytts-marytts_b443b5_bd7625src/test/java/marytts/tests/junit4/ByteStringTranslatorTest.java:123:123:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:maxymania-jxta-jxse_777caa_7ec2bdsrc/main/java/net/jxta/impl/endpoint/tls/TlsTransport.java:418:418:IS2_INCONSISTENT_SYNC -#Null_Violation_Hunk:maxymania-jxta-jxse_bf66fc_6e9cebsrc/main/java/net/jxta/impl/endpoint/tcp/TcpTransport.java:590:590:IS2_INCONSISTENT_SYNC -#Null_Violation_Hunk:maxymania-jxta-jxse_dcfde4_379efcsrc/main/java/net/jxta/document/Advertisement.java:131:131:IS2_INCONSISTENT_SYNC -#Null_Violation_Hunk:maxymania-jxta-jxse_dcfde4_379efcsrc/main/java/net/jxta/document/Advertisement.java:134:134:IS2_INCONSISTENT_SYNC -#Null_Violation_Hunk:maxymania-jxta-jxse_dcfde4_379efcsrc/main/java/net/jxta/impl/endpoint/WireFormatMessageBinary.java:1287:1396:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_045797_d4228esrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_045797_d4228esrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_057d69_1ccb4esrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_057d69_1ccb4esrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_1b464d_6ebceasrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_1b464d_6ebceasrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_2d9f7b_28db22src/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_2d9f7b_28db22src/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_57e397_da326asrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_57e397_da326asrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/CoreFiltersTest.java:110:115:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/CoreTokenParsersTest.java:89:94:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:139:140:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:115:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:135:136:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:143:144:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:127:128:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6e35aa_eab913src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:131:132:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_6f7b1f_bde07csrc/main/java/com/mitchellbosecke/pebble/node/expression/NodeExpressionBinary.java:23:23:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_6f7b1f_bde07csrc/main/java/com/mitchellbosecke/pebble/node/expression/NodeExpressionBinary.java:22:22:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_7e0046_6e5994src/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_7e0046_6e5994src/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_a652e1_301943src/main/java/com/mitchellbosecke/pebble/extension/i18n/i18nFunction.java:20:40:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/CoreFiltersTest.java:110:115:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/CoreTokenParsersTest.java:89:94:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:139:140:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:143:144:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:135:136:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:127:128:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:131:132:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_afe8db_787529src/test/java/com/mitchellbosecke/pebble/GetAttributeTest.java:115:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mbosecke-pebble_c13417_2396b4src/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_c13417_2396b4src/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_d6a410_549bdesrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:20:20:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mbosecke-pebble_d6a410_549bdesrc/main/java/com/mitchellbosecke/pebble/extension/AbstractNodeVisitor.java:27:27:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:mebigfatguy-fb-contrib_1555c2_7c04d4src/com/mebigfatguy/fbcontrib/detect/ImmatureClass.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:mebigfatguy-fb-contrib_2040c3_96f915src/com/mebigfatguy/fbcontrib/detect/CopiedOverriddenMethod.java:373:388:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mebigfatguy-fb-contrib_86166f_0614eesrc/com/mebigfatguy/fbcontrib/detect/LiteralStringComparison.java:221:240:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mebigfatguy-fb-contrib_adaf6a_72ef2fsrc/com/mebigfatguy/fbcontrib/detect/FieldCouldBeLocal.java:439:505:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mebigfatguy-fb-contrib_b72e07_126e18src/com/mebigfatguy/fbcontrib/detect/OverlyPermissiveMethod.java:132:132:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:mebigfatguy-fb-contrib_d28181_e732aesrc/com/mebigfatguy/fbcontrib/detect/LiteralStringComparison.java:221:240:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mebigfatguy-fb-contrib_ed3c9f_72b7ddsrc/com/mebigfatguy/fbcontrib/utils/Values.java:312:312:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:mebigfatguy-fb-contrib_ed3c9f_72b7ddsrc/com/mebigfatguy/fbcontrib/utils/Values.java:237:237:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:metamx-java-util_565992_70db32src/main/java/com/metamx/common/parsers/DelimitedParser.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:minusone13-InvoicingSystem_045a3b_bbb1b9src/main/java/presentation/saleui/JPmanageBills2.java:397:636:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:minusone13-InvoicingSystem_045a3b_bbb1b9src/main/java/presentation/saleui/JPmanageCustomer.java:634:695:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_08152e_0ee836src/main/java/presentation/financialui/JPmanageBills2.java:241:441:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_0bcb6a_f86c0bsrc/main/java/presentation/financialui/InitialInfoPanel.java:73:73:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_0bcb6a_f86c0bsrc/main/java/presentation/financialui/InitialInfoPanel.java:66:73:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_111daa_a1d2b8src/main/java/presentation/commodityui/JPmanageBills2.java:356:464:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_111daa_a1d2b8src/main/java/presentation/saleui/JPmanageBills2.java:392:611:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_111daa_a1d2b8src/main/java/presentation/saleui/JPmanageCustomer.java:258:415:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:minusone13-InvoicingSystem_11a8fe_94ce08src/main/java/po/SaleBackSheetPO.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_11a8fe_94ce08src/main/java/presentation/managerui/JPBill.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/customerbl/StubCustomer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/salebillbl/salebillController.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/salebillbl/salebillList.java:3:3:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/salebillbl/StubPurBackSheet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/salebillbl/StubPurSheet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/salebillbl/StubSaleBackSheet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/businesslogic/salebillbl/StubSaleSheet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_191470_9607bdsrc/main/java/po/CustomerPO.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_2b7622_624a17src/main/java/vo/VO.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_34ac0d_94ce08src/main/java/po/PurBackSheetPO.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:minusone13-InvoicingSystem_360e0e_32caeasrc/main/java/businesslogic/salebillbl/StubSale.java:65:65:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_3838b2_f33e79src/main/java/presentation/commodityui/StockCheckPanel.java:207:449:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_39d1f4_813ddfsrc/main/java/presentation/managerui/JPpassBill2.java:334:504:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_3b8026_2b4e06src/main/java/presentation/saleui/JPmanageBills2.java:397:636:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:minusone13-InvoicingSystem_3b8026_2b4e06src/main/java/presentation/saleui/JPmanageCustomer.java:634:695:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_4756fc_bfb244src/main/java/businesslogic/commoditybl/StubCategory.java:50:50:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_47f4de_0b4427src/main/java/presentation/commodityui/StockManagerDriver.java:10:10:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:minusone13-InvoicingSystem_4ace6d_96265bsrc/main/java/po/CommodityPO.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_523a4c_ed2410src/main/java/presentation/commodityui/JPmanageBills2.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_53ffb6_11c3e2src/main/java/presentation/commodityui/StockCheckPanel.java:207:449:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_5745ee_65d64csrc/main/java/presentation/financialui/InitialInfoPanel.java:73:73:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_5745ee_65d64csrc/main/java/presentation/financialui/InitialInfoPanel.java:66:73:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_5b233a_6be038src/main/java/presentation/userui/JPmanageUser.java:254:333:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6038a2_ffc29dsrc/main/java/presentation/commodityui/JPtreeContent.java:113:120:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_65d614_3479c7src/main/java/presentation/commodityui/JPtreeContent.java:113:120:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_667c1d_1a5283src/main/java/businesslogic/customerbl/Customer.java:67:67:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:minusone13-InvoicingSystem_667c1d_1a5283src/main/java/businesslogic/customerbl/customerList.java:7:7:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_667c1d_1a5283src/main/java/businesslogic/customerbl/customerList.java:7:7:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:minusone13-InvoicingSystem_6951f1_6adf51src/main/java/presentation/financialui/InitialInfoPanel.java:66:73:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6951f1_6adf51src/main/java/presentation/financialui/InitialInfoPanel.java:73:73:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_6a07d7_526f82src/main/java/presentation/commodityui/JPtreeContent.java:113:120:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6be038_111daasrc/main/java/presentation/financialui/JPmanageAccount.java:279:370:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6be038_111daasrc/main/java/presentation/financialui/JPmanageAccount.java:486:547:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6be038_111daasrc/main/java/presentation/userui/JPmanageUser.java:478:539:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6c2370_8bc71esrc/main/java/presentation/managerui/JPpassBill2.java:334:504:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_6e1fb8_73a4d1src/main/java/data/commoditydata/StubCommodityList.java:6:6:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:minusone13-InvoicingSystem_6ec4a6_b82993src/main/java/presentation/commodityui/JPManagerComOfStock.java:192:308:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:minusone13-InvoicingSystem_73110d_671c5asrc/main/java/po/PO.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:minusone13-InvoicingSystem_73a4d1_dbdc77src/main/java/data/commoditydata/StubCommodityList.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:minusone13-InvoicingSystem_76b873_64d897src/main/java/businesslogic/commoditybl/StubCategory.java:50:50:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_7914cf_31587fsrc/main/java/presentation/managerui/JPpassBill2.java:334:504:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_7fc3a8_25b43fsrc/main/java/presentation/financialui/BusinessProcessPanel.java:784:1089:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_7fc3a8_25b43fsrc/main/java/presentation/financialui/SaleDetailPanel.java:278:586:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_8c52ce_153e17src/main/java/presentation/saleui/JPmanageBills2.java:397:636:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:minusone13-InvoicingSystem_8c52ce_153e17src/main/java/presentation/saleui/JPmanageCustomer.java:634:695:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_8e977a_d73f22src/main/java/presentation/commodityui/JPtreeContent.java:113:120:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_8f528b_29fd9fsrc/main/java/presentation/managerui/JPBill.java:309:335:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_910050_f3e674src/main/java/presentation/userui/JPmanageUser.java:254:333:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_919c01_c3a32esrc/main/java/presentation/commodityui/JPmanageBills2.java:356:464:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_919c01_c3a32esrc/main/java/presentation/saleui/JPmanageBills2.java:392:611:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_919c01_c3a32esrc/main/java/presentation/saleui/JPmanageCustomer.java:258:415:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_930f4b_ce2103src/main/java/vo/financialBillVO/ReceiptVO.java:91:91:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:minusone13-InvoicingSystem_99e086_8fd37bsrc/main/java/po/PO.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:minusone13-InvoicingSystem_a03082_ba459fsrc/main/java/presentation/managerui/JPmanagerStrategy2.java:263:535:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_a03f1e_91352fsrc/main/java/presentation/financialui/InitialInfoPanel.java:56:63:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_a03f1e_91352fsrc/main/java/presentation/financialui/InitialInfoPanel.java:63:63:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_aff074_76b873src/main/java/presentation/financialui/JPmanageBills2.java:241:441:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_b7175d_6353c6src/main/java/presentation/managerui/JPpassBill2.java:334:504:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_bf5f15_ce32acsrc/main/java/businesslogic/commoditybl/StubCategory.java:50:50:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_bf5f15_ce32acsrc/main/java/presentation/financialui/JPmanageBills2.java:241:441:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_bfb244_64d897src/main/java/presentation/financialui/JPmanageBills2.java:241:441:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_bfd387_f6bb97src/main/java/businesslogic/strategybl/StubStrategyPool.java:75:75:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_bfd387_f6bb97src/main/java/businesslogic/strategybl/StubStrategyPool.java:79:79:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_bfd387_f6bb97src/main/java/businesslogic/strategybl/StubStrategyPool.java:71:71:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_c37a04_903e05src/main/java/businesslogic/managerbl/StubManager.java:37:37:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_c37a04_903e05src/main/java/businesslogic/managerbl/StubManager.java:61:61:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_c37a04_903e05src/main/java/businesslogic/managerbl/StubManager.java:57:57:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_c37a04_903e05src/main/java/businesslogic/managerbl/StubManager.java:53:53:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_c7aa53_6a87b8src/main/java/presentation/financialui/JPmanageAccount.java:279:370:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_c7aa53_6a87b8src/main/java/presentation/financialui/JPmanageAccount.java:486:547:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_c7aa53_6a87b8src/main/java/presentation/userui/JPmanageUser.java:478:539:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:minusone13-InvoicingSystem_cfa646_94c68csrc/main/java/businesslogic/examinebl/StubBillPool.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:minusone13-InvoicingSystem_d26296_8c52cesrc/main/java/presentation/commodityui/JPmanageBills2.java:356:464:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_d26296_8c52cesrc/main/java/presentation/saleui/JPmanageBills2.java:392:611:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_d26296_8c52cesrc/main/java/presentation/saleui/JPmanageCustomer.java:258:415:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_d422c1_169427src/main/java/vo/financialBillVO/ReceiptVO.java:91:91:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_d7ccc1_c19d89src/main/java/businesslogic/salebillbl/StubSale.java:65:65:NM_METHOD_NAMING_CONVENTION -#Null_Violation_Hunk:minusone13-InvoicingSystem_d8e94a_9ca421src/main/java/vo/financialBillVO/ReceiptVO.java:91:91:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:minusone13-InvoicingSystem_f3e674_b691ffsrc/main/java/presentation/financialui/JPmanageAccount.java:279:370:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_f3e674_b691ffsrc/main/java/presentation/financialui/JPmanageAccount.java:486:547:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_f3e674_b691ffsrc/main/java/presentation/userui/JPmanageUser.java:478:539:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:minusone13-InvoicingSystem_f6a518_afdb4bsrc/main/java/vo/financialBillVO/ReceiptVO.java:91:91:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:minusone13-InvoicingSystem_f7ae52_8f53e3src/main/java/businesslogic/salebillbl/salebillController.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:mkovatsc-Californium_0e9a09_0e0ae2californium/src/main/java/ch/ethz/inf/vs/californium/coap/registries/OptionNumberRegistry.java:47:48:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:mkovatsc-Californium_1ec0f5_90a109californium/src/test/java/ch/ethz/inf/vs/californium/test/lockstep/BlockwiseServerSide.java:594:594:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:mkovatsc-Californium_42eedf_a63ee5californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/resources/ProxyCacheResource.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:mkovatsc-Californium_42eedf_a63ee5californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/resources/ProxyCacheResource.java:358:358:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mkovatsc-Californium_484cf7_7b4f54californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/ProxyEndpoint.java:219:242:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mkovatsc-Californium_4cfc94_04600bcalifornium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:53:53:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_4cfc94_04600bcalifornium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:37:37:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_4cfc94_04600bcalifornium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:58:58:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_4cfc94_04600bcalifornium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:48:48:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_5bf1a0_3da6a7californium/src/main/java/ch/ethz/inf/vs/californium/coap/OptionNumberRegistry.java:74:79:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:mkovatsc-Californium_6d199b_84768ecf-browser/src/main/java/ch/ethz/inf/vs/californium/examples/GUIClient.java:247:257:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mkovatsc-Californium_735237_4d0822californium/src/test/java/ch/ethz/inf/vs/californium/test/lockstep/ObserveServerSide.java:255:255:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_86d96e_367d3acalifornium/src/test/java/ch/ethz/inf/vs/californium/test/lockstep/BlockwiseServerSide.java:594:594:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_8a27d4_035716californium/src/main/java/ch/ethz/inf/vs/californium/coap/Message.java:106:110:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:mkovatsc-Californium_a42a48_fc751ccf-plugtest-client/src/main/java/ch/ethz/inf/vs/californium/examples/PlugtestClient.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:mkovatsc-Californium_c3693c_f9ea4ccf-plugtest-client/src/main/java/ch/ethz/inf/vs/californium/examples/PlugtestClient.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:mkovatsc-Californium_d3b3bb_f45660californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:37:37:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_d3b3bb_f45660californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:48:48:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_d3b3bb_f45660californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:53:53:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_d3b3bb_f45660californium/src/main/java/ch/ethz/inf/vs/californium/endpoint/RDResource.java:58:58:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:mkovatsc-Californium_d77979_40eac2cf-plugtest-client/src/main/java/ch/ethz/inf/vs/californium/examples/block/TD_COAP_BLOCK_01.java:48:81:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_3ddb4e_44ea3dsrc/main/java/org/codehaus/mojo/nbm/CreateNetbeansFileStructureMojo.java:107:107:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:mojohaus-nbm-maven-plugin_40c5a1_054d80src/main/java/org/codehaus/mojo/nbm/CreateClusterMojo.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:mojohaus-nbm-maven-plugin_40c5a1_054d80src/main/java/org/codehaus/mojo/nbm/RunNetBeansMojo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_b97659_3392e5src/main/java/org/codehaus/mojo/nbm/AbstractNbmMojo.java:388:388:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_bdf3fe_0fd11csrc/main/java/org/codehaus/mojo/nbm/AbstractNbmMojo.java:464:482:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_bdf3fe_0fd11csrc/main/java/org/codehaus/mojo/nbm/CreateClusterAppMojo.java:638:646:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_bdf3fe_0fd11csrc/main/java/org/codehaus/mojo/nbm/PopulateRepositoryMojo.java:969:1016:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_bdf3fe_0fd11csrc/main/java/org/codehaus/mojo/nbm/PopulateRepositoryMojo.java:1021:1101:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_dac289_8090edsrc/main/java/org/codehaus/mojo/nbm/CreateNetbeansFileStructure.java:96:96:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_f71b29_d1057dsrc/main/java/org/codehaus/mojo/nbm/CreateNetbeansFileStructure.java:118:118:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:mojohaus-nbm-maven-plugin_fa517c_9703bcsrc/main/java/org/codehaus/mojo/nbm/CreateNetbeansFileStructureMojo.java:111:111:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:movsim-movsim_0d3876_e07086src/main/java/org/movsim/simulator/roadSection/impl/OnrampMobilImpl.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:movsim-movsim_371f60_fae14esrc/main/java/org/movsim/simulator/Simulator.java:232:232:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:movsim-movsim_4202b6_b271a9src/main/java/org/movsim/simulator/roadSection/impl/OnrampMobilImpl.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:movsim-movsim_4202b6_b271a9src/main/java/org/movsim/simulator/vehicles/lanechanging/impl/LaneChangingModelImpl.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:movsim-movsim_8841f5_f9f52fsrc/main/java/org/movsim/consumption/impl/EngineModelImpl.java:278:278:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:movsim-movsim_92717c_c45a8csrc/main/java/org/movsim/simulator/roadSection/impl/OnrampMobilImpl.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:mrniko-netty-socketio_1ef006_50bdf7src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:98:152:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mrniko-netty-socketio_1ef006_50bdf7src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:52:93:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mrniko-netty-socketio_1ef006_50bdf7src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:157:192:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mrniko-netty-socketio_1ef006_50bdf7src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:157:192:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:mrniko-netty-socketio_2525d5_f7da1asrc/main/java/com/corundumstudio/socketio/protocol/JacksonJsonSupport.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:mrniko-netty-socketio_2525d5_f7da1asrc/main/java/com/corundumstudio/socketio/protocol/JacksonJsonSupport.java:56:99:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:mrniko-netty-socketio_2d34e8_a20ce2src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:52:93:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mrniko-netty-socketio_2d34e8_a20ce2src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:98:152:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mrniko-netty-socketio_2d34e8_a20ce2src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:157:192:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:mrniko-netty-socketio_2d34e8_a20ce2src/main/java/com/corundumstudio/socketio/parser/JacksonJsonSupport.java:157:192:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:mrniko-netty-socketio_477336_3924d2src/main/java/com/corundumstudio/socketio/ack/AckManager.java:35:56:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:mrniko-netty-socketio_5e9ffb_512968src/main/java/com/corundumstudio/socketio/protocol/JacksonJsonSupport.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:mrniko-netty-socketio_5e9ffb_512968src/main/java/com/corundumstudio/socketio/protocol/JacksonJsonSupport.java:55:98:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:mrniko-netty-socketio_5e9ffb_512968src/main/java/com/corundumstudio/socketio/protocol/JacksonJsonSupport.java:103:158:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:mrniko-netty-socketio_5e9ffb_512968src/main/java/com/corundumstudio/socketio/protocol/JacksonJsonSupport.java:163:202:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:mrniko-netty-socketio_623c9f_a0d2b1src/main/java/com/corundumstudio/socketio/transport/WebSocketTransport.java:41:41:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:mrniko-redisson_7855cd_b0822fsrc/main/java/org/redisson/connection/ClusterConnectionManager.java:159:159:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:mrniko-redisson_925f14_2b06casrc/main/java/org/redisson/RedissonTopic.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:mrniko-redisson_f4424a_e4a325src/main/java/org/redisson/reactive/RedissonListReactive.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:mrniko-redisson_f4424a_e4a325src/main/java/org/redisson/reactive/RedissonSetReactive.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:msokolov-lux_019449_c246dasrc/main/java/lux/index/analysis/XmlTextTokenStream.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:msokolov-lux_136152_d9fef1src/main/java/lux/solr/LuxUpdateProcessor.java:146:151:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_1406a5_8b7895src/main/java/lux/api/QueryStats.java:39:39:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:msokolov-lux_15677c_4588e3src/main/java/lux/index/field/PathOccurrenceField.java:32:84:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_1fce3f_ad1259src/main/java/lux/functions/LuxFunctionLibrary.java:16:29:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_1fce3f_ad1259src/main/java/lux/index/field/PathOccurrenceField.java:32:84:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_309ad8_fb6157src/main/java/lux/saxon/LuxSearch.java:153:188:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_309ad8_fb6157src/main/java/lux/saxon/LuxSearch.java:153:188:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:msokolov-lux_3ac888_5408eesrc/main/java/lux/index/analysis/XmlTextTokenStream.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:msokolov-lux_4a45b1_f47459src/main/java/lux/Compiler.java:225:228:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_4d4791_ad1259src/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_4d4791_ad1259src/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_4d4791_ad1259src/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:msokolov-lux_60f4ba_af3c39src/main/java/lux/index/field/QNameTextTokenStream.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:msokolov-lux_60f4ba_af3c39src/main/java/lux/index/XmlIndexer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:msokolov-lux_610c03_e392dbsrc/main/java/lux/lucene/SurroundBoolean.java:10:25:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_610c03_e392dbsrc/main/java/lux/lucene/SurroundSpanQuery.java:17:48:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:msokolov-lux_610c03_e392dbsrc/main/java/lux/XPathQuery.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:msokolov-lux_64772c_1dd835src/main/java/lux/solr/SolrIndexConfig.java:202:210:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_64772c_1dd835src/main/java/lux/solr/SolrIndexConfig.java:219:225:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_692a67_7e3f85src/main/java/lux/solr/SolrIndexConfig.java:222:229:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_739098_019449src/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_739098_019449src/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_739098_019449src/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_7b9d9c_e4c823src/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_7b9d9c_e4c823src/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_7b9d9c_e4c823src/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_7e6180_d4f7fesrc/main/java/lux/index/analysis/QNameTokenFilter.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:msokolov-lux_80eb4b_448cbesrc/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_80eb4b_448cbesrc/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_80eb4b_448cbesrc/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_8b85f7_ec3933src/main/java/lux/api/QueryStats.java:35:35:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:msokolov-lux_96e484_366518src/main/java/lux/solr/SolrIndexConfig.java:222:229:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_b37235_617200src/main/java/lux/functions/FieldValues.java:92:145:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_b37235_617200src/main/java/lux/functions/FieldValues.java:92:145:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_b37235_617200src/main/java/lux/functions/FieldValues.java:92:145:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_b37235_617200src/main/java/lux/functions/LuxFunctionLibrary.java:16:29:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_b400fd_746973src/main/java/lux/solr/SolrIndexConfig.java:222:229:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_b7b96e_e177fdsrc/main/java/lux/api/QueryStats.java:118:118:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:msokolov-lux_b7b96e_e177fdsrc/main/java/lux/api/QueryStats.java:116:116:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:msokolov-lux_b7b96e_e177fdsrc/main/java/lux/saxon/LuxSearch.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:msokolov-lux_b7b96e_e177fdsrc/main/java/lux/saxon/XdmResultSet.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:msokolov-lux_b7b96e_e177fdsrc/main/java/lux/saxon/XdmResultSet.java:11:24:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_bc6c90_e4c823src/main/java/lux/functions/Count.java:27:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_bc6c90_e4c823src/main/java/lux/functions/Exists.java:27:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_c3bbf7_6464fbsrc/main/java/lux/functions/Count.java:27:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_c3bbf7_6464fbsrc/main/java/lux/functions/Exists.java:27:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_cdae07_cd4344src/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_cdae07_cd4344src/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_cdae07_cd4344src/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_d27d0d_bd7b6esrc/main/java/lux/api/QueryStats.java:142:142:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:msokolov-lux_d296c2_a92503src/main/java/lux/solr/SolrIndexConfig.java:347:354:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_d90442_2234cdsrc/main/java/lux/index/field/PathValueTokenStream.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:msokolov-lux_d90442_2234cdsrc/main/java/lux/solr/XmlUpdateProcessor.java:116:123:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_d9fe44_e15e4fsrc/main/java/lux/solr/SolrIndexConfig.java:347:354:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_d9fe44_f7af33src/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_d9fe44_f7af33src/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_d9fe44_f7af33src/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_da16d2_69a86bsrc/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_da16d2_69a86bsrc/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_da16d2_69a86bsrc/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_e53528_2b8385src/main/java/lux/functions/Key.java:94:147:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_e53528_2b8385src/main/java/lux/functions/Key.java:94:147:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_e53528_2b8385src/main/java/lux/functions/Key.java:94:147:SE_INNER_CLASS -#Null_Violation_Hunk:msokolov-lux_ecb648_69a5e2src/main/java/lux/index/field/PathOccurrenceField.java:32:84:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_f7af33_69a86bsrc/main/java/lux/solr/SolrIndexConfig.java:351:358:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_f86cd1_830f90src/main/java/lux/solr/SolrIndexConfig.java:219:225:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_f86cd1_830f90src/main/java/lux/solr/SolrIndexConfig.java:202:210:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:msokolov-lux_fa684b_0e41f6src/main/java/lux/functions/Count.java:27:60:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:msokolov-lux_fa684b_0e41f6src/main/java/lux/functions/Exists.java:27:60:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:mtedone-podam_00b936_a380b3src/main/java/uk/co/jemos/podam/api/MapKeyOrElementsArguments.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:mtedone-podam_26b100_e26a0fsrc/main/java/uk/co/jemos/podam/api/PodamFactoryImpl.java:-1:-1:JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS -#Illegal_Line_Position:mtedone-podam_37ffb4_a80d18src/main/java/uk/co/jemos/podam/api/PodamFactoryImpl.java:-1:-1:JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS -#Illegal_Line_Position:mtedone-podam_4443d0_c27e77src/main/java/uk/co/jemos/podam/api/PodamFactoryImpl.java:-1:-1:JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS -#Null_Violation_Hunk:mtedone-podam_48a40b_1075ffsrc/main/java/uk/co/jemos/podam/common/AbstractConstructorComparator.java:19:33:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:mtedone-podam_495238_45ac3fsrc/main/java/uk/co/jemos/podam/common/AbstractConstructorComparator.java:19:33:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:mtedone-podam_4e45c1_e24567src/main/java/uk/co/jemos/podam/common/AbstractMethodComparator.java:20:54:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:mtedone-podam_5c0d09_c6bf1csrc/main/java/uk/co/jemos/podam/api/PodamFactoryImpl.java:-1:-1:JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS -#Illegal_Line_Position:mtedone-podam_84270a_a87249src/main/java/uk/co/jemos/podam/api/PodamFactoryImpl.java:-1:-1:JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS -#Illegal_Line_Position:mtedone-podam_a00b9b_42e311src/main/java/uk/co/jemos/podam/api/RandomDataProviderStrategy.java:-1:-1:NM_FIELD_NAMING_CONVENTION 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-#Null_Violation_Hunk:netty-netty_0a217c_2127c8src/main/java/org/jboss/netty/channel/AbstractChannel.java:338:355:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:nodebox-nodebox_beb80f_fbcd62src/main/java/nodebox/client/Viewer.java:387:456:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:nodebox-nodebox_beb80f_fbcd62src/main/java/nodebox/client/Viewer.java:387:456:SE_INNER_CLASS -#Null_Violation_Hunk:notthebees-languagegames_594b74_5a1be0src/main/java/languagegames/Concept.java:33:33:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:notthebees-languagegames_7b767e_ad7cefsrc/test/java/paddy/conceptual/TestInteractAgentsIterationProcedure.java:17:17:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:notthebees-languagegames_fc6bfd_744138src/test/java/paddy/conceptual/TestAgentContainerImpl.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:nuodb-migration-tools_19f3dc_c3af0dsrc/main/java/com/nuodb/tools/migration/match/AntRegexCompiler.java:96:112:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:nuxeo-nuxeo-chemistry_46678f_ceb38dnuxeo-opencmis-impl/src/main/java/org/nuxeo/ecm/core/opencmis/impl/server/NuxeoCmisService.java:1841:1909:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:nuxeo-nuxeo-chemistry_79fb13_05c1ffnuxeo-opencmis-tests/src/test/java/org/nuxeo/ecm/core/opencmis/impl/CmisSuiteSession.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:nuxeo-nuxeo-diff_3af239_9c792dsrc/main/java/org/nuxeo/ecm/diff/service/impl/DiffDisplayServiceImpl.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:nuxeo-nuxeo-diff_cb36c2_e9eecfnuxeo-diff-content/src/main/java/org/nuxeo/ecm/diff/content/adapter/base/AbstractContentDiffAdapter.java:80:80:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:nuxeo-nuxeo-diff_e992ca_d70e3anuxeo-diff-content/src/main/java/org/nuxeo/ecm/diff/content/adapter/base/AbstractContentDiffAdapter.java:79:79:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR 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-#Illegal_Line_Position:nuxeo-nuxeo-platform-document-routing_b98db8_2b214anuxeo-platform-document-routing-dm/src/main/java/org/nuxeo/ecm/platform/routing/dm/operation/CreateRoutingTask.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:nuxeo-nuxeo-platform-document-routing_cfe5aa_fee6ffnuxeo-platform-document-routing-core/src/main/java/org/nuxeo/ecm/platform/routing/core/impl/GraphRunner.java:66:66:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:nuxeo-nuxeo-platform-forms-layout-demo_ddd2b5_477782nuxeo-platform-forms-layout-demo/src/main/java/org/nuxeo/ecm/platform/forms/layout/demo/jsf/LayoutDemoContext.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:objectify-objectify_3ca77e_1894b7src/main/java/com/googlecode/objectify/impl/engine/LoadEngine.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:objectify-objectify_3ca77e_1894b7src/main/java/com/googlecode/objectify/impl/engine/LoadEngine.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:objectify-objectify_e534ef_c1e5bdsrc/main/java/com/googlecode/objectify/util/jackson/BlobKeyDeserializer.java:14:25:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:objectify-objectify_e534ef_c1e5bdsrc/main/java/com/googlecode/objectify/util/jackson/KeyDeserializer.java:14:26:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:objectify-objectify_e534ef_c1e5bdsrc/main/java/com/googlecode/objectify/util/jackson/RawKeyDeserializer.java:15:26:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:objectify-objectify_e534ef_c1e5bdsrc/main/java/com/googlecode/objectify/util/jackson/RefDeserializer.java:18:34:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:objectos-way_17f414_419068src/test/java/br/com/objectos/way/etc/io/NameTemplateFileFilterTest.java:73:86:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/main/java/br/com/objectos/way/base/SeqNumCol.java:126:126:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/test/java/br/com/objectos/comuns/matematica/financeira/TesteDeNumeroAbstrato.java:233:243:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/test/java/br/com/objectos/comuns/matematica/financeira/TesteDeNumeroAbstrato.java:206:220:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/test/java/br/com/objectos/comuns/matematica/financeira/TesteDeNumeroAbstrato.java:233:243:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/test/java/br/com/objectos/comuns/matematica/financeira/TesteDeNumeroAbstrato.java:206:220:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/test/java/br/com/objectos/way/base/SeqNumColTest.java:68:71:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_27a598_436bd7way-base/src/test/java/br/com/objectos/way/base/SeqNumColTest.java:62:65:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_30eea0_fb1435src/main/java/br/com/objectos/way/gdrive/DriveExecValid.java:206:233:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_31083a_30eea0src/main/java/br/com/objectos/way/gdrive/GDrive.java:280:292:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_31083a_30eea0src/main/java/br/com/objectos/way/gdrive/GDrive.java:247:268:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_86db68_9aa1easrc/test/java/br/com/objectos/way/io/TableReaderTest.java:85:89:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_90e438_42fbe5src/test/java/br/com/objectos/way/io/TableReaderConverterTest.java:107:118:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:objectos-way_9a562a_69238fsrc/test/java/br/com/objectos/way/io/TableReaderTest.java:99:102:SIC_INNER_SHOULD_BE_STATIC 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-#Null_Violation_Hunk:Omertron-api-themoviedb_0e5760_1f1054src/main/java/com/omertron/themoviedbapi/model2/media/MediaState.java:72:83:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Omertron-api-themoviedb_0e5760_1f1054src/main/java/com/omertron/themoviedbapi/model2/media/MediaState.java:72:83:SE_INNER_CLASS -#Null_Violation_Hunk:Omertron-api-themoviedb_0e5760_1f1054src/main/java/com/omertron/themoviedbapi/model2/media/MediaState.java:72:83:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Omertron-api-themoviedb_28c814_8e11e9src/main/java/com/omertron/themoviedbapi/model/Genre.java:28:28:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Omertron-api-themoviedb_28c814_8e11e9src/main/java/com/omertron/themoviedbapi/model/keyword/Keyword.java:29:29:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Omertron-api-themoviedb_28c814_8e11e9src/main/java/com/omertron/themoviedbapi/model/movie/ProductionCompany.java:29:29:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:Omertron-api-themoviedb_2ef414_1ac805src/main/java/com/omertron/themoviedbapi/model/MovieDb.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:Omertron-api-themoviedb_3e1b0f_e4dc8esrc/main/java/com/omertron/themoviedbapi/wrapper/WrapperGenericList.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:Omertron-api-themoviedb_d0ec5c_aa6bb1src/main/java/com/omertron/themoviedbapi/model2/artwork/ArtworkMedia.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:Omertron-api-themoviedb_e00d93_8451a4src/main/java/com/omertron/themoviedbapi/model/account/Account.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:omnifaces-omnifaces_121a37_7c1a29src/main/java/org/omnifaces/component/output/cache/el/CachingValueExpression.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:omnifaces-omnifaces_121a37_7c1a29src/main/java/org/omnifaces/taghandler/ImportConstants.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS 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-#Null_Violation_Hunk:omnifaces-omnifaces_449432_4a1a8dsrc/org/omnifaces/util/concurrentlinkedhashmap/ConcurrentLinkedHashMap.java:1423:1434:SE_INNER_CLASS -#Null_Violation_Hunk:omnifaces-omnifaces_475ac8_0e397csrc/org/omnifaces/util/concurrentlinkedhashmap/ConcurrentLinkedHashMap.java:1365:1376:SE_INNER_CLASS -#Null_Violation_Hunk:omnifaces-omnifaces_500019_342124src/main/java/org/omnifaces/util/FacesLocal.java:238:238:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:omnifaces-omnifaces_60021d_b4850csrc/main/java/org/omnifaces/component/output/Cache.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:omnifaces-omnifaces_60021d_b4850csrc/main/java/org/omnifaces/util/FacesLocal.java:238:238:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:omnifaces-omnifaces_685ab5_110570src/main/java/org/omnifaces/util/Events.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:omnifaces-omnifaces_89fa05_bf940asrc/main/java/org/omnifaces/taghandler/ValidateBean.java:381:381:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:omnifaces-omnifaces_a0884a_5e76easrc/main/java/org/omnifaces/util/FacesLocal.java:238:238:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:omnifaces-omnifaces_acebe3_54a7f7src/main/java/org/omnifaces/component/output/cache/el/CachingValueExpression.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:omnifaces-omnifaces_acebe3_54a7f7src/main/java/org/omnifaces/taghandler/ImportConstants.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:omnifaces-omnifaces_afb3d8_ff18bbsrc/main/java/org/omnifaces/cdi/param/ParamValue.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:omnifaces-omnifaces_bf31d4_9c127fsrc/main/java/org/omnifaces/taghandler/ValidateBean.java:381:381:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:omnifaces-omnifaces_c67442_9fed2fsrc/main/java/org/omnifaces/util/FacesLocal.java:238:238:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:opendaylight-bgpcep_1dca38_71f45fframework/src/main/java/org/opendaylight/protocol/framework/DispatcherImpl.java:104:112:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:OpenHFT-Chronicle-Queue_0cba0d_d22551chronicle/src/main/java/net/openhft/chronicle/ChronicleQueueBuilder.java:284:292:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:OpenHFT-Chronicle-Queue_0cba0d_d22551chronicle/src/main/java/net/openhft/chronicle/ChronicleQueueBuilder.java:272:281:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:OpenHFT-Chronicle-Queue_0cba0d_d22551chronicle/src/main/java/net/openhft/chronicle/ChronicleQueueBuilder.java:261:269:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:OpenHFT-Java-Lang_0c3915_60cd7alang/src/main/java/net/openhft/lang/io/serialization/impl/ByteBufferMarshaller.java:9:44:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:OpenHFT-Java-Lang_0c3915_60cd7alang/src/main/java/net/openhft/lang/io/serialization/impl/StringZMapMarshaller.java:37:102:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:OpenHFT-Java-Lang_87816f_6053cflang/src/main/java/net/openhft/lang/io/serialization/impl/StringMarshaller.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:openpnp-openpnp_0bb975_4588ddsrc/main/java/org/openpnp/gui/MainFrame.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:openpnp-openpnp_0bb975_4588ddsrc/main/java/org/openpnp/machine/reference/ReferenceJobProcessor.java:837:841:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:openpnp-openpnp_0c1eb2_b4f319src/main/java/org/openpnp/machine/reference/ReferenceJobProcessor.java:837:841:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:openpnp-openpnp_102408_27cac9src/main/java/org/openpnp/machine/reference/ReferenceJobProcessor.java:837:841:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:openpnp-openpnp_357d57_18c1c1src/main/java/org/openpnp/model/Placement.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:openpnp-openpnp_4a4d3c_6a9a72src/main/java/org/openpnp/gui/MainFrame.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:openpnp-openpnp_5314b9_71899dsrc/main/java/org/openpnp/machine/reference/ReferenceJobProcessor.java:837:841:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:openpnp-openpnp_6a9a72_5c5eb0src/main/java/org/openpnp/gui/MainFrame.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:openpnp-openpnp_98d022_0bb975src/main/java/org/openpnp/gui/MainFrame.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:openpnp-openpnp_98d022_0bb975src/main/java/org/openpnp/model/Placement.java:-1:-1:UWF_NULL_FIELD -#Illegal_Line_Position:openpnp-openpnp_9f6532_800eecsrc/main/java/org/openpnp/gui/MainFrame.java:-1:-1:MS_CANNOT_BE_FINAL -#Illegal_Line_Position:openpnp-openpnp_ba1f6c_4550e9src/main/java/org/openpnp/gui/MainFrame.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:openpnp-openpnp_c831ea_2fb767src/main/java/org/openpnp/model/Placement.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:openpnp-openpnp_fb0a3e_b18889src/main/java/org/openpnp/machine/reference/ReferenceJobProcessor.java:837:841:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:openspim-SPIMAcquisition_6c55a0_0a7274src/main/java/spim/algorithm/AbstractAntiDrift.java:29:29:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:openspim-SPIMAcquisition_89ef59_6a6ccasrc/main/java/spim/SPIMAcquisition.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:openspim-SPIMAcquisition_9697f3_69fdafsrc/main/java/spim/algorithm/AbstractAntiDrift.java:29:29:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:openspim-SPIMAcquisition_9d1cee_38886csrc/main/java/spim/SPIMAcquisition.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:OpenTreeOfLife-taxomachine_0c184a_ea3d70src/main/java/opentree/tnrs/adaptersupport/gnr/GNRMatch.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:OpenTreeOfLife-taxomachine_0c184a_ea3d70src/main/java/opentree/tnrs/TNRSMatchSet.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:OpenTreeOfLife-taxomachine_25f38c_05e43dsrc/main/java/opentree/TaxonomyBase.java:44:44:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:OpenTreeOfLife-taxomachine_453340_2bcfffsrc/main/java/opentree/tnrs/TNRSQuery.java:180:233:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:OpenTreeOfLife-taxomachine_70d238_fbfd49src/main/java/opentree/TaxonomyBase.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:OpenTreeOfLife-taxomachine_70d238_fbfd49src/main/java/opentree/TaxonomyBase.java:-1:-1:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:OpenTreeOfLife-taxomachine_70d238_fbfd49src/main/java/opentree/TaxonomyBase.java:41:41:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:OpenTreeOfLife-taxomachine_70d238_fbfd49src/main/java/opentree/TaxonomyBase.java:40:40:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:OpenTreeOfLife-taxomachine_75ab8c_16020fsrc/main/java/opentree/TaxonomyBase.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:OpenTreeOfLife-treemachine_018d88_aa97f6src/main/java/opentree/GraphInitializer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:OpenTreeOfLife-treemachine_233d25_9e1becsrc/main/java/opentree/GraphImporter.java:1407:1407:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:OpenTreeOfLife-treemachine_59abce_534fd5src/main/java/opentree/plugins/PhylografterUpdater.java:24:24:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:OpenTreeOfLife-treemachine_5bb246_fab7c3src/main/java/opentree/TaxonomyBase.java:46:46:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:OpenTreeOfLife-treemachine_9e0b65_cc5fbbsrc/main/java/opentree/GraphImporter.java:1108:1108:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:OpenTreeOfLife-treemachine_c327ed_a23920src/main/java/opentree/plugins/PhylografterUpdater.java:24:24:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:optimizationBenchmarking-optimizationBenchmarking_66efb9_3349dfsrc/main/java/org/optimizationBenchmarking/utils/math/fitting/impl/opti/OptiFittingJob.java:138:148:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:optimizationBenchmarking-optimizationBenchmarking_6d438b_f1a471src/main/java/examples/org/optimizationBenchmarking/utils/graphics/GraphicsExample.java:30:30:MS_MUTABLE_ARRAY -#Null_Violation_Hunk:optimizationBenchmarking-optimizationBenchmarking_a69592_ba6923src/main/java/org/optimizationBenchmarking/experimentation/attributes/clusters/behavior/_BehaviorCluster.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:optimizationBenchmarking-optimizationBenchmarking_c212b7_6ede13src/main/java/org/optimizationBenchmarking/utils/math/fitting/impl/opti/OptiFittingJob.java:147:157:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:optimizationBenchmarking-optimizationBenchmarking_e82438_dad893src/main/java/org/optimizationBenchmarking/experimentation/data/impl/delegates/DelegatingRun.java:95:95:URF_UNREAD_FIELD -#Null_Violation_Hunk:optimizationBenchmarking-optimizationBenchmarking_f1a471_0e1bb2src/main/java/examples/org/optimizationBenchmarking/utils/graphics/GraphicsExample.java:32:32:MS_MUTABLE_ARRAY -#Illegal_Line_Position:osiam-connector4java_f39219_110a35src/main/java/org/osiam/client/query/metamodel/Group_.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:osiam-connector4java_f39219_110a35src/main/java/org/osiam/client/query/metamodel/User_.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ovgu-ccd-jchess_033a9a_1f173djchess/gui/GameTab.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ovgu-ccd-jchess_033a9a_e1c0c3jchess/Player.java:66:67:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_033a9a_e1c0c3jchess/Player.java:58:61:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_0831a9_0eeed9jchess/gui/BoardView.java:146:146:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:ovgu-ccd-jchess_08edcb_5a15bejchess/Moves.java:51:52:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_08edcb_5a15bejchess/Player.java:33:35:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_15d366_e595f7jchess/Moves.java:57:59:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_15d366_e595f7jchess/Player.java:34:37:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_15d366_e595f7jchess/Player.java:41:44:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_15d366_e595f7jchess/Settings.java:41:44:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_15d366_e595f7jchess/Settings.java:50:53:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_17eeb8_3517dbjchess/gui/GameTab.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ovgu-ccd-jchess_191416_0831a9jchess/gui/GameTab.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:ovgu-ccd-jchess_2aa025_eedf50jchess/Moves.java:55:56:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_2aa025_eedf50jchess/Settings.java:48:50:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_2aa025_eedf50jchess/Settings.java:40:42:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_309f93_d5a6c5jchess/Moves.java:55:56:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_309f93_d5a6c5jchess/Settings.java:48:50:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_309f93_d5a6c5jchess/Settings.java:40:42:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_6e0464_273695jchess/Player.java:66:67:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_6e0464_273695jchess/Player.java:58:61:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_77796f_679f5djchess/gui/GameTab.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:ovgu-ccd-jchess_77796f_679f5djchess/gui/JChessTabbedPane.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:ovgu-ccd-jchess_accad2_956deejchess/tests/game/MoveTest.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:ovgu-ccd-jchess_adfe39_d8d917jchess/gui/GameTab.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:ovgu-ccd-jchess_be45d3_c60cdcjchess/Game.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:ovgu-ccd-jchess_c3f4a0_bdca7bjchess/util/PixelCoordinateNotOnBoardException.java:6:6:NM_CLASS_NOT_EXCEPTION -#Null_Violation_Hunk:ovgu-ccd-jchess_cd1f73_c12258jchess/Moves.java:55:56:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_cd1f73_c12258jchess/Settings.java:40:42:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:ovgu-ccd-jchess_cd1f73_c12258jchess/Settings.java:48:50:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:ovgu-ccd-jchess_e1f7fd_117abajchess/Game.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:ovgu-ccd-jchess_e4ff68_4cbaa5jchess/Game.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:owlcs-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/profiles/OWL2QLProfile.java:351:387:SE_INNER_CLASS -#Null_Violation_Hunk:owlcs-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/profiles/OWL2RLProfile.java:356:415:SE_INNER_CLASS -#Null_Violation_Hunk:owlcs-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/profiles/OWL2RLProfile.java:288:345:SE_INNER_CLASS -#Null_Violation_Hunk:owlcs-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/util/HornAxiomVisitorEx.java:244:285:SE_INNER_CLASS -#Null_Violation_Hunk:owlcs-owlapi_09174b_38e827api/src/main/java/org/semanticweb/owlapi/util/HornAxiomVisitorEx.java:187:240:SE_INNER_CLASS -#Illegal_Line_Position:owlcs-owlapi_0b2270_b20fe9oboformat/src/main/java/org/obolibrary/oboformat/writer/OBOFormatWriter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:owlcs-owlapi_0b8d35_8e556coboformat/src/main/java/org/obolibrary/oboformat/parser/OBOFormatParser.java:44:162:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:owlcs-owlapi_0b8d35_8e556coboformat/src/main/java/org/obolibrary/owl/LabelFunctionalFormat.java:13:13:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_101e91_621073parsers/src/main/java/org/coode/owlapi/latex/LatexAxiomsListOntologyFormat.java:49:53:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_112983_d13ce3tools/src/main/java/uk/ac/manchester/cs/owl/explanation/ordering/ExplanationOrdererImpl.java:373:385:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/BinaryRdfOntologyFormatFactory.java:12:28:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/N3OntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/NQuadsOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/NTriplesOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/RdfJsonOntologyFormatFactory.java:12:20:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/RDFXMLOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/TrigOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/TrixOntologyFormatFactory.java:12:23:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/formats/TurtleOntologyFormatFactory.java:11:22:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioBinaryRdfOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioBinaryRdfParserFactory.java:46:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioJsonOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioJsonParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioN3OntologyStorerFactory.java:48:63:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioN3ParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNQuadsOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNQuadsParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNTriplesOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioNTriplesParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioRDFXMLOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioRDFXMLParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrigOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrigParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrixOntologyStorerFactory.java:48:64:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTrixParserFactory.java:49:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTurtleOntologyStorerFactory.java:50:67:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_206a4c_8c0ef9rio/src/main/java/org/semanticweb/owlapi/rio/RioTurtleParserFactory.java:47:52:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:owlcs-owlapi_3221dd_f67b95oboformat/src/main/java/org/obolibrary/oboformat/writer/OBOFormatWriter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Null_Violation_Hunk:owlcs-owlapi_3ce0c8_72a28fparsers/src/main/java/de/uulm/ecs/ai/owlapi/krssparser/KRSS2OWLParserFactory.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebapi/src/main/java/org/semanticweb/owlapi/io/OWLParserFactoryImpl.java:14:31:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebapi/src/main/java/org/semanticweb/owlapi/util/OWLOntologyStorerFactoryImpl.java:33:52:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioBinaryRdfOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioJsonOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioN3OntologyStorerFactory.java:49:58:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioNQuadsOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioNTriplesOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioRDFXMLOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioTrigOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioTrixOntologyStorerFactory.java:49:59:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_4defcc_e501ebrio/src/main/java/org/semanticweb/owlapi/rio/RioTurtleOntologyStorerFactory.java:51:61:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_570cfa_93df9fimpl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLOntologyBuilderImpl.java:50:54:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_621073_07de69parsers/src/main/java/org/coode/owl/krssparser/KRSSOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_621073_07de69parsers/src/main/java/org/coode/owlapi/latex/LatexOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_621073_07de69parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxHTMLOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_621073_07de69parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxOntologyFormat.java:48:51:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_70efa7_d41db2tools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:1258:1258:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:owlcs-owlapi_70efa7_d41db2tools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:878:878:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:owlcs-owlapi_743e4c_8a6a56impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:103:137:SE_INNER_CLASS -#Null_Violation_Hunk:owlcs-owlapi_743e4c_8a6a56impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:1657:1691:SE_INNER_CLASS -#Null_Violation_Hunk:owlcs-owlapi_777b3e_7b036eimpl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:94:128:SE_INNER_CLASS -#Illegal_Line_Position:owlcs-owlapi_9c42ae_2fab17parsers/src/main/java/org/coode/owlapi/functionalparser/OWLFunctionalSyntaxParser.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:owlcs-owlapi_b46875_8df833impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLOntologyManagerImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/io/RDFParserMetaData.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/DefaultPrefixManager.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:owlcs-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/HasPriorityComparator.java:29:45:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/HornAxiomVisitorEx.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4api/src/main/java/org/semanticweb/owlapi/util/OWLEntityComparator.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:owlcs-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:132:162:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:owlcs-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/Internals.java:132:162:SE_INNER_CLASS -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/MapPointer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLOntologyManagerImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/SWRLRuleImpl.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4rio/src/main/java/org/semanticweb/owlapi/formats/RioRDFOntologyFormat.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4rio/src/main/java/org/semanticweb/owlapi/rio/RioOntologyStorer.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:owlcs-owlapi_b4ba8c_e696d4rio/src/main/java/org/semanticweb/owlapi/rio/RioParserImpl.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:owlcs-owlapi_b4ba8c_e696d4tools/src/main/java/uk/ac/manchester/cs/owl/explanation/ordering/ExplanationOrdererImpl.java:358:371:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE 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-#Null_Violation_Hunk:owlcs-owlapi_e3c497_ce87batools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:878:878:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:owlcs-owlapi_e3c497_ce87batools/src/main/java/com/clarkparsia/owlapi/modularity/locality/SyntacticLocalityEvaluator.java:1258:1258:NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:owlcs-owlapi_e7634e_edbdc7parsers/src/main/java/org/coode/owl/krssparser/KRSSOntologyFormat.java:51:55:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_e7634e_edbdc7parsers/src/main/java/org/coode/owlapi/latex/LatexAxiomsListOntologyFormat.java:52:58:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_e7634e_edbdc7parsers/src/main/java/org/coode/owlapi/latex/LatexOntologyFormat.java:51:56:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_e7634e_edbdc7parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxHTMLOntologyFormat.java:51:56:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:owlcs-owlapi_e7634e_edbdc7parsers/src/main/java/uk/ac/manchester/cs/owlapi/dlsyntax/DLSyntaxOntologyFormat.java:51:56:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:paul-hammant-qdox_0411b3_7ee2f4src/main/java/com/thoughtworks/qdox/parser/structs/LocatedDef.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:paul-hammant-qdox_0d687f_1fdd47src/java/com/thoughtworks/qdox/model/JavaField.java:8:93:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:paul-hammant-qdox_232e92_0d5e54src/main/java/com/thoughtworks/qdox/model/expression/Constant.java:31:53:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:paul-hammant-qdox_2990cb_f4747asrc/java/com/thoughtworks/qdox/JavaDocBuilder.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:paul-hammant-qdox_30e892_a39527src/java/com/thoughtworks/qdox/builder/AnnotationTransformer.java:41:92:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:paul-hammant-qdox_30e892_a39527src/java/com/thoughtworks/qdox/parser/expression/AnnotationConstant.java:30:52:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:paul-hammant-qdox_7efec6_cfad0fsrc/main/java/com/thoughtworks/qdox/parser/expression/AnnotationConstant.java:31:49:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:paul-hammant-qdox_981863_2886c5src/main/java/com/thoughtworks/qdox/model/DefaultJavaConstructor.java:3:15:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:paul-hammant-qdox_bedc50_ba2b6dsrc/main/java/com/thoughtworks/qdox/model/impl/DefaultJavaTypeVariable.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:paul-hammant-qdox_ca85cc_a3f186src/main/java/com/thoughtworks/qdox/parser/ParseException.java:71:71:UC_USELESS_VOID_METHOD 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-#Null_Violation_Hunk:pcpratts-rootbeer1_c04680_2494basrc/org/trifort/rootbeer/testcases/rootbeertest/kerneltemplate/GpuVectorMapRunOnGpu2.java:60:60:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:pcpratts-rootbeer1_f1429d_32ed9csrc/org/trifort/rootbeer/runtime/Rootbeer.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:pendelhaven3-magic_12bf66_79bf6asrc/main/java/com/pj/magic/gui/itemstable/ItemsTable.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:pendelhaven3-magic_89a77d_8da63esrc/main/java/com/pj/magic/service/impl/ProductServiceImpl.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:pendelhaven3-magic_c89716_d7f052src/main/java/com/pj/magic/ItemsTable.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:pendelhaven3-magic_d91d93_c0fe8esrc/main/java/com/pj/magic/gui/panels/PurchaseOrderPanel.java:695:695:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:pendelhaven3-magic_e242be_1982f8src/main/java/com/pj/magic/model/SalesRequisition.java:72:72:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:PerfCake-PerfCake_021143_423c76src/main/java/org/perfcake/util/Utils.java:517:517:UPM_UNCALLED_PRIVATE_METHOD -#Illegal_Line_Position:PerfCake-PerfCake_050992_32c683src/main/java/org/perfcake/message/MessageTemplate.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:PerfCake-PerfCake_230523_8e471fsrc/main/java/org/perfcake/message/MessageTemplate.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:PerfCake-PerfCake_28c64f_59626esrc/main/java/org/perfcake/message/generator/AbstractMessageGenerator.java:144:144:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:PerfCake-PerfCake_34e689_9440fdsrc/main/java/org/perfcake/util/Utils.java:517:517:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:PerfCake-PerfCake_3de192_28a6a4src/main/java/org/perfcake/reporting/reporters/AbstractReporter.java:369:379:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:PerfCake-PerfCake_759c50_e9a291src/main/java/org/perfcake/message/MessageTemplate.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:PerfCake-PerfCake_80dee1_4189ebsrc/main/java/org/perfcake/reporting/reporters/AbstractReporter.java:369:379:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:PerfCake-PerfCake_859a1e_8807b1src/main/java/org/perfcake/nreporting/destinations/ConsoleDestination.java:44:44:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:PerfCake-PerfCake_a81318_62ae0dsrc/main/java/org/perfcake/nreporting/destinations/ConsoleDestination.java:44:44:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:PerfCake-PerfCake_cd0e97_87572asrc/main/java/org/perfcake/message/MessageTemplate.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:perfectsense-dari_0650ca_bae484util/src/main/java/com/psddev/dari/util/AuthenticationPolicy.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:perfectsense-dari_0650ca_bae484util/src/main/java/com/psddev/dari/util/CodeUtils.java:-1:-1:MS_PKGPROTECT 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-#Null_Violation_Hunk:phillipsic-SeleniumDriverFramework_5baf07_e84a04src/main/java/com/comverse/common/Main.java:37:42:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:phillipsic-SeleniumDriverFramework_8834e4_5a7a55src/main/java/com/comverse/css/csr/ChangeRoles.java:26:29:NM_CONFUSING -#Illegal_Line_Position:phillipsic-SeleniumDriverFramework_c5bab1_ca8629src/main/java/com/comverse/css/commonpages/MoveMemberCommon.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:phillipsic-SeleniumDriverFramework_d58803_f2ab74src/main/java/com/comverse/css/b2b/ChangeRoles.java:28:31:NM_CONFUSING -#Null_Violation_Hunk:phillipsic-SeleniumDriverFramework_d58803_f2ab74src/main/java/com/comverse/css/csr/ChangeRoles.java:26:29:NM_CONFUSING -#Null_Violation_Hunk:phillipsic-SeleniumDriverFramework_e61878_04eadesrc/main/java/com/comverse/upm/upmPages/UpmLoginPage.java:9:39:NM_CLASS_NAMING_CONVENTION -#Illegal_Line_Position:phillipsic-SeleniumDriverFramework_e8bb23_e1cf36src/main/java/com/framework/common/User.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:phillipsic-SeleniumDriverFramework_fd52e4_915a71src/main/java/com/comverse/common/Main.java:37:42:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:PIH-mirebalais-smoke-tests_16bf06_fdd0d3src/main/java/org/openmrs/module/mirebalais/smoke/pageobjects/PatientDashboard.java:247:257:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:PIH-mirebalais-smoke-tests_c3646c_7b7626src/main/java/org/openmrs/module/mirebalais/smoke/pageobjects/PatientDashboard.java:331:389:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:plutext-docx4j_1c96a4_074e1csrc/main/java/org/docx4j/model/datastorage/CustomXmlDataStoragePartSelector.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:plutext-docx4j_547d06_56ac6esrc/main/java/org/docx4j/convert/out/ModelConverter.java:65:65:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR 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-#Null_Violation_Hunk:Praqma-cool_151f76_b35b91src/main/java/net/praqma/clearcase/util/setup/HLinkTask.java:17:17:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:Praqma-cool_464473_f25762src/main/java/net/praqma/clearcase/ucm/utils/BaselineList.java:239:249:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Praqma-cool_464473_f25762src/main/java/net/praqma/clearcase/ucm/utils/BaselineList.java:253:262:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:Praqma-cool_b05f7d_932016src/main/java/net/praqma/clearcase/PVob.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:protegeproject-swrlapi_1b924c_232b58src/main/java/org/swrlapi/sqwrl/DefaultSQWRLResult.java:1233:1265:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Illegal_Line_Position:protegeproject-swrlapi_1b924c_232b58src/main/java/org/swrlapi/sqwrl/values/SQWRLResultValue.java:-1:-1:CO_ABSTRACT_SELF -#Null_Violation_Hunk:protegeproject-swrlapi_67292a_a413a4src/main/java/org/swrlapi/xsd/XSDDate.java:7:7:EQ_COMPARETO_USE_OBJECT_EQUALS 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-#Null_Violation_Hunk:rage-tmc-cli_d6ee70_54f64bsrc/main/java/hy/tmc/cli/frontend/communication/commands/AnswerQuestion.java:18:18:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:rage-tmc-cli_f7c957_817857src/main/java/hy/tmc/cli/frontend/communication/commands/Command.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:rasto-lcmc_07b20c_656559src/main/java/lcmc/gui/resources/CRMInfo.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:rasto-lcmc_19ace1_647956src/main/java/lcmc/view/MainPanel.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:rasto-lcmc_227005_94d58esrc/main/java/lcmc/LCMC.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:rasto-lcmc_2a09b8_a306f7src/main/java/lcmc/data/ResourceAgent.java:229:229:MS_MUTABLE_COLLECTION -#Null_Violation_Hunk:rasto-lcmc_3d1fdc_3a5057src/main/java/lcmc/data/ResourceAgent.java:254:254:MS_MUTABLE_COLLECTION 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-#Null_Violation_Hunk:rasto-lcmc_a7583a_5d4d00src/main/java/lcmc/data/crm/ResourceAgent.java:236:236:MS_MUTABLE_COLLECTION -#Null_Violation_Hunk:rasto-lcmc_aeaac1_4b3831src/main/java/lcmc/gui/resources/drbd/BlockDevInfo.java:79:79:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:rasto-lcmc_fbc427_562545src/main/java/lcmc/data/ResourceAgent.java:254:254:MS_MUTABLE_COLLECTION -#Null_Violation_Hunk:Razz0991-Minigames_6451fb_edd374Minigames/src/au/com/mineauz/minigames/Minigames.java:25:25:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:Razz0991-Minigames_ed57f0_50486bMinigames/src/au/com/mineauz/minigames/Minigames.java:25:25:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:Razz0991-Minigames_f136d5_b93528Minigames/src/au/com/mineauz/minigames/minigame/reward/scheme/ScoreRewardScheme.java:219:329:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:Razz0991-Minigames_f18777_b8ef5aMinigames/src/au/com/mineauz/minigames/Minigames.java:14:14:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:Razz0991-Minigames_fce53f_32c059Minigames/src/au/com/mineauz/minigames/Minigames.java:23:23:MS_CANNOT_BE_FINAL -#Illegal_Line_Position:reinert-requestor_8549b0_505029src/main/java/io/reinert/requestor/RequestProgress.java:-1:-1:NM_SAME_SIMPLE_NAME_AS_INTERFACE -#Null_Violation_Hunk:relayrides-pushy_3b384b_81ed0asrc/main/java/com/relayrides/pushy/apns/FeedbackServiceConnection.java:132:153:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:relayrides-pushy_68cc13_69f470src/main/java/com/relayrides/pushy/apns/FeedbackServiceClient.java:119:135:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:relayrides-pushy_cea7c3_fb232asrc/main/java/com/relayrides/pushy/apns/FeedbackServiceClient.java:119:130:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:relayrides-pushy_d20104_f5cbaasrc/main/java/com/relayrides/pushy/apns/FeedbackServiceClient.java:120:131:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:relayrides-pushy_e3658a_d05082src/main/java/com/relayrides/pushy/apns/FeedbackServiceConnection.java:136:185:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:relayrides-pushy_f79d6f_43c96bsrc/main/java/com/relayrides/pushy/apns/FeedbackConnection.java:124:149:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:renepickhardt-generalized-language-modeling-toolkit_7f97b8_d8e140src/de/typology/splitter/DataSetSplitter.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:renepickhardt-generalized-language-modeling-toolkit_92c300_15e6absrc/de/typology/smoother/KneserNeyResultAggregator.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:renepickhardt-generalized-language-modeling-toolkit_9f7c43_6890f4src/main/java/de/typology/executables/Glmtk.java:42:47:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:renepickhardt-generalized-language-modeling-toolkit_9f7c43_6890f4src/main/java/de/typology/executables/GlmtkCount.java:106:111:SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -#Null_Violation_Hunk:renepickhardt-generalized-language-modeling-toolkit_a3dfa3_35f28csrc/main/java/de/typology/utils/Config.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:renepickhardt-generalized-language-modeling-toolkit_b97586_0e78a5src/de/typology/splitter/SplitterTask.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:renepickhardt-generalized-language-modeling-toolkit_bd49fa_be7c03src/main/java/de/glmtk/querying/probability/QueryCacherCreator.java:58:58:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:renepickhardt-generalized-language-modeling-toolkit_c5e8c8_684562src/de/typology/splitter/Sequencer.java:36:36:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:renepickhardt-generalized-language-modeling-toolkit_d8e140_4ccd9dsrc/de/typology/utils/Config.java:-1:-1:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:renepickhardt-generalized-language-modeling-toolkit_e5e598_726e21src/de/typology/utilsOld/Config.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Illegal_Line_Position:renepickhardt-generalized-language-modeling-toolkit_fda5b9_271ddfsrc/de/typology/smoother/KneserNeyResultAggregator.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:Requinard-TeamTab_6fc0b8_e25afbsrc/main/java/Game/Instruction.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:Requinard-TeamTab_6fc0b8_e25afbsrc/main/java/Game/Team.java:57:57:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:Requinard-TeamTab_add6b1_616f86src/main/java/Game/Instruction.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_026ffb_65f42csrc/main/java/org/jolokia/docker/maven/AbstractDockerMojo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_060338_bb6123src/main/java/org/jolokia/docker/maven/log/LogDispatcher.java:103:141:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:rhuss-docker-maven-plugin_060338_bb6123src/main/java/org/jolokia/docker/maven/WatchMojo.java:54:54:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_2d1bd9_60eb31src/main/java/org/jolokia/docker/maven/AbstractDockerMojo.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_2d1bd9_60eb31src/main/java/org/jolokia/docker/maven/assembly/DockerFileBuilder.java:116:129:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:rhuss-docker-maven-plugin_376b8c_a47eeasrc/main/java/org/jolokia/docker/maven/config/AssemblyConfiguration.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_3b4574_670e55src/main/java/org/jolokia/docker/maven/config/WatchConfiguration.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_65f42c_8c423asrc/main/java/org/jolokia/docker/maven/BuildMojo.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_786ebd_e5f01asrc/main/java/org/jolokia/docker/maven/WatchMojo.java:53:53:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_84a19b_0ae55asrc/main/java/org/jolokia/docker/maven/log/LogDispatcher.java:103:141:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:rhuss-docker-maven-plugin_84a19b_0ae55asrc/main/java/org/jolokia/docker/maven/WatchMojo.java:54:54:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_a66547_f7829csrc/main/java/org/jolokia/docker/maven/config/AssemblyConfiguration.java:128:128:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_b6fca4_670e55src/main/java/org/jolokia/docker/maven/config/WatchConfiguration.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_bb97f1_f236dasrc/main/java/org/jolokia/docker/maven/WatchMojo.java:53:53:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_d33bc9_895828src/main/java/org/jolokia/docker/maven/WatchMojo.java:58:58:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_e0e618_ab3f52src/main/java/org/jolokia/docker/maven/WatchMojo.java:52:52:UWF_UNWRITTEN_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_e4ae7d_8a32c5src/main/java/org/jolokia/docker/maven/config/RunImageConfiguration.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:rhuss-docker-maven-plugin_ebf8c9_1230a2src/main/java/org/jolokia/maven/docker/assembly/DockerFileBuilder.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_ebf8c9_1230a2src/main/java/org/jolokia/maven/docker/StartMojo.java:128:128:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:rhuss-docker-maven-plugin_f8e572_8c800csrc/main/java/org/jolokia/docker/maven/log/LogDispatcher.java:113:144:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:rhuss-docker-maven-plugin_f8e572_8c800csrc/main/java/org/jolokia/docker/maven/WatchMojo.java:52:52:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:rinde-RinSim_0365b7_afe859central/src/test/java/com/github/rinde/rinsim/central/rt/RtSolverModelTest.java:67:67:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:rinde-RinSim_d59ab7_947d5aexperiment-base/src/main/java/com/github/rinde/rinsim/experiment/base/DefaultScenario.java:25:25:EQ_COMPARETO_USE_OBJECT_EQUALS -#Illegal_Line_Position:rinde-RinSim_d59ab7_947d5aexperiment-base/src/test/java/com/github/rinde/rinsim/experiment/base/ExperimentTest.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:rinde-RinSim_d59ab7_947d5aexperiment-base/src/test/java/com/github/rinde/rinsim/experiment/base/ExperimentTest.java:161:161:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:rinde-RinSim_d59ab7_947d5aexperiment-base/src/test/java/com/github/rinde/rinsim/experiment/base/ExperimentTest.java:146:157:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:roberth-pitest_329fb0_ca4f4csrc/main/java/org/pitest/junit/RunnerAdapterTestUnit.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:robovm-robovm_23cfac_a20267cocoatouch/src/main/java/org/robovm/apple/uikit/UIFontDescriptorAttribute.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:robovm-robovm_23cfac_a20267cocoatouch/src/main/java/org/robovm/apple/uikit/UIFontTextStyle.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:robovm-robovm_2c4699_aeff73cocoatouch/src/main/java/org/robovm/apple/mediatoolbox/MTAudioProcessingTap.java:60:60:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:robovm-robovm_395c01_9ad1adcocoatouch/src/main/java/org/robovm/apple/mediatoolbox/MTAudioProcessingTap.java:60:60:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:robovm-robovm_640595_6fe06ecocoatouch/src/main/java/org/robovm/apple/uikit/UIFontDescriptorAttribute.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:robovm-robovm_640595_6fe06ecocoatouch/src/main/java/org/robovm/apple/uikit/UIFontTextStyle.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:robovm-robovm_d0e478_b0cfe1cocoatouch/src/main/java/org/robovm/apple/mediatoolbox/MTAudioProcessingTap.java:60:60:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:robovm-robovm_e96bf5_17e813cocoatouch/src/main/java/org/robovm/apple/uikit/UIFontDescriptorAttribute.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:robovm-robovm_e96bf5_17e813cocoatouch/src/main/java/org/robovm/apple/uikit/UIFontTextStyle.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:roundrop-facebook4j_1760cd_7789f6facebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_217f99_0e3521src/main/java/facebook4j/internal/json/AchievementJSONImpl.java:199:224:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_217f99_0e3521src/main/java/facebook4j/internal/json/EventJSONImpl.java:181:216:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_217f99_0e3521src/main/java/facebook4j/internal/json/EventJSONImpl.java:181:216:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_217f99_0e3521src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:258:282:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_217f99_0e3521src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_217f99_0e3521src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_54e3ad_6e784efacebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_6a8c5a_e9ade1facebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_750f06_a11755facebook4j-core/src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:326:397:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_844370_2ed9d8src/main/java/facebook4j/internal/json/AchievementJSONImpl.java:199:224:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_844370_2ed9d8src/main/java/facebook4j/internal/json/EventJSONImpl.java:182:217:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_844370_2ed9d8src/main/java/facebook4j/internal/json/EventJSONImpl.java:182:217:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_844370_2ed9d8src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:258:282:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_844370_2ed9d8src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_844370_2ed9d8src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_8e1564_854230facebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_a3edae_6fe0f6src/main/java/facebook4j/internal/json/AchievementJSONImpl.java:199:224:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_a3edae_6fe0f6src/main/java/facebook4j/internal/json/EventJSONImpl.java:181:216:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_a3edae_6fe0f6src/main/java/facebook4j/internal/json/EventJSONImpl.java:181:216:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_a3edae_6fe0f6src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:258:282:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_a3edae_6fe0f6src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_a3edae_6fe0f6src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_ac0dac_4d7454facebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_b1100f_f12070facebook4j-core/src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:326:397:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_bd35c5_c41f35facebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_cbf648_331fb4facebook4j-core/src/main/java/facebook4j/internal/json/UserJSONImpl.java:875:915:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_cbf648_331fb4facebook4j-core/src/main/java/facebook4j/internal/json/UserJSONImpl.java:875:915:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_cca35d_866e6cfacebook4j-core/src/main/java/facebook4j/internal/json/EventJSONImpl.java:212:252:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_cca35d_866e6cfacebook4j-core/src/main/java/facebook4j/internal/json/EventJSONImpl.java:212:252:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_daf824_e6a2d0facebook4j-core/src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:326:397:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_e6e671_7486fafacebook4j-core/src/main/java/facebook4j/internal/json/InboxResponseListImpl.java:71:95:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_f6e72e_628cb4src/main/java/facebook4j/internal/json/AchievementJSONImpl.java:199:224:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_f6e72e_628cb4src/main/java/facebook4j/internal/json/EventJSONImpl.java:182:217:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_f6e72e_628cb4src/main/java/facebook4j/internal/json/EventJSONImpl.java:182:217:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_f6e72e_628cb4src/main/java/facebook4j/internal/json/PhotoJSONImpl.java:258:282:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_f6e72e_628cb4src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:roundrop-facebook4j_f6e72e_628cb4src/main/java/facebook4j/internal/json/UserJSONImpl.java:582:602:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_fdad8c_d01f8ffacebook4j-core/src/main/java/facebook4j/internal/json/EventJSONImpl.java:243:305:SE_INNER_CLASS -#Null_Violation_Hunk:roundrop-facebook4j_fdad8c_d01f8ffacebook4j-core/src/main/java/facebook4j/internal/json/EventJSONImpl.java:243:305:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:rovo89-public-transport-enabler-fork_e28210_9c7150src/de/schildbach/pte/dto/QueryConnectionsResult.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:sanity-quickml_ca649e_35941csrc/main/java/quickml/supervised/tree/branchFinders/branchFinderBuilders/BranchFinderBuilder.java:28:28:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:sanity-quickml_ca649e_35941csrc/main/java/quickml/supervised/tree/branchFinders/branchFinderBuilders/BranchFinderBuilder.java:38:38:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:sannies-mp4parser_17bdd4_31ca35src/main/java/com/googlecode/mp4parser/boxes/apple/AppleCoverBox.java:86:111:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:sannies-mp4parser_2430e6_ff7ca9src/main/java/com/googlecode/mp4parser/AbstractContainerBox.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:sannies-mp4parser_5dcfde_1a931esrc/main/java/com/googlecode/mp4parser/authoring/tracks/AACTrackImpl.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_6e3278_d72143src/main/java/com/googlecode/mp4parser/contentprotection/PlayReadyHeader.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:sannies-mp4parser_6e3278_d72143src/main/java/com/googlecode/mp4parser/contentprotection/PlayReadyHeader.java:25:25:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:sannies-mp4parser_99f022_05cf34src/main/java/com/googlecode/mp4parser/boxes/piff/TfrfBox.java:110:129:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:sannies-mp4parser_e15acd_db53c5src/main/java/com/coremedia/iso/IsoFile.java:-1:-1:MF_CLASS_MASKS_FIELD -#Null_Violation_Hunk:sannies-mp4parser_f21047_426a25src/main/java/com/googlecode/mp4parser/boxes/cenc/CencSampleAuxiliaryDataFormat.java:45:80:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:98:98:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:234:234:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:84:84:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:101:101:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:109:109:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:141:141:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:58:58:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:66:66:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:112:112:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:130:130:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:155:155:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:139:139:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:sannies-mp4parser_fa213e_bd5e43src/main/java/com/googlecode/mp4parser/h264/model/SliceHeader.java:133:133:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:sboesebeck-morphium_0919e4_113020src/de/caluga/morphium/ConfigElement.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:sboesebeck-morphium_281fca_3aa6ecsrc/de/caluga/morphium/LazyDeReferencingProxy.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:sboesebeck-morphium_2d2d40_037703src/de/caluga/morphium/ConfigElement.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Null_Violation_Hunk:sboesebeck-morphium_721c29_2b6fd8src/de/caluga/morphium/writer/WriterImpl.java:715:715:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:sboesebeck-morphium_7ebb12_0e3c27src/de/caluga/morphium/Morphium.java:343:343:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:sboesebeck-morphium_822690_b00c2bsrc/de/caluga/morphium/Morphium.java:1959:2012:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:sboesebeck-morphium_822690_b00c2bsrc/de/caluga/morphium/Morphium.java:1959:2012:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:sboesebeck-morphium_822690_b00c2bsrc/de/caluga/morphium/Morphium.java:2085:2133:SE_BAD_FIELD_INNER_CLASS -#Null_Violation_Hunk:sboesebeck-morphium_822690_b00c2bsrc/de/caluga/morphium/Morphium.java:2085:2133:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:sboesebeck-morphium_a1fee4_2b693bsrc/de/caluga/morphium/Morphium.java:1204:1232:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:sboesebeck-morphium_d1ba6d_8d69aesrc/de/caluga/morphium/Morphium.java:1946:1959:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:sboesebeck-morphium_eeb738_b7b13csrc/de/caluga/morphium/PartiallyUpdateableProxy.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:sbwhitecap-Phex-trunk_8ea6bd_073c01src/main/java/phex/gui/tabs/network/NetworkTab.java:805:831:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:sbwhitecap-Phex-trunk_8ea6bd_073c01src/main/java/phex/gui/tabs/network/NetworkTab.java:718:802:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:sbwhitecap-Phex-trunk_b0223b_4a79basrc/main/java/phex/prefs/api/PreferencesFactory.java:327:365:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:sdl-Testy_c077e3_4d851bsrc/main/java/com/sdl/selenium/web/WebLocator.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:searchbox-io-Jest_005792_beed2dsrc/main/java/io/searchbox/Indices/CreateIndex.java:19:45:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_1ce876_79400csrc/main/java/io/searchbox/indices/IndicesExists.java:13:20:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_1ce876_79400csrc/main/java/io/searchbox/indices/mapping/PutMapping.java:14:33:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_1e43c4_0d4774src/main/java/io/searchbox/indices/GetMapping.java:13:28:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_1e43c4_0d4774src/main/java/io/searchbox/indices/GetTemplate.java:12:25:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_1e43c4_0d4774src/main/java/io/searchbox/indices/PutMapping.java:13:29:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_1e43c4_0d4774src/main/java/io/searchbox/indices/PutTemplate.java:12:26:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_33815f_a684aesrc/main/java/io/searchbox/core/Get.java:18:146:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_33815f_a684aesrc/main/java/io/searchbox/Indices/CreateIndex.java:19:45:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:searchbox-io-Jest_4b1801_6281a1src/main/java/io/searchbox/core/MoreLikeThis.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:searchbox-io-Jest_4b7c25_470c71src/main/java/io/searchbox/core/Get.java:16:69:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_4b7c25_470c71src/main/java/io/searchbox/core/MultiGet.java:16:102:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_4b7c25_470c71src/main/java/io/searchbox/indices/DeleteIndex.java:15:30:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_4b7c25_470c71src/main/java/io/searchbox/indices/mapping/PutMapping.java:12:28:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_8c48e3_90718esrc/main/java/io/searchbox/indices/IndicesExists.java:13:20:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_8c48e3_90718esrc/main/java/io/searchbox/indices/mapping/PutMapping.java:14:33:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:searchbox-io-Jest_e2436d_f6ccc8src/main/java/io/searchbox/core/search/facet/TermsFacet.java:55:65:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:searchbox-io-Jest_f41ef7_0150edsrc/main/java/io/searchbox/core/Delete.java:14:21:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:sesuncedu-htmlparser_652684_9d1d76src/nu/validator/htmlparser/impl/StackNode.java:134:134:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:sesuncedu-htmlparser_f3e696_0ee8e0src/nu/validator/htmlparser/io/MetaSniffer.java:38:38:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:shabbies-clockwork_85dd0b_db98e1src/main/java/model/PostManager.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:simon-eastwood-DependencyCheckCM_193bba_e307cesrc/main/java/org/owasp/dependencycheck/data/lucene/VersionTokenizingFilter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:simon-eastwood-DependencyCheckCM_1ead96_ac8920src/main/java/org/owasp/dependencycheck/analyzer/FalsePositiveAnalyzer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:simon-eastwood-DependencyCheckCM_474018_367da7src/main/java/org/codesecure/dependencycheck/utils/Settings.java:39:39:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:simon-eastwood-DependencyCheckCM_836c1b_ab27a7src/main/java/org/owasp/dependencycheck/data/lucene/VersionTokenizingFilter.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:simon-eastwood-DependencyCheckCM_ae279d_065a80src/main/java/org/codesecure/dependencycheck/dependency/VulnerableSoftware.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:simon-eastwood-DependencyCheckCM_d02c31_5b310dsrc/main/java/org/codesecure/dependencycheck/utils/Settings.java:39:39:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:simon-eastwood-DependencyCheckCM_e31086_c177ffsrc/main/java/org/codesecure/dependencycheck/dependency/VulnerableSoftware.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:simon-eastwood-DependencyCheckCM_f91fcb_3ea0d7src/main/java/org/owasp/dependencycheck/analyzer/FalsePositiveAnalyzer.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:SINTEF-9012-ThingML_5d7673_711aa7org.thingml.parser/src/main/java-gen/org/sintef/thingml/resource/thingml/mopp/ThingmlParser.java:30904:30916:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:sk89q-CommandBook_2039e3_8d4224src/main/java/com/sk89q/commandbook/CommandBook.java:-1:-1:CI_CONFUSED_INHERITANCE -#Illegal_Line_Position:sk89q-CommandBook_42fb8d_cd8af1src/main/java/com/sk89q/commandbook/profiles/binary/implementations/BinaryProfile_E1_R0.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:sk89q-CommandBook_bc032d_01bc41src/main/java/com/sk89q/commandbook/profiles/ProfilesComponent.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:skillcoyne-IGCSA_c720c1_b2a958src/main/java/org/lcsb/lu/igcsa/genome/Chromosome.java:112:112:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:slipcor-pvparena_0df1a3_c78b23src/net/slipcor/pvparena/arena/Arena.java:23:23:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:slipcor-pvparena_9a1bc7_192c0fsrc/net/slipcor/pvparena/commands/PAA_Install.java:217:217:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:slipcor-pvparena_9a1bc7_192c0fsrc/net/slipcor/pvparena/commands/PAA_Uninstall.java:142:142:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:slipcor-pvparena_e7ec82_7790c9src/net/slipcor/pvparena/loadables/ArenaRegionShape.java:20:61:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:slowenthal-classproject_fddaaf_f7f8e6src/main/java/playlist/model/UserDAO.java:94:94:UC_USELESS_VOID_METHOD -#Illegal_Line_Position:soluvas-soluvas-framework_5d8924_ad85cdjson/src/main/java/org/soluvas/json/LowerEnumDeserializer.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Null_Violation_Hunk:SomMeri-less4j_369c74_d07b47src/main/java/com/github/sommeri/less4j/core/compiler/scopes/LocalScope.java:85:108:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:SomMeri-less4j_a57522_1f8425src/main/java/com/github/sommeri/less4j/core/compiler/scopes/ScopeView.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:SomMeri-less4j_b1e20c_8377e6src/main/java/com/github/sommeri/less4j/utils/ListsComparator.java:179:210:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:SomMeri-less4j_c80f02_bf7fabsrc/main/java/com/github/sommeri/less4j/core/compiler/stages/MediaBubblerAndMerger.java:52:52:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:SomMeri-less4j_c80f02_bf7fabsrc/main/java/com/github/sommeri/less4j/core/compiler/stages/MediaBubblerAndMerger.java:47:47:UPM_UNCALLED_PRIVATE_METHOD -#Null_Violation_Hunk:SomMeri-less4j_d59a7e_369c74src/main/java/com/github/sommeri/less4j/core/compiler/scopes/Scope.java:357:380:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:SomMeri-less4j_e43ec1_c17807src/main/java/com/github/sommeri/less4j/core/compiler/scopes/LocalScope.java:85:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:SomMeri-less4j_e43ec1_c17807src/main/java/com/github/sommeri/less4j/core/compiler/scopes/LocalScope.java:148:163:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:SomMeri-less4j_f87f95_1d10easrc/main/java/com/github/sommeri/less4j/core/compiler/stages/SimpleImportsSolver.java:-1:-1:DMI_COLLECTION_OF_URLS -#Illegal_Line_Position:SonarSource-jenkins-sonar-plugin_067829_1691c4src/main/java/hudson/plugins/sonar/SonarBuildWrapper.java:-1:-1:VO_VOLATILE_REFERENCE_TO_ARRAY -#Illegal_Line_Position:SonarSource-jenkins-sonar-plugin_afb60b_b6fbc3src/main/java/hudson/plugins/sonar/SonarPublisher.java:-1:-1:UWF_NULL_FIELD -#Null_Violation_Hunk:SonarSource-sonar-python_308675_cad0e7src/main/java/org/sonar/plugins/python/PythonComplexityAnalyzer.java:132:135:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:SophieKoonin-JavaDecaf_5b8507_545859src/main/java/ast/SimpleNode.java:30:30:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Illegal_Line_Position:SophieKoonin-JavaDecaf_cf3fa7_18d909src/main/java/parser/JavaCharStream.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:SophieKoonin-JavaDecaf_cf3fa7_18d909src/main/java/parser/JDCParser.java:-1:-1:MS_PKGPROTECT -#Illegal_Line_Position:SophieKoonin-JavaDecaf_cf3fa7_18d909src/main/java/parser/JDCParserTokenManager.java:-1:-1:MS_PKGPROTECT -#Null_Violation_Hunk:SpigotMC-BungeeCord_bcaafc_e12bc1proxy/src/main/java/net/md_5/bungee/UserConnection.java:72:72:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:SpigotMC-BungeeCord_bcaafc_e12bc1proxy/src/main/java/net/md_5/bungee/UserConnection.java:73:73:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:SpigotMC-BungeeCord_e12bc1_4fb857proxy/src/main/java/net/md_5/bungee/UserConnection.java:-1:-1:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:SpigotMC-BungeeCord_e12bc1_4fb857proxy/src/main/java/net/md_5/bungee/UserConnection.java:25:25:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:SpigotMC-Spigot-API_0b3a14_184d57src/main/java/org/bukkit/fillr/Fillr.java:9:9:MS_SHOULD_BE_FINAL -#Null_Violation_Hunk:SpigotMC-Spigot-API_105925_8e142esrc/main/java/org/bukkit/fillr/Fillr.java:9:9:MS_SHOULD_BE_FINAL -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockBreakEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockDamageEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockDispenseEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockFormEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockFromToEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockIgniteEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockPistonExtendEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/block/BlockSpreadEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/enchantment/EnchantItemEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/enchantment/PrepareItemEnchantEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityChangeBlockEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityCombustByBlockEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityCombustByEntityEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityDamageByBlockEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityDamageByEntityEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityDeathEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityTameEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/EntityTargetEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/ItemSpawnEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/entity/PigZapEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/inventory/FurnaceSmeltEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/painting/PaintingPlaceEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerBedLeaveEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerChatEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerFishEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerInteractEntityEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerInteractEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerMoveEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerPortalEvent.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerPortalEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/player/PlayerRespawnEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleBlockCollisionEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleDestroyEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleEnterEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/vehicle/VehicleEntityCollisionEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/weather/LightningStrikeEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/world/PortalCreateEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_219d00_ca71besrc/main/java/org/bukkit/event/world/StructureGrowEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_380b5c_0b03f7src/main/java/org/bukkit/event/player/PlayerBlockItemEvent.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_5c8bc6_e35037src/main/java/org/bukkit/event/entity/ItemSpawnEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_5c8bc6_e35037src/main/java/org/bukkit/event/player/PlayerChatEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:SpigotMC-Spigot-API_5c8bc6_e35037src/main/java/org/bukkit/event/vehicle/VehicleEntityCollisionEvent.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:spotify-cassandra-reaper_264985_1b88d4src/main/java/com/spotify/reaper/core/RepairRun.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:spotify-cassandra-reaper_3b1eed_df3952src/main/java/com/spotify/reaper/core/RepairSegment.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:spotify-cassandra-reaper_df3952_5dc93asrc/main/java/com/spotify/reaper/core/Cluster.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:SpoutDev-Spout_2eecae_2a6771src/main/java/org/getspout/api/command/SimpleCommandsManager.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:SpoutDev-Spout_3bec58_035cd9src/main/java/org/getspout/api/inventory/Inventory.java:9:32:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:SpoutDev-Spout_4e46cc_ce20acsrc/main/java/org/spout/math/Matrix2.java:321:329:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:SpoutDev-Spout_4e46cc_ce20acsrc/main/java/org/spout/math/Matrix3.java:444:452:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:SpoutDev-Spout_4e46cc_ce20acsrc/main/java/org/spout/math/Matrix4.java:583:591:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:SpoutDev-Spout_7af7c1_7cd2c9src/main/java/org/spout/math/matrix/Matrix.java:600:612:SE_NO_SERIALVERSIONID -#Illegal_Line_Position:SpoutDev-Spout_d3e912_9f07c9src/main/java/org/getspout/api/math/Vector3.java:-1:-1:NM_FIELD_NAMING_CONVENTION -#Illegal_Line_Position:SpoutDev-Spout_e693d9_8bd6f8src/main/java/org/getspout/api/math/Vector3.java:-1:-1:NM_FIELD_NAMING_CONVENTION 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-#Null_Violation_Hunk:swagger-api-swagger-core_400662_b4fbe3modules/swagger-models/src/main/java/io/swagger/models/properties/DoubleProperty.java:8:86:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:swagger-api-swagger-core_400662_b4fbe3modules/swagger-models/src/main/java/io/swagger/models/properties/FloatProperty.java:8:86:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:swagger-api-swagger-core_400662_b4fbe3modules/swagger-models/src/main/java/io/swagger/models/properties/IntegerProperty.java:9:87:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:swagger-api-swagger-core_400662_b4fbe3modules/swagger-models/src/main/java/io/swagger/models/properties/LongProperty.java:8:86:RI_REDUNDANT_INTERFACES -#Illegal_Line_Position:swagger-api-swagger-core_e46368_1485e6modules/swagger-models/src/main/java/com/wordnik/swagger/models/Operation.java:-1:-1:UUF_UNUSED_FIELD 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-#Null_Violation_Hunk:teanutella-AppEmployee_83fc11_3e082bsrc/main/java/ca/ulaval/glo4003/appemployee/web/dto/UserDto.java:17:17:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:tehbeard-BeardStat_233110_ec664aspigot/src/main/java/com/tehbeard/beardstat/bukkit/identifier/GrahamIdentifierService.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:tehbeard-BeardStat_38428f_525045src/main/java/com/tehbeard/beardstat/bukkit/identifier/GrahamIdentifierService.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:tehbeard-BeardStat_38428f_525045src/main/java/com/tehbeard/beardstat/bukkit/identifier/GrahamIdentifierService.java:62:62:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:tehbeard-BeardStat_39ec62_ed1ca3src/main/java/com/tehbeard/BeardStat/DataProviders/JDBCStatDataProvider.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD 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-#Null_Violation_Hunk:tengstrand-Laja_dd37e3_21eb52src/test/java/net/sf/laja/cdd/testgen/Person.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:tengstrand-Laja_dd37e3_21eb52src/test/java/net/sf/laja/cdd/testgen/SpecialAddress.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:tengstrand-Laja_dd37e3_21eb52src/test/java/net/sf/laja/cdd/testgen/SpecialPerson.java:1:1:EQ_DOESNT_OVERRIDE_EQUALS -#Null_Violation_Hunk:tengstrand-Laja_dd37e3_21eb52src/test/java/net/sf/laja/cdd/testgen/state/AddressState.java:126:264:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:tengstrand-Laja_dd37e3_21eb52src/test/java/net/sf/laja/cdd/testgen/state/PersonState.java:229:481:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:tengstrand-Laja_ec9e70_15dfcdsrc/main/java/net/sf/laja/cdd/testgen/state/AddressState.java:230:260:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:tengstrand-Laja_ec9e70_15dfcdsrc/main/java/net/sf/laja/cdd/testgen/state/PersonState.java:427:502:SE_NO_SERIALVERSIONID 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-#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_262b14_6ea2a6src/main/java/net/bootsfaces/render/H.java:172:172:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_3b207b_074c39src/main/java/net/bootsfaces/render/H.java:175:175:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_3b207b_074c39src/main/java/net/bootsfaces/render/H.java:169:169:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_3b207b_074c39src/main/java/net/bootsfaces/render/H.java:172:172:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_3b207b_074c39src/main/java/net/bootsfaces/render/H.java:173:173:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_3b207b_074c39src/main/java/net/bootsfaces/render/H.java:171:171:MS_PKGPROTECT -#Illegal_Line_Position:TheCoder4eu-BootsFaces-OSP_634812_c80707src/main/java/net/bootsfaces/component/tabView/TabView.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_8385b7_db33aesrc/main/java/net/bootsfaces/component/switchComponent/Switch.java:46:53:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_b55074_210515src/main/java/net/bootsfaces/render/H.java:171:171:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_b55074_210515src/main/java/net/bootsfaces/render/H.java:175:175:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_b55074_210515src/main/java/net/bootsfaces/render/H.java:173:173:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_b55074_210515src/main/java/net/bootsfaces/render/H.java:172:172:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_b55074_210515src/main/java/net/bootsfaces/render/H.java:174:174:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_b55074_210515src/main/java/net/bootsfaces/render/H.java:169:169:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_f05180_8385b7src/main/java/net/bootsfaces/render/H.java:174:174:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_f05180_8385b7src/main/java/net/bootsfaces/render/H.java:169:169:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_f05180_8385b7src/main/java/net/bootsfaces/render/H.java:171:171:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_f05180_8385b7src/main/java/net/bootsfaces/render/H.java:170:170:MS_PKGPROTECT -#Null_Violation_Hunk:TheCoder4eu-BootsFaces-OSP_f05180_8385b7src/main/java/net/bootsfaces/render/H.java:172:172:MS_PKGPROTECT -#Null_Violation_Hunk:thervh70-SEM_Team9_0c9e8d_b07216src/main/java/nl/tudelft/ti2206/group9/entities/Coin.java:31:31:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:thinkaurelius-titan_02f228_22ccebsrc/main/java/com/thinkaurelius/faunus/hdfs/GraphFilter.java:15:25:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:thinkaurelius-titan_104742_6723c0src/main/java/com/thinkaurelius/faunus/hdfs/OnlyGraphFilter.java:15:25:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:thinkaurelius-titan_99e32d_74a81csrc/main/java/com/thinkaurelius/faunus/io/graph/FaunusElement.java:17:17:EQ_COMPARETO_USE_OBJECT_EQUALS -#Null_Violation_Hunk:thinkaurelius-titan_9f8867_f1e139src/main/java/com/thinkaurelius/faunus/FaunusGraph.java:650:655:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:thinkaurelius-titan_b696b7_730e9fsrc/main/java/com/thinkaurelius/faunus/hdfs/NoSideEffectFilter.java:15:25:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:thinkaurelius-titan_c28673_c311d3src/main/java/com/thinkaurelius/faunus/mapreduce/FaunusCompiler.java:637:647:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:thinkaurelius-titan_c311d3_57a932src/main/java/com/thinkaurelius/faunus/hdfs/HDFSTools.java:100:110:SE_NO_SERIALVERSIONID -#Null_Violation_Hunk:thinkaurelius-titan_e6fe1d_c349a2src/main/java/com/thinkaurelius/faunus/io/formats/FaunusTextInputFormat.java:17:17:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:thinkofdeath-ThinkMap_a9ba1b_ea8eecclient/src/main/java/uk/co/thinkofdeath/mapviewer/worker/Worker.java:49:49:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:thinkofdeath-ThinkMap_cea619_639205bukkit/src/main/java/think/webglmap/bukkit/ChunkManager.java:77:117:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:thomasjungblut-thomasjungblut-common_536bfe_c40d4asrc/de/jungblut/classification/nn/MultilayerPerceptronCostFunction.java:253:253:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:threerings-clyde_7d9052_2c8783src/main/java/com/threerings/config/ManagedConfig.java:59:59:URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:timmolter-XChart_0c9e93_4e918dsrc/main/java/com/xeiam/xchart/swing/SwingWrapper.java:162:176:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tinkerpop-blueprints_6f6ce4_fca85bblueprints-neo4j2-graph/src/main/java/com/tinkerpop/blueprints/impls/neo4j2/Neo4j2Vertex.java:92:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tinkerpop-blueprints_6f6ce4_fca85bblueprints-neo4j2-graph/src/main/java/com/tinkerpop/blueprints/impls/neo4j2/Neo4j2Vertex.java:135:160:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tinkerpop-blueprints_bf2c57_16bd1cblueprints-neo4j2-graph/src/main/java/com/tinkerpop/blueprints/impls/neo4j2/Neo4j2Vertex.java:135:160:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tinkerpop-blueprints_bf2c57_16bd1cblueprints-neo4j2-graph/src/main/java/com/tinkerpop/blueprints/impls/neo4j2/Neo4j2Vertex.java:92:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tomp2p-TomP2P_1236d8_3b963esrc/main/java/net/tomp2p/connection/ChannelCreator.java:166:171:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:tomp2p-TomP2P_1236d8_3b963esrc/main/java/net/tomp2p/connection/ChannelCreator.java:286:291:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:tomp2p-TomP2P_371cb9_051ca1src/main/java/net/tomp2p/connection/Scheduler.java:525:556:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:tomp2p-TomP2P_371cb9_051ca1src/main/java/net/tomp2p/connection/Scheduler.java:137:144:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tomp2p-TomP2P_371cb9_051ca1src/main/java/net/tomp2p/connection/Scheduler.java:148:239:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:tomp2p-TomP2P_371cb9_051ca1src/main/java/net/tomp2p/connection/Scheduler.java:426:503:RI_REDUNDANT_INTERFACES -#Null_Violation_Hunk:tomp2p-TomP2P_371cb9_051ca1src/main/java/net/tomp2p/peers/PeerMap.java:78:102:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tomp2p-TomP2P_371cb9_051ca1src/main/java/net/tomp2p/upnp/ActionMessage.java:593:593:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tomp2p-TomP2P_4a6971_6f2a7csrc/main/java/net/tomp2p/p2p/builder/DHTBuilder.java:237:237:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:tomp2p-TomP2P_4a6971_6f2a7csrc/main/java/net/tomp2p/upnp/ActionMessage.java:526:526:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:tomp2p-TomP2P_77ad45_6f71a2core/src/main/java/net/tomp2p/storage/Data.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:tomp2p-TomP2P_c2f081_ed8a9acore/src/main/java/net/tomp2p/message/Message.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:tomp2p-TomP2P_c2f081_ed8a9acore/src/main/java/net/tomp2p/message/Message.java:-1:-1:SE_TRANSIENT_FIELD_NOT_RESTORED -#Illegal_Line_Position:tomp2p-TomP2P_c2f081_ed8a9acore/src/main/java/net/tomp2p/storage/Data.java:-1:-1:SE_BAD_FIELD -#Null_Violation_Hunk:tomp2p-TomP2P_f650c9_541772src/main/java/net/tomp2p/connection/ChannelCreator.java:282:287:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:tranzero-SoftServe_Java-105_Project_218277_adac44src/main/java/com/ita/edu/softserve/web/TripsController.java:30:30:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:tranzero-SoftServe_Java-105_Project_2eb3b1_2c1f09src/main/java/com/ita/edu/softserve/web/TripsController.java:30:30:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:tranzero-SoftServe_Java-105_Project_3bc585_a3b038src/main/java/com/ita/edu/softserve/web/TripsController.java:30:30:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:treasure-data-td-import-java_264e2e_aba834src/main/java/com/treasure_data/file/AlasTimeFormatProcessor.java:22:22:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:treasure-data-td-import-java_8a4bdd_9dd3f1src/main/java/com/treasure_data/bulk_import/BulkImportMain.java:307:307:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:treasure-data-td-import-java_b85804_bb89a7src/main/java/com/treasure_data/bulk_import/upload_parts/TaskResult.java:23:24:NM_SAME_SIMPLE_NAME_AS_SUPERCLASS -#Null_Violation_Hunk:TridentSDK-TridentSDK_38e880_c1099fsrc/main/java/net/tridentsdk/plugin/PluginClassLoader.java:83:83:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:TridentSDK-TridentSDK_58ba68_48be58src/main/java/net/tridentsdk/plugin/cmd/CommandHandler.java:120:142:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:TridentSDK-TridentSDK_79820f_72357esrc/main/java/net/tridentsdk/api/event/player/PlayerInteractEvent.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:TridentSDK-TridentSDK_79820f_72357esrc/main/java/net/tridentsdk/api/event/player/PlayerMoveEvent.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:TridentSDK-TridentSDK_98d727_daa2f0src/main/java/net/tridentsdk/util/WeakEntity.java:367:370:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:TridentSDK-TridentSDK_98d727_daa2f0src/main/java/net/tridentsdk/util/WeakEntity.java:593:593:WMI_WRONG_MAP_ITERATOR -#Null_Violation_Hunk:TridentSDK-TridentSDK_b93a8a_72adb6src/main/java/net/tridentsdk/plugin/cmd/CommandHandler.java:116:138:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:TridentSDK-TridentSDK_c5d69a_e36819src/main/java/net/tridentsdk/world/ChunkLocation.java:32:46:CN_IDIOM -#Illegal_Line_Position:TridentSDK-TridentSDK_c784df_3a2feesrc/main/java/net/tridentsdk/api/Location.java:-1:-1:SE_BAD_FIELD -#Illegal_Line_Position:TridentSDK-TridentSDK_d5dc75_c1dbc8src/main/java/net/tridentsdk/api/event/player/PlayerInteractEvent.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:TridentSDK-TridentSDK_d5dc75_c1dbc8src/main/java/net/tridentsdk/api/event/player/PlayerMoveEvent.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:TridentSDK-TridentSDK_d64633_fcf5a6src/main/java/net/tridentsdk/api/scheduling/TridentRunnable.java:95:95:UWF_UNWRITTEN_FIELD -#Null_Violation_Hunk:TridentSDK-TridentSDK_ff2fba_5d5dbesrc/main/java/net/tridentsdk/plugin/cmd/CommandHandler.java:115:137:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_0eee6d_bac0afcore/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:298:298:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_0eee6d_bac0afcore/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:122:122:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_113b20_969203core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:170:170:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_113b20_969203core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:164:164:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_31bffc_e9bc3fcore/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:130:130:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_31bffc_e9bc3fcore/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:118:118:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_31bffc_e9bc3fcore/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:124:124:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_36e66f_7910e7core/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:166:166:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_3a104b_346272core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:234:234:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_3a104b_346272core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:230:230:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_3a104b_346272core/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:215:215:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_434121_c41c73core/src/main/java/org/fiteagle/core/aaa/CertificateAuthority.java:180:180:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_434121_c41c73core/src/main/java/org/fiteagle/core/aaa/CertificateAuthority.java:172:172:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_434121_c41c73core/src/main/java/org/fiteagle/core/aaa/CertificateAuthority.java:177:177:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_434121_c41c73core/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:35:35:NM_CLASS_NAMING_CONVENTION -#Null_Violation_Hunk:tubav-fiteagle_434121_c41c73core/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:212:212:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:tubav-fiteagle_47ed2a_20e3a1core/src/main/java/org/fiteagle/core/persistence/SQLiteDatabase.java:-1:-1:MS_CANNOT_BE_FINAL -#Null_Violation_Hunk:tubav-fiteagle_5d4f8d_e8e4ddcore/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:210:210:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_7ae1d4_1bfdaccore/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:204:204:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_8ae30a_3420eacore/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:265:265:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_a912f0_575c75core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:221:221:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_a912f0_575c75core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:215:215:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_b2be0b_c17596core/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:298:298:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_b2be0b_c17596core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:122:122:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_c1894a_6aa330core/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:298:298:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_c1894a_6aa330core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:122:122:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_d9594c_44b4d0core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:124:124:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_d9594c_44b4d0core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:130:130:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_dd2dfa_a912f0core/src/main/java/org/fiteagle/core/aaa/AuthenticationHandler.java:130:130:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_deff26_32f8afcore/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:298:298:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_deff26_32f8afcore/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:122:122:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_e89a8a_3bd8edcore/src/main/java/org/fiteagle/core/aaa/CertificateAuthority.java:159:159:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_e89a8a_3bd8edcore/src/main/java/org/fiteagle/core/aaa/CertificateAuthority.java:154:154:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_e89a8a_3bd8edcore/src/main/java/org/fiteagle/core/groupmanagement/SQLiteGroupDatabase.java:116:116:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_e89a8a_3bd8edcore/src/main/java/org/fiteagle/core/groupmanagement/SQLiteGroupDatabase.java:120:120:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_e8da92_da460ecore/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:265:265:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_e9bc3f_e8e4ddcore/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:158:158:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f1503a_d7c963core/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:298:298:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f1503a_d7c963core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:122:122:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f3cf3c_04ea73core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:230:230:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f3cf3c_04ea73core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:234:234:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f3cf3c_04ea73core/src/main/java/org/fiteagle/core/userdatabase/UserDBManager.java:215:215:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f6b16f_b538b1core/src/main/java/org/fiteagle/core/aaa/KeyManagement.java:298:298:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tubav-fiteagle_f6b16f_b538b1core/src/main/java/org/fiteagle/core/aaa/KeyStoreManagement.java:122:122:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:tuwiendsg-rSYBL_08cc08_589cf7rSYBL-control-service-pom/rSYBL-learning-engine/src/main/java/at/ac/tuwien/dsg/rSybl/learningEngine/advise/kMeans/Clustering.java:105:121:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:twilio-twilio-java_21242f_0f2a8dsrc/main/java/com/twilio/sdk/AppEngineClientConnectionManager.java:28:38:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:twilio-twilio-java_482120_2c8b2dsrc/main/java/com/twilio/sdk/resource/NextGenInstanceResource.java:-1:-1:STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE -#Null_Violation_Hunk:twilio-twilio-java_51a41b_593584src/main/java/com/twilio/sdk/AppEngineClientConnectionManager.java:28:38:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:twilio-twilio-java_531510_e63ae5src/main/java/com/twilio/sdk/resource/InstanceResource.java:-1:-1:STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE -#Illegal_Line_Position:twilio-twilio-java_6e52b6_8d9c16src/main/java/com/twilio/sdk/taskrouter/TaskRouterCapability.java:-1:-1:MF_CLASS_MASKS_FIELD -#Illegal_Line_Position:twilio-twilio-java_761e45_378c17src/main/java/com/twilio/sdk/resource/InstanceResource.java:-1:-1:STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE -#Null_Violation_Hunk:twilio-twilio-java_d32130_0620eesrc/main/java/com/twilio/sdk/AppEngineClientConnectionManager.java:28:38:SIC_INNER_SHOULD_BE_STATIC -#Illegal_Line_Position:ucam-cl-dtg-urop-2013-questions_583746_1e0e63src/main/java/uk/ac/cam/sup/models/QuestionSet.java:-1:-1:UUF_UNUSED_FIELD -#Illegal_Line_Position:ucam-cl-dtg-urop-2013-questions_72921e_d9311csrc/main/java/uk/ac/cam/sup/models/QuestionSet.java:-1:-1:UUF_UNUSED_FIELD -#Null_Violation_Hunk:UnifiedViews-Plugin-DevEnv_6b5c02_1a23dduv-dpu-helpers/src/main/java/eu/unifiedviews/helpers/dpu/extension/faulttolerance/FaultTolerance.java:131:169:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Null_Violation_Hunk:UnifiedViews-Plugin-DevEnv_878992_bcf189uv-dpu-helpers/src/main/java/eu/unifiedviews/helpers/dpu/extension/faulttolerance/FaultTolerance.java:131:169:SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -#Illegal_Line_Position:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Illegal_Line_Position:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:-1:-1:UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:254:254:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:254:254:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:233:233:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:254:254:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -#Null_Violation_Hunk:UniTime-unitime_78be2f_616163JavaSource/org/unitime/timetable/onlinesectioning/custom/purdue/XEInterface.java:98:98:UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD 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-#Null_Violation_Hunk:void256-nifty-gui_e0f940_2bb2ecsrc/main/java/de/lessvoid/nifty/controls/scrollbar/UpdateScrollpanelPositionToDisplayElement.java:54:54:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:void256-nifty-gui_ef7352_4e9550src/main/java/de/lessvoid/nifty/renderer/lwjgl/render/font/ColorValueParser.java:11:36:SIC_INNER_SHOULD_BE_STATIC -#Null_Violation_Hunk:void256-nifty-gui_f154ff_64cfb3nifty/src/main/java/de/lessvoid/niftyinternal/node/NiftyNodeImplContent.java:57:57:UC_USELESS_VOID_METHOD -#Null_Violation_Hunk:webbit-webbit_a307e8_33e7aesrc/main/java/org/webbitserver/handler/AbstractResourceHandler.java:80:80:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:webbit-webbit_a307e8_33e7aesrc/main/java/org/webbitserver/handler/AbstractResourceHandler.java:88:88:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:webbit-webbit_c7b531_ad9db4src/main/java/org/webbitserver/handler/AbstractResourceHandler.java:75:75:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:webbit-webbit_f98005_3ec690src/main/java/org/webbitserver/handler/AbstractResourceHandler.java:80:80:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:webbit-webbit_f98005_3ec690src/main/java/org/webbitserver/handler/AbstractResourceHandler.java:88:88:UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -#Null_Violation_Hunk:weld-core_68dc85_d4e945src/main/java/org/jboss/weld/environment/se/Weld.java:74:74:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:weld-core_d4e945_e91ce1src/main/java/org/jboss/weld/environment/se/discovery/SEBeanDeploymentArchive.java:49:49:SIC_INNER_SHOULD_BE_STATIC_ANON -#Null_Violation_Hunk:weld-core_d4e945_e91ce1src/main/java/org/jboss/weld/environment/se/Weld.java:100:100:SIC_INNER_SHOULD_BE_STATIC_ANON -#Illegal_Line_Position:Weltraumschaf-commons_0cde07_2f8250src/main/java/de/weltraumschaf/commons/shell/DefaultParser.java:-1:-1:UWF_NULL_FIELD 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51 : 297 -prev_VincSch-Photoplatform_Angular_Spring_9a7764_15560bsrc#main#java#de#htw#sdf#photoplatform#webservice#dto#PurchaseData.java : 27 : 82 -prev_VincSch-Photoplatform_Angular_Spring_f98c9b_4e7165src#main#java#de#htw#sdf#photoplatform#webservice#dto#PurchaseData.java : 27 : 82 -prev_wildfly-security-wildfly-elytron_db2858_dd2ef6src#main#java#org#wildfly#security#password#impl#UnixSHACryptPasswordImpl.java : 40 : 108 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_649efa_615e32zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 46 : 214 -prev_zanata-zanata-api_8d4828_aeeb97zanata-common-api#src#main#java#org#zanata#rest#dto#stats#contribution#ContributionStatistics.java : 13 : 94 -prev_zanata-zanata-api_e377f3_b5c470zanata-common-api#src#main#java#org#zanata#common#TranslationStatistics.java : 60 : 259 -prev_zendesk-maxwell_23869d_024cf8src#main#java#com#zendesk#maxwell#RowMap.java : 16 : 135 -prev_zendesk-maxwell_2c9ae7_a203bdsrc#main#java#com#zendesk#maxwell#RowMap.java : 16 : 135 -prev_zendesk-maxwell_3fdf2a_23869dsrc#main#java#com#zendesk#maxwell#RowMap.java : 9 : 47 -prev_zendesk-maxwell_71a288_f50122src#main#java#com#zendesk#maxwell#MaxwellAbstractRowsEvent.java : 200 : 237 -prev_zendesk-maxwell_739033_e6c89bsrc#main#java#com#zendesk#maxwell#MaxwellAbstractRowsEvent.java : 199 : 233 -prev_zendesk-maxwell_8aec1e_534cf7src#main#java#com#zendesk#maxwell#RowMap.java : 9 : 47 -prev_zendesk-maxwell_9bb17d_2272b2src#main#java#com#zendesk#maxwell#MaxwellAbstractRowsEvent.java : 200 : 237 -prev_zendesk-maxwell_d9b984_d0f921src#main#java#com#zendesk#maxwell#RowMap.java : 9 : 47 -prev_zendesk-maxwell_e6c89b_8f1f0fsrc#main#java#com#zendesk#maxwell#MaxwellAbstractRowsEvent.java : 200 : 237 -prev_zendesk-maxwell_f50122_2c9ae7src#main#java#com#zendesk#maxwell#RowMap.java : 9 : 47 -CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE -prev_ClemsonRSRG-RESOLVE_9ee405_202d6dsrc#main#java#edu#clemson#cs#r2jt#absyn#FunctionArgList.java : 100 : 109 diff --git a/logs/Null.txt b/logs/Null.txt deleted file mode 100644 index 3b1b8cd..0000000 --- a/logs/Null.txt +++ /dev/null @@ -1,124 +0,0 @@ -1 - BC_VACUOUS_INSTANCEOF Ignore it. no source code, no source code change - CN_IDIOM_NO_SUPER_CALL Ignore it. no source code, no source code change - CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE Ignore it. no source code, no source code change - DLS_DEAD_LOCAL_STORE Ignore it. no source code, no source code change - DM_DEFAULT_ENCODING - DM_NUMBER_CTOR - DM_STRING_CTOR - DM_STRING_VOID_CTOR - DP_DO_INSIDE_DO_PRIVILEGED - EI_EXPOSE_REP - EQ_COMPARETO_USE_OBJECT_EQUALS - EQ_DOESNT_OVERRIDE_EQUALS - EQ_SELF_USE_OBJECT - HE_EQUALS_USE_HASHCODE - HE_HASHCODE_USE_OBJECT_EQUALS - HE_INHERITS_EQUALS_USE_HASHCODE - IS2_INCONSISTENT_SYNC - MS_CANNOT_BE_FINAL - MS_MUTABLE_ARRAY - MS_PKGPROTECT - MS_SHOULD_BE_FINAL - NM_CLASS_NAMING_CONVENTION - NM_CLASS_NOT_EXCEPTION - NM_SAME_SIMPLE_NAME_AS_SUPERCLASS - OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE - OS_OPEN_STREAM - OS_OPEN_STREAM_EXCEPTION_PATH - RI_REDUNDANT_INTERFACES - SA_FIELD_DOUBLE_ASSIGNMENT - SE_COMPARATOR_SHOULD_BE_SERIALIZABLE - SE_NO_SERIALVERSIONID - SIO_SUPERFLUOUS_INSTANCEOF - UCF_USELESS_CONTROL_FLOW - UG_SYNC_SET_UNSYNC_GET - UPM_UNCALLED_PRIVATE_METHOD - URF_UNREAD_FIELD - URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD - UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR - UWF_UNWRITTEN_FIELD - UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD - WMI_WRONG_MAP_ITERATOR --1 - CI_CONFUSED_INHERITANCE - CO_ABSTRACT_SELF - DMI_COLLECTION_OF_URLS - EQ_ABSTRACT_SELF - HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS - JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS - ME_MUTABLE_ENUM_FIELD - MF_CLASS_MASKS_FIELD - MS_CANNOT_BE_FINAL - MS_PKGPROTECT - MS_SHOULD_BE_FINAL - NM_FIELD_NAMING_CONVENTION - NM_SAME_SIMPLE_NAME_AS_INTERFACE - SE_BAD_FIELD - SE_TRANSIENT_FIELD_NOT_RESTORED - STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE - UPM_UNCALLED_PRIVATE_METHOD - UUF_UNUSED_FIELD - UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD - UWF_NULL_FIELD - UWF_UNWRITTEN_FIELD - UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD - VO_VOLATILE_REFERENCE_TO_ARRAY - - - - CI_CONFUSED_INHERITANCE change modifier of fields from protected to private or public, or remove final of class. - CO_ABSTRACT_SELF Interface, remove compareTo() method. - - SE_NO_SERIALVERSIONID add a field: serialVersionUID - EQ_ABSTRACT_SELF Interface, remove compareTo() method. - EQ_COMPARETO_USE_OBJECT_EQUALS: Update or Delete compareTo(), Add equals() - EQ_DOESNT_OVERRIDE_EQUALS override equals() - HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS remove equals() only one instance - ME_MUTABLE_ENUM_FIELD enum, field add final. - MF_CLASS_MASKS_FIELD, change super class or delete the field with a same name in super class. - MS_SHOULD_BE_FINAL Add final key word - STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE remove public static final DateFormat DATE_FORMAT.... or SimpleDateFormat - UUF_UNUSED_FIELD remove unused fields. not sure - UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD field - UWF_NULL_FIELD update field, remove field - UWF_UNWRITTEN_FIELD field - UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD remove field - VO_VOLATILE_REFERENCE_TO_ARRAY field - - all GumTree results. class, field, method, //statements. - -NM_SAME_SIMPLE_NAME_AS_INTERFACE rename class name or remove super class -NM_SAME_SIMPLE_NAME_AS_SUPERCLASS, class name -NM_METHOD_NAMING_CONVENTION -NM_CLASS_NAMING_CONVENTION class name -NM_CLASS_NOT_EXCEPTION class name -RI_REDUNDANT_INTERFACES class implemented interface -SE_NO_SUITABLE_CONSTRUCTOR Serializable Class level remove Serializable interface and serialVersionUID - -SIC_INNER_SHOULD_BE_STATIC add static to inner class, not sure, delete it, 如果是匿名内部类，该如何处理？ ，其他的直接内部类的范围。 -SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS 同上 -=== -CO_ABSTRACT_SELF inner class -SE_INNER_CLASS inner class -SE_COMPARATOR_SHOULD_BE_SERIALIZABLE, inner class, 读definition -SE_BAD_FIELD_INNER_CLASS inner class -SIC_INNER_SHOULD_BE_STATIC_ANON inner class - -HE_INHERITS_EQUALS_USE_HASHCODE inner class or class -CN_IDIOM add clone method. or update clone method - -DM_NUMBER_CTOR multi v multi patches -EQ_COMPARETO_USE_OBJECT_EQUALS, the same as before -IC_INIT_CIRCULARITY, multi V, multi patches> - - - -SE_NO_SUITABLE_CONSTRUCTOR_FOR_EXTERNALIZATION, add a constructor or add public to old constructor, - - - -NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR - -SE_NO_SERIALVERSIONID change superclass or interface, add field or remove @SuppressWarnings("serial"), some are inner class - \ No newline at end of file diff --git a/logs/NullSourceCode.txt b/logs/NullSourceCode.txt deleted file mode 100644 index 75e1853..0000000 --- a/logs/NullSourceCode.txt +++ /dev/null @@ -1,1305 +0,0 @@ -UUF_UNUSED_FIELD : prev_0xCopy-RelaxFactory_aa9d34_931213rxf-couch#src#main#java#rxf#couch#driver#CouchMetaDriver.java : -1 : -1 -NM_FIELD_NAMING_CONVENTION : prev_aaron-santos-lanterna_4eac0e_33c490src#main#java#com#googlecode#lanterna#gui#component#TextGrid.java : -1 : -1 -NM_FIELD_NAMING_CONVENTION : 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prev_Activiti-Activiti_7dce14_94b753modules#activiti-engine#src#main#java#org#activiti#engine#impl#bpmn#helper#MessageThrowingEventListener.java : -1 : -1 -MS_SHOULD_BE_FINAL : prev_Activiti-Activiti_7dce14_94b753modules#activiti-engine#src#main#java#org#activiti#engine#impl#calendar#DurationBusinessCalendar.java : 22 : 22 -UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR : prev_Activiti-Activiti_8646b1_b13e7cmodules#activiti-engine#src#main#java#org#activiti#engine#ProcessEngineConfiguration.java : 507 : 507 -MS_SHOULD_BE_FINAL : prev_Activiti-Activiti_90446c_2d592dmodules#activiti-engine#src#main#java#org#activiti#engine#impl#calendar#DurationBusinessCalendar.java : 22 : 22 -MF_CLASS_MASKS_FIELD : prev_Activiti-Activiti_90446c_2d592dmodules#activiti-engine#src#main#java#org#activiti#engine#impl#cmd#SubmitTaskFormCmd.java : -1 : -1 -MF_CLASS_MASKS_FIELD : 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-1 : -1 -MS_SHOULD_BE_FINAL : prev_Activiti-Activiti_f6c242_fc85e3modules#activiti-engine#src#main#java#org#activiti#engine#impl#calendar#DurationBusinessCalendar.java : 22 : 22 -MF_CLASS_MASKS_FIELD : prev_Activiti-Activiti_f6c242_fc85e3modules#activiti-engine#src#main#java#org#activiti#engine#impl#cmd#SubmitTaskFormCmd.java : -1 : -1 -MF_CLASS_MASKS_FIELD : prev_Activiti-Activiti_fce83e_08c2b8modules#activiti-engine#src#main#java#org#activiti#engine#impl#bpmn#helper#MessageThrowingEventListener.java : -1 : -1 -UUF_UNUSED_FIELD : prev_adangel-pmd_3aa04a_ddacf7pmd#src#main#java#net#sourceforge#pmd#util#datasource#ReaderDataSource.java : -1 : -1 -UUF_UNUSED_FIELD : prev_adangel-pmd_4f50ec_4a49e6pmd#src#main#java#net#sourceforge#pmd#lang#plsql#rule#codesize#TooManyFieldsRule.java : -1 : -1 -UWF_NULL_FIELD : prev_adangel-pmd_782135_cb5feapmd#src#main#java#net#sourceforge#pmd#cli#PMDParameters.java : -1 : -1 -UUF_UNUSED_FIELD : prev_aeshell-aesh_1780ee_938c76src#test#java#org#jboss#aesh#console#aesh#AeshCommandDynamicTest.java : -1 : -1 -MS_CANNOT_BE_FINAL : prev_aherbert-GDSC-SMLM_b6538a_2db8f3src#main#java#gdsc#smlm#ij#utils#Utils.java : -1 : -1 -UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR : prev_aherbert-GDSC-SMLM_e23773_c6e912src#main#java#gdsc#smlm#fitting#function#gaussian#FreeCircularGaussian2DFunction.java : 59 : 59 -UWF_NULL_FIELD : prev_aherbert-GDSC-SMLM_f32d6c_47ab63src#main#java#gdsc#smlm#fitting#function#PoissonGammaGaussianLikelihoodWrapper.java : -1 : -1 -UWF_NULL_FIELD : prev_aherbert-GDSC-SMLM_f32d6c_47ab63src#main#java#gdsc#smlm#fitting#function#PoissonGaussianLikelihoodWrapper.java : -1 : -1 -UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD : prev_aht-group-ofx_0e06e8_180211core#src#main#java#org#openfuxml#renderer#latex#AbstractOfxLatexRenderer.java : 113 : 113 -EQ_ABSTRACT_SELF : prev_airlift-airlift_dd0c0a_a06897src#main#java#com#facebook#presto#Cursor.java : -1 : -1 -UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR : prev_alibaba-druid_3eb0b6_aaf1f2src#main#java#com#alibaba#druid#sql#ast#statement#SQLJoinTableSource.java : 73 : 73 -SE_TRANSIENT_FIELD_NOT_RESTORED : prev_allanbank-mongodb-async-driver_222a77_541915src#main#java#com#allanbank#mongodb#Credential.java : -1 : -1 -SE_TRANSIENT_FIELD_NOT_RESTORED : prev_allanbank-mongodb-async-driver_2df4f3_405b07src#main#java#com#allanbank#mongodb#MongoClientConfiguration.java : -1 : -1 -SE_TRANSIENT_FIELD_NOT_RESTORED : prev_allanbank-mongodb-async-driver_4481cc_2bbf92src#main#java#com#allanbank#mongodb#bson#impl#RootDocument.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_5ca324_112eb3src#main#java#com#allanbank#mongodb#bson#builder#impl#AbstractBuilder.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_98a1be_348fccsrc#main#java#com#allanbank#mongodb#connection#FutureCallback.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_98a1be_348fccsrc#main#java#com#allanbank#mongodb#connection#FutureCallback.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_98a901_e8cac9src#main#java#com#allanbank#mongodb#builder#AggregationGeoNear.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_98a901_e8cac9src#main#java#com#allanbank#mongodb#builder#GeoJson.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_98a901_e8cac9src#main#java#com#allanbank#mongodb#Credential.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_98a901_e8cac9src#main#java#com#allanbank#mongodb#error#MongoClientClosedException.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_a264bd_c87300src#main#java#com#allanbank#mongodb#builder#AggregationGeoNear.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_a264bd_c87300src#main#java#com#allanbank#mongodb#builder#GeoJson.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_a264bd_c87300src#main#java#com#allanbank#mongodb#Credential.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_a264bd_c87300src#main#java#com#allanbank#mongodb#error#MongoClientClosedException.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#bson#io#SizeOfVisitor.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#commands#Distinct.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#commands#Find.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#commands#FindAndModify.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#commands#GroupBy.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#commands#MapReduce.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#error#ReplyException.java : -1 : -1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#MongoDbConfiguration.java : -1 : -1 -CI_CONFUSED_INHERITANCE : prev_allanbank-mongodb-async-driver_c760f4_8c7984src#main#java#com#allanbank#mongodb#util#IOUtils.java : -1 : -1 -EQ_DOESNT_OVERRIDE_EQUALS : prev_allanbank-mongodb-async-driver_cfb78d_436794src#main#java#com#allanbank#mongodb#client#message#AggregateCommand.java : 1 : 1 -SE_BAD_FIELD : prev_allanbank-mongodb-async-driver_e9d4ca_c3ef67src#main#java#com#allanbank#mongodb#error#ServerVersionException.java : -1 : -1 -UWF_NULL_FIELD : prev_anba-es6draft_2c2cc7_74ade4src#main#java#com#github#anba#es6draft#repl#Repl.java : -1 : -1 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-EQ_COMPARETO_USE_OBJECT_EQUALS -SQL_NONCONSTANT_STRING_PASSED_TO_EXECUTE -NP_NULL_ON_SOME_PATH_EXCEPTION -NP_UNWRITTEN_FIELD -MS_MUTABLE_COLLECTION_PKGPROTECT -UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE -DMI_HARDCODED_ABSOLUTE_FILENAME -SE_BAD_FIELD -DM_STRING_TOSTRING -UUF_UNUSED_FIELD -ICAST_INTEGER_MULTIPLY_CAST_TO_LONG -EC_UNRELATED_TYPES -BC_VACUOUS_INSTANCEOF -ICAST_IDIV_CAST_TO_DOUBLE -RCN_REDUNDANT_NULLCHECK_OF_NULL_VALUE -ES_COMPARING_PARAMETER_STRING_WITH_EQ -RV_RETURN_VALUE_IGNORED -CI_CONFUSED_INHERITANCE -DB_DUPLICATE_SWITCH_CLAUSES -ODR_OPEN_DATABASE_RESOURCE_EXCEPTION_PATH -NP_ALWAYS_NULL -RpC_REPEATED_CONDITIONAL_TEST -SE_BAD_FIELD_STORE -NP_NULL_PARAM_DEREF -GC_UNRELATED_TYPES -DLS_DEAD_LOCAL_STORE_OF_NULL -RC_REF_COMPARISON_BAD_PRACTICE -MS_MUTABLE_ARRAY -SE_INNER_CLASS -UL_UNRELEASED_LOCK_EXCEPTION_PATH -SE_COMPARATOR_SHOULD_BE_SERIALIZABLE -CN_IDIOM_NO_SUPER_CALL -NP_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD -UC_USELESS_VOID_METHOD -NP_NONNULL_PARAM_VIOLATION -DMI_INVOKING_TOSTRING_ON_ARRAY -DP_DO_INSIDE_DO_PRIVILEGED -SF_SWITCH_FALLTHROUGH -NP_BOOLEAN_RETURN_NULL -NM_CLASS_NOT_EXCEPTION -SIO_SUPERFLUOUS_INSTANCEOF -NP_GUARANTEED_DEREF - -UL_UNRELEASED_LOCK -IP_PARAMETER_IS_DEAD_BUT_OVERWRITTEN -HE_INHERITS_EQUALS_USE_HASHCODE -MS_CANNOT_BE_FINAL -DB_DUPLICATE_BRANCHES -STCAL_INVOKE_ON_STATIC_DATE_FORMAT_INSTANCE -MS_MUTABLE_COLLECTION -IL_INFINITE_RECURSIVE_LOOP -VO_VOLATILE_INCREMENT -JLM_JSR166_UTILCONCURRENT_MONITORENTER -NP_NULL_PARAM_DEREF_NONVIRTUAL -DM_STRING_CTOR -UR_UNINIT_READ -XFB_XML_FACTORY_BYPASS -RV_EXCEPTION_NOT_THROWN -UI_INHERITANCE_UNSAFE_GETRESOURCE -VA_FORMAT_STRING_EXTRA_ARGUMENTS_PASSED -IT_NO_SUCH_ELEMENT -NM_CLASS_NAMING_CONVENTION -RC_REF_COMPARISON -RC_REF_COMPARISON_BAD_PRACTICE_BOOLEAN -DLS_DEAD_LOCAL_STORE_SHADOWS_FIELD -HE_EQUALS_NO_HASHCODE -NS_NON_SHORT_CIRCUIT -NP_DEREFERENCE_OF_READLINE_VALUE -NP_GUARANTEED_DEREF_ON_EXCEPTION_PATH -EQ_DOESNT_OVERRIDE_EQUALS -DM_STRING_VOID_CTOR -DP_CREATE_CLASSLOADER_INSIDE_DO_PRIVILEGED -BIT_SIGNED_CHECK -ME_ENUM_FIELD_SETTER -BC_EQUALS_METHOD_SHOULD_WORK_FOR_ALL_OBJECTS -NS_DANGEROUS_NON_SHORT_CIRCUIT -NP_EQUALS_SHOULD_HANDLE_NULL_ARGUMENT -SR_NOT_CHECKED -RR_NOT_CHECKED -UUF_UNUSED_PUBLIC_OR_PROTECTED_FIELD -VA_FORMAT_STRING_MISSING_ARGUMENT -EC_BAD_ARRAY_COMPARE -NP_NONNULL_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR -DM_BOXED_PRIMITIVE_FOR_COMPARE -NP_NULL_ON_SOME_PATH_MIGHT_BE_INFEASIBLE -UMAC_UNCALLABLE_METHOD_OF_ANONYMOUS_CLASS -UWF_NULL_FIELD -CO_COMPARETO_INCORRECT_FLOATING -NP_NULL_PARAM_DEREF_ALL_TARGETS_DANGEROUS -NO_NOTIFY_NOT_NOTIFYALL -SC_START_IN_CTOR -RV_RETURN_VALUE_IGNORED_INFERRED -UM_UNNECESSARY_MATH -SA_FIELD_SELF_ASSIGNMENT -BC_IMPOSSIBLE_CAST -LI_LAZY_INIT_UPDATE_STATIC -NP_TOSTRING_COULD_RETURN_NULL -SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS -AT_OPERATION_SEQUENCE_ON_CONCURRENT_ABSTRACTION -EQ_UNUSUAL -SE_NO_SUITABLE_CONSTRUCTOR -UW_UNCOND_WAIT -MF_CLASS_MASKS_FIELD -FE_TEST_IF_EQUAL_TO_NOT_A_NUMBER -IA_AMBIGUOUS_INVOCATION_OF_INHERITED_OR_OUTER_METHOD -SE_BAD_FIELD_INNER_CLASS -RV_NEGATING_RESULT_OF_COMPARETO -ISC_INSTANTIATE_STATIC_CLASS -HE_HASHCODE_USE_OBJECT_EQUALS -DM_BOOLEAN_CTOR -DMI_RANDOM_USED_ONLY_ONCE -EQ_CHECK_FOR_OPERAND_NOT_COMPATIBLE_WITH_THIS -DM_GC -NM_SAME_SIMPLE_NAME_AS_SUPERCLASS -EC_NULL_ARG -EQ_SELF_USE_OBJECT -RV_ABSOLUTE_VALUE_OF_RANDOM_INT -SE_NO_SUITABLE_CONSTRUCTOR_FOR_EXTERNALIZATION -MS_EXPOSE_REP -SE_TRANSIENT_FIELD_NOT_RESTORED -IM_AVERAGE_COMPUTATION_COULD_OVERFLOW -NP_METHOD_PARAMETER_TIGHTENS_ANNOTATION -NP_METHOD_RETURN_RELAXING_ANNOTATION -UG_SYNC_SET_UNSYNC_GET -NM_FIELD_NAMING_CONVENTION -MS_OOI_PKGPROTECT -UCF_USELESS_CONTROL_FLOW_NEXT_LINE -VA_FORMAT_STRING_BAD_CONVERSION -BX_BOXING_IMMEDIATELY_UNBOXED_TO_PERFORM_COERCION -SA_FIELD_DOUBLE_ASSIGNMENT -BC_BAD_CAST_TO_CONCRETE_COLLECTION -SF_DEAD_STORE_DUE_TO_SWITCH_FALLTHROUGH -MS_FINAL_PKGPROTECT -DMI_COLLECTION_OF_URLS -INT_BAD_COMPARISON_WITH_SIGNED_BYTE -RV_CHECK_FOR_POSITIVE_INDEXOF -RE_CANT_USE_FILE_SEPARATOR_AS_REGULAR_EXPRESSION -RU_INVOKE_RUN -BC_IMPOSSIBLE_DOWNCAST_OF_TOARRAY -ICAST_BAD_SHIFT_AMOUNT -ICAST_INT_CAST_TO_FLOAT_PASSED_TO_ROUND -DM_BOXED_PRIMITIVE_TOSTRING -UR_UNINIT_READ_CALLED_FROM_SUPER_CONSTRUCTOR -WA_NOT_IN_LOOP -CN_IDIOM -DMI_BLOCKING_METHODS_ON_URL -EC_UNRELATED_CLASS_AND_INTERFACE -SWL_SLEEP_WITH_LOCK_HELD -IM_BAD_CHECK_FOR_ODD -RE_POSSIBLE_UNINTENDED_PATTERN -INT_BAD_COMPARISON_WITH_NONNEGATIVE_VALUE -ICAST_INT_CAST_TO_DOUBLE_PASSED_TO_CEIL -EQ_OVERRIDING_EQUALS_NOT_SYMMETRIC -LG_LOST_LOGGER_DUE_TO_WEAK_REFERENCE -DLS_DEAD_LOCAL_STORE_IN_RETURN -J2EE_STORE_OF_NON_SERIALIZABLE_OBJECT_INTO_SESSION -NP_STORE_INTO_NONNULL_FIELD -RANGE_ARRAY_INDEX -IL_INFINITE_LOOP -DC_DOUBLECHECK -NN_NAKED_NOTIFY -EC_UNRELATED_TYPES_USING_POINTER_EQUALITY -SE_PRIVATE_READ_RESOLVE_NOT_INHERITED -INT_VACUOUS_BIT_OPERATION -DM_NEXTINT_VIA_NEXTDOUBLE -VA_FORMAT_STRING_ILLEGAL -DMI_INVOKING_HASHCODE_ON_ARRAY -RV_DONT_JUST_NULL_CHECK_READLINE -RE_BAD_SYNTAX_FOR_REGULAR_EXPRESSION -SA_LOCAL_SELF_ASSIGNMENT_INSTEAD_OF_FIELD -NM_VERY_CONFUSING -MSF_MUTABLE_SERVLET_FIELD -BC_IMPOSSIBLE_INSTANCEOF -SA_LOCAL_SELF_COMPARISON -SA_LOCAL_SELF_ASSIGNMENT -IC_SUPERCLASS_USES_SUBCLASS_DURING_INITIALIZATION -CNT_ROUGH_CONSTANT_VALUE -SI_INSTANCE_BEFORE_FINALS_ASSIGNED -DLS_DEAD_STORE_OF_CLASS_LITERAL -RV_ABSOLUTE_VALUE_OF_HASHCODE -NM_SAME_SIMPLE_NAME_AS_INTERFACE -HE_HASHCODE_NO_EQUALS -DM_NEW_FOR_GETCLASS -SA_FIELD_SELF_COMPARISON -NM_METHOD_CONSTRUCTOR_CONFUSION -EQ_COMPARING_CLASS_NAMES -UC_USELESS_CONDITION_TYPE -RV_01_TO_INT -SA_LOCAL_DOUBLE_ASSIGNMENT -SQL_BAD_RESULTSET_ACCESS -EQ_GETCLASS_AND_CLASS_CONSTANT -BSHIFT_WRONG_ADD_PRIORITY -HRS_REQUEST_PARAMETER_TO_HTTP_HEADER -DMI_USING_REMOVEALL_TO_CLEAR_COLLECTION -STCAL_STATIC_SIMPLE_DATE_FORMAT_INSTANCE -FI_FINALIZER_NULLS_FIELDS -ML_SYNC_ON_FIELD_TO_GUARD_CHANGING_THAT_FIELD -JCIP_FIELD_ISNT_FINAL_IN_IMMUTABLE_CLASS -CO_COMPARETO_RESULTS_MIN_VALUE -IMSE_DONT_CATCH_IMSE -QF_QUESTIONABLE_FOR_LOOP -MWN_MISMATCHED_NOTIFY -RV_RETURN_VALUE_OF_PUTIFABSENT_IGNORED -DMI_NONSERIALIZABLE_OBJECT_WRITTEN -BC_BAD_CAST_TO_ABSTRACT_COLLECTION -SW_SWING_METHODS_INVOKED_IN_SWING_THREAD -EC_ARRAY_AND_NONARRAY -NP_NULL_INSTANCEOF -MTIA_SUSPECT_SERVLET_INSTANCE_FIELD -EQ_ALWAYS_FALSE -INT_BAD_COMPARISON_WITH_INT_VALUE -NP_OPTIONAL_RETURN_NULL -BX_BOXING_IMMEDIATELY_UNBOXED -VA_FORMAT_STRING_EXPECTED_MESSAGE_FORMAT_SUPPLIED -BIT_IOR -FI_MISSING_SUPER_CALL -VO_VOLATILE_REFERENCE_TO_ARRAY -SF_DEAD_STORE_DUE_TO_SWITCH_FALLTHROUGH_TO_THROW -DMI_CONSTANT_DB_PASSWORD -NP_IMMEDIATE_DEREFERENCE_OF_READLINE -ML_SYNC_ON_UPDATED_FIELD -HE_USE_OF_UNHASHABLE_CLASS -FI_PUBLIC_SHOULD_BE_PROTECTED -DMI_BIGDECIMAL_CONSTRUCTED_FROM_DOUBLE -TQ_NEVER_VALUE_USED_WHERE_ALWAYS_REQUIRED -XSS_REQUEST_PARAMETER_TO_SERVLET_WRITER -NP_ALWAYS_NULL_EXCEPTION -DM_INVALID_MIN_MAX -NM_WRONG_PACKAGE -MS_SHOULD_BE_REFACTORED_TO_BE_FINAL -DC_PARTIALLY_CONSTRUCTED -WA_AWAIT_NOT_IN_LOOP -INT_VACUOUS_COMPARISON -RV_CHECK_COMPARETO_FOR_SPECIFIC_RETURN_VALUE -RCN_REDUNDANT_COMPARISON_OF_NULL_AND_NONNULL_VALUE -DL_SYNCHRONIZATION_ON_SHARED_CONSTANT -EQ_ALWAYS_TRUE -DMI_EMPTY_DB_PASSWORD -DMI_ENTRY_SETS_MAY_REUSE_ENTRY_OBJECTS -WL_USING_GETCLASS_RATHER_THAN_CLASS_LITERAL -FI_USELESS -VA_FORMAT_STRING_BAD_CONVERSION_FROM_ARRAY -SP_SPIN_ON_FIELD -BOA_BADLY_OVERRIDDEN_ADAPTER -MWN_MISMATCHED_WAIT -NP_CLONE_COULD_RETURN_NULL -CO_ABSTRACT_SELF -DMI_COLLECTIONS_SHOULD_NOT_CONTAIN_THEMSELVES -QBA_QUESTIONABLE_BOOLEAN_ASSIGNMENT -IC_INIT_CIRCULARITY -ICAST_INT_2_LONG_AS_INSTANT -FI_EXPLICIT_INVOCATION -ME_MUTABLE_ENUM_FIELD -RCN_REDUNDANT_COMPARISON_TWO_NULL_VALUES -HE_SIGNATURE_DECLARES_HASHING_OF_UNHASHABLE_CLASS -RS_READOBJECT_SYNC -SQL_BAD_PREPARED_STATEMENT_ACCESS -VA_FORMAT_STRING_BAD_CONVERSION_TO_BOOLEAN -EQ_ABSTRACT_SELF -NP_CLOSING_NULL -RV_REM_OF_HASHCODE -PT_RELATIVE_PATH_TRAVERSAL -TLW_TWO_LOCK_WAIT -INT_BAD_REM_BY_1 -ICAST_QUESTIONABLE_UNSIGNED_RIGHT_SHIFT -VA_PRIMITIVE_ARRAY_PASSED_TO_OBJECT_VARARG -DM_USELESS_THREAD -DMI_DOH -IJU_ASSERT_METHOD_INVOKED_FROM_RUN_METHOD -BIT_IOR_OF_SIGNED_BYTE -DMI_THREAD_PASSED_WHERE_RUNNABLE_EXPECTED -SA_LOCAL_SELF_COMPUTATION - This method performs a nonsensical computation of a local variable with another reference to the same variable (e.g., x&x or x-x). - Because of the nature of the computation, this operation doesn't seem to make sense, and may indicate a typo or a logic error. Double check the computation. -IM_MULTIPLYING_RESULT_OF_IREM - The code multiplies the result of an integer remaining by an integer constant. - Be sure you don't have your operator precedence confused. For example i % 60 * 1000 is (i % 60) * 1000, not i % (60 * 1000). -MS_MUTABLE_HASHTABLE - Field is a mutable Hashtable (MS_MUTABLE_HASHTABLE) - A final static field references a Hashtable and can be accessed by malicious code or by accident from another package. - This code can freely modify the contents of the Hashtable. \ No newline at end of file diff --git a/logs/myLog.log b/logs/myLog.log deleted file mode 100644 index e69de29..0000000 diff --git a/pom.xml b/pom.xml index 016c216..20628f7 100644 --- a/pom.xml +++ b/pom.xml @@ -25,11 +25,11 @@ 1.2 - - edu.lu.uni - simple-utils - 0.0.1-SNAPSHOT - + + + + + @@ -69,17 +69,12 @@ ${logback.version} + - + - - - edu.lu.uni.serval - GitTraveller - 0.0.1-SNAPSHOT - junit diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java deleted file mode 100644 index 648449c..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPattern/utils/CNodeMap.java +++ /dev/null @@ -1,101 +0,0 @@ -package edu.lu.uni.serval.FixPattern.utils; - -import java.util.HashMap; -import java.util.Map; - -public class CNodeMap { - - public static Map map; - - static { - map = new HashMap(); - map.put(20100,"Left"); - map.put(30100,"ActMisc"); - map.put(40000,"FullType"); - map.put(50000,"TypeQualifier"); - map.put(60100,"BaseType"); - map.put(60200,"Pointer"); - map.put(60800,"EnumName"); - map.put(60900,"StructUnionName"); - map.put(61000,"TypeName"); - map.put(70002,"SizeType"); - map.put(70100,"IntType"); - map.put(80001,"CChar"); - map.put(80100,"Si"); - map.put(90002,"UnSigned"); - map.put(100003,"CInt"); - map.put(200000,"ParamList"); - map.put(210000,"DotsParameter"); - map.put(220100,"ParameterType"); - map.put(240100,"Ident"); - map.put(240200,"Constant"); - map.put(240400,"FunCall"); - map.put(240500,"CondExpr"); - map.put(240600,"Sequence"); - map.put(240700,"Assignment"); - map.put(240800,"Postfix"); - map.put(240900,"Infix"); - map.put(241000,"Unary"); - map.put(241100,"Binary"); - map.put(241200,"ArrayAccess"); - map.put(241300,"RecordAccess"); - map.put(241400,"RecordPtAccess"); - map.put(241500,"SizeOfExpr"); - map.put(241600,"SizeOfType"); - map.put(241700,"Cast"); - map.put(241900,"Constructor"); - map.put(242000,"ParenExpr"); - map.put(260300,"ExprStatement"); - map.put(260800,"Asm"); - map.put(270100,"Label"); - map.put(270200,"Case"); - map.put(270300,"CaseRange"); - map.put(270400,"Default"); - map.put(280001,"Continue"); - map.put(280002,"Break"); - map.put(280003,"Return"); - map.put(280100,"Goto"); - map.put(280200,"ReturnExpr"); - map.put(290001,"None"); - map.put(290100,"Some"); - map.put(300100,"If"); - map.put(300200,"Switch"); - map.put(310100,"While"); - map.put(310200,"DoWhile"); - map.put(310300,"For"); - map.put(310400,"MacroIteration"); - map.put(330000,"Compound"); - map.put(340000,"Storage"); - map.put(350100,"DeclList"); - map.put(350200,"MacroDecl"); - map.put(360100,"InitExpr"); - map.put(360200,"InitList"); - map.put(360300,"InitDesignators"); - map.put(370100,"DesignatorField"); - map.put(370200,"DesignatorIndex"); - map.put(370300,"DesignatorRange"); - map.put(380000,"Definition"); - map.put(400100,"Define"); - map.put(400200,"Include"); - map.put(400400,"OtherDirective"); - map.put(410001,"DefineVar"); - map.put(410002,"Undef"); - map.put(410100,"DefineFunc"); - map.put(420001,"DefineEmpty"); - map.put(420100,"DefineExpr"); - map.put(420200,"DefineStmt"); - map.put(420400,"DefineDoWhileZero"); - map.put(420600,"DefineInit"); - map.put(440100,"IfdefDirective"); - map.put(450100,"Declaration"); - map.put(450200,"Definition"); - map.put(450300,"CppTop"); - map.put(450400,"IfdefTop"); - map.put(450700,"NotParsedCorrectly"); - map.put(450800,"FinalDef"); - map.put(460000,"Program"); - map.put(470000,"GenericList"); - map.put(480000,"GenericString"); - map.put(490100,"IfToken"); - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiff.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiff.java new file mode 100644 index 0000000..acec7ff --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiff.java @@ -0,0 +1,98 @@ +package edu.lu.uni.serval.FixPattern.utils; + +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.TreeContext; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; + +import java.io.IOException; +import java.util.List; + +/** + * Created by anilkoyuncu on 17/09/2018. + */ +public class EDiff { + private static Logger log = LoggerFactory.getLogger(EDiff.class); + public static ITree getSimpliedTree(String fn, JedisPool outerPool) { + + ITree tree = null; + Jedis inner = null; + try { + inner = outerPool.getResource(); + while (!inner.ping().equals("PONG")){ + log.info("wait"); + } + inner.select(1); + String dist2load = inner.get(fn); + inner.select(0); + String s = inner.get(dist2load); + HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.fromString(s); + + ITree parent = null; + ITree children =null; + TreeContext tc = new TreeContext(); + tree = EDiffHelper.getASTTree(actionSet, parent, children,tc); + tree.setParent(null); + tc.validate(); + + } catch (IOException e) { + e.printStackTrace(); + } catch (ClassNotFoundException e) { + e.printStackTrace(); + }finally { + if (inner != null) { + inner.close(); + } + } + return tree; + + } + public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ + + int newType = 0; + + Action action = actionSet.getAction(); + if (action instanceof Update){ + newType = 101; + }else if(action instanceof Insert){ + newType =100; + }else if(action instanceof Move){ + newType = 102; + }else if(action instanceof Delete){ + newType=103; + }else{ + new Exception("unknow action"); + } + if(actionSet.getParent() == null){ + //root + + parent = tc.createTree(newType, "", null); + tc.setRoot(parent); + +// parent = new Tree(newType,""); + }else{ + children = tc.createTree(newType, "", null); + children.setParentAndUpdateChildren(parent); +// children = new Tree(newType,""); +// parent.addChild(children); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getActionTree(subAction,children,null,tc); + + } + + + } + return parent; + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiffHelper.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiffHelper.java new file mode 100644 index 0000000..b6f7980 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/EDiffHelper.java @@ -0,0 +1,88 @@ +package edu.lu.uni.serval.FixPattern.utils; + +import com.github.gumtreediff.tree.ITree; +import com.github.gumtreediff.tree.TreeContext; +import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.util.Base64; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.stream.Collectors; + +/** + * Created by anilkoyuncu on 17/09/2018. + */ +public class EDiffHelper { + private static Logger log = LoggerFactory.getLogger(EDiffHelper.class); + /** Read the object from Base64 string. */ + public static Object fromString( String s ) throws IOException, + ClassNotFoundException { + byte [] data = Base64.getDecoder().decode( s ); + ObjectInputStream ois = new ObjectInputStream( + new ByteArrayInputStream( data ) ); + Object o = ois.readObject(); + ois.close(); + return o; + } + + /** Write the object to a Base64 string. */ + public static String toString( Serializable o ) throws IOException { + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + ObjectOutputStream oos = new ObjectOutputStream( baos ); + oos.writeObject( o ); + oos.close(); + return Base64.getEncoder().encodeToString(baos.toByteArray()); + } + + public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children, TreeContext tc){ + + int newType = 0; + + String astNodeType = actionSet.getAstNodeType(); + List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); + + if(keysByValue.size() != 1){ + log.error("More than 1"); + } + newType = keysByValue.get(0); + if(actionSet.getParent() == null){ + //root + +// parent = new Tree(newType,""); + parent = tc.createTree(newType, "", null); + tc.setRoot(parent); + }else{ +// children = new Tree(newType,""); +// parent.addChild(children); + children = tc.createTree(newType, "", null); + children.setParentAndUpdateChildren(parent); + } + List subActions = actionSet.getSubActions(); + if (subActions.size() != 0){ + for (HierarchicalActionSet subAction : subActions) { + + if(actionSet.getParent() == null){ + children = parent; + } + getASTTree(subAction,children,null,tc); + + } + + + } + return parent; + } + + + public static List getKeysByValue(Map map, E value) { + return map.entrySet() + .stream() + .filter(entry -> Objects.equals(entry.getValue(), value)) + .map(Map.Entry::getKey) + .collect(Collectors.toList()); + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPattern/utils/PoolBuilder.java b/src/main/java/edu/lu/uni/serval/FixPattern/utils/PoolBuilder.java new file mode 100644 index 0000000..fba3f04 --- /dev/null +++ b/src/main/java/edu/lu/uni/serval/FixPattern/utils/PoolBuilder.java @@ -0,0 +1,33 @@ +package edu.lu.uni.serval.FixPattern.utils; + +import redis.clients.jedis.JedisPoolConfig; + +import java.time.Duration; + +/** + * Created by anilkoyuncu on 17/09/2018. + */ +public class PoolBuilder { + public static JedisPoolConfig getPoolConfig() { + return poolConfig; + } + + static final JedisPoolConfig poolConfig = buildPoolConfig(); + + + private static JedisPoolConfig buildPoolConfig() { + final JedisPoolConfig poolConfig = new JedisPoolConfig(); + poolConfig.setMaxTotal(128); + poolConfig.setMaxIdle(128); + poolConfig.setMinIdle(16); + poolConfig.setTestOnBorrow(true); + poolConfig.setTestOnReturn(true); + poolConfig.setTestWhileIdle(true); + poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); + poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); + poolConfig.setNumTestsPerEvictionRun(3); + poolConfig.setBlockWhenExhausted(true); + + return poolConfig; + } +} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/CUCreator.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/CUCreator.java index f495837..ec47e1a 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/CUCreator.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/CUCreator.java @@ -1,15 +1,11 @@ package edu.lu.uni.serval.FixPatternParser; -import java.io.BufferedReader; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileReader; -import java.io.IOException; - import org.eclipse.jdt.core.dom.AST; import org.eclipse.jdt.core.dom.ASTParser; import org.eclipse.jdt.core.dom.CompilationUnit; +import java.io.*; + /** * Creator of a CompilationUnit. * diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java index fe86e18..2b7367b 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/Parser.java @@ -1,19 +1,6 @@ package edu.lu.uni.serval.FixPatternParser; import java.io.File; -import java.util.ArrayList; -import java.util.List; -import java.util.Locale; - -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.gumtree.GumTreeComparer; -import edu.lu.uni.serval.gumtree.regroup.ActionFilter; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; /** * Parse fix patterns with GumTree. @@ -33,435 +20,7 @@ public abstract class Parser implements ParserInterface { public abstract void parseFixPatterns(File prevFile, File revFile, File diffEntryFile,String project); - protected List parseChangedSourceCodeWithGumTree(File prevFile, File revFile) { - List actionSets = new ArrayList<>(); - // GumTree results - List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTree(prevFile, revFile); -// List gumTreeResults = new GumTreeComparer().compareTwoFilesWithGumTreeForCCode(prevFile, revFile); - if (gumTreeResults != null && gumTreeResults.size() > 0) { - // Regroup GumTre results. - List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); - - // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. - // TODO: variable effects range, sub-actions are these kinds of modification? - actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); - } - - return actionSets; - } - - protected List getFirstAndLastMoveAction(HierarchicalActionSet gumTreeResult) { - List firstAndLastMoveActions = new ArrayList<>(); - List actions = gumTreeResult.getSubActions(); - if (actions.size() == 0) { - return null; - } - Move firstMoveAction = null; - Move lastMoveAction = null; - while (actions.size() > 0) { - List subActions = new ArrayList<>(); - for (HierarchicalActionSet action : actions) { - subActions.addAll(action.getSubActions()); - if (action.toString().startsWith("MOV")) { - if (firstMoveAction == null) { - firstMoveAction = (Move) action.getAction(); - lastMoveAction = (Move) action.getAction(); - } else { - int startPosition = action.getStartPosition(); - int length = action.getLength(); - int startPositionFirst = firstMoveAction.getPosition(); - int startPositionLast = lastMoveAction.getPosition(); - int lengthLast = lastMoveAction.getNode().getLength(); - if (startPosition < startPositionFirst || (startPosition == startPositionFirst && length > firstMoveAction.getLength())) { - firstMoveAction = (Move) action.getAction(); - } - if ((startPosition + length) > (startPositionLast + lengthLast)) { - lastMoveAction = (Move) action.getAction(); - } - } - } - } - - actions.clear(); - actions.addAll(subActions); - } - if (firstMoveAction == null) { - return null; - } - firstAndLastMoveActions.add(firstMoveAction); - firstAndLastMoveActions.add(lastMoveAction); - return firstAndLastMoveActions; - } - - protected String getSemiSourceCodeEditScripts(HierarchicalActionSet actionSet) { - // TODO Auto-generated method stub - return null; - } - protected String getAbstractIdentifiersEditScripts(HierarchicalActionSet actionSet) { - // TODO Auto-generated method stub - return null; - } - - protected String getRawTokenEditScripts(HierarchicalActionSet actionSet) { - // TODO Auto-generated method stub - return null; - } - - protected int getEndPosition(List children) { - int endPosition = 0; - for (ITree child : children) { - if (child.getLabel().endsWith("Body")) { - endPosition = child.getPos() - 1; - break; - } - } - return endPosition; - } - - /** - * Get the AST node based edit script of patches in terms of breadth first. - * - * @param actionSet - * @return - */ - protected String getASTEditScriptsBreadthFirst(HierarchicalActionSet actionSet) { - String editScript = ""; - - List actionSets = new ArrayList<>(); - actionSets.add(actionSet); - while (actionSets.size() != 0) { - List subSets = new ArrayList<>(); - for (HierarchicalActionSet set : actionSets) { - subSets.addAll(set.getSubActions()); - String actionStr = set.getActionString(); - int index = actionStr.indexOf("@@"); - String singleEdit = actionStr.substring(0, index).replace(" ", ""); - - singleEdit = handleSimpleNameNode(singleEdit, actionStr, index); - - editScript += singleEdit + " "; - } - actionSets.clear(); - actionSets.addAll(subSets); - } - return editScript; - } - - private String handleSimpleNameNode(String singleEdit, String actionStr, int index) { - // TODO - if (singleEdit.endsWith("SimpleName")) { - actionStr = actionStr.substring(index + 2); - if (actionStr.startsWith("MethodName")) { - singleEdit = singleEdit.replace("SimpleName", "MethodName"); - } else if (actionStr.startsWith("ClassName")) { - singleEdit = singleEdit.replace("SimpleName", "ClassName"); - } else { - if (actionStr.startsWith("Name")) { - char c = actionStr.charAt(5); - if (Character.isUpperCase(c)) { - singleEdit = singleEdit.replace("SimpleName", "Name"); - } else { - singleEdit = singleEdit.replace("SimpleName", "Variable"); - } - } else { - singleEdit = singleEdit.replace("SimpleName", "Variable"); - } - } - } - return singleEdit; - } - - /** - * Get the AST node based edit script of patches in terms of deep first. - * - * @param actionSet - * @return - */ - protected String getASTEditScriptsDeepFirst(HierarchicalActionSet actionSet) { - String editScript = ""; - String actionStr = actionSet.getActionString(); - int index = actionStr.indexOf("@@"); - String singleEdit = actionStr.substring(0, index).replace(" ", ""); - - singleEdit = handleSimpleNameNode(singleEdit, actionStr, index); - - editScript = singleEdit + " "; - - List subActionSets = actionSet.getSubActions();; - for (HierarchicalActionSet subActionSet : subActionSets) { - editScript += getASTEditScriptsDeepFirst(subActionSet); - } - return editScript; - } - - /** - * - * @param hunkActionSets - * @param bugStartLine - * @param bugEndLine - * @param fixStartLine - * @param fixEndLine - * @return - */ - protected String getASTEditScriptsBreadthFirst(List hunkActionSets, int bugEndPosition, int fixEndPosition) { - String editScript = ""; - - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - editScript += getASTEditScriptsBreadthFirst(hunkActionSet, bugEndPosition, fixEndPosition); - } - return editScript; - } - - private String getASTEditScriptsBreadthFirst(HierarchicalActionSet hunkActionSet, int bugEndPosition, int fixEndPosition) { - String editScript = ""; - List actionSets = new ArrayList<>(); - actionSets.add(hunkActionSet); - while (actionSets.size() != 0) { - List subSets = new ArrayList<>(); - for (HierarchicalActionSet set : actionSets) { - int position = set.getAction().getPosition(); - String actionStr = set.getActionString(); - if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) { - continue; - } - - subSets.addAll(set.getSubActions()); - int index = actionStr.indexOf("@@"); - String singleEdit = actionStr.substring(0, index).replace(" ", ""); - - singleEdit = handleSimpleNameNode(singleEdit, actionStr, index); - - editScript += singleEdit + " "; - } - actionSets.clear(); - actionSets.addAll(subSets); - } - return editScript; - } - - private boolean isOutofPosition(String actionStr, int actionPosition, int bugEndPosition, int fixEndPosition) { - if (actionStr.startsWith("INS")) { - if (actionPosition > fixEndPosition) { - return true; - } - } else if (!actionStr.startsWith("MOV") && actionPosition > bugEndPosition) { - return true; - } - return false; - } - - protected String getASTEditScriptsDeepFirst(List hunkActionSets, int bugEndPosition, int fixEndPosition) { - StringBuilder editScript = new StringBuilder(); - - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - editScript.append(getASTEditScriptsDeepFirst2(hunkActionSet, bugEndPosition, fixEndPosition)); - } - return editScript.toString(); - } - - private String getASTEditScriptsDeepFirst(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition) { - String editScripts = ""; - String actionStr = actionSet.getActionString(); - int index = actionStr.indexOf("@@"); - String singleEdit = actionStr.substring(0, index).replace(" ", ""); - - singleEdit = handleSimpleNameNode(singleEdit, actionStr, index); - - editScripts += singleEdit + " "; - - for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) { - int position = subActionSet.getAction().getPosition(); - actionStr = subActionSet.getActionString(); - if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) { - continue; - } - editScripts += getASTEditScriptsDeepFirst(subActionSet, bugEndPosition, fixEndPosition); - } - - return editScripts; - } - - private String getASTEditScriptsDeepFirst2(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition) { - StringBuilder editScripts = new StringBuilder(); - String actionStr = actionSet.getActionString(); - int index = actionStr.indexOf("@@"); - String singleEdit = actionStr.substring(0, index); - - if (singleEdit.endsWith("Statement")) { - singleEdit = singleEdit + " " + singleEdit.substring(4, singleEdit.indexOf("Statement")).toLowerCase(Locale.ENGLISH); - } else { - singleEdit = handleSimpleNameNode2(singleEdit, actionStr, index, actionSet); - } - editScripts.append(singleEdit).append(" "); - - for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) { - int position = subActionSet.getAction().getPosition(); - actionStr = subActionSet.getActionString(); - if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) { - continue; - } - editScripts.append(getASTEditScriptsDeepFirst2(subActionSet, bugEndPosition, fixEndPosition)); - } - - return editScripts.toString(); - } - - private String handleSimpleNameNode2(String singleEdit, String actionStr, int index, HierarchicalActionSet actionSet) { - if (singleEdit.endsWith("SimpleName")) { - actionStr = actionStr.substring(index + 2); - if (actionStr.startsWith("MethodName")) { - singleEdit = singleEdit.replace("SimpleName", "MethodName"); - String methodName = actionStr.substring(actionStr.indexOf("MethodName:") + 11); - int index1 = methodName.indexOf(":"); - int index2 = methodName.indexOf(" "); - index = (index1 < 0 || index1 > index2) ? index2 : index1; - methodName = methodName.substring(0, index); - singleEdit += " " + methodName; - } else if (actionStr.startsWith("ClassName")) { - singleEdit = singleEdit.replace("SimpleName", "ClassName"); - String className = actionStr.substring(actionStr.indexOf("ClassName:") + 10); - int index1 = className.indexOf(" "); - index = index1 < 0 ? className.length() : index1; - className = className.substring(0, index); - singleEdit += " " + className; - } else { - if (actionStr.startsWith("Name")) { - char c = actionStr.charAt(5); - if (Character.isUpperCase(c)) { - singleEdit = singleEdit.replace("SimpleName", "Name"); - String name = actionStr.substring(actionStr.indexOf("Name:") + 5); - int index1 = name.indexOf(" "); - index = index1 < 0 ? name.length() : index1; - name = name.substring(0, index); - singleEdit += " " + name; - } else { - singleEdit = singleEdit.replace("SimpleName", "Variable"); - int index1 = actionStr.indexOf(" "); - index = index1 < 0 ? actionStr.length() : index1; - String var = actionStr.substring(0, index); - var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode()); - singleEdit += " " + var.replaceAll(" ", ""); - } - } else { - singleEdit = singleEdit.replace("SimpleName", "Variable"); - String var = actionStr.substring(0, (actionStr.indexOf(" ") < 0 ? actionStr.length() : actionStr.indexOf(" "))); - var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode()); - singleEdit += " " + var.replaceAll(" ", ""); - } - } - } else { - if (actionSet.getSubActions() != null && actionSet.getSubActions().size() > 0) { - singleEdit += " " + actionSet.getAstNodeType()+ "exp"; - } else { - if (singleEdit.endsWith("CharacterLiteral")) { - singleEdit += " charLiteral"; - } else if (singleEdit.endsWith("NumberLiteral")) { - singleEdit += " numLiteral"; - } else if (singleEdit.endsWith("StringLiteral")) { - singleEdit += " strLiteral"; - } else if (singleEdit.endsWith("BooleanLiteral") || singleEdit.endsWith("NullLiteral") || singleEdit.endsWith("Operator") || - singleEdit.endsWith("ThisExpression") || singleEdit.endsWith("TypeLiteral") || singleEdit.endsWith("Instanceof") || - singleEdit.endsWith("New") || singleEdit.endsWith("WildcardType") || singleEdit.endsWith("SimpleType") || - singleEdit.endsWith("QualifiedType") || singleEdit.endsWith("PrimitiveType") || singleEdit.endsWith("NameQualifiedType")) { - singleEdit += " " + actionSet.getNode().getLabel(); - } else if (singleEdit.endsWith("SuperConstructorInvocation")) { - singleEdit += " super"; - } else if (singleEdit.endsWith("ConstructorInvocation")) { - singleEdit += " this"; - } else if (singleEdit.endsWith("SimpleName")) { - actionStr = actionStr.substring(index + 2); - if (actionStr.startsWith("MethodName")) { - singleEdit = singleEdit.replace("SimpleName", "MethodName"); - String methodName = actionStr.substring(actionStr.indexOf("MethodName:") + 11); - int index1 = methodName.indexOf(":"); - int index2 = methodName.indexOf(" "); - index = (index1 < 0 || index1 > index2) ? index2 : index1; - methodName = methodName.substring(0, index); - singleEdit += " " + methodName; - } else if (actionStr.startsWith("ClassName")) { - singleEdit = singleEdit.replace("SimpleName", "ClassName"); - String className = actionStr.substring(actionStr.indexOf("ClassName:") + 10); - int index1 = className.indexOf(" "); - index = index1 < 0 ? className.length() : index1; - className = className.substring(0, index); - singleEdit += " " + className; - } else { - if (actionStr.startsWith("Name")) { - char c = actionStr.charAt(5); - if (Character.isUpperCase(c)) { - singleEdit = singleEdit.replace("SimpleName", "Name"); - String name = actionStr.substring(actionStr.indexOf("Name:") + 5); - int index1 = name.indexOf(" "); - index = index1 < 0 ? name.length() : index1; - name = name.substring(0, index); - singleEdit += " " + name; - } else { - singleEdit = singleEdit.replace("SimpleName", "Variable"); - int index1 = actionStr.indexOf(" "); - index = index1 < 0 ? actionStr.length() : index1; - String var = actionStr.substring(0, index); - var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode()); - singleEdit += " " + var.replaceAll(" ", ""); - } - } else { - singleEdit = singleEdit.replace("SimpleName", "Variable"); - String var = actionStr.substring(0, (actionStr.indexOf(" ") < 0 ? actionStr.length() : actionStr.indexOf(" "))); - var = new SimplifyTree().canonicalVariableName(var, actionSet.getAction().getNode()); - singleEdit += " " + var.replaceAll(" ", ""); - } - } - } else { - ITree nodeTree = actionSet.getNode(); - if (nodeTree.getChildren().size() > 0) { - singleEdit += " " + actionSet.getAstNodeType()+ "exp"; - } else { - singleEdit += " " + nodeTree.getLabel().replaceAll(" ", ""); - } - } - } - } - return singleEdit; - } - - protected String getAstEditScripts(List actionSets, int bugEndLine, int fixEndLine) { - String editScripts = ""; - for (HierarchicalActionSet actionSet : actionSets) { - editScripts += getActionString(actionSet, bugEndLine, fixEndLine, ""); - } - return editScripts; - } - - private String getActionString(HierarchicalActionSet actionSet, int bugEndPosition, int fixEndPosition, String hierarchicalLabel) { - String editScripts = ""; - - String actionStr = actionSet.getActionString(); - int index = actionStr.indexOf("@@"); - String singleEdit = actionStr.substring(0, index); - - singleEdit = handleSimpleNameNode(singleEdit, actionStr, index); - - editScripts += hierarchicalLabel + singleEdit + "\n"; - - for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) { - int position = subActionSet.getAction().getPosition(); - actionStr = subActionSet.getActionString(); - if (isOutofPosition(actionStr, position, bugEndPosition, fixEndPosition)) { - continue; - } - editScripts += getActionString(subActionSet, bugEndPosition, fixEndPosition, hierarchicalLabel + "---"); - } - - return editScripts; - } - - protected void clearITree(HierarchicalActionSet actionSet) { - actionSet.getAction().setNode(null); - for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) { - clearITree(subActionSet); - } - } - @Override public String getAstEditScripts() { return astEditScripts; @@ -472,10 +31,10 @@ public abstract class Parser implements ParserInterface { return patchesSourceCode; } - @Override - public String getBuggyTrees() { - return buggyTrees; - } +// @Override +// public String getBuggyTrees() { +// return buggyTrees; +// } @Override public String getSizes() { @@ -487,13 +46,13 @@ public abstract class Parser implements ParserInterface { return tokensOfSourceCode; } - @Override - public String getOriginalTree() { - return originalTree; - } - - @Override - public String getActionSets() { - return actionSets; - } +// @Override +// public String getOriginalTree() { +// return originalTree; +// } +// +// @Override +// public String getActionSets() { +// return actionSets; +// } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/ParserInterface.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/ParserInterface.java index 2245087..2a4c517 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/ParserInterface.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/ParserInterface.java @@ -1,23 +1,21 @@ package edu.lu.uni.serval.FixPatternParser; -import java.io.File; - public interface ParserInterface { - public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile); +// public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile); public String getAstEditScripts(); public String getPatchesSourceCode(); - public String getBuggyTrees(); +// public String getBuggyTrees(); public String getSizes(); public String getTokensOfSourceCode(); - public String getOriginalTree(); +// public String getOriginalTree(); - public String getActionSets(); +// public String getActionSets(); } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/Tokenizer.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/Tokenizer.java deleted file mode 100644 index b9a9030..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/Tokenizer.java +++ /dev/null @@ -1,75 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser; - -import java.util.List; - -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; - -public class Tokenizer { - - public static String getTokensDeepFirst(SimpleTree simpleTree) { - String tokens = ""; - List children = simpleTree.getChildren(); - String astNodeType = simpleTree.getNodeType(); - - if (children.isEmpty()) { // BreakStatement, ContinueStatement, ReturnStatement, TryStatement - if (astNodeType.endsWith("Statement")) { - String label = astNodeType; - label = label.substring(0, label.lastIndexOf("S")).toLowerCase(); - tokens += astNodeType + " " + label + " "; - } else if ("SuperConstructorInvocation".equals(astNodeType)) { - tokens += astNodeType + " super "; - } else if ("ConstructorInvocation".equals(astNodeType)) { - tokens += astNodeType + " this "; - } else if ("StringLiteral".equals(astNodeType)) { - tokens += astNodeType + " stringLiteral "; - } else if ("CharacterLiteral".equals(astNodeType)) { - tokens += astNodeType + " charLiteral "; - } else if ("ArrayInitializer".equals(astNodeType)) { - tokens += astNodeType + " arrayInitializer "; - } else if ("LambdaExpression".equals(astNodeType)) { - tokens += astNodeType + " lambda "; - } else if ("NumberLiteral".equals(astNodeType)) { - tokens += astNodeType + " numberLiteral "; - } else { - tokens += astNodeType + " " + simpleTree.getLabel() + " "; - } - } else { - if ("AssertStatement".equals(astNodeType) || "DoStatement".equals(astNodeType) - || "ForStatement".equals(astNodeType) || "IfStatement".equals(astNodeType) - || "ReturnStatement".equals(astNodeType) || "SwitchStatement".equals(astNodeType) - || "SynchronizedStatement".equals(astNodeType) || "ThrowStatement".equals(astNodeType) - || "TryStatement".equals(astNodeType) || "WhileStatement".equals(astNodeType)) { - String label = astNodeType; - label = label.substring(0, label.lastIndexOf("S")).toLowerCase(); - tokens += astNodeType + " " + label + " "; - } else if ("EnhancedForStatement".equals(astNodeType)) { - tokens += astNodeType + " " + "for "; - } else if ("CatchClause".equals(astNodeType)) { - tokens += astNodeType + " " + "catch "; - } else if ("SwitchCase".equals(astNodeType)) { - tokens += astNodeType + " case "; - } else if ("SuperConstructorInvocation".equals(astNodeType)) { - tokens += astNodeType + " super "; - } else if ("ConstructorInvocation".equals(astNodeType)) { - tokens += astNodeType + " this "; - } else if ("FinallyBody".equals(astNodeType)) { - tokens += astNodeType + " finally "; - } else if ("LabeledStatement".equals(astNodeType)) { - tokens += "LabeledStatement " + simpleTree.getLabel(); - } else if ("SuperMethodInvocation".equals(astNodeType)) { - tokens += astNodeType + " super "; - } else if ("MethodName".equals(astNodeType)) { - tokens += "MethodName " + simpleTree.getLabel() + " "; - } - - if ("ArrayInitializer".equals(astNodeType)) { - tokens += astNodeType + " arrayInitializer "; - } else { - for (SimpleTree child : children) { - tokens += getTokensDeepFirst(child); - } - } - } - return tokens; - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchHunkParser.java deleted file mode 100644 index a100e28..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchHunkParser.java +++ /dev/null @@ -1,113 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.patch; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; -import edu.lu.uni.serval.diffentry.DiffEntryReader; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter; -import edu.lu.uni.serval.gumtree.regroup.HunkFixPattern; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; - -/** - * Parse fix patterns with GumTree. - * - * Multiple statements bugs. - * - * @author kui.liu - * - */ -public class CommitPatchHunkParser extends CommitPatchParser { - - - @Override - public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { - - // GumTree results - List actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile); - - if (actionSets.size() > 0) { - // DiffEntry size: filter out big hunks. - List diffentryHunks = new DiffEntryReader().readHunks(diffEntryFile); - //Filter out the modify actions, which are not in the DiffEntry hunks. - HunkActionFilter hunkFilter = new HunkActionFilter(); - List allHunkFixPatterns = hunkFilter.filterActionsByDiffEntryHunk2(diffentryHunks, actionSets, revFile, prevFile); - - for (HunkFixPattern hunkFixPattern : allHunkFixPatterns) { - // Range of buggy source code - int startLine = 0; - int endLine = 0; - // Range of fixing source code - int startLine2 = 0; - int endLine2 = 0; - /* - * Convert the ITree of buggy code to a simple tree. - * It will be used to compute the similarity. - */ - List hunkActionSets = hunkFixPattern.getHunkActionSets(); - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - String astEditScripts = ""; - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - SimplifyTree abstractIdentifier = new SimplifyTree(); - abstractIdentifier.abstractTree(hunkActionSet); - SimpleTree simpleT = hunkActionSet.getSimpleTree(); - if (simpleT == null) { // Failed to get the simple tree for INS actions. - continue; - } - children.add(simpleT); - - /** - * Select edit scripts for deep learning. - * Edit scripts will be used to mine common fix patterns. - */ - // 1. First level: AST node type. - astEditScripts += getASTEditScriptsBreadthFirst(hunkActionSet); - // 2. source code: raw tokens - // 3. abstract identifiers: - // 4. semi-source code: - - if (startLine == 0) { - startLine = hunkActionSet.getBugStartLineNum(); - endLine = hunkActionSet.getBugEndLineNum(); - startLine2 = hunkActionSet.getFixStartLineNum(); - endLine2 = hunkActionSet.getFixEndLineNum(); - } else { - if (startLine > hunkActionSet.getBugStartLineNum()) startLine = hunkActionSet.getBugStartLineNum(); - if (startLine2 > hunkActionSet.getFixStartLineNum()) startLine2 = hunkActionSet.getFixStartLineNum(); - if (endLine < hunkActionSet.getBugEndLineNum()) endLine = hunkActionSet.getBugEndLineNum(); - if (endLine2 < hunkActionSet.getFixEndLineNum()) endLine2 = hunkActionSet.getFixEndLineNum(); - } - } - if (children.size() == 0) continue; - if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2 ) continue; - - simpleTree.setChildren(children); - simpleTree.setParent(null); - - // Source Code of patches. - String patchSourceCode = getPatchSourceCode(hunkFixPattern.getHunk(), startLine, endLine, startLine2, endLine2); - if ("".equals(patchSourceCode)) continue; - - this.patchesSourceCode += "PATCH###\n" + patchSourceCode + "\n"; - int size = astEditScripts.split(" ").length; - this.sizes += size + "\n"; - this.astEditScripts += astEditScripts + "\n"; - -// this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + simpleTree.toString() + "\n"; - this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n"; -// this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" + readActionSet(actionSet, "") + "\n"; -// this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" + actionSet.getOriginalTree().toString() + "\n"; - - } - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java deleted file mode 100644 index b1edcc3..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchParser.java +++ /dev/null @@ -1,105 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.patch; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.List; - -import edu.lu.uni.serval.FixPatternParser.Parser; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; - -/** - * Parse fix patterns with GumTree. - * - * @author kui.liu - * - */ -public class CommitPatchParser extends Parser{ - - @Override - public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { - } - - protected DiffEntryHunk matchHunk(int startLine, int endLine, int startLine2, int endLine2, String actionStr, List hunks) { - for (DiffEntryHunk hunk : hunks) { - int bugStartLine = hunk.getBugLineStartNum(); - int bugRange = hunk.getBugRange(); - int fixStartLine = hunk.getFixLineStartNum(); - int fixRange = hunk.getFixRange(); - - if (actionStr.startsWith("INS")) { - if (fixStartLine + fixRange < startLine2) { - continue; - } - if (endLine2 < fixStartLine ) { - return null; - } - return hunk; - } else { - if (bugStartLine + bugRange < startLine) { - continue; - } - if (endLine < bugStartLine ) { - return null; - } - return hunk; - } - } - return null; - } - - protected String getPatchSourceCode(DiffEntryHunk hunk, int startLineNum, int endLineNum, int startLineNum2, int endLineNum2) { - String sourceCode = hunk.getHunk(); - int bugStartLine = hunk.getBugLineStartNum(); - int fixStartLine = hunk.getFixLineStartNum(); - String buggyStatements = ""; - String fixedStatements = ""; - BufferedReader reader = null; - try { - reader = new BufferedReader(new StringReader(sourceCode)); - String line = null; - int bugLines = 0; - int fixLines = 0; - int contextLines = 0; // counter of non-buggy code line. - while ((line = reader.readLine()) != null) { - int bugLineIndex = bugLines + contextLines; - int fixLineIndex = fixLines + contextLines; - if (line.startsWith("-")) { - if (bugStartLine + bugLineIndex >= startLineNum && bugStartLine + bugLineIndex <= endLineNum) { - buggyStatements += line + "\n"; - } - bugLines ++; - } else if (line.startsWith("+")) { - if (fixStartLine + fixLineIndex >= startLineNum2 && fixStartLine + fixLineIndex <= endLineNum2) { - fixedStatements += line + "\n"; - } - fixLines ++; - } else { - contextLines ++; - } - - if (bugStartLine + bugLineIndex > endLineNum && fixStartLine + fixLineIndex > endLineNum2) { - break; - } - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - if (reader != null) { - reader.close(); - reader = null; - } - } catch (IOException e) { - e.printStackTrace(); - } - } - return buggyStatements + fixedStatements; - } - - @Override - public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile, String project) { - - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchSingleStatementParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchSingleStatementParser.java deleted file mode 100644 index 63e31b7..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchSingleStatementParser.java +++ /dev/null @@ -1,158 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.patch; - -import java.io.File; -import java.util.List; - -import org.eclipse.jdt.core.dom.CompilationUnit; - -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.actions.model.Update; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.FixPatternParser.CUCreator; -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; -import edu.lu.uni.serval.diffentry.DiffEntryReader; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; - -/** - * Parse fix patterns with GumTree. - * - * Single Statement bugs. - * - * @author kui.liu - * - */ -public class CommitPatchSingleStatementParser extends CommitPatchParser { - - @Override - public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { - // GumTree results - List actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile); - - if (actionSets.size() > 0) { - // DiffEntry Hunks: filter out big hunks. - List diffentryHunks = new DiffEntryReader().readHunks(diffEntryFile); - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return; - } - for (HierarchicalActionSet actionSet : actionSets) { - // position of buggy statements - int startPosition = 0; - int endPosition = 0; - // position of fixed statements - int startPosition2 = 0; - int endPosition2 = 0; - - String actionStr = actionSet.getActionString(); - String astNodeType = actionSet.getAstNodeType(); - if (actionStr.startsWith("INS")) { - startPosition2 = actionSet.getStartPosition(); - endPosition2 = startPosition2 + actionSet.getLength(); - List firstAndLastMov = getFirstAndLastMoveAction(actionSet); - if (firstAndLastMov != null) { - startPosition = firstAndLastMov.get(0).getNode().getPos(); - ITree lastTree = firstAndLastMov.get(1).getNode(); - endPosition = lastTree.getPos() + lastTree.getLength(); - } else { // Ignore the pure insert actions without any move actions. - continue; - } - } else if (actionStr.startsWith("UPD")) { - startPosition = actionSet.getStartPosition(); - endPosition = startPosition + actionSet.getLength(); - Update update = (Update) actionSet.getAction(); - ITree newNode = update.getNewNode(); - startPosition2 = newNode.getPos(); - endPosition2 = startPosition2 + newNode.getLength(); - - if (Checker.containsBodyBlock(astNodeType)) { - List children = update.getNode().getChildren(); - endPosition = getEndPosition(children); - List newChildren = newNode.getChildren(); - endPosition2 = getEndPosition(newChildren); - - if (endPosition == 0) { - endPosition = startPosition + actionSet.getLength(); - } - if (endPosition2 == 0) { - endPosition2 = startPosition2 + newNode.getLength(); - } - } - } else {// DEL actions and MOV actions: we don't need these actions, as for now. - continue; - } - if (startPosition == 0 || startPosition2 == 0) { - continue; - } - - // Get line numbers. - int startLine = prevUnit.getLineNumber(startPosition); - int endLine = prevUnit.getLineNumber(endPosition); - int startLine2 = revUnit.getLineNumber(startPosition2); - int endLine2 = revUnit.getLineNumber(endPosition2); - if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2) - continue; - // Filter out the modify actions, which are not in the DiffEntry hunks. - DiffEntryHunk hunk = matchHunk(startLine, endLine, startLine2, endLine2, actionStr, diffentryHunks); - if (hunk == null) { - continue; - } - - /* - * Convert the ITree of buggy code to a simple tree. It will be - * used to compute the similarity. - */ - SimplifyTree abstractIdentifier = new SimplifyTree(); - abstractIdentifier.abstractTree(actionSet); - SimpleTree simpleTree = actionSet.getSimpleTree(); - if (simpleTree == null) { // Failed to get the simple tree for INS actions. - continue; - } - - /** - * Select edit scripts for deep learning. Edit scripts will be - * used to mine common fix patterns. - */ - // 1. First level: AST node type. - String astEditScripts = getASTEditScriptsBreadthFirst(actionSet); - int size = astEditScripts.split(" ").length; - if (size < 2) { - // System.out.println(actionSet); - continue; - } - - // Source Code of patches. - String patchSourceCode = getPatchSourceCode(hunk, startLine, endLine, startLine2, endLine2); - if ("".equals(patchSourceCode)) - continue; - - this.patchesSourceCode += Configuration.PATCH_SIGNAL + "\n" + patchSourceCode + "\n"; - this.sizes += size + "\n"; - this.astEditScripts += astEditScripts + "\n"; -// // 2. source code: raw tokens -// String rawTokenEditScripts = getRawTokenEditScripts(actionSet); -// // 3. abstract identifiers: -// String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet); -// // 4. semi-source code: -// String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet); - - // this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + - // simpleTree.toString() + "\n"; - this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n"; - // this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" + - // readActionSet(actionSet, "") + "\n"; - // this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" + - // actionSet.getOriginalTree().toString() + "\n"; - } - actionSets.clear(); - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java deleted file mode 100644 index 1c5981b..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/CSVUtils.java +++ /dev/null @@ -1,62 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import java.io.IOException; -import java.io.Writer; -import java.util.List; - -/** - * Created by anilkoyuncu on 19/03/2018. - */ -public class CSVUtils { - - private static final char DEFAULT_SEPARATOR = ','; - - public static void writeLine(Writer w, List values) throws IOException { - writeLine(w, values, DEFAULT_SEPARATOR, ' '); - } - - public static void writeLine(Writer w, List values, char separators) throws IOException { - writeLine(w, values, separators, ' '); - } - - //https://tools.ietf.org/html/rfc4180 - private static String followCVSformat(String value) { - - String result = value; - if (result.contains("\"")) { - result = result.replace("\"", "\"\""); - } - return result; - - } - - public static void writeLine(Writer w, List values, char separators, char customQuote) throws IOException { - - boolean first = true; - - //default customQuote is empty - - if (separators == ' ') { - separators = DEFAULT_SEPARATOR; - } - - StringBuilder sb = new StringBuilder(); - for (String value : values) { - if (!first) { - sb.append(separators); - } - if (customQuote == ' ') { - sb.append(followCVSformat(value)); - } else { - sb.append(customQuote).append(followCVSformat(value)).append(customQuote); - } - - first = false; - } - sb.append("\n"); - w.append(sb.toString()); - - - } - -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java deleted file mode 100644 index 9cda090..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Consumer.java +++ /dev/null @@ -1,226 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.matchers.Matcher; -import com.github.gumtreediff.matchers.Matchers; -import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.Tree; -import com.rabbitmq.client.*; -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import redis.clients.jedis.Jedis; -import redis.clients.jedis.JedisPool; -import redis.clients.jedis.JedisPoolConfig; - -import java.io.*; -import java.util.List; -import java.util.Map; -import java.util.Objects; -import java.util.concurrent.TimeoutException; -import java.util.stream.Collectors; - -/** - * Created by anilkoyuncu on 03/04/2018. - */ -public class Consumer { - - private static Logger log = LoggerFactory.getLogger(Consumer.class); - private static String inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; - - public static void main(String[] args) { - - ConnectionFactory factory = new ConnectionFactory(); - factory.setHost("10.240.5.10"); -// factory.setVirtualHost("treeCompare"); - factory.setPort(5672); - factory.setUsername("anil"); - factory.setPassword("changeme2018"); - factory.setConnectionTimeout(1000); - Connection connection = null; - Channel channel = null; - try { - connection = factory.newConnection(); - - channel = connection.createChannel(); - channel.queueDeclare("tree_queue", false, false, false, null); - - - boolean autoAck = false; - Channel finalChannel = channel; - channel.basicConsume("tree_queue", autoAck,"myConsumerTag", - new DefaultConsumer(finalChannel) { - @Override - public void handleDelivery( - String consumerTag, - Envelope envelope, - AMQP.BasicProperties properties, - byte[] body) throws IOException { - - String message = new String(body, "UTF-8"); - String[] split = message.split(","); - String key = split[0]; - String firstV = split[1]; - String secondV = split[2]; - try{ - calculateSimi(firstV,secondV,key); - }catch (Exception e){ - finalChannel.basicNack(envelope.getDeliveryTag(),false,false); - } - finalChannel.basicAck(envelope.getDeliveryTag(),false); - - // process the message - } - }); - -// channel.basicConsume("tree_queue", true, consumer); - - } catch (IOException e) { - e.printStackTrace(); - } catch (TimeoutException e) { - e.printStackTrace(); - } - } - - public static void calculateSimi(String firstVal,String secondVal, String key){ - - String[] split = key.split("_"); - - - String i = split[1]; - String j = split[2]; - - String[] firstValueSplit = firstVal.split("GumTreeOutput2"); - String[] secondValueSplit = secondVal.split("GumTreeOutput2"); - - String firstValue; - if (firstValueSplit.length == 1) { - firstValue = inputPath + firstValueSplit[0]; - } else { - firstValue = inputPath + firstValueSplit[1]; - } - - String secondValue; - if (secondValueSplit.length == 1) { - secondValue = inputPath + secondValueSplit[0]; - } else { - secondValue = inputPath + secondValueSplit[1]; - } - - ITree oldTree = getSimpliedTree(firstValue); - - ITree newTree = getSimpliedTree(secondValue); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - - double chawatheSimilarity1 = m.chawatheSimilarity(oldTree, newTree); - String chawatheSimilarity = String.format("%1.2f", chawatheSimilarity1); - double diceSimilarity1 = m.diceSimilarity(oldTree, newTree); - String diceSimilarity = String.format("%1.2f", diceSimilarity1); - double jaccardSimilarity1 = m.jaccardSimilarity(oldTree, newTree); - String jaccardSimilarity = String.format("%1.2f", jaccardSimilarity1); - - String editDistance = String.valueOf(actions.size()); - - String result = firstVal + "," + secondVal + "," + chawatheSimilarity + "," + diceSimilarity + "," + jaccardSimilarity + "," + editDistance; - - - if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0) - || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) { - String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j); - log.info(matchKey); -// JedisPool jedisPool = new JedisPool(new JedisPoolConfig(), "127.0.0.1", Integer.valueOf(port), 20000000); -// try (Jedis outer = jedisPool.getResource()) { -// outer.select(1); -// outer.set(matchKey, result); -// } - } - - -// try (Jedis jedis = pool.getResource()) { -// jedis.del("pair_"+ (String.valueOf(i)) + "_" + String.valueOf(j)); -// } - - } - - public static ITree getSimpliedTree(String fn) { - HierarchicalActionSet actionSet = null; - try { - FileInputStream fi = new FileInputStream(new File(fn)); - ObjectInputStream oi = new ObjectInputStream(fi); - actionSet = (HierarchicalActionSet) oi.readObject(); - oi.close(); - fi.close(); - - - } catch (FileNotFoundException e) { - log.error("File not found"); - e.printStackTrace(); - } catch (IOException e) { - log.error("Error initializing stream"); - e.printStackTrace(); - } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - ITree parent = null; - ITree children =null; - ITree tree = getASTTree(actionSet, parent, children); - tree.setParent(null); - - return tree; - - } - - public static List getKeysByValue(Map map, E value) { - return map.entrySet() - .stream() - .filter(entry -> Objects.equals(entry.getValue(), value)) - .map(Map.Entry::getKey) - .collect(Collectors.toList()); - } - - public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ - - int newType = 0; - - String astNodeType = actionSet.getAstNodeType(); - List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); - - if(keysByValue.size() != 1){ - log.error("Birden cok astnodemapmapping"); - } - newType = keysByValue.get(0); - if(actionSet.getParent() == null){ - //root - - parent = new Tree(newType,""); - }else{ - children = new Tree(newType,""); - parent.addChild(children); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getASTTree(subAction,children,null); - - } - - - } - return parent; - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FieldViolation.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FieldViolation.java deleted file mode 100644 index a011853..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FieldViolation.java +++ /dev/null @@ -1,121 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -public enum FieldViolation { - UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR, - ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD, - LI_LAZY_INIT_STATIC, - URF_UNREAD_FIELD, - MS_SHOULD_BE_FINAL, - URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD, - UWF_UNWRITTEN_FIELD, - MS_PKGPROTECT, - SS_SHOULD_BE_STATIC, - NP_UNWRITTEN_FIELD, - UWF_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD, - SE_BAD_FIELD, - UUF_UNUSED_FIELD, - SE_BAD_FIELD_STORE, - MS_MUTABLE_ARRAY, - NP_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD, -} - -enum ClassViolation{ - SIC_INNER_SHOULD_BE_STATIC_ANON, //inner class. ClassInstanceCreation by overriding some methods. - SIC_INNER_SHOULD_BE_STATIC, - RI_REDUNDANT_INTERFACES, - SE_COMPARATOR_SHOULD_BE_SERIALIZABLE, - - SE_NO_SERIALVERSIONID, - CI_CONFUSED_INHERITANCE, - SE_INNER_CLASS, - - NM_CLASS_NOT_EXCEPTION, -} - -enum MethodViolation { - NM_METHOD_NAMING_CONVENTION, - UPM_UNCALLED_PRIVATE_METHOD, - DE_MIGHT_IGNORE, - - NM_CONFUSING, - CN_IMPLEMENTS_CLONE_BUT_NOT_CLONEABLE, - UC_USELESS_VOID_METHOD, -} - -enum StmtViolation { - DLS_DEAD_LOCAL_STORE, //Assignment statement. false positives may be high. - //This instruction assigns a value to a local variable, but the value is not read or used in any subsequent instruction. - - DM_BOXED_PRIMITIVE_FOR_PARSING, - - DM_CONVERT_CASE, - DM_DEFAULT_ENCODING, - IS2_INCONSISTENT_SYNC, - - NP_GUARANTEED_DEREF, - SIO_SUPERFLUOUS_INSTANCEOF, - NP_BOOLEAN_RETURN_NULL, - SF_SWITCH_FALLTHROUGH, - DP_DO_INSIDE_DO_PRIVILEGED, - DMI_INVOKING_TOSTRING_ON_ARRAY, - NP_NONNULL_PARAM_VIOLATION, - CN_IDIOM_NO_SUPER_CALL, - UL_UNRELEASED_LOCK_EXCEPTION_PATH, - RC_REF_COMPARISON_BAD_PRACTICE, - NP_ALWAYS_NULL, - NP_NULL_PARAM_DEREF, - GC_UNRELATED_TYPES, - DLS_DEAD_LOCAL_STORE_OF_NULL, - RpC_REPEATED_CONDITIONAL_TEST, - ODR_OPEN_DATABASE_RESOURCE_EXCEPTION_PATH, - DB_DUPLICATE_SWITCH_CLAUSES, - RV_RETURN_VALUE_IGNORED, - ES_COMPARING_PARAMETER_STRING_WITH_EQ, - RCN_REDUNDANT_NULLCHECK_OF_NULL_VALUE, - ICAST_IDIV_CAST_TO_DOUBLE, - BC_VACUOUS_INSTANCEOF, - EC_UNRELATED_TYPES, - ICAST_INTEGER_MULTIPLY_CAST_TO_LONG, - DM_STRING_TOSTRING, - DMI_HARDCODED_ABSOLUTE_FILENAME, - MS_MUTABLE_COLLECTION_PKGPROTECT, - NP_NULL_ON_SOME_PATH_EXCEPTION, - SQL_NONCONSTANT_STRING_PASSED_TO_EXECUTE, - EQ_COMPARETO_USE_OBJECT_EQUALS, - BX_UNBOXING_IMMEDIATELY_REBOXED, - HE_EQUALS_USE_HASHCODE, - DM_EXIT, - FE_FLOATING_POINT_EQUALITY, - RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE, - BC_UNCONFIRMED_CAST, - REC_CATCH_EXCEPTION, - BC_UNCONFIRMED_CAST_OF_RETURN_VALUE, - VA_FORMAT_STRING_USES_NEWLINE, - RV_RETURN_VALUE_IGNORED_BAD_PRACTICE, - EI_EXPOSE_REP2, - WMI_WRONG_MAP_ITERATOR, - EI_EXPOSE_REP, - NP_LOAD_OF_KNOWN_NULL_VALUE, - DM_NUMBER_CTOR, - SBSC_USE_STRINGBUFFER_CONCATENATION, - OS_OPEN_STREAM_EXCEPTION_PATH, - NP_NONNULL_RETURN_VIOLATION, - SF_SWITCH_NO_DEFAULT, - RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT, - ODR_OPEN_DATABASE_RESOURCE, - PZLA_PREFER_ZERO_LENGTH_ARRAYS, - NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE, - UCF_USELESS_CONTROL_FLOW, - UC_USELESS_CONDITION, - NP_NULL_ON_SOME_PATH, - DM_FP_NUMBER_CTOR, - SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING, - OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE, - ES_COMPARING_STRINGS_WITH_EQ, - OS_OPEN_STREAM, - RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE, - NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE, - - UC_USELESS_OBJECT, - OBL_UNSATISFIED_OBLIGATION, -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java index ccf4804..4d885ea 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java @@ -1,25 +1,11 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import java.io.*; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import com.github.gumtreediff.actions.model.Delete; -import com.github.gumtreediff.actions.model.Insert; -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.actions.model.Update; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; -import edu.lu.uni.serval.diffentry.DiffEntryReader; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; -import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; + +import java.io.*; +import java.util.List; + + /** * Parse fix violations with GumTree in terms of multiple statements. @@ -97,232 +83,5 @@ public class FixedViolationHunkParser extends FixedViolationParser { } -// public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { -// // GumTree results -// List actionSets = parseChangedSourceCodeWithGumTree2(prevFile, revFile); -// -// -// if (this.resultType != 0) { -//// String type = ""; -//// if (this.resultType == 1) { -//// type = "#NullGumTreeResult:"; -//// } else if (this.resultType == 2) { -//// type = "#NoSourceCodeChange:"; -//// } else if (this.resultType == 3) { -//// type = "#NoStatementChange:"; -//// } -// } else { -// List diffentryHunks = new DiffEntryReader().readHunks3(diffentryFile); -// -// //Filter out the modify actions, which are not in the DiffEntry hunks. -// HunkActionFilter hunkFilter = new HunkActionFilter(); -// List selectedPatchHunks = hunkFilter.filterActionsByModifiedRange2(diffentryHunks, actionSets, revFile, prevFile); -// -// for (DiffEntryHunk patchHunk : selectedPatchHunks) { -// List hunkActionSets = patchHunk.getActionSets(); -// // multiple UPD, and some UPD contain other UPD. -// removeOverlapperdUPD(hunkActionSets); -// -// // Range of buggy source code -// int bugStartLine = 0; -// int bugEndLine = 0; -// // Range of fixing source code -// int fixStartLine = 0; -// int fixEndLine = 0; -// int bugEndPosition = 0; -// int fixEndPosition = 0; -// int hunkSet = 0; -// for (HierarchicalActionSet hunkActionSet : hunkActionSets) { -// -// -// FileOutputStream f = null; -// try { -// String pj = diffentryFile.getParent().split("GumTreeInputBug4")[1]; -// String root = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; -// String hunkTreeFileName = root+pj.replace("DiffEntries","ASTDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet); -// f = new FileOutputStream(new File(hunkTreeFileName)); -// ObjectOutputStream o = new ObjectOutputStream(f); -// o.writeObject(hunkActionSet.getNode()); -// -// o.close(); -// f.close(); -// } catch (FileNotFoundException e) { -// e.printStackTrace(); -// } catch (IOException e) { -// e.printStackTrace(); -// } -// hunkSet++; -// -// -// -// int actionBugStart = hunkActionSet.getBugStartLineNum(); -// int actionBugEnd = hunkActionSet.getBugEndLineNum(); -// int actionFixStart = hunkActionSet.getFixStartLineNum(); -// int actionFixEnd = hunkActionSet.getFixEndLineNum(); -// if (bugStartLine == 0) { -// bugStartLine = actionBugStart; -// } else if (actionBugStart != 0 && actionBugStart < bugStartLine) { -// bugStartLine = actionBugStart; -// } -// if (fixStartLine == 0) { -// fixStartLine = actionFixStart; -// } else if (actionFixStart != 0 && actionFixStart < fixStartLine) { -// fixStartLine = actionFixStart; -// } -// if (bugEndLine < actionBugEnd) { -// bugEndLine = actionBugEnd; -// bugEndPosition = hunkActionSet.getBugEndPosition(); -// } -// if (fixEndLine < actionFixEnd) { -// fixEndLine = actionFixEnd; -// fixEndPosition = hunkActionSet.getFixEndPosition(); -// } -// } -// -// if (fixStartLine == 0 && bugStartLine == 0) { -// this.unfixedViolations += "#WRONG: " + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; -// this.nullMappingGumTreeResult ++; -// continue; -// } -// -// if (fixStartLine == 0 && bugStartLine != 0) {// pure delete actions. -// // get the exact buggy code by violation's position. TODO later -// } -// -//// if (children.size() == 0) continue; -// boolean isPureInsert = false; -// if (bugStartLine == 0 && patchHunk.getBugLineStartNum() > 0) { -// bugStartLine = patchHunk.getBugLineStartNum(); -// bugEndLine = bugStartLine + patchHunk.getBuggyHunkSize() - 1; -// isPureInsert = true; -//// continue; -// } -//// if ((bugEndLine - bugStartLine > Configuration.HUNK_SIZE ) || fixEndLine - fixStartLine > Configuration.HUNK_SIZE) { -//// continue; //TODO hunk size -//// } -// if(patchHunk.getBuggyHunkSize() > Configuration.HUNK_SIZE || patchHunk.getFixedHunkSize() > Configuration.HUNK_SIZE){ -// continue; -// } -// -// /** -// * Select edit scripts for deep learning. -// * Edit scripts will be used to mine common fix patterns. -// */ -// // 1. First level: AST node type. -// String astEditScripts = getASTEditScriptsDeepFirst(hunkActionSets, bugEndPosition, fixEndPosition); -// if (astEditScripts.contains("\n") || astEditScripts.split(" ").length % 3 != 0) { -// System.err.println("===+++===: " + revFile.getName() + ":" +patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize()); -// } -// // 2. source code: raw tokens -// // 3. abstract identifiers: -// // 4. semi-source code: -// String[] editScriptTokens = astEditScripts.split(" "); -// int size = editScriptTokens.length; -// if (size == 1) { -// this.nullMappingGumTreeResult ++; -// this.unfixedViolations += "#NullMatchedGumTreeResult1:" + revFile.getName() + ":" + patchHunk.getBugLineStartNum() + ", " + patchHunk.getBuggyHunkSize() + "\n"; -// continue; -// } -// -// String patchPosition = "\n" + revFile.getName() + "\n@@ -" + bugStartLine + ", " + bugEndLine + " +" + fixStartLine + ", " + fixEndLine + "@@\n"; -//// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets, bugEndPosition, fixEndPosition) + "\n"; -////TODO uncomment the line below for more detailed gumtree input. -// String info = Configuration.PATCH_SIGNAL + "\n" + patchPosition + patchHunk.getHunk() + "\nAST Diff###:\n" + getAstEditScripts(hunkActionSets) + "\n"; -//// if (noUpdate(editScriptTokens)) { -//// } -// -// String canonicalVariableNames = getBuggyCodeTree(patchHunk, prevFile, revFile); -// this.patchesSourceCode += info; -// this.patchesSourceCode += "\nRenamed_Variables###:\n" + canonicalVariableNames; -// this.sizes += size + "\n"; -// this.astEditScripts += astEditScripts + "\n"; -//// String tokens = Tokenizer.getTokensDeepFirst(simpleTree).trim(); -//// this.tokensOfSourceCode += tokens + "\n"; -// } -// } -// } - - private String getAstEditScripts(List hunkActionSets) { - String scripts = ""; - for (HierarchicalActionSet hunkActionSet : hunkActionSets) { - scripts += hunkActionSet.toString() + "\n"; - } - return scripts; - } - - private String getBuggyCodeTree(DiffEntryHunk patchHunk, File prevFile, File revFile) { - int bugStartLine = patchHunk.getBugLineStartNum(); - int bugEndLine = bugStartLine + patchHunk.getBugRange() - 1; - - ViolationSourceCodeTree parser = new ViolationSourceCodeTree(prevFile, bugStartLine, bugEndLine); - parser.extract(); - List matchedTrees = parser.getViolationSourceCodeTrees(); - Map renamedVariablesMap = new HashMap<>(); - Map canonicalVariables = new HashMap<>(); - if (matchedTrees.size() > 0) { - SimplifyTree st = new SimplifyTree(); - for (ITree matchedTree : matchedTrees) { - st.canonicalizeSourceCodeTree(matchedTree); - } - renamedVariablesMap = st.canonicalVariableMap; - canonicalVariables = st.canonicalVariables; - } - - int fixStartLine = patchHunk.getFixLineStartNum(); - int fixEndLine = fixStartLine + patchHunk.getFixRange() - 1; - ViolationSourceCodeTree fixedParser = new ViolationSourceCodeTree(revFile, fixStartLine, fixEndLine); - fixedParser.extract(); - matchedTrees = fixedParser.getViolationSourceCodeTrees(); - if (matchedTrees.size() > 0) { - SimplifyTree st = new SimplifyTree(); - st.canonicalVariableMap = renamedVariablesMap; - st.canonicalVariables = canonicalVariables; - for (ITree matchedTree : matchedTrees) { - st.canonicalizeSourceCodeTree(matchedTree); - } - renamedVariablesMap = st.canonicalVariableMap; - } - - StringBuilder builder = new StringBuilder(); - for (Map.Entry entry : renamedVariablesMap.entrySet()) { - builder.append(entry.getKey()).append(" = ").append(entry.getValue()).append("\n"); - } - return builder.toString(); - } - - private void removeOverlapperdUPD(List actionSets) { - if (actionSets.size() == 1) { - return; - } - List updates = new ArrayList<>(); - for (HierarchicalActionSet actionSet : actionSets) { - if (actionSet.getActionString().startsWith("UPD")) { - updates.add(actionSet); - } - } - - List overlappedUpdates = new ArrayList<>(); - if (updates.size() > 1) { - for (HierarchicalActionSet update : updates) { - int startLine = update.getBugStartLineNum(); - int endLine = update.getBugEndLineNum(); - int endPosition = update.getBugEndPosition(); - for (HierarchicalActionSet update2 : updates) { - if (update.equals(update2)) continue; - int startLine2 = update2.getBugStartLineNum(); - int endLine2 = update2.getBugEndLineNum(); - int endPosition2 = update2.getBugEndPosition(); - if (startLine <= startLine2 - && endLine2 <= endLine && endPosition2 < endPosition) { - if (!overlappedUpdates.contains(update)) { - overlappedUpdates.add(update); - } - break; - } - } - } - } - actionSets.removeAll(overlappedUpdates); - } } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java index 264e854..3bbc4eb 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java +++ b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java @@ -1,21 +1,16 @@ package edu.lu.uni.serval.FixPatternParser.violations; -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; - import com.github.gumtreediff.actions.model.Action; - import edu.lu.uni.serval.FixPatternParser.Parser; import edu.lu.uni.serval.gumtree.GumTreeComparer; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.gumtree.regroup.HierarchicalRegrouper; -import edu.lu.uni.serval.utils.FileHelper; import edu.lu.uni.serval.utils.ListSorter; +import java.io.File; +import java.util.ArrayList; +import java.util.List; + /** * Parse fix patterns with GumTree. * @@ -60,16 +55,7 @@ public class FixedViolationParser extends Parser { } else { // Regroup GumTre results. List allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults); -// for (HierarchicalActionSet actionSet : allActionSets) { -// String astNodeType = actionSet.getAstNodeType(); -// if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) { -// actionSets.add(actionSet); -// } -// } - - // Filter out modified actions of changing method names, method parameters, variable names and field names in declaration part. - // variable effects range, sub-actions are these kinds of modification? -// actionSets.addAll(new ActionFilter().filterOutUselessActions(allActionSets)); + ListSorter sorter = new ListSorter<>(allActionSets); actionSets = sorter.sortAscending(); @@ -82,63 +68,14 @@ public class FixedViolationParser extends Parser { } } - /** - * Read patch source code from buggy and fixed files. - * @param prevFile - * @param revFile - * @param bugStartLineNum - * @param bugEndLineNum - * @param fixStartLineNum - * @param fixEndLineNum - * @param isInsert - * @return - */ - protected String getPatchSourceCode(File prevFile, File revFile, int bugStartLineNum, int bugEndLineNum, int fixStartLineNum, int fixEndLineNum, boolean isInsert) { - String buggyStatements = ""; - if (isInsert) { - buggyStatements = readSourceCode(prevFile, bugStartLineNum, bugEndLineNum, ""); - } else { - buggyStatements = readSourceCode(prevFile, bugStartLineNum, bugEndLineNum, "-"); - } - String fixedStatements = readSourceCode(revFile, fixStartLineNum, fixEndLineNum, "+"); - return buggyStatements + fixedStatements; - } - private String readSourceCode(File file, int startLineNum, int endLineNum, String type) { - String sourceCode = ""; - String fileContent = FileHelper.readFile(file); - BufferedReader reader = null; - try { - reader = new BufferedReader(new StringReader(fileContent)); - String line = null; - int lineIndex = 0; - while ((line = reader.readLine()) != null) { - lineIndex ++; - if (lineIndex >= startLineNum && lineIndex <= endLineNum) { - sourceCode += type + line + "\n"; - } - if (lineIndex == endLineNum) break; - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return sourceCode; - } - public String getAlarmTypes() { - return violationTypes; - } - @Override - public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { - } +// @Override +// public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) { +// +// } // public void setUselessViolations(List uselessViolations) { // this.uselessViolations = uselessViolations; diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java deleted file mode 100644 index 6fe1e46..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java +++ /dev/null @@ -1,156 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import java.io.File; -import java.util.List; - -import org.eclipse.jdt.core.dom.CompilationUnit; - -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.actions.model.Update; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.FixPatternParser.CUCreator; -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; - -/** - * Parse fixed violations with GumTree in terms of single statement. - * - * @author kui.liu - * - */ -public class FixedViolationSingleStatementParser extends FixedViolationParser { - - @Override - public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) { - // GumTree results - List actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile); - - if (actionSets.size() > 0) { - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return; - } - - // Read the positions of checked violations - for (HierarchicalActionSet actionSet : actionSets) { - // position of buggy statements - int startPosition = 0; - int endPosition = 0; - // position of fixed statements - int startPosition2 = 0; - int endPosition2 = 0; - - String actionStr = actionSet.getActionString(); - String astNodeType = actionSet.getAstNodeType(); - if (actionStr.startsWith("INS")) { - startPosition2 = actionSet.getStartPosition(); - endPosition2 = startPosition2 + actionSet.getLength(); - List firstAndLastMov = getFirstAndLastMoveAction(actionSet); - if (firstAndLastMov != null) { - startPosition = firstAndLastMov.get(0).getNode().getPos(); - ITree lastTree = firstAndLastMov.get(1).getNode(); - endPosition = lastTree.getPos() + lastTree.getLength(); - } else { // Ignore the pure insert actions without any move actions. - continue; - } - } else if (actionStr.startsWith("UPD")) { - startPosition = actionSet.getStartPosition(); - endPosition = startPosition + actionSet.getLength(); - Update update = (Update) actionSet.getAction(); - ITree newNode = update.getNewNode(); - startPosition2 = newNode.getPos(); - endPosition2 = startPosition2 + newNode.getLength(); - - if (Checker.containsBodyBlock(astNodeType)) { - List children = update.getNode().getChildren(); - endPosition = getEndPosition(children); - List newChildren = newNode.getChildren(); - endPosition2 = getEndPosition(newChildren); - - if (endPosition == 0) { - endPosition = startPosition + actionSet.getLength(); - } - if (endPosition2 == 0) { - endPosition2 = startPosition2 + newNode.getLength(); - } - } - } else {// DEL actions and MOV actions: we don't need these actions, as for now. - continue; - } - if (startPosition == 0 || startPosition2 == 0) { - continue; - } - - // Get line numbers. - int startLine = prevUnit.getLineNumber(startPosition); - int endLine = prevUnit.getLineNumber(endPosition); - int startLine2 = revUnit.getLineNumber(startPosition2); - int endLine2 = revUnit.getLineNumber(endPosition2); - - Violation violation = null;//findViolation(startLine, endLine, violations); - if (violation == null) continue; - - if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2 ) continue; - - /* - * Convert the ITree of buggy code to a simple tree. - * It will be used to compute the similarity. - */ - SimplifyTree abstractIdentifier = new SimplifyTree(); - abstractIdentifier.abstractTree(actionSet); - SimpleTree simpleTree = actionSet.getSimpleTree(); - if (simpleTree == null) { // Failed to get the simple tree for INS actions. - continue; - } - - /** - * Select edit scripts for deep learning. - * Edit scripts will be used to mine common fix patterns. - */ - // 1. First level: AST node type. - String astEditScripts = getASTEditScriptsBreadthFirst(actionSet); - int size = astEditScripts.split(" ").length; - if (size == 1) { - continue; - } - - // Source Code of patches. - String patchSourceCode = getPatchSourceCode(prevFile, revFile, startLine, endLine, startLine2, endLine2, false); - this.patchesSourceCode += Configuration.PATCH_SIGNAL + "\n" + revFile.getName() + "\n" + patchSourceCode + "\n"; - this.sizes += size + "\n"; - this.astEditScripts += astEditScripts + "\n"; - this.violationTypes += violation.getViolationType() + "\n"; - // 2. source code: raw tokens -// String rawTokenEditScripts = getRawTokenEditScripts(actionSet); -// // 3. abstract identifiers: -// String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet); -// // 4. semi-source code: -// String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet); - -// this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + simpleTree.toString() + "\n"; - this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n"; -// this.actionSets += Configuration.BUGGY_TREE_TOKEN + "\n" + readActionSet(actionSet, "") + "\n"; -// this.originalTree += Configuration.BUGGY_TREE_TOKEN + "\n" + actionSet.getOriginalTree().toString() + "\n"; - } - actionSets.clear(); - } else { - System.out.println(1); - } - } - - protected Violation findViolation(int startLine, int endLine, List violations) { - for (Violation violation : violations) { - int vStartLine = violation.getStartLineNum(); - int vEndLine = violation.getEndLineNum(); - if (!(startLine > vEndLine && endLine< vStartLine)) return violation; - } - return null; - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java deleted file mode 100644 index 969a4c2..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Message.java +++ /dev/null @@ -1,20 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import java.io.File; - -public class Message { - - private String name; - private String inputPath; - private String innerPort; - - public Message(String name , String inputPath, String innerPort) { - super(); - this.name = name; - this.inputPath = inputPath; - this.innerPort = innerPort; - } - - - -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java deleted file mode 100644 index 53bd576..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Producer.java +++ /dev/null @@ -1,150 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import com.rabbitmq.client.Channel; -import com.rabbitmq.client.Connection; -import com.rabbitmq.client.ConnectionFactory; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.File; -import java.io.FilenameFilter; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; -import java.util.concurrent.TimeoutException; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -/** - * Created by anilkoyuncu on 03/04/2018. - */ -public class Producer { - private static Logger log = LoggerFactory.getLogger(Producer.class); - public static void main(String[] args) { - - - String inputPath; - String outputPath; - String port; - String portInner; - String pairsCSVPath; - String importScript; - String pairsCompletedPath; - String serverWait; - if (args.length > 0) { - inputPath = args[0]; - port = args[1]; - portInner = args[2]; - serverWait = args[3]; -// pairsCSVPath = args[3]; -// importScript = args[4]; -// pairsCompletedPath = args[3]; - } else { - inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; - outputPath = "/Users/anilkoyuncu/bugStudy/dataset/"; - port = "6379"; - portInner = "6380"; - serverWait = "10000"; - pairsCSVPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test"; - importScript = "/Users/anilkoyuncu/bugStudy/dataset/pairs/test2.sh"; - pairsCompletedPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs_completed"; - } - - - calculatePairs(inputPath, port); - log.info("Calculate pairs done"); - - - - } - public static void calculatePairs(String inputPath,String port) { - File folder = new File(inputPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - List fileToCompare = new ArrayList<>(); - for (File pj : pjs) { - File[] files = pj.listFiles(new FilenameFilter() { - public boolean accept(File dir, String name) { - return name.startsWith("ActionSetDumps"); - } - }); - Collections.addAll(fileToCompare, files[0].listFiles()); - - } - System.out.println("a"); -// compareAll(fileToCompare); - readMessageFiles(fileToCompare, port); - } - - private static void readMessageFiles(List folders, String port) { - - List treesFileNames = new ArrayList<>(); - - - for (File target : folders) { - - treesFileNames.add(target.toString()); - } - - - log.info("Calculating pairs"); - - int fileCounter = 0; - - ConnectionFactory factory = new ConnectionFactory(); - factory.setHost("10.240.5.10"); -// factory.setVirtualHost("treeCompare"); - factory.setPort(5672); - factory.setUsername("anil"); - factory.setPassword("changeme2018"); - factory.setConnectionTimeout(1000); - Connection connection = null; - Channel channel = null; - try { - connection = factory.newConnection(); - - channel = connection.createChannel(); - channel.queueDeclare("tree_queue", false, false, false, null); - - } catch (IOException e) { - e.printStackTrace(); - } catch (TimeoutException e) { - e.printStackTrace(); - } - - - for (int i = 0; i < treesFileNames.size(); i++) { - for (int j = i + 1; j < treesFileNames.size(); j++) { - - - // do operations with jedis resource - - String key = "pair_" + String.valueOf(i) + "_" + String.valueOf(j); -// String value = treesFileNames.get(i).split("GumTreeOutput2")[1] +","+treesFileNames.get(j).split("GumTreeOutput2")[1]; -// jedis.set(key,value); - - String message = key +","+treesFileNames.get(i).split("GumTreeOutput2")[1] + "," + treesFileNames.get(j).split("GumTreeOutput2")[1]; - try { - channel.basicPublish("", "tree_queue", null, message.getBytes()); - } catch (IOException e) { - e.printStackTrace(); - } - - - - - } - } - - - - - log.info("Done pairs"); - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Violation.java b/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Violation.java deleted file mode 100644 index b22530a..0000000 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/Violation.java +++ /dev/null @@ -1,133 +0,0 @@ -package edu.lu.uni.serval.FixPatternParser.violations; - -import java.util.ArrayList; -import java.util.List; - -import edu.lu.uni.serval.diffentry.DiffEntryHunk; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; - -public class Violation implements Comparable { - - private String fileName = ""; - private Integer startLineNum; - private int endLineNum; - private int bugStartLineNum; - private int bugEndLineNum; - private int fixStartLineNum = 0; - private int fixEndLineNum; - private String violationType; - private List hunks = new ArrayList<>(); - private List actionSets; - private int bugFixStartLineNum = 0; // the heuristic matched fix start line of a violation - private int bugFixEndLineNum = 0; // the heuristic matched fix end line of a violation - - public Violation(Integer startLineNum, int endLineNum, String violationType) { - super(); - this.startLineNum = startLineNum; - this.endLineNum = endLineNum; - this.violationType = violationType; - this.actionSets = new ArrayList<>(); - } - - public String getFileName() { - return fileName; - } - - public void setFileName(String fileName) { - this.fileName = fileName; - } - - public Integer getStartLineNum() { - return startLineNum; - } - - public int getEndLineNum() { - return endLineNum; - } - - public int getBugStartLineNum() { - return bugStartLineNum; - } - - public void setBugStartLineNum(int bugStartLineNum) { - this.bugStartLineNum = bugStartLineNum; - } - - public int getBugEndLineNum() { - return bugEndLineNum; - } - - public void setBugEndLineNum(int bugEndLineNum) { - this.bugEndLineNum = bugEndLineNum; - } - - public int getFixStartLineNum() { - return fixStartLineNum; - } - - public void setFixStartLineNum(int fixStartLineNum) { - this.fixStartLineNum = fixStartLineNum; - } - - public int getFixEndLineNum() { - return fixEndLineNum; - } - - public void setFixEndLineNum(int fixEndLineNum) { - this.fixEndLineNum = fixEndLineNum; - } - - public List getHunks() { - return hunks; - } - - public void setHunks(List hunks) { - this.hunks = hunks; - } - - public String getViolationType() { - return violationType; - } - - public List getActionSets() { - return actionSets; - } - - public int getBugFixStartLineNum() { - return bugFixStartLineNum; - } - - public void setBugFixStartLineNum(int bugFixStartLineNum) { - this.bugFixStartLineNum = bugFixStartLineNum; - } - - public int getBugFixEndLineNum() { - return bugFixEndLineNum; - } - - public void setBugFixEndLineNum(int bugFixEndLineNum) { - this.bugFixEndLineNum = bugFixEndLineNum; - } - - @Override - public int compareTo(Violation v) { - return this.startLineNum.compareTo(v.startLineNum); - } - - @Override - public String toString() { - return this.startLineNum + " : " + this.endLineNum + " : " + this.violationType; - } - - @Override - public boolean equals(Object obj) { - if (obj instanceof Violation) { - Violation v = (Violation) obj; - if (this.fileName.equals(v.fileName) && this.violationType.equals(v.violationType) && this.startLineNum == v.startLineNum && this.endLineNum == v.endLineNum) { - return true; - } - } - return false; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java deleted file mode 100644 index c1c1d7b..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java +++ /dev/null @@ -1,121 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser; - -import java.io.File; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -/** - * Multi-thread parser of parsing the difference between buggy code file and fixed code file. - * - * @author kui.liu - * - */ -public class AkkaParser { - - private static Logger log = LoggerFactory.getLogger(AkkaParser.class); - - /** - * Two parameters: - * First one: the root path of input data. - * Second one: the number of threads. - * Third one: the threshold of selecting patch hunks. - * @param args - */ - @SuppressWarnings("deprecation") - public static void main(String[] args) { -// String inputRootPath = args[0]; - int numberOfWorkers = 5; //Integer.parseInt(args[1]); - int hunkThreshold = 10; -// try { -// hunkThreshold = Integer.parseInt(args[2]); -// } catch (NumberFormatException e1) { -// hunkThreshold = 10; -// } - -// Configuration.ROOT_PATH = inputRootPath; - Configuration.HUNK_SIZE = hunkThreshold; - - List pjList = Arrays.asList("APACHE-CAMEL","APACHE-HBASE","APACHE-HIVE","COMMONS-CODEC","COMMONS-COLLECTIONS", - "COMMONS-COMPRESS","COMMONS-CONFIGURATION","COMMONS-CRYPTO","COMMONS-CSV","COMMONS-IO","COMMONS-LANG", - "COMMONS-MATH","COMMONS-WEAVER","JBOSS-ENTESB","JBOSS-JBMETA","SPRING-AMQP","SPRING-ANDROID","SPRING-BATCH", - "SPRING-BATCHADM","SPRING-DATACMNS","SPRING-DATAGRAPH","SPRING-DATAJPA","SPRING-DATAMONGO","SPRING-DATAREDIS", - "SPRING-DATAREST","SPRING-LDAP","SPRING-MOBILE","SPRING-ROO","SPRING-SEC","SPRING-SECOAUTH","SPRING-SGF","SPRING-SHDP", - "SPRING-SOCIAL","SPRING-SOCIALFB","SPRING-SOCIALLI","SPRING-SOCIALTW","SPRING-SPR","SPRING-SWF","SPRING-SWS","WILDFLY-ELY", - "WILDFLY-SWARM","WILDFLY-WFARQ","WILDFLY-WFCORE","WILDFLY-WFLY","WILDFLY-WFMP"); - for (String pj : pjList) { - String[] split = pj.split("-"); - String pjPath = split[0]; - String pjName = split[1]; -// String rootPath = "/Volumes/data/bugStudy/"; -// String DATASET_FILE_PATH = rootPath + "/dataset/GumTreeInput/" + pjName; -// String GIT_REPOSITORY_PATH = "/Users/anilkoyuncu/bugLocalizationStudy/irblsensitivity/data/" + pjPath + "/" + pjName + "/gitrepo/.git"; - log.info(pjName); - // input data - log.info("Get the input data..."); - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT +pjName +"gitrepo/"); - log.info("MessageFiles: " + msgFiles.size()); - - // output path - final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH + pjName + "/"; - final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH+ pjName + "/"; - final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH+ pjName + "/"; - final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH+ pjName + "/"; - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - - ActorSystem system = null; - ActorRef parsingActor = null; - final WorkMessage msg = new WorkMessage(0, msgFiles); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Mining-FixPattern-System"); -// parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, -// patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); - } - } - - } - - /** - * Get violation-related files. - * - * @param gumTreeInput - * @return - */ - public static List getMessageFiles(String gumTreeInput) { - String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile - File revFilesPath = new File(inputPath + "revFiles/"); - File[] revFiles = revFilesPath.listFiles(); // project folders - List msgFiles = new ArrayList<>(); - - for (File revFile : revFiles) { - if (revFile.getName().endsWith(".java")) { - String fileName = revFile.getName(); - File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file - fileName = fileName.replace(".java", ".txt"); - File diffentryFile = new File(gumTreeInput + "diffentries/" + fileName); // DiffEntry file - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file - MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); - } - } - - return msgFiles; - } -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java deleted file mode 100644 index b0057ae..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser2.java +++ /dev/null @@ -1,146 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser; - -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.File; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -/** - * Multi-thread parser of parsing the difference between buggy code file and fixed code file. - * - * @author kui.liu - * - */ -public class AkkaParser2 { - - private static Logger log = LoggerFactory.getLogger(AkkaParser2.class); - - /** - * Two parameters: - * First one: the root path of input data. - * Second one: the number of threads. - * Third one: the threshold of selecting patch hunks. - * @param args - */ - @SuppressWarnings("deprecation") - public static void main(String[] args) { - String inputRootPath; - String outputRootPath; - int numberOfWorkers; - if(args.length > 0){ - inputRootPath = args[0]; - outputRootPath = args[1]; - numberOfWorkers = Integer.parseInt(args[2]); - }else{ - inputRootPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug"; - outputRootPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputBug/"; - numberOfWorkers = 1; - } - -// try { -// hunkThreshold = Integer.parseInt(args[2]); -// } catch (NumberFormatException e1) { -// hunkThreshold = 10; -// } - -// Configuration.ROOT_PATH = inputRootPath; -// log.info(Configuration.ROOT_PATH); -// Configuration.HUNK_SIZE = hunkThreshold; - - - - // input data -// String GUM_TREE_INPUT = inputRootPath + "GumTreeInput/"; - log.info("Get the input data..." + inputRootPath ); - - log.info("Set the output data..." + outputRootPath ); - - - File folder = new File(inputRootPath); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List folders = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - - for (File target : folders) { - log.info("MessageFiles: " + target.toString()); - final List msgFiles = getMessageFiles(target.toString() + "/"); - log.info("MessageFiles: " + msgFiles.size()); - // output path - - - String pjName = target.getName(); - // output path - String GUM_TREE_OUTPUT = outputRootPath + pjName + "/"; - final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts/"; - final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode/"; - final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens/"; - final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes/"; - final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes/"; - - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - - ActorSystem system = null; - ActorRef parsingActor = null; - final WorkMessage msg = new WorkMessage(0, msgFiles); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Mining-FixPattern-System"); -// parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, editScriptsFilePath, -// patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); - } - - - } - - - } - - /** - * Get violation-related files. - * - * @param gumTreeInput - * @return - */ - public static List getMessageFiles(String gumTreeInput) { - String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile - File revFilesPath = new File(inputPath + "revFiles/"); - File[] revFiles = revFilesPath.listFiles(); // project folders - List msgFiles = new ArrayList<>(); - - for (File revFile : revFiles) { -// if (revFile.getName().endsWith(".c") || revFile.getName().endsWith(".h")) { - if (revFile.getName().endsWith(".java")) { - String fileName = revFile.getName(); - File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file - fileName = fileName.replace(".java", ".txt"); - File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file - MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); - - } -// } - } - - return msgFiles; //.subList(10,20); - } -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java index 3e8fdf5..46ea6df 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternActor.java @@ -1,15 +1,14 @@ package edu.lu.uni.serval.MultipleThreadsParser; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - import akka.actor.ActorRef; import akka.actor.Props; import akka.actor.UntypedActor; import akka.japi.Creator; import akka.routing.RoundRobinPool; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.List; public class ParseFixPatternActor extends UntypedActor { diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java index 8f88ce3..3084dbe 100644 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java +++ b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/ParseFixPatternWorker.java @@ -1,28 +1,17 @@ package edu.lu.uni.serval.MultipleThreadsParser; -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.List; -import java.util.concurrent.ExecutionException; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.Future; -import java.util.concurrent.TimeUnit; -import java.util.concurrent.TimeoutException; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - import akka.actor.Props; import akka.actor.UntypedActor; import akka.japi.Creator; import edu.lu.uni.serval.FixPatternParser.RunnableParser; import edu.lu.uni.serval.FixPatternParser.violations.FixedViolationHunkParser; -import edu.lu.uni.serval.FixPatternParser.violations.Violation; import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.util.List; +import java.util.concurrent.*; public class ParseFixPatternWorker extends UntypedActor { private static Logger log = LoggerFactory.getLogger(ParseFixPatternActor.class); @@ -79,10 +68,6 @@ public class ParseFixPatternWorker extends UntypedActor { File diffentryFile = msgFile.getDiffEntryFile(); -// File positionFile = msgFile.getPositionFile(); - /*if (revFile.getName().toLowerCase().contains("test")) { - continue; - }*/ FixedViolationHunkParser parser = new FixedViolationHunkParser(); final ExecutorService executor = Executors.newSingleThreadExecutor(); @@ -103,13 +88,7 @@ public class ParseFixPatternWorker extends UntypedActor { String editScript = parser.getAstEditScripts(); if ("".equals(editScript)) { -// if (parser.resultType == 1) { -// nullGumTreeResults += countAlarms(positionFile, ""); -// } else if (parser.resultType == 2) { -// noSourceCodeChanges += countAlarms(positionFile, ""); -// } else if (parser.resultType == 3) { -// noStatementChanges += countAlarms(positionFile, ""); -// } + } else { editScripts.append(editScript); patchesSourceCode.append(parser.getPatchesSourceCode()); @@ -118,29 +97,21 @@ public class ParseFixPatternWorker extends UntypedActor { counter ++; if (counter % 100 == 0) { -// FileHelper.outputToFile(editScriptsFilePath + "edistScripts_" + id + ".list", editScripts, true); -// FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); -// FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); -// FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); editScripts.setLength(0); patchesSourceCode.setLength(0); sizes.setLength(0); tokens.setLength(0); log.info("Worker #" + id +" finialized parsing " + counter + " files..."); -// FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); testingInfo.setLength(0); } } } catch (TimeoutException e) { future.cancel(true); -// timeouts += countAlarms(positionFile, "#Timeout:"); System.err.println("#Timeout: " + revFile.getName()); } catch (InterruptedException e) { -// timeouts += countAlarms(positionFile, "#TimeInterrupted:"); System.err.println("#TimeInterrupted: " + revFile.getName()); e.printStackTrace(); } catch (ExecutionException e) { -// timeouts += countAlarms(positionFile, "#TimeAborted:"); System.err.println("#TimeAborted: " + revFile.getName()); e.printStackTrace(); } finally { @@ -149,24 +120,13 @@ public class ParseFixPatternWorker extends UntypedActor { } if (sizes.length() > 0) { -// FileHelper.outputToFile(editScriptsFilePath + "editScripts_" + id + ".list", editScripts, true); -// FileHelper.outputToFile(patchesSourceCodeFilePath + "patches_" + id + ".list", patchesSourceCode, true); -// FileHelper.outputToFile(editScriptSizesFilePath + "sizes_" + id + ".list", sizes, true); -// FileHelper.outputToFile(buggyTokensFilePath + "tokens_" + id + ".list", tokens, true); editScripts.setLength(0); patchesSourceCode.setLength(0); sizes.setLength(0); tokens.setLength(0); -// FileHelper.outputToFile("OUTPUT/testingInfo_" + id + ".list", testingInfo, true); testingInfo.setLength(0); } -// String statistic = "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + -// "\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults + -// "\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + -// "\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts; -// FileHelper.outputToFile("OUTPUT/statistic_" + id + ".list", statistic, false); -// FileHelper.outputToFile("OUTPUT/UnfixedV_" + id + ".list", builder, false); log.info("Worker #" + id +"finialized parsing " + counter + " files..."); log.info("Worker #" + id + " finialized the work..."); diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java deleted file mode 100644 index 80b03db..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser/SingleThreadParser.java +++ /dev/null @@ -1,190 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.List; -import java.util.concurrent.ExecutionException; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.Future; -import java.util.concurrent.TimeUnit; -import java.util.concurrent.TimeoutException; - -import edu.lu.uni.serval.FixPatternParser.RunnableParser; -import edu.lu.uni.serval.FixPatternParser.violations.FixedViolationHunkParser; -import edu.lu.uni.serval.FixPatternParser.violations.Violation; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -public class SingleThreadParser { - - public static void main(String[] args) { - // output path - final String editScriptsFilePath = Configuration.EDITSCRIPTS_FILE_PATH; - final String patchesSourceCodeFilePath = Configuration.PATCH_SOURCECODE_FILE_PATH; - final String buggyTokensFilePath = Configuration.BUGGY_CODE_TOKEN_FILE_PATH; - final String editScriptSizesFilePath = Configuration.EDITSCRIPT_SIZES_FILE_PATH; - final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE_PATH; - FileHelper.deleteDirectory(editScriptsFilePath); - FileHelper.deleteDirectory(patchesSourceCodeFilePath); - FileHelper.deleteDirectory(buggyTokensFilePath); - FileHelper.deleteDirectory(editScriptSizesFilePath); - FileHelper.deleteDirectory(alarmTypesFilePath); - - final List files = AkkaParser.getMessageFiles(Configuration.GUM_TREE_INPUT); - - StringBuilder editScripts = new StringBuilder(); - StringBuilder patchesSourceCode = new StringBuilder(); - StringBuilder sizes = new StringBuilder(); - StringBuilder tokens = new StringBuilder(); - StringBuilder alarmTypes = new StringBuilder(); - StringBuilder testingInfo = new StringBuilder(); - - int counter = 0; - - int testViolations = 0; - int nullGumTreeResults = 0; - int noSourceCodeChanges = 0; - int noStatementChanges = 0; - int nullDiffEntry = 0; - int nullMappingGumTreeResults = 0; - int pureDeletion = 0; - int largeHunk = 0; - int nullSourceCode = 0; - int testInfos = 0; - int timeouts = 0; - StringBuilder builder = new StringBuilder(); - - for (MessageFile msgFile : files) { - File revFile = msgFile.getRevFile(); - File prevFile = msgFile.getPrevFile(); - File diffentryFile = msgFile.getDiffEntryFile(); - File positionFile = msgFile.getPositionFile(); - if (revFile.getName().toLowerCase().contains("test#") || revFile.getName().toLowerCase().contains("tests#")) { - testViolations += countAlarms(positionFile, "#TestViolation:"); - continue; - } - FixedViolationHunkParser parser = new FixedViolationHunkParser(); -// parser.setUselessViolations(uselessViolations); - - final ExecutorService executor = Executors.newSingleThreadExecutor(); - // schedule the work - final Future future = executor.submit(new RunnableParser(prevFile, revFile, diffentryFile, parser)); - try { - // wait for task to complete - future.get(Configuration.SECONDS_TO_WAIT, TimeUnit.SECONDS); - - nullDiffEntry += parser.nullMatchedDiffEntry; - nullMappingGumTreeResults += parser.nullMappingGumTreeResult; - pureDeletion += parser.pureDeletions; - largeHunk += parser.largeHunk; - nullSourceCode += parser.nullSourceCode; - testInfos += parser.testInfos; - testingInfo.append(parser.testingInfo); - builder.append(parser.unfixedViolations); - - String editScript = parser.getAstEditScripts(); - if ("".equals(editScript)) { - if (parser.resultType == 1) { - nullGumTreeResults += countAlarms(positionFile, ""); - } else if (parser.resultType == 2) { - noSourceCodeChanges += countAlarms(positionFile, ""); - } else if (parser.resultType == 3) { - noStatementChanges += countAlarms(positionFile, ""); -// } else if (parser.resultType == 4) { - } - } else { - editScripts.append(editScript); - patchesSourceCode.append(parser.getPatchesSourceCode()); - sizes.append(parser.getSizes()); - alarmTypes.append(parser.getAlarmTypes()); - tokens.append(parser.getTokensOfSourceCode()); - - counter ++; - if (counter % 5000 == 0) { - FileHelper.outputToFile(editScriptsFilePath + "edistScripts.list", editScripts, true); - FileHelper.outputToFile(patchesSourceCodeFilePath + "patches.list", patchesSourceCode, true); - FileHelper.outputToFile(editScriptSizesFilePath + "sizes.list", sizes, true); - FileHelper.outputToFile(buggyTokensFilePath + "tokens.list", tokens, true); - editScripts.setLength(0); - patchesSourceCode.setLength(0); - sizes.setLength(0); - tokens.setLength(0); - FileHelper.outputToFile(alarmTypesFilePath + "alarmTypes.list", alarmTypes, true); - alarmTypes.setLength(0); - FileHelper.outputToFile("OUTPUT/testingInfo.list", testingInfo, true); - testingInfo.setLength(0); - } - } - } catch (TimeoutException e) { -// err.println("task timed out"); - future.cancel(true); - timeouts += countAlarms(positionFile, "#Timeout:"); -// System.err.println("#Timeout: " + revFile.getName()); - } catch (InterruptedException e) { - timeouts += countAlarms(positionFile, "#TimeInterrupted:"); -// err.println("task interrupted"); -// System.err.println("#TimeInterrupted: " + revFile.getName()); - } catch (ExecutionException e) { - timeouts += countAlarms(positionFile, "#TimeAborted:"); -// err.println("task aborted"); -// System.err.println("#TimeAborted: " + revFile.getName()); - } finally { - executor.shutdownNow(); - } - } - - if (sizes.length() > 0) { - FileHelper.outputToFile(editScriptsFilePath + "edistScripts.list", editScripts, true); - FileHelper.outputToFile(patchesSourceCodeFilePath + "patches.list", patchesSourceCode, true); - FileHelper.outputToFile(editScriptSizesFilePath + "sizes.list", sizes, true); - FileHelper.outputToFile(buggyTokensFilePath + "tokens.list", tokens, true); - editScripts.setLength(0); - patchesSourceCode.setLength(0); - sizes.setLength(0); - tokens.setLength(0); - - FileHelper.outputToFile(alarmTypesFilePath + "alarmTypes.list", alarmTypes, true); - alarmTypes.setLength(0); - FileHelper.outputToFile("OUTPUT/testingInfo.list", testingInfo, true); - testingInfo.setLength(0); - } - String statistic = "TestViolations: " + testViolations + "\nNullGumTreeResults: " + nullGumTreeResults + "\nNoSourceCodeChanges: " + noSourceCodeChanges + - "\nNoStatementChanges: " + noStatementChanges + "\nNullDiffEntry: " + nullDiffEntry + "\nNullMatchedGumTreeResults: " + nullMappingGumTreeResults + - "\nPureDeletion: " + pureDeletion + "\nLargeHunk: " + largeHunk + "\nNullSourceCode: " + nullSourceCode + - "\nTestingInfo: " + testInfos + "\nTimeout: " + timeouts; - FileHelper.outputToFile("OUTPUT/statistic.list", statistic, false); - FileHelper.outputToFile("OUTPUT/UnfixedV.list", builder, false); - } - - private static int countAlarms(File positionFile, String type) {//, List uselessViolations) { - int counter = 0; - String content = FileHelper.readFile(positionFile); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - String[] elements = line.split(":"); - Violation v = new Violation(Integer.parseInt(elements[1]), Integer.parseInt(elements[2]), elements[0]); - String fileName = positionFile.getName().replace(".txt", ".java"); - v.setFileName(fileName); - counter ++; - if (!"".equals(type)) { - System.err.println(type + fileName + ":" + elements[1] + ":" + elements[2] + ":" + elements[0]); - } - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return counter; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/AkkaMatcher.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/AkkaMatcher.java deleted file mode 100644 index 0f59221..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/AkkaMatcher.java +++ /dev/null @@ -1,214 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.MapSorter; - -/** - * Multi-thread parser of parsing the difference between buggy code file and fixed code file. - * - * @author kui.liu - * - */ -public class AkkaMatcher { - - private static Logger log = LoggerFactory.getLogger(AkkaMatcher.class); - - public static void main(String[] args) { - List extractedFeatures = readStringList(Configuration.ROOT_PATH + "TestData/2_CNNinput.csv"); - int size = extractedFeatures.size(); - List trainingFeatures = extractedFeatures.subList(0, size - 178); - List bugFeatures = extractedFeatures.subList(size - 178, size); - - - for (int index = 0; index < 178; index ++) { -// AkkaMatcher computor = new AkkaMatcher(); -// computor.matchFixPatterns(bugFeatures.get(index), index, trainingFeatures); - Map similarities = new HashMap<>(); - for (int i = 0; i < size - 178; i ++) { - Double similarity = Math.abs(computeSimilarity(bugFeatures.get(index), trainingFeatures.get(i))); - similarities.put(i + 1, similarity); - } - - MapSorter mapSorter = new MapSorter(); - Map sortedSimilarities = mapSorter.sortByValueDescending(similarities); - - List similarityList = new ArrayList<>(); - double similarity = 0; - int num = 0; - for (Map.Entry entry : sortedSimilarities.entrySet()) { - if (entry.getValue().equals(Double.NaN)) { - continue; - } - if (entry.getValue() == similarity) { - continue; - } - similarityList.add(entry.getKey()); - similarity = entry.getValue(); - if (++ num % 100 == 0) { - break; - } - } - outputMatchedPatterns(similarityList, index + 1); - } - - } - - private static Double computeSimilarity(Double[] feature, Double[] trainingFeature) { - Double similarity = DistanceCalculator.cosineSimilarityDistance(trainingFeature, feature); - return similarity; - } - - private static void outputMatchedPatterns(List similarityList, int bugId) { - String outputFile = Configuration.ROOT_PATH + "TestData/MatchedFixPatterns/Bug_" + bugId + ".list"; - StringBuilder builder = new StringBuilder("BugId: " + bugId + "\n\n\n"); - - for (int i = 0, size = similarityList.size(); i < size; i ++) { - int patternPosition = similarityList.get(i); - builder.append(readPattern(patternPosition)); - } - - FileHelper.outputToFile(outputFile, builder, false); - } - - private static String readPattern(int patternPosition) { - String patternInfo = ""; - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(Configuration.SELECTED_PATCHES_SOURE_CODE_FILE); - scanner = new Scanner(fis); - int index = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - if (line.equals("PATCH###")) { - if (patternPosition == index) { - break; - } - index ++; - patternInfo = ""; - } - patternInfo += line + "\n"; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return patternInfo; - } - - @SuppressWarnings("deprecation") - public void matchFixPatterns(Double[] bugFeature, int bugIndex, List trainingFeatures) { - ActorSystem system = null; - ActorRef parsingActor = null; - int numberOfWorkers = 100; - final WorkMessage msg = new WorkMessage(bugIndex, bugFeature, trainingFeatures); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Matching-FixPattern-System"); - parsingActor = system.actorOf(MatchFixPatternActor.props(numberOfWorkers), "match-fix-pattern-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); - } - } - - - /** - * Get bug commit-related files. - * - * @return - */ - public static List getMessageFiles() { - String inputPath = Configuration.GUM_TREE_INPUT; //DiffEntries prevFiles revFiles - File inputFileDirector = new File(inputPath); - File[] files = inputFileDirector.listFiles(); // project folders - log.info("Projects: " + files.length); - List msgFiles = new ArrayList<>(); - - for (File file : files) { - if (!file.isDirectory()) continue; -// if (!(file.getName().startsWith("k") || file.getName().startsWith("l"))) continue; - if (file.getName().startsWith("a") || file.getName().startsWith("b") - || file.getName().startsWith("c") || file.getName().startsWith("d") - || file.getName().startsWith("e") || file.getName().startsWith("f") - || file.getName().startsWith("g") || file.getName().startsWith("h") - ||file.getName().startsWith("h") || file.getName().startsWith("i") - || file.getName().startsWith("k") || file.getName().startsWith("l") - || file.getName().startsWith("j") || file.getName().startsWith("t")) continue; -// if (!file.getName().startsWith("j")) continue; - log.info("Project name: " + file.getName()); - String projectFolder = file.getPath(); - File revFileFolder = new File(projectFolder + "/revFiles/");// revised file folder - File[] revFiles = revFileFolder.listFiles(); - for (File revFile : revFiles) { - if (revFile.getName().endsWith(".java")) { - File prevFile = new File(projectFolder + "/prevFiles/prev_" + revFile.getName());// previous file - File diffentryFile = new File(projectFolder + "/DiffEntries/" + revFile.getName().replace(".java", ".txt")); // DiffEntry file - MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); - msgFiles.add(msgFile); - } - } - } - - return msgFiles; - } - - public static List readStringList(String inputFile) { - List list = new ArrayList<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(inputFile); - scanner = new Scanner(fis); - while(scanner.hasNextLine()) { - String line = scanner.nextLine(); - Double[] features = doubleParseFeature(line); - list.add(features); - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return list; - } - - private static Double[] doubleParseFeature(String feature) { - String[] features = feature.split(", "); - int length = features.length; - Double[] doubleFeatures = new Double[length]; - for (int i = 0; i < length; i ++) { - doubleFeatures[i] = Double.parseDouble(features[i]); - } - return doubleFeatures; - } -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceCalculator.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceCalculator.java deleted file mode 100644 index 8ce4a9a..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceCalculator.java +++ /dev/null @@ -1,68 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -public class DistanceCalculator { - - public static double calculateDistance(DistanceFunction distanceType, Double[] targetPoint, Double[] selfPoint) { - double distance = 0; - switch (distanceType) { - case EUCLIDEAN: - distance = DistanceCalculator.euclideanDistance(targetPoint, selfPoint); - break; - case COSINESIMILARITY: - distance = DistanceCalculator.cosineSimilarityDistance(targetPoint, selfPoint); - break; - case MANHATTAN: - distance = DistanceCalculator.manhattanDistance(targetPoint, selfPoint); - break; - default: - distance = DistanceCalculator.euclideanDistance(targetPoint, selfPoint); - break; - } - return distance; - } - - public static double euclideanDistance(Double[] targetPoint, Double[] selfPoint) { - double sum = 0.0; - - for (int i = 0, length = targetPoint.length; i < length; i++) { - double diff = targetPoint[i] - selfPoint[i]; - sum += diff * diff; - } - return Math.sqrt(sum); - } - - public static Double cosineSimilarityDistance(Double[] targetPoint, Double[] selfPoint) { - Double sim = 0.0d; - int length = targetPoint.length; - double dot = 0.0d; - double mag1 = 0.0d; - double mag2 = 0.0d; - - for (int i = 0; i < length; i ++) { - dot += targetPoint[i] * selfPoint[i]; - mag1 += Math.pow(targetPoint[i], 2); - mag2 += Math.pow(selfPoint[i], 2); - } - - sim = dot / (Math.sqrt(mag1) * Math.sqrt(mag2)); - return sim; - } - - public static Double manhattanDistance(Double[] targetPoint, Double[] selfPoint) { - double result = 0.0; - for (int i = 0; i < targetPoint.length; i++) { - result += Math.abs(selfPoint[i] - targetPoint[i]); - } - return result; - } - - public static Double minkowskiDistance(Double[] targetPoint, Double[] selfPoint) { - return null; - } - - public static Double jaccardSimilarity(Double[] targetPoint, Double[] selfPoint) { - return null; - } - -} - diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceFunction.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceFunction.java deleted file mode 100644 index a54b3a3..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/DistanceFunction.java +++ /dev/null @@ -1,5 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -public enum DistanceFunction { - EUCLIDEAN, COSINESIMILARITY, MANHATTAN -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternActor.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternActor.java deleted file mode 100644 index 754375b..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternActor.java +++ /dev/null @@ -1,172 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.ActorRef; -import akka.actor.Props; -import akka.actor.UntypedActor; -import akka.japi.Creator; -import akka.routing.RoundRobinPool; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; -import edu.lu.uni.serval.utils.MapSorter; - -public class MatchFixPatternActor extends UntypedActor { - - private static Logger logger = LoggerFactory.getLogger(MatchFixPatternActor.class); - - private ActorRef mineRouter; - private final int numberOfWorkers; - private int counter = 0; - - public MatchFixPatternActor(int numberOfWorkers) { - mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) - .props(MatchFixPatternWorker.props()), "match-fix-pattern-router"); - this.numberOfWorkers = numberOfWorkers; - } - - public static Props props(final int numberOfWorkers) { - - return Props.create(new Creator() { - - private static final long serialVersionUID = 9207427376110704705L; - - @Override - public MatchFixPatternActor create() throws Exception { - return new MatchFixPatternActor(numberOfWorkers); - } - - }); - } - - @SuppressWarnings("deprecation") - @Override - public void onReceive(Object message) throws Exception { - if (message instanceof WorkMessage) { - WorkMessage msg = (WorkMessage) message; - List trainingFeatures = msg.getTrainingFeatures(); - int size = trainingFeatures.size(); - int average = size / numberOfWorkers; - this.bugId = msg.getId(); - Double[] bugFeature = msg.getBugFeature(); - - for (int i = 0; i < numberOfWorkers; i ++) { - int fromIndex = i * average; - int toIndex = (i + 1) * average; - if (i == numberOfWorkers - 1) { - toIndex = size; - } - - List subTrainingFeatures = new ArrayList<>(); - subTrainingFeatures.addAll(trainingFeatures.subList(fromIndex, toIndex)); - final WorkMessage workMsg = new WorkMessage(bugId, bugFeature, subTrainingFeatures); - workMsg.setNum(i + 1); - mineRouter.tell(workMsg, getSelf()); - logger.info("Assign a task to worker #" + (i + 1) + "..."); - } - } else if (message instanceof ReturnMessage) { - counter ++; - logger.info(counter + " workers finished their work..."); - ReturnMessage rMsg = (ReturnMessage) message; - returnMessages.add(rMsg); - - if (counter >= numberOfWorkers) { - ListSorter sorter = new ListSorter(returnMessages); - returnMessages = sorter.sortAscending(); - - Map similarities = new HashMap<>(); - int index = 0; - for (int i = 0; i < numberOfWorkers; i ++) { - ReturnMessage returnMessage = returnMessages.get(i); - List similarity = returnMessage.getSimilarities(); - for (int j = 0, size = similarity.size(); j < size; j ++) { - index ++; - similarities.put(index, similarity.get(j)); - } - } - - MapSorter mapSorter = new MapSorter(); - Map sortedSimilarities = mapSorter.sortByValueDescending(similarities); - - List similarityList = new ArrayList<>(); - double similarity = 0; - int num = 0; - for (Map.Entry entry : sortedSimilarities.entrySet()) { - if (entry.getValue() == similarity) { - continue; - } - similarityList.add(entry.getKey()); - similarity = entry.getValue(); - if (++ num % 100 == 0) { - break; - } - } - outputMatchedPatterns(similarityList); - logger.info("All workers finished their work..."); - this.getContext().stop(mineRouter); - this.getContext().stop(getSelf()); - this.getContext().system().shutdown(); - } - } else { - unhandled(message); - } - } - - private void outputMatchedPatterns(List similarityList) { - String outputFile = Configuration.ROOT_PATH + "TestData/MatchedFixPatterns/Bug_" + bugId + ".list"; - StringBuilder builder = new StringBuilder("BugId: " + bugId + "\n\n\n"); - - for (int i = 0, size = similarityList.size(); i < size; i ++) { - int patternPosition = similarityList.get(i); - builder.append(readPattern(patternPosition)); - } - - FileHelper.outputToFile(outputFile, builder, false); - } - - private String readPattern(int patternPosition) { - String patternInfo = ""; - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(Configuration.SELECTED_PATCHES_SOURE_CODE_FILE); - scanner = new Scanner(fis); - int index = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - if (line.equals("PATCH###")) { - if (patternPosition == index) { - break; - } - index ++; - patternInfo = ""; - } - patternInfo += line + "\n"; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return patternInfo; - } - - private int bugId; - private List returnMessages = new ArrayList<>(); -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternWorker.java deleted file mode 100644 index 5470afb..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/MatchFixPatternWorker.java +++ /dev/null @@ -1,60 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -import java.util.ArrayList; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.Props; -import akka.actor.UntypedActor; -import akka.japi.Creator; - -public class MatchFixPatternWorker extends UntypedActor { - private static Logger log = LoggerFactory.getLogger(MatchFixPatternActor.class); - - public MatchFixPatternWorker() { - } - - public static Props props() { - return Props.create(new Creator() { - - private static final long serialVersionUID = -7615153844097275009L; - - @Override - public MatchFixPatternWorker create() throws Exception { - return new MatchFixPatternWorker(); - } - - }); - } - - @Override - public void onReceive(Object message) throws Exception { - if (message instanceof WorkMessage) { - WorkMessage msg = (WorkMessage) message; - List trainingFeatures = msg.getTrainingFeatures(); - Double[] bugFeature = msg.getBugFeature(); - int bugID = msg.getId(); - int workNum = msg.getNum(); - - List similarities = new ArrayList<>(); - for (int i = 0, size = trainingFeatures.size(); i < size; i ++) { - Double similarity = Math.abs(computeSimilarity(bugFeature, trainingFeatures.get(i))); - similarities.add(similarity); - } - - final ReturnMessage rMsg = new ReturnMessage(bugID, workNum, similarities); - log.info("Worker #" + workNum + " finished the work..."); - this.getSender().tell(rMsg, getSelf()); - } else { - unhandled(message); - } - } - - private Double computeSimilarity(Double[] feature, Double[] trainingFeature) { - Double similarity = DistanceCalculator.cosineSimilarityDistance(trainingFeature, feature); - return similarity; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/ReturnMessage.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/ReturnMessage.java deleted file mode 100644 index af52dd7..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/ReturnMessage.java +++ /dev/null @@ -1,35 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -import java.util.List; - -public class ReturnMessage implements Comparable{ - - private int bugId; - private Integer workerId; - private List similarities; - - public ReturnMessage(int bugId, int workerId, List similarities) { - super(); - this.bugId = bugId; - this.workerId = workerId; - this.similarities = similarities; - } - - public int getBugId() { - return bugId; - } - - public int getWorkerId() { - return workerId; - } - - public List getSimilarities() { - return similarities; - } - - @Override - public int compareTo(ReturnMessage o) { - return this.workerId.compareTo(o.workerId); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/WorkMessage.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/WorkMessage.java deleted file mode 100644 index b6e8356..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser2/WorkMessage.java +++ /dev/null @@ -1,39 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser2; - -import java.util.List; - -public class WorkMessage { - - private int id; - private Double[] bugFeature; - private List trainingFeatures; - private int num; - - public WorkMessage(int id, Double[] bugFeature, List trainingFeatures) { - super(); - this.id = id; - this.bugFeature = bugFeature; - this.trainingFeatures = trainingFeatures; - } - - public int getId() { - return id; - } - - public Double[] getBugFeature() { - return bugFeature; - } - - public List getTrainingFeatures() { - return trainingFeatures; - } - - public int getNum() { - return num; - } - - public void setNum(int num) { - this.num = num; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser.java deleted file mode 100644 index 40a8917..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser.java +++ /dev/null @@ -1,90 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser3; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -/** - * Multi-thread parser of parsing source code of unfixed violations. - * - * @author kui.liu - * - */ -public class AkkaParser { - - private static Logger log = LoggerFactory.getLogger(AkkaParser.class); - - @SuppressWarnings("deprecation") - public static void main(String[] args) { - String violationType = Configuration.GUM_TREE_INPUT + "UnfixedViolations/"; - File file = new File(violationType); - File[] violationTypes = file.listFiles(); - for (File violationT : violationTypes) { - if (violationT.isDirectory()) { - violationType = violationT.getName(); - if (//violationType.equals("SF_SWITCH_NO_DEFAULT") || -// violationType.equals("SE_NO_SERIALVERSIONID") || - violationType.equals("DM_DEFAULT_ENCODING")) { - // input data - log.info("Get the input data..."); - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT, violationType); - log.info("MessageFiles: " + msgFiles.size()); - - // output path - final String sourceCodeFilesPath = Configuration.ROOT_PATH + "UnfixedViolations_RQ3/" + violationType + "/"; - FileHelper.deleteDirectory(sourceCodeFilesPath); - - ActorSystem system = null; - ActorRef parsingActor = null; - int numberOfWorkers = 200; - final WorkMessage msg = new WorkMessage(0, msgFiles); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Mining-Pattern-System-" + violationType); - parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, sourceCodeFilesPath, violationType), "mine-pattern-actor-" + violationType); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); - } - } - } - } - } - - - /** - * Get violation-related files. - * - * @param gumTreeInput - * @return - */ - public static List getMessageFiles(String inputPath, String violationType) { - File sourceCodeFilesPath = new File(inputPath + "UnfixedViolations/" + violationType + "/"); - File[] sourceCodeFiles = sourceCodeFilesPath.listFiles(); // project folders - List msgFiles = new ArrayList<>(); - - for (File sourceCodeFile : sourceCodeFiles) { - if (sourceCodeFile.getName().endsWith(".java")) { - String fileName = sourceCodeFile.getName(); - fileName = fileName.substring(8).replace(".java", ".txt"); - File positionFile = new File(inputPath + "UnFV_positions/" + violationType + "/" + fileName); // position file - MessageFile msgFile = new MessageFile(null, sourceCodeFile, null); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); - } - } - - return msgFiles; - } -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser2.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser2.java deleted file mode 100644 index 6354a9f..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/AkkaParser2.java +++ /dev/null @@ -1,78 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser3; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.ActorRef; -import akka.actor.ActorSystem; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -/** - * Multi-thread parser of parsing source code of fixed violations. - * - * @author kui.liu - * - */ -public class AkkaParser2 { - - private static Logger log = LoggerFactory.getLogger(AkkaParser2.class); - - @SuppressWarnings("deprecation") - public static void main(String[] args) { - // input data - log.info("Get the input data..."); - final List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); - log.info("MessageFiles: " + msgFiles.size()); - - // output path - final String sourceCodeFilesPath = Configuration.ROOT_PATH + "fixedViolations/"; - FileHelper.deleteDirectory(sourceCodeFilesPath); - - ActorSystem system = null; - ActorRef parsingActor = null; - int numberOfWorkers = 431; - final WorkMessage msg = new WorkMessage(0, msgFiles); - try { - log.info("Akka begins..."); - system = ActorSystem.create("Mining-Pattern-System"); - parsingActor = system.actorOf(ParseFixPatternActor.props(numberOfWorkers, sourceCodeFilesPath, "Type"), "mine-pattern-actor"); - parsingActor.tell(msg, ActorRef.noSender()); - } catch (Exception e) { - system.shutdown(); - e.printStackTrace(); - } - } - - - /** - * Get violation-related files. - * - * @param gumTreeInput - * @return - */ - public static List getMessageFiles(String inputPath) { - File sourceCodeFilesPath = new File(inputPath + "prevFiles/"); - File[] sourceCodeFiles = sourceCodeFilesPath.listFiles(); - List msgFiles = new ArrayList<>(); - - for (File sourceCodeFile : sourceCodeFiles) { - if (sourceCodeFile.getName().endsWith(".java")) { - String fileName = sourceCodeFile.getName(); - fileName = fileName.substring(5).replace(".java", ".txt"); - File positionFile = new File(inputPath + "positions/" + fileName); // position file - MessageFile msgFile = new MessageFile(null, sourceCodeFile, null); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); - } - } - - return msgFiles; - } -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternActor.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternActor.java deleted file mode 100644 index 4c30d3a..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternActor.java +++ /dev/null @@ -1,80 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser3; - -import java.util.ArrayList; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.ActorRef; -import akka.actor.Props; -import akka.actor.UntypedActor; -import akka.japi.Creator; -import akka.routing.RoundRobinPool; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; - -public class ParseFixPatternActor extends UntypedActor { - - private static Logger logger = LoggerFactory.getLogger(ParseFixPatternActor.class); - - private ActorRef mineRouter; - private final int numberOfWorkers; - private int counter = 0; - - public ParseFixPatternActor(int numberOfWorkers, String sourceCodeFilesPath, String vType) { - mineRouter = this.getContext().actorOf(new RoundRobinPool(numberOfWorkers) - .props(ParseFixPatternWorker.props(sourceCodeFilesPath)), "mine-pattern-router-" + vType); - this.numberOfWorkers = numberOfWorkers; - } - - public static Props props(final int numberOfWorkers, final String sourceCodeFilesPath, final String vType) { - - return Props.create(new Creator() { - - private static final long serialVersionUID = 9207427376110704705L; - - @Override - public ParseFixPatternActor create() throws Exception { - return new ParseFixPatternActor(numberOfWorkers, sourceCodeFilesPath, vType); - } - - }); - } - - @SuppressWarnings("deprecation") - @Override - public void onReceive(Object message) throws Exception { - if (message instanceof WorkMessage) { - List files = ((WorkMessage) message).getMsgFiles(); - int size = files.size(); - int average = size / numberOfWorkers; - - for (int i = 0; i < numberOfWorkers; i ++) { - int fromIndex = i * average; - int toIndex = (i + 1) * average; - if (i == numberOfWorkers - 1) { - toIndex = size; - } - - List filesOfWorkers = new ArrayList<>(); - filesOfWorkers.addAll(files.subList(fromIndex, toIndex)); - final WorkMessage workMsg = new WorkMessage(i + 1, filesOfWorkers); - mineRouter.tell(workMsg, getSelf()); - logger.info("Assign a task to worker #" + (i + 1) + "..."); - } - } else if ("STOP".equals(message.toString())) { - counter ++; - logger.info(counter + " workers finished their work..."); - if (counter >= numberOfWorkers) { - logger.info("All workers finished their work..."); - this.getContext().stop(mineRouter); - this.getContext().stop(getSelf()); - this.getContext().system().shutdown(); - } - } else { - unhandled(message); - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternWorker.java b/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternWorker.java deleted file mode 100644 index 5137cd7..0000000 --- a/src/main/java/edu/lu/uni/serval/MultipleThreadsParser3/ParseFixPatternWorker.java +++ /dev/null @@ -1,122 +0,0 @@ -package edu.lu.uni.serval.MultipleThreadsParser3; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import akka.actor.Props; -import akka.actor.UntypedActor; -import akka.japi.Creator; -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.violation.code.parser.ViolationCodeParser; - -public class ParseFixPatternWorker extends UntypedActor { - private static Logger log = LoggerFactory.getLogger(ParseFixPatternActor.class); - - private String sourceCodeFilesPath; - - public ParseFixPatternWorker(String sourceCodeFilesPath) { - this.sourceCodeFilesPath = sourceCodeFilesPath; - } - - public static Props props(final String sourceCodeFilesPath) { - return Props.create(new Creator() { - - private static final long serialVersionUID = -7615153844097275009L; - - @Override - public ParseFixPatternWorker create() throws Exception { - return new ParseFixPatternWorker(sourceCodeFilesPath); - } - - }); - } - - @Override - public void onReceive(Object message) throws Exception { - if (message instanceof WorkMessage) { - WorkMessage msg = (WorkMessage) message; - List files = msg.getMsgFiles(); - StringBuilder sourceCode = new StringBuilder(); - StringBuilder sizes = new StringBuilder(); - StringBuilder tokens = new StringBuilder(); - - List violationTypes = readTypes(); - - int id = msg.getId(); - int counter = 0; - - for (MessageFile msgFile : files) { - File prevFile = msgFile.getPrevFile(); - File positionFile = msgFile.getPositionFile(); - if (prevFile.getName().toLowerCase().contains("test")) { - continue; - } - ViolationCodeParser parser = new ViolationCodeParser(); - parser.parse(prevFile, positionFile); - parser.setTypes(violationTypes); - - String sourceCodeStr = parser.sourceCode; - if ("".equals(sourceCodeStr)) { - } else { - sourceCode.append(sourceCodeStr); - sizes.append(parser.sizes); - tokens.append(parser.tokens); - - counter ++; - if (counter % 100 == 0) { - FileHelper.outputToFile(sourceCodeFilesPath + "SourceCode/worker_" + id + ".list", sourceCode, true); - FileHelper.outputToFile(sourceCodeFilesPath + "Sizes/worker_" + id + ".list", sizes, true); - FileHelper.outputToFile(sourceCodeFilesPath + "Tokens/worker_" + id + ".list", tokens, true); - sourceCode.setLength(0); - sizes.setLength(0); - tokens.setLength(0); - } - } - } - - if (sizes.length() > 0) { - FileHelper.outputToFile(sourceCodeFilesPath + "SourceCode/worker_" + id + ".list", sourceCode, true); - FileHelper.outputToFile(sourceCodeFilesPath + "Sizes/worker_" + id + ".list", sizes, true); - FileHelper.outputToFile(sourceCodeFilesPath + "Tokens/worker_" + id + ".list", tokens, true); - sourceCode.setLength(0); - sizes.setLength(0); - tokens.setLength(0); - } - - log.info("Worker #" + id +"Finish of parsing " + counter + " files..."); - log.info("Worker #" + id + " finished the work..."); - this.getSender().tell("STOP", getSelf()); - } else { - unhandled(message); - } - } - - private List readTypes() { - String fileName = Configuration.ROOT_PATH + "fixedViolations/types.list"; - String content = FileHelper.readFile(fileName); - List types = new ArrayList<>(); - BufferedReader reader = new BufferedReader(new StringReader(content)); - try { - String line = null; - while ((line = reader.readLine()) != null) { - types.add(line); - } - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } -// System.err.println(types.size()); - return types; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/TreeToString.java b/src/main/java/edu/lu/uni/serval/TreeToString.java deleted file mode 100644 index e234b69..0000000 --- a/src/main/java/edu/lu/uni/serval/TreeToString.java +++ /dev/null @@ -1,47 +0,0 @@ -package edu.lu.uni.serval; - -import java.util.ArrayList; -import java.util.List; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; - -public class TreeToString { - - private List strList = new ArrayList<>(); - - public String toString(ITree tree) { - List children = tree.getChildren(); - String str = ASTNodeMap.map.get(tree.getType()); - if (strList.size() == 0) { - strList.add(str); - for (ITree child : children) { - TreeToString t2s = new TreeToString(); - t2s.toString(child); - List strList1 = t2s.strList; - for (String str1 : strList1) { - strList.add("---" + str1); - } - } - } else { - strList.clear(); - strList.add(str); - for (ITree child : children) { - TreeToString t2s = new TreeToString(); - t2s.toString(child); - List strList1 = t2s.strList; - for (String str1 : strList1) { - strList.add("---" + str1); - } - } - } - - str = ""; - for (String str1 : strList) { - str += str1 + "\n"; - } - - return str; - } -} diff --git a/src/main/java/edu/lu/uni/serval/config/Configuration.java b/src/main/java/edu/lu/uni/serval/config/Configuration.java index 3325840..4421c72 100644 --- a/src/main/java/edu/lu/uni/serval/config/Configuration.java +++ b/src/main/java/edu/lu/uni/serval/config/Configuration.java @@ -4,88 +4,4 @@ public class Configuration { public static final long SECONDS_TO_WAIT = 900L; -// public static String ROOT_PATH = "/Volumes/data/bugStudy/dataset/"; // The root path of all output data. - public static String ROOT_PATH = "/Users/anilkoyuncu/bugStudy/dataset/"; // The root path of all output data. - - public static int HUNK_SIZE = 10; // The limitation of source code lines of each DiffEntry, which will be selected as training data. - public static final String BUGGY_TREE_SIGNAL = "BUGGY_TREE###"; // The starting signal of the tree of buggy source code . - public static final String PATCH_SIGNAL = "PATCH###"; // Th starting signal of each patch. - - // input path of GumTree. (i.e., Fix patterns parser) - public static final String GUM_TREE_INPUT = ROOT_PATH + "GumTreeInput/";// Buggy version file VS. Fixing version file, (DiffEntry File) - - - // the output path of GumTree results. - public static final String GUM_TREE_OUTPUT = ROOT_PATH + "GumTreeResults/"; - public static final String EDITSCRIPTS_FILE_PATH = GUM_TREE_OUTPUT + "editScripts/"; - public static final String PATCH_SOURCECODE_FILE_PATH = GUM_TREE_OUTPUT + "sourceCode/"; - public static final String BUGGYTREE_FILE_PATH = GUM_TREE_OUTPUT + "buggyTrees/"; - public static final String BUGGY_CODE_TOKEN_FILE_PATH = GUM_TREE_OUTPUT + "tokens/"; - public static final String EDITSCRIPT_SIZES_FILE_PATH = GUM_TREE_OUTPUT + "editScriptSizes/"; - public static final String ALARM_TYPES_FILE_PATH = GUM_TREE_OUTPUT + "alarmTypes/"; - - public static final String EDITSCRIPTS_FILE = GUM_TREE_OUTPUT + "editScripts.list"; - public static final String PATCH_SOURCECODE_FILE = GUM_TREE_OUTPUT + "patchSourceCode.list"; - public static final String BUGGYTREES_FILE = GUM_TREE_OUTPUT + "buggyTrees.list"; - public static final String BUGGY_CODE_TOKENS_FILE = GUM_TREE_OUTPUT + "tokens.list"; - public static final String EDITSCRIPT_SIZES_FILE = GUM_TREE_OUTPUT + "editScriptSizes.csv"; - public static final String ALARM_TYPES_FILE = GUM_TREE_OUTPUT + "alarmTypes.list"; - - public static final int VECTOR_SIZE_OF_EMBEDED_TOKEN1 = 100; // tokens of edit scripts. - public static final int VECTOR_SIZE_OF_EMBEDED_TOKEN2 = 200; // tokens of source code - - // the input path of fix patterns mining. - private static final String MINING_INPUT = ROOT_PATH + "MiningInput/"; - public static final String MAX_TOKEN_VECTORS_SIZE_OF_EDIT_SCRIPTS = MINING_INPUT + "/MaxTokenVectorSizeOfEditScripts.list"; // The max size of edit scripts: upper limitation of max size. - public static final String MAX_TOKEN_VECTORS_SIZE_OF_SOURCE_CODE = MINING_INPUT + "/MaxTokenVectorSizeOfBuggySourceCode.list"; // The max size of all buggy source code token vectors. - // the input path of token embedding. - public static final String EMBEDDING_INPUT = MINING_INPUT + "Embedding/"; - public static final String SELECTED_PATCHES_SOURE_CODE_FILE = EMBEDDING_INPUT + "patchSourceCode.list";// Selected patches. - public static final String SELECTED_BUGGY_TREE_FILE = EMBEDDING_INPUT + "buggyTrees.list"; - public static final String SELECTED_BUGGY_TOKEN_FILE = EMBEDDING_INPUT + "tokens.list"; // Selected token vectors of buggy source code. - public static final String SELECTED_EDITSCRIPTES_FILE = EMBEDDING_INPUT + "editScripts.list"; // Selected edit script vectors. - public static final String SELECTED_ALARM_TYPES_FILE = EMBEDDING_INPUT + "alarmTypes.list"; // Selected edit script vectors. - // the input path of feature learning. - public static final String FEATURE_LEARNING_INPUT = MINING_INPUT + "FeatureLearning/"; - public static final String EMBEDDED_EDIT_SCRIPT_TOKENS = FEATURE_LEARNING_INPUT + "embeddedEditScriptTokens.list"; // All embedded tokens of selected edit scripts. - public static final String VECTORIED_EDIT_SCRIPTS = FEATURE_LEARNING_INPUT + "vectorizedEditScripts.csv"; // Embedded and vectorized edit script vectors. - // the input path of clustering. - public static final String EXTRACTED_FEATURES = MINING_INPUT + "ExtractedFeatures/"; // Extracted features of all edit scripts. - public static final String CLUSTER_INPUT = MINING_INPUT + "ClusteringInput/input.arff"; - - // the output path of fix patterns mining. - private static final String MINING_OUTPUT = ROOT_PATH + "MiningOutput/"; - public static final String CLUSTER_OUTPUT = MINING_OUTPUT + "ClusteringOutput/clusterResults.list"; - public static final String CLUSTERED_PATCHES_FILE = MINING_OUTPUT + "ClusteredPatches/"; - public static final String CLUSTERED_TOKENSS_FILE = MINING_OUTPUT + "ClusteredTokens/"; // Token vectors of buggy source code. - public static final String COMMON_CLUSTERS_SIZES = MINING_OUTPUT + "ClusteringOutput/CommonClusterSizes.list"; - - // evaluation data - public static final String TEST_INPUT = ROOT_PATH + "TestProjects/"; - public static final String TEST_POSITION_FILE = ROOT_PATH + "TestData/Positions/"; // Positions of all test statements. - public static final String TEST_DATA_FILE = ROOT_PATH + "TestData/TestStatements/"; // Token vectors of all test statements. - - public static final String NUMBER_OF_TRAINING_DATA = ROOT_PATH + "TestData/NumberOfTrainingData.list";; - - // data of unsupervised learning - public static final String EMBEDDING_DATA_TOKENS1 = ROOT_PATH + "TestData/AllTokenVectorsForEvaluation.list"; - public static final String EMBEDDED_ALL_TOKENS1 = ROOT_PATH + "TestData/AllEmbeddedTokens.list"; - public static final String VECTORIED_ALL_SOURCE_CODE1 = ROOT_PATH + "TestData/AllVectorizedSourceCode/"; - public static final String EXTRACTED_FEATURES_EVALUATION = ROOT_PATH + "TestDataExtractedFeatures/"; // extracted features of all source code (training data and testing data) - - // Data of supervised learning - public static final String CLUSTERNUMBER_LABEL_MAP = ROOT_PATH + "TestData/clusterMappingLabel.list"; - public static final String EMBEDDING_DATA_TOKENS2 = ROOT_PATH + "TestData/AllTokenVectorsForSupervisedEvaluation.list"; - public static final String EMBEDDED_ALL_TOKENS2 = ROOT_PATH + "TestData/AllEmbeddedTokensForSuperVisedEvaluation.list"; - public static final String TRAINING_DATA = ROOT_PATH + "TestData/TrainingData.csv"; // Training data of supervised learning - public static final String TESTING_DATA = ROOT_PATH + "TestData/SupervisedLearning/"; // testing data of supervised learning - public static final String FEATURES_OF_TRAINING_DATA = ROOT_PATH + "TestingOutput/TraingFeatures/"; - public static final String FEATURES_OF_TESTING_DATA = ROOT_PATH + "TestingOutput/TestingFeatures/"; - public static final String POSSIBILITIES_OF_TESTING_DATA = ROOT_PATH + "TestingOutput/Posibilities/"; - public static final String PREDICTED_RESULTS_OF_TESTING_DATA = ROOT_PATH + "TestingOutput/Prediction/"; - - public static final String SUPERVISED_LEARNING_MODEL = ROOT_PATH + "TestingOutput/SupervisedLearningModel.zip"; - - public static final String FEATURES_OF_COMMON_CLUSTERS = ROOT_PATH + "FeaturesOfCommonClusters/"; - } diff --git a/src/main/java/edu/lu/uni/serval/defects4j/Bug.java b/src/main/java/edu/lu/uni/serval/defects4j/Bug.java deleted file mode 100644 index e169ddd..0000000 --- a/src/main/java/edu/lu/uni/serval/defects4j/Bug.java +++ /dev/null @@ -1,43 +0,0 @@ -package edu.lu.uni.serval.defects4j; - -public class Bug { - private String project; - - private String fileName; - - private int startLine; - - private int endLine; - - private String type; - - public Bug(String project, String fileName, int startLine, int endLine, String type) { - super(); - this.project = project; - this.fileName = fileName; - this.startLine = startLine; - this.endLine = endLine; - this.type = type; - } - - public String getProject() { - return project; - } - - public String getFileName() { - return fileName; - } - - public int getStartLine() { - return startLine; - } - - public int getEndLine() { - return endLine; - } - - public String getType() { - return type; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/defects4j/BugParser.java b/src/main/java/edu/lu/uni/serval/defects4j/BugParser.java deleted file mode 100644 index 8a30ee0..0000000 --- a/src/main/java/edu/lu/uni/serval/defects4j/BugParser.java +++ /dev/null @@ -1,206 +0,0 @@ -package edu.lu.uni.serval.defects4j; - -import java.io.BufferedReader; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; -import java.util.Scanner; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; - -public class BugParser { - - public static void main(String[] args) throws IOException { - List bugs = new ArrayList<>(); - String bugsFile = "Dataset/Defects4j/Bugs.txt"; - String content = FileHelper.readFile(bugsFile); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - - StringBuilder tokensBuilder = new StringBuilder(); - StringBuilder buggyCodeBuilder = new StringBuilder(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(" : "); - String type = elements[0]; - String project = elements[1]; - project = project.substring(0, project.lastIndexOf(".")); - String fileName = elements[2]; - int startLine = Integer.parseInt(elements[3]); - int endLine = Integer.parseInt(elements[4]); - - Bug bug = new Bug(project, fileName, startLine, endLine, type); - bugs.add(bug); - } - int i = 0; - for (Bug bug : bugs) { - String type = bug.getType(); - String project = bug.getProject(); - String fileName = bug.getFileName(); - int startLine = bug.getStartLine(); - int endLine = bug.getEndLine(); - File buggyFile = null; - - String[] elements = project.split("_"); - if (elements.length < 2) System.out.println(type + "-" + project + "-" + fileName + "-" + startLine + "-" + endLine); - List javaFiles = FileHelper.getAllFiles(Configuration.ROOT_PATH + "Testing/projects1/" + elements[0] + "/" + elements[1] + "-b", ".java"); - for (File javaFile : javaFiles) { - if (javaFile.getPath().endsWith(fileName)) { - buggyFile = javaFile; - break; - } - } - if (i == 31) { - i = i + 1 - 1; - } - SimpleTree simpleTree = null; - if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(type)|| "HE_EQUALS_USE_HASHCODE".equals(type) || "HE_INHERITS_EQUALS_USE_HASHCODE".equals(type)|| - "SE_NO_SUITABLE_CONSTRUCTOR".equals(type) || "RI_REDUNDANT_INTERFACES".equals(type) -// ||"CN_IDIOM_NO_SUPER_CALL".equals(type) - ||"SE_NO_SERIALVERSIONID".equals(type) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(type)) { - ViolationSourceCodeTree parser = new ViolationSourceCodeTree(buggyFile, startLine, endLine); - ITree classNameTree = parser.getClassNameTokens(); - simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(classNameTree, null); - - startLine = parser.getViolationFinalStartLine(); - endLine = parser.getViolationFinalEndLine(); - } else { - ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(buggyFile, startLine, endLine); - alarmTree.extract(); - List matchedTrees = alarmTree.getViolationSourceCodeTrees(); - if (matchedTrees.size() == 0) { - System.err.println("#Null_Violation_Hunk: " + buggyFile.getName() + ":" + startLine + ":" + endLine); - continue; - } - simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, null); - children.add(simpleT); - } - simpleTree.setChildren(children); - - startLine = alarmTree.getViolationFinalStartLine(); - endLine = alarmTree.getViolationFinalEndLine(); - } - - String tokens = Tokenizer.getTokensDeepFirst(simpleTree); - String[] tokensArray = tokens.split(" "); - int length = tokensArray.length; - System.out.println((++ i) + "==" + length); -// sizes += length + "\n"; -// this.tokens += tokens + "\n"; - String sourceCode = readSourceCode(buggyFile, startLine, endLine, type); -// this.sourceCode += sourceCode + "\n"; -// tokensBuilder.append(type).append(":").append(tokens).append("\n"); - tokensBuilder.append(tokens).append("\n"); - buggyCodeBuilder.append(sourceCode).append("\n"); - } - - FileHelper.outputToFile("Dataset/Defects4j/buggyTokens.list", tokensBuilder, false); - FileHelper.outputToFile("Dataset/Defects4j/buggySourceCode.list", buggyCodeBuilder, false); - } - - private static String readSourceCode(File javaFile, int startLine, int endLine, String violationType) { - StringBuilder sourceCode = new StringBuilder("##Source_Code:\n"); - sourceCode.append(violationType).append("\n"); - sourceCode.append(javaFile.getName().replaceAll("#", "/")).append("\nPosition: ").append(startLine).append(" : ").append(endLine).append("\n"); - FileInputStream fis = null; - Scanner scanner = null; - - try { - fis = new FileInputStream(javaFile); - scanner = new Scanner(fis); - int counter = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - counter ++; - if (startLine <= counter && counter <= endLine) { - sourceCode.append(line + "\n"); - } - if (counter == endLine) break; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return sourceCode.toString(); - } -} - - - -/* -20 -32 -20 -8 -8 -16 -22 -10 -10 -10 -12 -16 -18 -10 -12 -8 -14 -44 -8 -26 -20 -10 -12 -12 -10 -4 -10 -8 -8 -12 -16 -1776 -8 -10 -10 -12 -8 -50 -18 -8 -12 -38 -4 -4 -14 -16 -20 -26 -8 -14 -12 -14 -*/ \ No newline at end of file diff --git a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java b/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java deleted file mode 100644 index ece32e5..0000000 --- a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryHunk.java +++ /dev/null @@ -1,85 +0,0 @@ -package edu.lu.uni.serval.diffentry; - -import java.util.ArrayList; -import java.util.List; - -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; - -public class DiffEntryHunk { - - private int bugLineStartNum; - private int fixLineStartNum; - private int bugRange; - private int fixRange; - private String hunk; - private int buggyHunkSize; - private int fixedHunkSize; - private String file; - private List actionSets = new ArrayList<>(); - - public DiffEntryHunk(int bugLineStartNum, int fixLineStartNum, int bugRange, int fixRange) { - super(); - this.bugLineStartNum = bugLineStartNum; - this.fixLineStartNum = fixLineStartNum; - this.bugRange = bugRange; - this.fixRange = fixRange; - } - - public int getBugLineStartNum() { - return bugLineStartNum; - } - - public int getFixLineStartNum() { - return fixLineStartNum; - } - - public int getBugRange() { - return bugRange; - } - - public int getFixRange() { - return fixRange; - } - - public String getHunk() { - return hunk; - } - - public void setHunk(String hunk) { - this.hunk = hunk; - } - - public int getBuggyHunkSize() { - return buggyHunkSize; - } - - public void setBuggyHunkSize(int buggyHunkSize) { - this.buggyHunkSize = buggyHunkSize; - } - - public int getFixedHunkSize() { - return fixedHunkSize; - } - - public void setFixedHunkSize(int fixedHunkSize) { - this.fixedHunkSize = fixedHunkSize; - } - - public String getFile() { - return file; - } - - public void setFile(String file) { - this.file = file; - } - - public List getActionSets() { - return actionSets; - } - - @Override - public String toString() { - return "@@ -" + this.bugLineStartNum + ", " + this.bugRange + " +" + this.fixLineStartNum + ", " + this.fixRange + "\n" + this.hunk; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java b/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java deleted file mode 100644 index 0e4806b..0000000 --- a/src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java +++ /dev/null @@ -1,250 +0,0 @@ -package edu.lu.uni.serval.diffentry; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; -import java.util.regex.Pattern; - -import edu.lu.uni.serval.utils.FileHelper; - -public class DiffEntryReader { - - public List readHunks(File diffentryFile) { - List diffentryHunks = new ArrayList<>(); - String content = FileHelper.readFile(diffentryFile); - BufferedReader reader = null; - try { - reader = new BufferedReader(new StringReader(content)); - String line = null; - int startLine = 0; - int range = 0; - int startLine2 = 0; - int range2 = 0; - StringBuilder hunk = new StringBuilder(); - boolean sourceCode = false; - - while ((line = reader.readLine()) != null) { - if (RegExp.filterSignal(line.trim())) { - sourceCode = true; - if (hunk.length() > 0) { - if ((range < 7 && range2 < 7) || range == 0 || range2 == 0) { // filter out big hunks - DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2); - diffEntryHunk.setHunk(hunk.toString()); - diffentryHunks.add(diffEntryHunk); - } - hunk.setLength(0); - } - int plusIndex = line.indexOf("+"); - String lineNum = line.substring(4, plusIndex); - String[] nums = lineNum.split(","); - startLine = Integer.parseInt(nums[0].trim()); - if (nums.length == 2) { - range = Integer.parseInt(nums[1].trim()); - } - - String lineNum2 = line.substring(plusIndex) .trim(); - lineNum2 = lineNum2.substring(1, lineNum2.length() - 2); - String[] nums2 = lineNum2.split(","); - startLine2 = Integer.parseInt(nums2[0].trim()); - if (nums2.length == 2) { - range2 = Integer.parseInt(nums2[1].trim()); - } - continue; - } - if (sourceCode) hunk.append(line + "\n"); - } - - if ((range < 7 && range2 < 7) || range == 0 || range2 == 0) { // filter out big hunks - DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2); - diffEntryHunk.setHunk(hunk.toString()); - diffentryHunks.add(diffEntryHunk); - } - hunk.setLength(0); - - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - if (reader != null) { - reader.close(); - reader = null; - } - } catch (IOException e) { - e.printStackTrace(); - } - } - - return diffentryHunks; - } - - /** - * Read all hunks without considering their sizes. - * - * @param diffentryFile - * @return - */ - public List readHunks2(File diffentryFile) { - List diffentryHunks = new ArrayList<>(); - String content = FileHelper.readFile(diffentryFile); - BufferedReader reader = null; - try { - reader = new BufferedReader(new StringReader(content)); - String line = null; - int startLine = 0; - int range = 0; - int startLine2 = 0; - int range2 = 0; - StringBuilder hunk = new StringBuilder(); - boolean sourceCode = false; - - while ((line = reader.readLine()) != null) { - if (RegExp.filterSignal(line.trim())) { -// line = Pattern.compile("^@@\\s\\-\\d+,*\\d*\\s\\+\\d+,*\\d*\\s@@").split(line)[1]; - sourceCode = true; - if (hunk.length() > 0) { - if (startLine > 0) { - DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2); - diffEntryHunk.setHunk(hunk.toString()); - diffentryHunks.add(diffEntryHunk); - } - hunk.setLength(0); - } - int plusIndex = line.indexOf("+"); - String lineNum = line.substring(4, plusIndex); - String[] nums = lineNum.split(","); - startLine = Integer.parseInt(nums[0].trim()); - if (nums.length == 2) { - range = Integer.parseInt(nums[1].trim()); - } - - String lineNum2 = line.substring(plusIndex) .trim(); - lineNum2 = lineNum2.substring(1, lineNum2.length() - 2); - String[] nums2 = lineNum2.split(","); - startLine2 = Integer.parseInt(nums2[0].trim()); - if (nums2.length == 2) { - range2 = Integer.parseInt(nums2[1].trim()); - } - continue; - } - if (sourceCode) hunk.append(line + "\n"); - } - - if (startLine > 0) { - DiffEntryHunk diffEntryHunk = new DiffEntryHunk(startLine, startLine2, range, range2); - diffEntryHunk.setHunk(hunk.toString()); - diffentryHunks.add(diffEntryHunk); - } - hunk.setLength(0); - - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - if (reader != null) { - reader.close(); - reader = null; - } - } catch (IOException e) { - e.printStackTrace(); - } - } - - return diffentryHunks; - } - - /** - * Read all hunks with pure deleted lines and added lines. - * - * @param diffentryFile - * @return - */ - public List readHunks3(File diffentryFile) { - List diffentryHunks = new ArrayList<>(); - String content = FileHelper.readFile(diffentryFile); - BufferedReader reader = null; - try { - reader = new BufferedReader(new StringReader(content)); - String line = null; - int buggyStartLine = 0; - int buggyRange = 0; - int fixedStartLine = 0; - int fixedRange = 0; - int buggyHunkSize = 0; - int fixedHunkSize = 0; - StringBuilder hunk = new StringBuilder(); - boolean sourceCode = false; - - while ((line = reader.readLine()) != null) { - if (RegExp.filterSignal(line.trim())) { - sourceCode = true; - if (hunk.length() > 0) { - if (buggyStartLine > 0) { - DiffEntryHunk diffEntryHunk = new DiffEntryHunk(buggyStartLine, fixedStartLine, buggyRange, fixedRange); - diffEntryHunk.setHunk(hunk.toString()); - diffEntryHunk.setBuggyHunkSize(buggyHunkSize); - diffEntryHunk.setFixedHunkSize(fixedHunkSize); - diffEntryHunk.setFile(diffentryFile.getPath()); - diffentryHunks.add(diffEntryHunk); - } - hunk.setLength(0); - buggyStartLine = 0; - buggyRange = 0; - fixedStartLine = 0; - fixedRange = 0; - buggyHunkSize = 0; - fixedHunkSize = 0; - } - int plusIndex = line.indexOf("+"); - String lineNum = line.substring(4, plusIndex); - String[] nums = lineNum.split(","); - buggyStartLine = Integer.parseInt(nums[0].trim()); - if (nums.length == 2) { - buggyRange = Integer.parseInt(nums[1].trim()); - } - - String lineNum2 = line.substring(plusIndex) .trim(); - lineNum2 = lineNum2.substring(1, lineNum2.length() - 2); - String[] nums2 = lineNum2.split(","); - fixedStartLine = Integer.parseInt(nums2[0].trim()); - if (nums2.length == 2) { - fixedRange = Integer.parseInt(nums2[1].trim()); - } - continue; - } else if (sourceCode) { - if (line.startsWith("-")) { - buggyHunkSize ++; - } else if (line.startsWith("+")) { - fixedHunkSize ++; - } - hunk.append(line + "\n"); - } - } - - if (buggyStartLine > 0 && hunk.length() > 0) { - DiffEntryHunk diffEntryHunk = new DiffEntryHunk(buggyStartLine, fixedStartLine, buggyRange, fixedRange); - diffEntryHunk.setHunk(hunk.toString()); - diffEntryHunk.setBuggyHunkSize(buggyHunkSize); - diffEntryHunk.setFixedHunkSize(fixedHunkSize); - diffEntryHunk.setFile(diffentryFile.getPath()); - diffentryHunks.add(diffEntryHunk); - hunk.setLength(0); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - if (reader != null) { - reader.close(); - reader = null; - } - } catch (IOException e) { - e.printStackTrace(); - } - } - - return diffentryHunks; - } -} diff --git a/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java b/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java deleted file mode 100644 index b1d017d..0000000 --- a/src/main/java/edu/lu/uni/serval/diffentry/RegExp.java +++ /dev/null @@ -1,20 +0,0 @@ -package edu.lu.uni.serval.diffentry; - -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -public class RegExp { - private static final String REGULAR_EXPRESSION = "^@@\\s\\-\\d+,*\\d*\\s\\+\\d+,*\\d*\\s@@$"; //@@ -21,0 +22,2 @@ - private static Pattern pattern = Pattern.compile(REGULAR_EXPRESSION); - - public static boolean filterSignal(String string) { - boolean flag = false; - - Matcher res = pattern.matcher(string); - if (res.matches()) { - flag = true; - } - - return flag; - } -} diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java b/src/main/java/edu/lu/uni/serval/fixminer/EnhancedASTDiff.java similarity index 59% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java rename to src/main/java/edu/lu/uni/serval/fixminer/EnhancedASTDiff.java index 3d8916e..43895e0 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParser.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/EnhancedASTDiff.java @@ -1,4 +1,4 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer; import akka.actor.ActorRef; import akka.actor.ActorSystem; @@ -16,10 +16,10 @@ import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -public class TestHunkParser { +public class EnhancedASTDiff { + + private static Logger log = LoggerFactory.getLogger(EnhancedASTDiff.class); - private static Logger log = LoggerFactory.getLogger(TestHunkParser.class); -// public static void main(String[] args) { public static void main(String inputPath, String outputPath,String numOfWorkers,String project) { @@ -44,29 +44,13 @@ public class TestHunkParser { continue; String GUM_TREE_OUTPUT = outputPath + "/"+ pjName + "/"; -// final String editScriptsFilePath = GUM_TREE_OUTPUT + "editScripts.list"; -// final String patchesSourceCodeFilePath =GUM_TREE_OUTPUT + "patchSourceCode.list"; -// final String buggyTokensFilePath = GUM_TREE_OUTPUT + "tokens.list"; -// final String editScriptSizesFilePath = GUM_TREE_OUTPUT + "editScriptSizes.csv"; -// final String alarmTypesFilePath = GUM_TREE_OUTPUT + "alarmTypes.list"; - FileHelper.createDirectory(GUM_TREE_OUTPUT + "/UPD"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/INS"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/DEL"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/MOV"); FileHelper.createDirectory(GUM_TREE_OUTPUT + "/ALL"); -// FileHelper.deleteDirectory(editScriptsFilePath); -// FileHelper.deleteDirectory(patchesSourceCodeFilePath); -// FileHelper.deleteDirectory(buggyTokensFilePath); -// FileHelper.deleteDirectory(editScriptSizesFilePath); -// FileHelper.deleteDirectory(alarmTypesFilePath); -// StringBuilder astEditScripts = new StringBuilder(); -// StringBuilder tokens = new StringBuilder(); -// StringBuilder sizes = new StringBuilder(); -// StringBuilder patches = new StringBuilder(); -// StringBuilder alarmTypes = new StringBuilder(); int a = 0; @@ -76,7 +60,7 @@ public class TestHunkParser { try { log.info("Akka begins..."); system = ActorSystem.create("Mining-FixPattern-System"); - System.out.println(system.settings()); + parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), project), "mine-fix-pattern-actor"); parsingActor.tell(msg, ActorRef.noSender()); } catch (Exception e) { @@ -84,20 +68,6 @@ public class TestHunkParser { e.printStackTrace(); } - -// FileHelper.outputToFile(editScriptsFilePath, astEditScripts, true); -// FileHelper.outputToFile(buggyTokensFilePath, tokens, true); -// FileHelper.outputToFile(editScriptSizesFilePath, sizes, true); -// FileHelper.outputToFile(patchesSourceCodeFilePath, patches, true); -// FileHelper.outputToFile(alarmTypesFilePath, alarmTypes, true); -// astEditScripts.setLength(0); -// tokens.setLength(0); -// sizes.setLength(0); -// patches.setLength(0); -// alarmTypes.setLength(0); -// System.out.println(a); - -// classifyByAlarmTypes(); } } @@ -109,16 +79,15 @@ public class TestHunkParser { List msgFiles = new ArrayList<>(); if (revFiles.length >= 0) { for (File revFile : revFiles) { -// if (revFile.getName().endsWith(".java")) { String fileName = revFile.getName(); File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file fileName = fileName.replace(".java", ".txt"); File diffentryFile = new File(gumTreeInput + "DiffEntries/" + fileName); // DiffEntry file -// File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file + MessageFile msgFile = new MessageFile(revFile, prevFile, diffentryFile); -// msgFile.setPositionFile(positionFile); + msgFiles.add(msgFile); -// } + } return msgFiles; diff --git a/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java b/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java index 6848d2c..d4cf22b 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java @@ -1,6 +1,5 @@ package edu.lu.uni.serval.fixminer; -import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser; import edu.lu.uni.serval.fixminer.cluster.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -27,34 +26,34 @@ public class Launcher { appProps.load(new FileInputStream(appConfigPath)); String portInner = appProps.getProperty("portInner","6380"); - String serverWait = appProps.getProperty("serverWait", "50000"); +// String serverWait = appProps.getProperty("serverWait", "50000"); String numOfWorkers = appProps.getProperty("numOfWorkers", "10"); String jobType = appProps.getProperty("jobType","ALL"); String portDumps = appProps.getProperty("portDumps","6399"); String pythonPath = appProps.getProperty("pythonPath","/Users/anilkoyuncu/bugStudy/code/python"); String datasetPath = appProps.getProperty("datasetPath","/Users/anilkoyuncu/bugStudy/dataset"); String pjName = appProps.getProperty("pjName","allDataset"); - String dbNo = appProps.getProperty("dbNo","0"); +// String dbNo = appProps.getProperty("dbNo","0"); String actionType = appProps.getProperty("actionType","ALL"); String threshold = appProps.getProperty("threshold","1"); String cursor = appProps.getProperty("cursor","10000000"); String chunk = appProps.getProperty("chunk","1.txt"); String parameters = String.format("\nportInner %s " + - "\nserverWait %s \nnumOfWorkers %s " + + "\nnumOfWorkers %s " + "\njobType %s \nport %s " + "\npythonPath %s \ndatasetPath %s" + - "\npjName %s \ndbNo %s \nactionType %s \nthreshold %s \ncursor %s" - , portInner, serverWait, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,dbNo,actionType,threshold,cursor); + "\npjName %s \nactionType %s \nthreshold %s \ncursor %s" + , portInner, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,actionType,threshold,cursor); log.info(parameters); - mainLaunch(portInner, serverWait, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,dbNo,actionType,threshold,cursor,chunk); + mainLaunch(portInner, numOfWorkers, jobType, portDumps, pythonPath,datasetPath,pjName,actionType,threshold,cursor,chunk); } - public static void mainLaunch(String portInner, String serverWait, String numOfWorkers, String jobType, String portDumps, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType, String threshold, String cursor, String chunk){ + public static void mainLaunch(String portInner, String numOfWorkers, String jobType, String portDumps, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String cursor, String chunk){ String dbDir; @@ -72,43 +71,35 @@ public class Launcher { try { switch (jobType) { case "ENHANCEDASTDIFF": - TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); + EnhancedASTDiff.main(gumInput, gumOutput, numOfWorkers, pjName); break; case "CACHE": - StoreFile.main(gumOutput, portDumps, serverWait, dbDir, actionType+dumpsName,actionType); + StoreEDiffInCache.main(gumOutput, portDumps, dbDir, actionType+dumpsName,actionType); break; - case "COMP": - CalculatePairs.main(serverWait, dbDir, actionType+dumpsName, portDumps, pairsPath+actionType, pjName+actionType); - - ImportPairs2DB.main(pairsPath+actionType, portInner, serverWait, dbDir,datasetPath); + case "SI": + CalculatePairs.main(dbDir, actionType+dumpsName, portDumps, pairsPath+actionType, pjName+actionType); + ImportPairs2DB.main(pairsPath+actionType, portInner, dbDir,datasetPath); break; - case "AKKA": - AkkaTreeLoader.main(portInner, serverWait, dbDir, pjName +actionType+chunk+".rdb" , portDumps, actionType+dumpsName,pairsPath+actionType,numOfWorkers,cursor); + case "SIMI": + AkkaTreeLoader.main(portInner, dbDir, pjName +actionType+chunk+".rdb" , portDumps, actionType+dumpsName,pairsPath+actionType,numOfWorkers,cursor,chunk); break; case "LEVEL1": - level1(portInner, serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); + level1(portInner, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); break; //CALC python abstractPatch.py to from cluster folder case "LEVEL2": - level2(serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); + level2(portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; //CALC via python case "LEVEL3": - level3(serverWait, portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); - break; - case "ALL": -// TestHunkParser.main(gumInput, gumOutput, numOfWorkers, pjName); -// StoreFile.main(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType); -// level1(portInner, serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, pairsPath, dumpsName, gumInput); -// level2(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); -// level3(serverWait, port, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); + level3(portDumps, pythonPath, datasetPath, pjName, actionType, threshold, dbDir, dumpsName, gumInput); break; case "EXTRACTPATTERN": - PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + PatternExtractor.mainLaunch(portInner,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,actionType,threshold); break; case "GETPATTERN": - PatternExtractor.mainLaunch(portInner,serverWait,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,dbNo,actionType,threshold); + PatternExtractor.mainLaunch(portInner,numOfWorkers,jobType,portDumps,pythonPath,datasetPath,pjName,actionType,threshold); break; } } catch (Exception e) { @@ -120,63 +111,63 @@ public class Launcher { } - private static void level1(String portInner, String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception { + private static void level1(String portInner, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String pairsPath, String dumpsName, String gumInput) throws Exception { - TreeLoaderClusterL1.main(portInner, serverWait, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); + TreeLoaderClusterL1.main(portInner, port, dbDir, "level1-"+pjName+ actionType+".rdb", dbDir ,pjName + actionType); CallShell cs1 =new CallShell(); String db1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String db11 = String.format(db1, dbDir,"level1-"+pjName+ actionType+".rdb" ,Integer.valueOf(port)); - cs1.runShell(db11,serverWait, port); + cs1.runShell(db11, port); String runpy = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; String formatRunPy = String.format(runpy,pythonPath +"/abstractPatch.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, "matches" + pjName + actionType, threshold); cs1.runShell(formatRunPy); String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(port)); - cs1.runShell(stopServer,serverWait, port); + cs1.runShell(stopServer, port); } - private static void level2(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { + private static void level2(String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { String stopServer; MultiThreadTreeLoaderCluster.calculatePairsOfClusters(datasetPath + "/cluster"+pjName+ actionType, datasetPath,actionType); - MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); + MultiThreadTreeLoaderCluster.mainCompare("6300", datasetPath+"/pairs"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl1-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",actionType); CallShell cs3 =new CallShell(); String db22 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String db1b = String.format(db22, dbDir,"clusterl1-"+pjName+actionType+".rdb",Integer.valueOf(port)); - cs3.runShell(db1b,serverWait, port); + cs3.runShell(db1b, port); String runpy2 = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; String formatRunPy1a = String.format(runpy2,pythonPath +"/abstractPatchCluster.py", gumInput, datasetPath + "/cluster"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); cs3.runShell(formatRunPy1a); String stopServer1a = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer1a,Integer.valueOf(port)); - cs3.runShell(stopServer,serverWait, port); + cs3.runShell(stopServer, port); } - private static void level3(String serverWait, String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { + private static void level3(String port, String pythonPath, String datasetPath, String pjName, String actionType, String threshold, String dbDir, String dumpsName, String gumInput) throws Exception { String stopServer; MultiThreadTreeLoaderCluster3.calculatePairsOfClusters(datasetPath + "/cluster-2l"+pjName+ actionType, datasetPath,actionType); - MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",serverWait,actionType); + MultiThreadTreeLoaderCluster3.mainCompare("6300", datasetPath+"/pairs-2l"+actionType, datasetPath + "/redisSingleImport.sh", dbDir, "clusterl2-"+pjName+actionType+".rdb", actionType+dumpsName, "6301",actionType); CallShell cs5 =new CallShell(); String dba = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String dbaa = String.format(dba, dbDir,"clusterl2-"+pjName+actionType+".rdb",Integer.valueOf(port)); - cs5.runShell(dbaa,serverWait, port); + cs5.runShell(dbaa, port); String runpya = "bash "+datasetPath + "/" + "launchPy.sh" +" %s %s %s %s %s %s"; String formatRunPya = String.format(runpya,pythonPath +"/abstractPatchClusterLevel3.py", gumInput, datasetPath + "/cluster-3l"+pjName+ actionType, port, datasetPath + "/cluster-2l"+pjName+ actionType,threshold); cs5.runShell(formatRunPya); String stopServera = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServera,Integer.valueOf(port)); - cs5.runShell(stopServer,serverWait, port); + cs5.runShell(stopServer, port); return; } -// System.exit(1); + } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java b/src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java index edd65c1..bbc33a5 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/PatternExtractor.java @@ -1,7 +1,5 @@ package edu.lu.uni.serval.fixminer; -import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.TreeContext; import edu.lu.uni.serval.FixPattern.utils.Checker; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; @@ -21,7 +19,6 @@ import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.getASTTree; /** * Created by anilkoyuncu on 02/08/2018. @@ -30,7 +27,7 @@ public class PatternExtractor { private static Logger log = LoggerFactory.getLogger(PatternExtractor.class); - public static void mainLaunch(String portInner,String serverWait, String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String dbNo, String actionType,String threshold) { + public static void mainLaunch(String portInner,String numOfWorkers,String jobType,String port, String pythonPath, String datasetPath, String pjName, String actionType,String threshold) { String dbDir; @@ -55,7 +52,7 @@ public class PatternExtractor { switch (jobType) { case "EXTRACTPATTERN": - loadDB(gumOutput, portInner, serverWait, dbDir, actionType+dumpsName,actionType,fixes); + loadDB(gumOutput, portInner, dbDir, actionType+dumpsName,actionType,fixes); break; case "GETPATTERN": getPattern(fixes,actionType); @@ -67,7 +64,7 @@ public class PatternExtractor { } - public static void loadDB(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String operation,List fixes) throws Exception { + public static void loadDB(String inputPath,String portInner,String dbDir,String chunkName,String operation,List fixes) throws Exception { // String inputPath; // String portInner; // String serverWait; @@ -246,24 +243,24 @@ public class PatternExtractor { } } - public static ITree getSimpliedTree(HierarchicalActionSet actionSet) { - - ITree tree = null; - Jedis inner = null; - try { - - ITree parent = null; - ITree children = null; - TreeContext tc = new TreeContext(); - tree = getASTTree(actionSet, parent, children, tc); -// tree.setParent(null); - tc.validate(); - - } catch (Exception e) { - e.printStackTrace(); - } - return tree; - } +// public static ITree getSimpliedTree(HierarchicalActionSet actionSet) { +// +// ITree tree = null; +// Jedis inner = null; +// try { +// +// ITree parent = null; +// ITree children = null; +// TreeContext tc = new TreeContext(); +// tree = getASTTree(actionSet, parent, children, tc); +//// tree.setParent(null); +// tc.validate(); +// +// } catch (Exception e) { +// e.printStackTrace(); +// } +// return tree; +// } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java b/src/main/java/edu/lu/uni/serval/fixminer/TestHunkParserSingleFile.java similarity index 72% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java rename to src/main/java/edu/lu/uni/serval/fixminer/TestHunkParserSingleFile.java index 58ad0dc..44575a7 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestHunkParserSingleFile.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/TestHunkParserSingleFile.java @@ -1,20 +1,18 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer; import akka.actor.ActorRef; import akka.actor.ActorSystem; import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor; import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage; -import edu.lu.uni.serval.config.Configuration; import edu.lu.uni.serval.utils.FileHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -232,131 +230,10 @@ public class TestHunkParserSingleFile { // } } - public static void classifyByAlarmTypes() { - final String alarmTypesFilePath = Configuration.ALARM_TYPES_FILE; - List alarmTypes = readStringList(alarmTypesFilePath); - //edit scripts, sizes of edit scripts, buggy tokens, patches. - classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPT_SIZES_FILE); - classifyByAlarmTypes(alarmTypes, Configuration.EDITSCRIPTS_FILE); - classifyByAlarmTypes(alarmTypes, Configuration.BUGGY_CODE_TOKENS_FILE); - classifyByAlarmTypes2(alarmTypes, Configuration.PATCH_SOURCECODE_FILE); - } - private static void classifyByAlarmTypes(List alarmTypes, String file) { - Map buildersMap = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(file); - scanner = new Scanner(fis); - int counter = 0; - while (scanner.hasNextLine()) { - String alarmType = alarmTypes.get(counter); - StringBuilder builder = getBuilder(buildersMap, alarmType); - builder.append(scanner.nextLine() + "\n"); - counter ++; - if (counter % 1000 == 0) { - outputBuilders(buildersMap, file); - } - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - outputBuilders(buildersMap, file); - } - - private static void classifyByAlarmTypes2(List alarmTypes, String patchSourcecodeFile) { - Map buildersMap = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(patchSourcecodeFile); - scanner = new Scanner(fis); - int counter = 0; - String singlePatch = ""; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - if (Configuration.PATCH_SIGNAL.equals(line)) { - if (!"".equals(singlePatch)) { - String alarmType = alarmTypes.get(counter); - StringBuilder builder = getBuilder(buildersMap, alarmType); - builder.append(scanner.nextLine() + "\n"); - counter ++; - if (counter % 2000 == 0) { - outputBuilders(buildersMap, patchSourcecodeFile); - } - } - singlePatch = line + "\n"; - } - singlePatch += line + "\n"; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - outputBuilders(buildersMap, patchSourcecodeFile); - } - private static void outputBuilders(Map map, String fileNameStr) { - File file = new File(fileNameStr); - String fileName = file.getName(); - String parentPath = file.getParent(); - for (Map.Entry entry : map.entrySet()) { - String alarmType = entry.getKey(); - StringBuilder builder = entry.getValue(); - - FileHelper.outputToFile(parentPath + "/" + alarmType + "/" + fileName, builder, true); - - builder.setLength(0); - entry.setValue(builder); - } - } - public static List readStringList(String inputFile) { - List list = new ArrayList<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(inputFile); - scanner = new Scanner(fis); - while(scanner.hasNextLine()) { - list.add(scanner.nextLine()); - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return list; - } - private static StringBuilder getBuilder(Map buildersMap, String alarmType) { - if (buildersMap.containsKey(alarmType)) { - return buildersMap.get(alarmType); - } else { - StringBuilder builder = new StringBuilder(); - buildersMap.put(alarmType, builder); - return builder; - } - } + } diff --git a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java b/src/main/java/edu/lu/uni/serval/fixminer/TestTreeLoader.java similarity index 54% rename from src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java rename to src/main/java/edu/lu/uni/serval/fixminer/TestTreeLoader.java index ad23b9c..9beb253 100644 --- a/src/main/java/edu/lu/uni/serval/FixPatternParser/violations/TestTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/TestTreeLoader.java @@ -1,15 +1,16 @@ -package edu.lu.uni.serval.FixPatternParser.violations; +package edu.lu.uni.serval.fixminer; import com.github.gumtreediff.actions.ActionGenerator; import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.matchers.Mapping; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; import java.io.*; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -132,98 +133,98 @@ public class TestTreeLoader { } - public static void compareAll(List folders){ - List trees = new ArrayList<>(); - HashMap hmap = new HashMap(); - for (File target : folders) { - - try { - FileInputStream fi = new FileInputStream(new File(target.toString())); - ObjectInputStream oi = new ObjectInputStream(fi); - ITree pr1 = (ITree) oi.readObject(); - oi.close(); - fi.close(); - trees.add(pr1); - hmap.put(folders.indexOf(target), target.toString()); - - } catch (FileNotFoundException e) { - System.out.println("File not found"); - } catch (IOException e) { - System.out.println("Error initializing stream"); - } catch (ClassNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - } - - for (ITree tree : trees) { -// SimplifyTree simplifyTree = new SimplifyTree(); -// simplifyTree.canonicalizeSourceCodeTree(tree); - tree.setLabel(""); - tree.setParent(null); - List descendants = tree.getDescendants(); - for (ITree descendant : descendants) { - descendant.setLabel(""); - } - - } - System.out.println("a"); - - try { - - - - for (int i = 0; i < trees.size(); i++) { - for (int j = i + 1; j < trees.size(); j++) { - // compare list.get(i) and list.get(j) - BufferedWriter writer = new BufferedWriter(new FileWriter("output.txt",true)); - ITree oldTree = trees.get(i); - - ITree newTree = trees.get(j); - - Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); - m.match(); - - ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); - ag.generate(); - List actions = ag.getActions(); - writer.write(String.valueOf(i)); - writer.write("\t"); - writer.write(String.valueOf(j)); - writer.write("\t"); - - writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); - writer.write("\t"); - writer.write(String.valueOf(actions.size())); - writer.write("\t"); - writer.write(hmap.get(i)); - writer.write("\t"); - writer.write(hmap.get(j)); - writer.write("\n"); - - writer.close(); - } - } - - - } catch (FileNotFoundException e) { - System.out.println("File not found"); - } catch (IOException e) { - System.out.println("Error initializing stream"); - - } - - -// if (actions.size() > 1) { -// Matcher m1 = Matchers.getInstance().getMatcher(actions.get(0).getNode(), actions.get(0).getNode()); -// m1.match(); -// Set mappingSet1 = m1.getMappingSet(); +// public static void compareAll(List folders){ +// List trees = new ArrayList<>(); +// HashMap hmap = new HashMap(); +// for (File target : folders) { +// +// try { +// FileInputStream fi = new FileInputStream(new File(target.toString())); +// ObjectInputStream oi = new ObjectInputStream(fi); +// ITree pr1 = (ITree) oi.readObject(); +// oi.close(); +// fi.close(); +// trees.add(pr1); +// hmap.put(folders.indexOf(target), target.toString()); +// +// } catch (FileNotFoundException e) { +// System.out.println("File not found"); +// } catch (IOException e) { +// System.out.println("Error initializing stream"); +// } catch (ClassNotFoundException e) { +// // TODO Auto-generated catch block +// e.printStackTrace(); +// } +// } +// +// for (ITree tree : trees) { +//// SimplifyTree simplifyTree = new SimplifyTree(); +//// simplifyTree.canonicalizeSourceCodeTree(tree); +// tree.setLabel(""); +// tree.setParent(null); +// List descendants = tree.getDescendants(); +// for (ITree descendant : descendants) { +// descendant.setLabel(""); +// } // // } - } +// System.out.println("a"); +// +// try { +// +// +// +// for (int i = 0; i < trees.size(); i++) { +// for (int j = i + 1; j < trees.size(); j++) { +// // compare list.get(i) and list.get(j) +// BufferedWriter writer = new BufferedWriter(new FileWriter("output.txt",true)); +// ITree oldTree = trees.get(i); +// +// ITree newTree = trees.get(j); +// +// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); +// m.match(); +// +// ActionGenerator ag = new ActionGenerator(oldTree, newTree, m.getMappings()); +// ag.generate(); +// List actions = ag.getActions(); +// writer.write(String.valueOf(i)); +// writer.write("\t"); +// writer.write(String.valueOf(j)); +// writer.write("\t"); +// +// writer.write(String.format("%1.2f", m.chawatheSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.format("%1.2f", m.diceSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.format("%1.2f", m.jaccardSimilarity(oldTree, newTree))); +// writer.write("\t"); +// writer.write(String.valueOf(actions.size())); +// writer.write("\t"); +// writer.write(hmap.get(i)); +// writer.write("\t"); +// writer.write(hmap.get(j)); +// writer.write("\n"); +// +// writer.close(); +// } +// } +// +// +// } catch (FileNotFoundException e) { +// System.out.println("File not found"); +// } catch (IOException e) { +// System.out.println("Error initializing stream"); +// +// } +// +// +//// if (actions.size() > 1) { +//// Matcher m1 = Matchers.getInstance().getMatcher(actions.get(0).getNode(), actions.get(0).getNode()); +//// m1.match(); +//// Set mappingSet1 = m1.getMappingSet(); +//// +//// } +// } } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java index 2e2c19b..2cc115b 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/AkkaTreeLoader.java @@ -1,20 +1,17 @@ package edu.lu.uni.serval.fixminer.cluster; -import com.github.gumtreediff.tree.ITree; -import com.github.gumtreediff.tree.TreeContext; -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import org.junit.Assert; +import edu.lu.uni.serval.FixPattern.utils.PoolBuilder; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.*; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; -import java.io.*; -import java.time.Duration; -import java.util.*; -import java.util.concurrent.Executors; -import java.util.function.Consumer; -import java.util.stream.Collectors; +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; +import java.util.regex.Pattern; import static edu.lu.uni.serval.fixminer.cluster.akka.AkkaTreeParser.akkaCompare; @@ -23,58 +20,13 @@ import static edu.lu.uni.serval.fixminer.cluster.akka.AkkaTreeParser.akkaCompare */ public class AkkaTreeLoader { - private static class StreamGobbler implements Runnable { - private InputStream inputStream; - private Consumer consumer; - - public StreamGobbler(InputStream inputStream, Consumer consumer) { - this.inputStream = inputStream; - this.consumer = consumer; - } - - @Override - public void run() { - new BufferedReader(new InputStreamReader(inputStream)).lines() - .forEach(consumer); - } - } - private static Logger log = LoggerFactory.getLogger(AkkaTreeLoader.class); - public static void loadRedis(String cmd,String serverWait){ - Process process; - - try { -// String comd = String.format(cmd, f.getAbsoluteFile()); - process = Runtime.getRuntime() - - .exec(cmd); + public static void main(String portInner, String dbDir, String chunkName, String port, String dumpsName, String pairsPath, String numOfWorkers, String cursor,String chunk) throws Exception { - StreamGobbler streamGobbler = - new StreamGobbler(process.getInputStream(), System.out::println); - Executors.newSingleThreadExecutor().submit(streamGobbler); - int exitCode = process.waitFor(); - assert exitCode == 0; -// Thread.sleep(Integer.valueOf(serverWait)); - - } catch (IOException e) { - e.printStackTrace(); - } - catch (InterruptedException e) { - e.printStackTrace(); - } - log.info("Load done"); - } - - private static Consumer consumer = Assert::assertNotNull; - - - public static void main(String portInner, String serverWait, String dbDir, String chunkName, String port, String dumpsName, String pairsPath, String numOfWorkers, String cursor) throws Exception { - - - String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,serverWait,chunkName,dbDir,dumpsName); + String parameters = String.format("\nportInner %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,chunkName,dbDir,dumpsName); log.info(parameters); @@ -82,243 +34,76 @@ public class AkkaTreeLoader { String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port)); // - cs.runShell(cmd1,serverWait,port); + cs.runShell(cmd1,port); String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; String cmd2 = String.format(cmdInner, dbDir,chunkName,Integer.valueOf(portInner)); log.info(cmd1); log.info(cmd2); // - cs.runShell(cmd2,serverWait, portInner); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); - JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); - - -// Jedis jedis = new Jedis(new URI("redis://localhost:"+port)); -// while (!jedis.ping().equals("PONG")){ -// log.info("wait"); -// } -// -// jedis = new Jedis(new URI("redis://localhost:"+portInner)); -// while (!jedis.ping().equals("PONG")){ -// log.info("wait"); -// } - - -// String pairsIndexFile = pairsPath + "/"+ chunkName; -// pairsIndexFile = pairsIndexFile.replace("csv.rdb","index"); -// -// -// Pattern pattern = Pattern.compile(","); -// String csvFile = pairsIndexFile; -// try { -// try (BufferedReader in = new BufferedReader(new FileReader(csvFile));){ -// Map namefreq = in -// .lines() -// // .skip(1) -// .map(x -> pattern.split(x)) -// // .filter(x -> x[4].equals("CA") && x[3].equals("F")) -// .collect(HashMap::new, (map, x) -> -// map.put(x[0], x[1]), -// Map::putAll); -// // namefreq.forEach((k, v) -> System.out.println(k + " => " + v)); -// -// Jedis inner = null; -// try { -// inner = outerPool.getResource(); -// -// for (Map.Entry entry : namefreq.entrySet()) { -// String key = entry.getKey(); -// String value = entry.getValue(); -// inner.select(1); -// inner.set(key,value); -// // ... -// } -// -// -// }finally { -// if (inner != null) { -// inner.close(); -// } -// } -// -// -// } -// } catch (IOException e) { -// e.printStackTrace(); -// } + cs.runShell(cmd2, portInner); + JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000); -// comparePairs(innerPool,outerPool); - Thread.sleep(Integer.valueOf(serverWait)); - akkaCompare(innerPool,outerPool,numOfWorkers,cursor); - -// String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; -// String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); -// -// cs.runShell(stopServer1,serverWait); -// stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; -// String stopServer2 = String.format(stopServer,Integer.valueOf(port)); -// -// cs.runShell(stopServer2,serverWait); + String pairsIndexFile = pairsPath + "/"+ chunkName; + //0.txt.rdb + pairsIndexFile = pairsIndexFile.replace(chunk+".rdb",".index"); - } + Pattern pattern = Pattern.compile(","); + String csvFile = pairsIndexFile; + try { + try (BufferedReader in = new BufferedReader(new FileReader(csvFile));){ + Map namefreq = in + .lines() + .map(x -> pattern.split(x)) + .collect(HashMap::new, (map, x) -> + map.put(x[0], x[1]), + Map::putAll); - public static void comparePairs(JedisPool innerPool,JedisPool outerPool){ + Jedis inner = null; + try { + inner = outerPool.getResource(); - - ScanResult scan; - - try (Jedis inner = innerPool.getResource()) { - while (!inner.ping().equals("PONG")){ - log.info("wait"); + for (Map.Entry entry : namefreq.entrySet()) { + String key = entry.getKey(); + String value = entry.getValue(); + inner.select(1); + inner.set(key,value); } - ScanParams sc = new ScanParams(); - //150000000 - log.info("Scanning "); - sc.count(250000000); - sc.match("pair_[0-9]*"); - - scan = inner.scan("0", sc); - int size = scan.getResult().size(); - log.info("Scanned " + String.valueOf(size)); + }finally { + if (inner != null) { + inner.close(); + } } - List result = scan.getResult(); - log.info("Getting results"); - result - .parallelStream() - .forEach(m -> - { - Compare compare = new Compare(); - compare.coreCompare(m, innerPool, outerPool); - ; - } - ); - - -// } - - - - - } - - /** Read the object from Base64 string. */ - private static Object fromString( String s ) throws IOException , - ClassNotFoundException { - byte [] data = Base64.getDecoder().decode( s ); - ObjectInputStream ois = new ObjectInputStream( - new ByteArrayInputStream( data ) ); - Object o = ois.readObject(); - ois.close(); - return o; - } - public static ITree getSimpliedTree(String fn,JedisPool outerPool) { - - ITree tree = null; - Jedis inner = null; - try { - inner = outerPool.getResource(); - while (!inner.ping().equals("PONG")){ - log.info("wait"); } - inner.select(1); - String dist2load = inner.get(fn); - inner.select(0); - String s = inner.get(dist2load); - HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(s); - - ITree parent = null; - ITree children =null; - TreeContext tc = new TreeContext(); - tree = getASTTree(actionSet, parent, children,tc); - tree.setParent(null); - tc.validate(); - } catch (IOException e) { e.printStackTrace(); - } catch (ClassNotFoundException e) { - e.printStackTrace(); - }finally { - if (inner != null) { - inner.close(); - } } - return tree; + + + + + akkaCompare(innerPool,outerPool,numOfWorkers,cursor); + + + } - public static List getKeysByValue(Map map, E value) { - return map.entrySet() - .stream() - .filter(entry -> Objects.equals(entry.getValue(), value)) - .map(Map.Entry::getKey) - .collect(Collectors.toList()); - } - - public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ - - int newType = 0; - - String astNodeType = actionSet.getAstNodeType(); - List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); - - if(keysByValue.size() != 1){ - log.error("More than 1"); - } - newType = keysByValue.get(0); - if(actionSet.getParent() == null){ - //root - -// parent = new Tree(newType,""); - parent = tc.createTree(newType, "", null); - tc.setRoot(parent); - }else{ -// children = new Tree(newType,""); -// parent.addChild(children); - children = tc.createTree(newType, "", null); - children.setParentAndUpdateChildren(parent); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getASTTree(subAction,children,null,tc); - - } - } - return parent; - } - static final JedisPoolConfig poolConfig = buildPoolConfig(); - private static JedisPoolConfig buildPoolConfig() { - final JedisPoolConfig poolConfig = new JedisPoolConfig(); - poolConfig.setMaxTotal(128); - poolConfig.setMaxIdle(128); - poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(false); - poolConfig.setTestOnReturn(false); - poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); -// poolConfig.setNumTestsPerEvictionRun(3); - poolConfig.setBlockWhenExhausted(true); - return poolConfig; - } + diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java index 5a80670..87ab887 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CalculatePairs.java @@ -1,5 +1,6 @@ package edu.lu.uni.serval.fixminer.cluster; +import edu.lu.uni.serval.FixPattern.utils.PoolBuilder; import edu.lu.uni.serval.utils.FileHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -13,7 +14,6 @@ import java.nio.ByteBuffer; import java.nio.channels.FileChannel; import java.util.List; -import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig; /** * Created by anilkoyuncu on 05/04/2018. @@ -21,21 +21,21 @@ import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig; public class CalculatePairs { private static Logger log = LoggerFactory.getLogger(CalculatePairs.class); - public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName) throws Exception { + public static void main(String dbDir,String chunkName,String port,String outputPath,String pjName) throws Exception { - String parameters = String.format("\nport %s \nserverWait %s \nchunkName %s \ndbDir %s",port,serverWait,chunkName,dbDir); + String parameters = String.format("\nport %s \nchunkName %s \ndbDir %s",port,chunkName,dbDir); log.info(parameters); CallShell cs =new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port)); - cs.runShell(cmd,serverWait, port); + cs.runShell(cmd, port); FileHelper.createDirectory(outputPath); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000); ScanResult scan; try (Jedis outer = outerPool.getResource()) { diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java index 3c32292..9c1d05d 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/CallShell.java @@ -26,7 +26,7 @@ public class CallShell { } - public static void runShell(String command, String serverWait, String port) throws Exception { + public static void runShell(String command, String port) throws Exception { Process process = Runtime.getRuntime().exec(command); BufferedReader reader = new BufferedReader(new InputStreamReader( @@ -101,7 +101,7 @@ try{ public static void main(String[] args) throws Exception { // runPing("redis-cli -p 6380 ping"); - runShell("bash /Users/anilkoyuncu/bugStudy/release/code/redis/startServer.sh /Users/anilkoyuncu/bugStudy/release/code/redis Defects4JALL0.txt.rdb 6380","1","6380"); + runShell("bash /Users/anilkoyuncu/bugStudy/release/code/redis/startServer.sh /Users/anilkoyuncu/bugStudy/release/code/redis Defects4JALL0.txt.rdb 6380","6380"); } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java index 27ea1c1..49c03af 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/Compare.java @@ -5,6 +5,7 @@ import com.github.gumtreediff.actions.model.Action; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPattern.utils.EDiff; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.Jedis; @@ -13,7 +14,6 @@ import redis.clients.jedis.JedisPool; import java.util.List; import java.util.Map; -import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.getSimpliedTree; /** * Created by anilkoyuncu on 03/04/2018. @@ -44,9 +44,9 @@ public class Compare { // String firstValue = resultMap.get("0"); // String secondValue = resultMap.get("1"); - oldTree = getSimpliedTree(i,outerPool); + oldTree = EDiff.getSimpliedTree(i,outerPool); - newTree = getSimpliedTree(j,outerPool); + newTree = EDiff.getSimpliedTree(j,outerPool); Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); m.match(); diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java index b6a303f..6249a4a 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/ImportPairs2DB.java @@ -9,9 +9,6 @@ import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -//import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis; -//import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedisWait; - /** * Created by anilkoyuncu on 05/04/2018. @@ -19,10 +16,10 @@ import java.util.stream.Stream; public class ImportPairs2DB { private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class); - public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String datasetPath) throws Exception { + public static void main(String csvInputPath,String portInner,String dbDir,String datasetPath) throws Exception { - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \ndbDir %s",csvInputPath,portInner,serverWait,dbDir); + String parameters = String.format("\nInput path %s \nportInner %s \ndbDir %s",csvInputPath,portInner,dbDir); log.info(parameters); @@ -40,7 +37,7 @@ public class ImportPairs2DB { cmd = String.format(cmd, dbDir,pj.getName() +".rdb", portInt); log.info(cmd); CallShell cs = new CallShell(); - cs.runShell(cmd,serverWait, portInner); + cs.runShell(cmd, portInner); cmd = "bash "+datasetPath + "/redisSingleImport.sh" +" %s %s"; @@ -50,7 +47,7 @@ public class ImportPairs2DB { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,portInt); - cs.runShell(stopServer2,serverWait, portInner); + cs.runShell(stopServer2, portInner); portInt++; diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java index baa1c42..e4e0441 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoader.java @@ -1,14 +1,13 @@ package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.actions.model.Action; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.Tree; import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; -import edu.lu.uni.serval.utils.FileHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.*; @@ -291,17 +290,17 @@ public class MultiThreadTreeLoader { readMessageFiles(fileToCompare,port); } - public static void processMessages(String inputPath, String outputPath) { - File folder = new File(outputPath + "pairs_splitted/"); - File[] listOfFiles = folder.listFiles(); - Stream stream = Arrays.stream(listOfFiles); - List pjs = stream - .filter(x -> !x.getName().startsWith(".")) - .collect(Collectors.toList()); - FileHelper.createDirectory(outputPath + "comparison_splitted/"); - pjs.parallelStream() - .forEach(m -> coreLoop(m, outputPath,inputPath)); - } +// public static void processMessages(String inputPath, String outputPath) { +// File folder = new File(outputPath + "pairs_splitted/"); +// File[] listOfFiles = folder.listFiles(); +// Stream stream = Arrays.stream(listOfFiles); +// List pjs = stream +// .filter(x -> !x.getName().startsWith(".")) +// .collect(Collectors.toList()); +// FileHelper.createDirectory(outputPath + "comparison_splitted/"); +// pjs.parallelStream() +// .forEach(m -> coreLoop(m, outputPath,inputPath)); +// } public static ITree getSimpliedTree(String fn) { @@ -377,45 +376,45 @@ public class MultiThreadTreeLoader { return parent; } - public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ - - int newType = 0; - - Action action = actionSet.getAction(); - if (action instanceof Update){ - newType = 101; - }else if(action instanceof Insert){ - newType =100; - }else if(action instanceof Move){ - newType = 102; - }else if(action instanceof Delete){ - newType=103; - }else{ - new Exception("unknow action"); - } - if(actionSet.getParent() == null){ - //root - - parent = new Tree(newType,""); - }else{ - children = new Tree(newType,""); - parent.addChild(children); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getActionTree(subAction,children,null); - - } - - - } - return parent; - } +// public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children){ +// +// int newType = 0; +// +// Action action = actionSet.getAction(); +// if (action instanceof Update){ +// newType = 101; +// }else if(action instanceof Insert){ +// newType =100; +// }else if(action instanceof Move){ +// newType = 102; +// }else if(action instanceof Delete){ +// newType=103; +// }else{ +// new Exception("unknow action"); +// } +// if(actionSet.getParent() == null){ +// //root +// +// parent = new Tree(newType,""); +// }else{ +// children = new Tree(newType,""); +// parent.addChild(children); +// } +// List subActions = actionSet.getSubActions(); +// if (subActions.size() != 0){ +// for (HierarchicalActionSet subAction : subActions) { +// +// if(actionSet.getParent() == null){ +// children = parent; +// } +// getActionTree(subAction,children,null); +// +// } +// +// +// } +// return parent; +// } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java index 09d0eb4..fa6ed79 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster.java @@ -1,22 +1,29 @@ package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.actions.ActionGenerator; -import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.actions.model.Action; import com.github.gumtreediff.matchers.Matcher; import com.github.gumtreediff.matchers.Matchers; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.TreeContext; +import edu.lu.uni.serval.FixPattern.utils.EDiff; +import edu.lu.uni.serval.FixPattern.utils.EDiffHelper; +import edu.lu.uni.serval.FixPattern.utils.PoolBuilder; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.utils.FileHelper; - import org.javatuples.Pair; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.*; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.ScanParams; +import redis.clients.jedis.ScanResult; import java.io.*; -import java.time.Duration; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -28,28 +35,27 @@ public class MultiThreadTreeLoaderCluster { private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster.class); - public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait,String type) throws Exception { + public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String type) throws Exception { CallShell cs = new CallShell(); String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); -// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - cs.runShell(cmd1,serverWait, port); + cs.runShell(cmd1, port); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); - cs.runShell(cmd2,serverWait, port); -// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); + cs.runShell(cmd2, port); + String cmd3; cmd3 = "bash " + importScript +" %s %s"; - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + JedisPool jedisPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000); File folder = new File(pairsCSVPath); @@ -104,29 +110,16 @@ public class MultiThreadTreeLoaderCluster { } String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); -// loadRedis(stopServer2,serverWait); - cs.runShell(stopServer1,serverWait, port); + cs.runShell(stopServer1, port); String stopServer2 = String.format(stopServer,Integer.valueOf(port)); -// loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait, port); + cs.runShell(stopServer2, port); } - /** Read the object from Base64 string. */ - public static Object fromString( String s ) throws IOException , - ClassNotFoundException { - byte [] data = Base64.getDecoder().decode( s ); - ObjectInputStream ois = new ObjectInputStream( - new ByteArrayInputStream( data ) ); - Object o = ois.readObject(); - ois.close(); - return o; - } - public static Pair getTree(String firstValue, JedisPool outerPool,String type){ @@ -148,13 +141,13 @@ public class MultiThreadTreeLoaderCluster { inner = outerPool.getResource(); String filename = project + "/"+type+"/" + pureFileName + ".txt_" + actionSetPosition; String si= inner.get(filename); - HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); + HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.fromString(si); ITree parent = null; ITree children =null; TreeContext tc = new TreeContext(); - tree = getActionTree(actionSet, parent, children,tc); + tree = EDiff.getActionTree(actionSet, parent, children,tc); tree.setParent(null); tc.validate(); @@ -179,50 +172,7 @@ public class MultiThreadTreeLoaderCluster { } - public static ITree getActionTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ - int newType = 0; - - Action action = actionSet.getAction(); - if (action instanceof Update){ - newType = 101; - }else if(action instanceof Insert){ - newType =100; - }else if(action instanceof Move){ - newType = 102; - }else if(action instanceof Delete){ - newType=103; - }else{ - new Exception("unknow action"); - } - if(actionSet.getParent() == null){ - //root - - parent = tc.createTree(newType, "", null); - tc.setRoot(parent); - -// parent = new Tree(newType,""); - }else{ - children = tc.createTree(newType, "", null); - children.setParentAndUpdateChildren(parent); -// children = new Tree(newType,""); -// parent.addChild(children); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getActionTree(subAction,children,null,tc); - - } - - - } - return parent; - } private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool,String type) { @@ -383,26 +333,6 @@ public class MultiThreadTreeLoaderCluster { - static final JedisPoolConfig poolConfig = buildPoolConfig(); - - - private static JedisPoolConfig buildPoolConfig() { - final JedisPoolConfig poolConfig = new JedisPoolConfig(); - poolConfig.setMaxTotal(128); - poolConfig.setMaxIdle(128); - poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(true); - poolConfig.setTestOnReturn(true); - poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); - poolConfig.setNumTestsPerEvictionRun(3); - poolConfig.setBlockWhenExhausted(true); - - return poolConfig; - } - - // return msgFiles; } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java index 5cea1b4..661595a 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/MultiThreadTreeLoaderCluster3.java @@ -2,24 +2,26 @@ package edu.lu.uni.serval.fixminer.cluster; import com.github.gumtreediff.tree.ITree; import com.github.gumtreediff.tree.TreeContext; -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.FixPattern.utils.EDiffHelper; +import edu.lu.uni.serval.FixPattern.utils.PoolBuilder; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import edu.lu.uni.serval.utils.FileHelper; import org.apache.commons.lang3.StringUtils; import org.apache.commons.text.similarity.JaroWinklerDistance; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.*; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.ScanParams; +import redis.clients.jedis.ScanResult; import java.io.*; -import java.time.Duration; import java.util.*; import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoader.getKeysByValue; -import static edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoaderCluster.fromString; + /** * Created by anilkoyuncu on 19/03/2018. @@ -30,27 +32,24 @@ public class MultiThreadTreeLoaderCluster3 { private static Logger log = LoggerFactory.getLogger(MultiThreadTreeLoaderCluster3.class); -// public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) { - public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String serverWait, String type) throws Exception { + public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner,String type) throws Exception { CallShell cs = new CallShell(); String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner)); -// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000"); - cs.runShell(cmd1,serverWait, port); + cs.runShell(cmd1, port); String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port)); -// edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000"); - cs.runShell(cmd2,serverWait, port); + cs.runShell(cmd2, port); String cmd3; cmd3 = "bash " + importScript +" %s %s"; - JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + JedisPool jedisPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000); @@ -79,8 +78,7 @@ public class MultiThreadTreeLoaderCluster3 { if (size == 0) { String comd = String.format(cmd3, f.getPath(), portInner); cs.runShell(comd); -// edu.lu.uni.serval.fixminer.cluster.MultiThreadTreeLoaderCluster. -// loadRedis(comd); + scan = jedis.scan("0", sc); size = scan.getResult().size(); @@ -103,17 +101,10 @@ public class MultiThreadTreeLoaderCluster3 { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer1 = String.format(stopServer,Integer.valueOf(portInner)); -// loadRedis(stopServer2,serverWait); - cs.runShell(stopServer1,serverWait, port); + cs.runShell(stopServer1, port); String stopServer2 = String.format(stopServer,Integer.valueOf(port)); -// loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait, port); - - - - -// } + cs.runShell(stopServer2, port); @@ -151,13 +142,13 @@ public class MultiThreadTreeLoaderCluster3 { inner = outerPool.getResource(); String fn = project + "/"+type+"/" + s + ".txt_" + actionSetPosition; String si= inner.get(fn); - HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si); + HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.fromString(si); ITree parent = null; ITree children =null; TreeContext tc = new TreeContext(); - tree = getASTTree(actionSet, parent, children,tc); + tree = EDiffHelper.getASTTree(actionSet, parent, children,tc); // tree.setParent(null); tc.validate(); @@ -176,46 +167,7 @@ public class MultiThreadTreeLoaderCluster3 { } - public static ITree getASTTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){ - int newType = 0; - - String astNodeType = actionSet.getAstNodeType(); - - String label = actionSet.getAction().toString(); - List keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType); - - if(keysByValue.size() != 1){ - log.error("Birden cok astnodemapmapping"); - } - newType = keysByValue.get(0); - if(actionSet.getParent() == null){ - //root - -// parent = new Tree(newType,""); - parent = tc.createTree(newType, label, null); - tc.setRoot(parent); - }else{ -// children = new Tree(newType,""); -// parent.addChild(children); - children = tc.createTree(newType, label, null); - children.setParentAndUpdateChildren(parent); - } - List subActions = actionSet.getSubActions(); - if (subActions.size() != 0){ - for (HierarchicalActionSet subAction : subActions) { - - if(actionSet.getParent() == null){ - children = parent; - } - getASTTree(subAction,children,null,tc); - - } - - - } - return parent; - } public static List getNames(ITree oldTree, List oldTokens){ @@ -489,31 +441,6 @@ public class MultiThreadTreeLoaderCluster3 { String firstValue = resultMap.get("0"); String secondValue = resultMap.get("1"); -// if(firstValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL") || secondValue.equals("7/0/7af9e0_e674f1_spring-social-web#src#main#java#org#springframework#social#connect#web#ConnectController.txt_0_SOCIAL")){ -// log.info(""); -// } - - ///35/1/22b5f7_84bf27_ui#org.eclipse.pde.runtime#src#org#eclipse#pde#internal#runtime#registry#RegistryBrowserLabelProvider.txt_2_PDE - - - -// firstValue = inputPath + firstValue; -// secondValue = inputPath + secondValue; - -// String[] firstValueSplit = firstValue.split("/"); -// String[] secondValueSplit = secondValue.split("/"); -// -// if (firstValueSplit.length == 1) { -// firstValue = inputPath + firstValueSplit[0]; -// } else { -// firstValue = inputPath + firstValueSplit[1]; -// } -// -// if (secondValueSplit.length == 1) { -// secondValue = inputPath + secondValueSplit[0]; -// } else { -// secondValue = inputPath + secondValueSplit[1]; -// } try { ITree oldTree = getTree(firstValue,outerPool,type); @@ -526,30 +453,18 @@ public class MultiThreadTreeLoaderCluster3 { return; } -// ITree oldTree = oldPair.getValue0(); -// ITree newTree = newPair.getValue0(); -// -// String oldProject = oldPair.getValue1(); -// String newProject = newPair.getValue1(); + List oldTokens = new ArrayList<>(); List newTokens = new ArrayList<>(); -// if(secondValue.startsWith("/2/")){ -// log.info("newss"); -// } - // 41 return statement oldTokens = getNames(oldTree,oldTokens); newTokens = getNames(newTree,newTokens); -// if(oldTokens.size() == 0 || newTokens.size() == 0){ -// log.error("Cluster {} has no tokens on pair {}",clusterName , name); -// } -// Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree); -// m.match(); + CharSequence[] oldSequences = oldTokens.toArray(new CharSequence[oldTokens.size()]); CharSequence[] newSequences = newTokens.toArray(new CharSequence[newTokens.size()]); JaroWinklerDistance jwd = new JaroWinklerDistance(); @@ -572,14 +487,7 @@ public class MultiThreadTreeLoaderCluster3 { int retval = Double.compare(overallSimi, Double.valueOf(0.8)); if(retval >= 0){ -// log.info("YES"); -// log.info(name); -// log.info(firstValue); -// log.info(secondValue); -// log.info("************"); -// if(!overallSimi.equals(1.0)){ -// log.info(""); -// } + String matchKey = "match-"+clusterName+"_" + (String.valueOf(i)) + "_" + String.valueOf(j); String result = firstValue + "," + secondValue + ","+String.join(",", oldTokens); jedis.select(1); @@ -705,30 +613,6 @@ public class MultiThreadTreeLoaderCluster3 { - - - static final JedisPoolConfig poolConfig = buildPoolConfig(); - - - private static JedisPoolConfig buildPoolConfig() { - final JedisPoolConfig poolConfig = new JedisPoolConfig(); - poolConfig.setMaxTotal(128); - poolConfig.setMaxIdle(128); - poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(true); - poolConfig.setTestOnReturn(true); - poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); - poolConfig.setNumTestsPerEvictionRun(3); - poolConfig.setBlockWhenExhausted(true); - - return poolConfig; - } - - - -// return msgFiles; } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreEDiffInCache.java similarity index 64% rename from src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java rename to src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreEDiffInCache.java index f6b9eb4..39bba51 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreFile.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/StoreEDiffInCache.java @@ -1,5 +1,7 @@ package edu.lu.uni.serval.fixminer.cluster; +import edu.lu.uni.serval.FixPattern.utils.EDiffHelper; +import edu.lu.uni.serval.FixPattern.utils.PoolBuilder; import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -9,50 +11,28 @@ import redis.clients.jedis.JedisPool; import java.io.*; import java.util.ArrayList; import java.util.Arrays; -import java.util.Base64; import java.util.List; import java.util.stream.Collectors; import java.util.stream.Stream; -import static edu.lu.uni.serval.fixminer.cluster.TreeLoaderClusterL1.poolConfig; /** * Created by anilkoyuncu on 03/04/2018. */ -public class StoreFile { +public class StoreEDiffInCache { - private static Logger log = LoggerFactory.getLogger(StoreFile.class); + private static Logger log = LoggerFactory.getLogger(StoreEDiffInCache.class); -// public static void main(String[] args) { - public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String operation) throws Exception { -// String inputPath; -// String portInner; -// String serverWait; -// String dbDir; -// String chunkName; -// String numOfWorkers; -// if (args.length > 0) { -// inputPath = args[0]; -// portInner = args[1]; -// serverWait = args[2]; -// chunkName = args[3]; -// numOfWorkers = args[4]; -// dbDir = args[5]; -// } else { -// inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput2"; -// portInner = "6399"; -// serverWait = "10000"; -// chunkName ="dumps.rdb"; -// dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis"; -// numOfWorkers = "1"; -// } - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \noperation %s",inputPath,portInner,serverWait,chunkName,dbDir,operation); + + public static void main(String inputPath,String portInner,String dbDir,String chunkName,String operation) throws Exception { + + String parameters = String.format("\nInput path %s \nportInner %s \nchunkName %s \ndbDir %s \noperation %s",inputPath,portInner,chunkName,dbDir,operation); log.info(parameters); CallShell cs = new CallShell(); String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner)); -// loadRedis(cmd,serverWait); - cs.runShell(cmd,serverWait, portInner); + + cs.runShell(cmd, portInner); File folder = new File(inputPath); File[] subFolders = folder.listFiles(); @@ -98,7 +78,7 @@ public class StoreFile { } log.info(String.valueOf(workList.size())); - JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000); workList.stream().parallel() .forEach(m -> storeCore(innerPool, m.split(",")[1],m.split(",")[0])); @@ -107,10 +87,12 @@ public class StoreFile { String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s"; String stopServer2 = String.format(stopServer,Integer.valueOf(portInner)); -// loadRedis(stopServer2,serverWait); - cs.runShell(stopServer2,serverWait, portInner); + + cs.runShell(stopServer2, portInner); } + + public static void storeCore(JedisPool innerPool,String path,String key){ try { @@ -141,7 +123,7 @@ public class StoreFile { try (Jedis inner = innerPool.getResource()) { - inner.set(key,toString(actionSet)); + inner.set(key, EDiffHelper.toString(actionSet)); } @@ -155,25 +137,7 @@ public class StoreFile { } - /** Read the object from Base64 string. */ - private static Object fromString( String s ) throws IOException , - ClassNotFoundException { - byte [] data = Base64.getDecoder().decode( s ); - ObjectInputStream ois = new ObjectInputStream( - new ByteArrayInputStream( data ) ); - Object o = ois.readObject(); - ois.close(); - return o; - } - /** Write the object to a Base64 string. */ - private static String toString( Serializable o ) throws IOException { - ByteArrayOutputStream baos = new ByteArrayOutputStream(); - ObjectOutputStream oos = new ObjectOutputStream( baos ); - oos.writeObject( o ); - oos.close(); - return Base64.getEncoder().encodeToString(baos.toByteArray()); - } } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java index 443d889..939c129 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeActor.java @@ -8,13 +8,10 @@ import akka.routing.RoundRobinPool; import edu.lu.uni.serval.fixminer.cluster.akka.TreeMessage; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.Jedis; import redis.clients.jedis.JedisPool; import java.util.List; -import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.loadRedis; - public class TreeActor extends UntypedActor { private static Logger logger = LoggerFactory.getLogger(TreeActor.class); diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java index e7e15b4..36a480a 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeLoaderClusterL1.java @@ -1,11 +1,14 @@ package edu.lu.uni.serval.fixminer.cluster; +import edu.lu.uni.serval.FixPattern.utils.PoolBuilder; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import redis.clients.jedis.*; +import redis.clients.jedis.Jedis; +import redis.clients.jedis.JedisPool; +import redis.clients.jedis.ScanParams; +import redis.clients.jedis.ScanResult; import java.io.File; -import java.time.Duration; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; @@ -18,19 +21,19 @@ public class TreeLoaderClusterL1 { private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class); - public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path,String innerTypePrefix) throws Exception { + public static void main(String portInner,String port,String inputPath,String level1DB,String level1Path,String innerTypePrefix) throws Exception { - String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nport %s",inputPath,portInner,serverWait,port); + String parameters = String.format("\nInput path %s \nportInner %s \nport %s",inputPath,portInner,port); log.info(parameters); String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port)); CallShell cs = new CallShell(); - cs.runShell(cmd,serverWait, port); - JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000); + cs.runShell(cmd, port); + JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(port),20000000); File chunks = new File(level1Path); @@ -44,8 +47,8 @@ public class TreeLoaderClusterL1 { String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s"; cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner)); - cs.runShell(cmdInner,serverWait, port); - JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000); + cs.runShell(cmdInner, port); + JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000); Jedis inner = null; @@ -97,38 +100,21 @@ public class TreeLoaderClusterL1 { String stopServer = "bash "+inputPath + "/" + "stopServer.sh" +" %s"; stopServer = String.format(stopServer,Integer.valueOf(portInner)); -// loadRedis(stopServer,serverWait); - cs.runShell(stopServer,serverWait, port); + + cs.runShell(stopServer, port); } String stopServer1 = "bash "+inputPath + "/" + "stopServer.sh" +" %s"; stopServer1 = String.format(stopServer1,Integer.valueOf(port)); -// loadRedis(stopServer,serverWait); - cs.runShell(stopServer1,serverWait, port); + + cs.runShell(stopServer1, port); } - static final JedisPoolConfig poolConfig = buildPoolConfig(); - private static JedisPoolConfig buildPoolConfig() { - final JedisPoolConfig poolConfig = new JedisPoolConfig(); - poolConfig.setMaxTotal(128); - poolConfig.setMaxIdle(128); - poolConfig.setMinIdle(16); - poolConfig.setTestOnBorrow(true); - poolConfig.setTestOnReturn(true); - poolConfig.setTestWhileIdle(true); - poolConfig.setMinEvictableIdleTimeMillis(Duration.ofMinutes(60).toMillis()); - poolConfig.setTimeBetweenEvictionRunsMillis(Duration.ofHours(30).toMillis()); - poolConfig.setNumTestsPerEvictionRun(3); - poolConfig.setBlockWhenExhausted(true); - - return poolConfig; - } - } diff --git a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java index 4c0e6a0..cfc7bb9 100644 --- a/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java +++ b/src/main/java/edu/lu/uni/serval/fixminer/cluster/TreeWorker.java @@ -8,14 +8,10 @@ import edu.lu.uni.serval.fixminer.cluster.akka.TreeMessage; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import redis.clients.jedis.JedisPool; -import redis.clients.jedis.JedisPoolConfig; -import java.time.Duration; import java.util.List; import java.util.concurrent.*; -import static edu.lu.uni.serval.fixminer.cluster.AkkaTreeLoader.poolConfig; - public class TreeWorker extends UntypedActor { private static Logger log = LoggerFactory.getLogger(TreeWorker.class); diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/ActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/ActionFilter.java deleted file mode 100644 index c8a1ce9..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/ActionFilter.java +++ /dev/null @@ -1,254 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.util.ArrayList; -import java.util.List; - -public class ActionFilter { - - private List methodNames = new ArrayList<>(); - private List variableNames = new ArrayList<>(); - - /** - * Filter out the modify actions of changing method names, method parameters, variable names and field names in declaration part. - * - * @param actionSets - * @return - */ - public List filterOutUselessActions(List actionSets) { - // Filter out modifications of variable names and method names. - List uselessActions = findoutUselessActions(actionSets); - actionSets.removeAll(uselessActions); - uselessActions.clear(); - - // Filter out non-UPD modifications, and modifications of variable names and method names. - uselessActions = findoutUselessActionSets(actionSets, true); - actionSets.removeAll(uselessActions); - uselessActions.clear(); - return actionSets; - } - - private List findoutUselessActionSets(List actionSets, boolean isRoot) { - List uselessActions = new ArrayList<>(); - - FindActionSet: { - for (HierarchicalActionSet actionSet : actionSets) { - if (!isRoot) { - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("UPD MethodInvocation") || actionStr.startsWith("INS MethodInvocation") || actionStr.startsWith("DEL MethodInvocation")) { - String label = actionSet.getAction().getNode().getLabel(); - for (String methodName : methodNames) { - if (actionSet.getActionString().startsWith("UPD MethodInvocation@@" + methodName + "(") - || actionSet.getActionString().startsWith("INS MethodInvocation@@" + methodName + "(") - || actionSet.getActionString().startsWith("DEL MethodInvocation@@" + methodName + "(") - || label.contains("." + methodName + "(")) { - addToUselessActions(actionSet, uselessActions); - break FindActionSet; - } - } - } else if (actionStr.startsWith("UPD SimpleName") || actionStr.startsWith("INS SimpleName") || actionStr.startsWith("DEL SimpleName")) { - String label = actionSet.getAction().getNode().getLabel(); - for (String variableName : variableNames) { - if (label.equals(variableName) || label.equals("Name:" + variableName)) { - addToUselessActions(actionSet, uselessActions); - break FindActionSet; - } - } - } else if (actionStr.startsWith("UPD StringLiteral") || actionStr.startsWith("INS StringLiteral") - || actionStr.startsWith("DEL StringLiteral") || actionStr.startsWith("MOV StringLiteral") - || actionStr.startsWith("UPD CharacterLiteral") || actionStr.startsWith("INS CharacterLiteral") - || actionStr.startsWith("DEL CharacterLiteral") || actionStr.startsWith("MOV CharacterLiteral")) { - addToUselessActions(actionSet, uselessActions); - break FindActionSet; - } - - List uselessActionSets = findoutUselessActionSets(actionSet.getSubActions(), false); - if (uselessActionSets.size() > 0) { - uselessActions.addAll(uselessActionSets); - break; - } - } else { - if (actionSet.getAstNodeType().endsWith("Statement") || "FieldDeclaration".equals(actionSet.getAstNodeType())) { - uselessActions.addAll(findoutUselessActionSets(actionSet.getSubActions(), false)); - } else { - uselessActions.add(actionSet); - } - } - } - } - - return uselessActions; - } - - private void addToUselessActions(HierarchicalActionSet actionSet, List uselessActions) { - while (actionSet.getParent() != null) { - actionSet = actionSet.getParent(); - } - if (!uselessActions.contains(actionSet)) { - uselessActions.add(actionSet); - } - } - - /** - * Identify the the modify actions of changing method names, method parameters, variable names and field names in declaration part. - * - * @param actionSets - * @return - */ - private List findoutUselessActions(List actionSets) { - List uselessActions = new ArrayList<>(); - - for (HierarchicalActionSet actionSet : actionSets) { - String actionType = actionSet.getAstNodeType(); - if (actionType.equals("MethodDeclaration")) { - addToUselessActions(actionSet, uselessActions);// INS, DEL: useful?, UPD, except the modifier actions - if (!actionSet.getActionString().startsWith("MOV ")) { - String label = actionSet.getNode().getLabel(); - String methodName = label.substring(label.indexOf("MethodName:")); - methodName = methodName.substring(11, methodName.indexOf(",")); - methodNames.add(methodName); // "MethodName:***" - - // UPD, DEL, INS parameters. - List subActionSets = actionSet.getSubActions(); - for (HierarchicalActionSet subActionSet : subActionSets) { - if (subActionSet.getAstNodeType().equals("SingleVariableDeclaration")) { - List subActionSets2 = subActionSet.getSubActions(); // - if (subActionSets2.size() == 0) { - String actSetStr = subActionSet.getActionString(); - int index1 = actSetStr.indexOf("@@"); - int index2 = 0; - if (actSetStr.startsWith("DEL")) { - index2 = actSetStr.indexOf("@AT@"); - } else { - index2 = actSetStr.indexOf("@TO@");; - } - actSetStr = actSetStr.substring(index1, index2).trim(); - String variableName = actSetStr.substring(actSetStr.lastIndexOf(" ")); - variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range - } else { - HierarchicalActionSet actSet = subActionSets2.get(subActionSets2.size() - 1); - String actStr = actSet.getActionString(); - if (actStr.startsWith("UPD SimpleName") || actStr.startsWith("INS SimpleName") || actStr.startsWith("DEL SimpleName")) { - String variableName = actSet.getNode().getLabel(); - variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range - } - } - } - } - } - } else if (actionType.equals("FieldDeclaration") || actionType.equals("VariableDeclarationStatement")) { - // UPD VariableDeclarationFragment - if (!actionSet.getActionString().startsWith("MOV ")) { - List subActionSets = actionSet.getSubActions(); - if (subActionSets.size() > 0) { - for (HierarchicalActionSet subActionSet : subActionSets) { // VariableDeclarationFragments - if (identifyUpdateVDF(subActionSet)) { - addToUselessActions(actionSet, uselessActions); - } - } - } - } - } else if (actionType.equals("TryStatement")) { - if (actionSet.getActionString().startsWith("UPD ")) { - List subActionSets = actionSet.getSubActions(); - if (subActionSets.size() > 0) { - for (HierarchicalActionSet subActionSet : subActionSets) { - if (subActionSet.getActionString().startsWith("UPD VariableDeclarationExpression")) { - List subActionSets2 = subActionSet.getSubActions(); // VariableDeclarationFragments - for (HierarchicalActionSet subActionSet2 : subActionSets2) { - if (identifyUpdateVDF(subActionSet2)) { - addToUselessActions(actionSet, uselessActions); - } - } - } else { - break; - } - } - } - } - } else if (actionType.equals("EnhancedForStatement")) { // SingleVariableDeclaration - if (!actionSet.getActionString().startsWith("MOV ")) { - List subActionSets = actionSet.getSubActions(); - if (subActionSets.size() > 0) { - HierarchicalActionSet subActionSet = subActionSets.get(0); - if (subActionSet.getActionString().startsWith("UPD SingleVariableDeclaration")) { - List subActionSets2 = subActionSet.getSubActions(); - for (HierarchicalActionSet subActionSet2 : subActionSets2) { // Type or Identifier - if (subActionSet2.getActionString().startsWith("UPD SimpleName")) { - String variableName = subActionSet2.getNode().getLabel(); - variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range - addToUselessActions(actionSet, uselessActions); - } - } - } - } - } - } else if (actionType.equals("SingleVariableDeclaration")) { - if (!actionSet.getActionString().startsWith("MOV ")) { - List subActionSets2 = actionSet.getSubActions(); // - if (subActionSets2.size() == 0) { - String actSetStr = actionSet.getActionString(); - int index1 = actSetStr.indexOf("@@"); - int index2 = 0; - if (actSetStr.startsWith("DEL")) { - index2 = actSetStr.indexOf("@AT@"); - } else { - index2 = actSetStr.indexOf("@TO@");; - } - actSetStr = actSetStr.substring(index1, index2).trim(); - String variableName = actSetStr.substring(actSetStr.lastIndexOf(" ")); - variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range - addToUselessActions(actionSet, uselessActions); - } else { - HierarchicalActionSet actSet = subActionSets2.get(subActionSets2.size() - 1); - String actStr = actSet.getActionString(); - if (actStr.startsWith("UPD SimpleName") || actStr.startsWith("INS SimpleName") || actStr.startsWith("DEL SimpleName")) { - String variableName = actSet.getNode().getLabel(); - variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range - addToUselessActions(actionSet, uselessActions); - } - } - } - } else { - if (actionSet.getParent() != null) { - while (actionSet.getParent() != null) { - actionSet = actionSet.getParent(); - } - if (uselessActions.contains(actionSet)) { - return uselessActions; - } else { - uselessActions.addAll(findoutUselessActions(actionSet.getSubActions())); - } - } - } - } - return uselessActions; - } - - /** - * Identify the AST node of this ActionSet is VariableDeclarationFragment or not. - * And, whether the action is happened on the Variable name or not. - * - * @param actionSet - */ - private boolean identifyUpdateVDF(HierarchicalActionSet actionSet) { - String actStr = actionSet.getActionString(); - if (actStr.startsWith("UPD VariableDeclarationFragment") - || actStr.startsWith("INS VariableDeclarationFragment") - || actStr.startsWith("DEL VariableDeclarationFragment")) { - List subActionSets = actionSet.getSubActions(); - if (subActionSets == null || subActionSets.size() == 0) { - // modification of Dimension - return true; - } - HierarchicalActionSet actSet = subActionSets.get(0); - String actSetStr = actSet.getActionString(); - if (actSetStr.startsWith("UPD SimpleName") || actSetStr.startsWith("INS SimpleName") || actSetStr.startsWith("DEL SimpleName")) { - String variableName = actSet.getNode().getLabel(); - variableNames.add(variableName); // "SimpleName:" + variableName TODO: effect range - return true; - } - } - return false; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java index 1bff3ac..4b5fb60 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalActionSet.java @@ -1,12 +1,12 @@ package edu.lu.uni.serval.gumtree.regroup; +import com.github.gumtreediff.actions.model.Action; +import com.github.gumtreediff.tree.ITree; + import java.io.Serializable; import java.util.ArrayList; import java.util.List; -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.tree.ITree; - /** * Hierarchical-level results of GumTree results * @@ -29,11 +29,16 @@ public class HierarchicalActionSet implements Comparable, private List subActions = new ArrayList<>(); private ITree node; - private SimpleTree abstractSimpleTree = null; // semi-source code tree. and AST node type tree - private SimpleTree abstractIdentifierTree = null; // abstract identifier tree - private SimpleTree simpleTree = null; // source code tree and AST node type tree - private SimpleTree originalTree = null; // source code tree. - + // source code tree. + + public int getBugEndPosition() { + return bugEndPosition; + } + + public int getFixEndPosition() { + return fixEndPosition; + } + private int bugEndPosition; private int fixEndPosition; @@ -147,49 +152,12 @@ public class HierarchicalActionSet implements Comparable, this.subActions = subActions; } - public SimpleTree getAbstractSimpleTree() { - return abstractSimpleTree; - } - - public void setAbstractSimpleTree(SimpleTree simpleTree) { - this.abstractSimpleTree = simpleTree; - } - - public SimpleTree getAbstractIdentifierTree() { - return abstractIdentifierTree; - } - - public void setAbstractIdentifierTree(SimpleTree abstractIdentifierTree) { - this.abstractIdentifierTree = abstractIdentifierTree; - } - - public SimpleTree getSimpleTree() { - return simpleTree; - } - - public void setSimpleTree(SimpleTree rawTokenTree) { - this.simpleTree = rawTokenTree; - } - - public SimpleTree getOriginalTree() { - return originalTree; - } - - public void setOriginalTree(SimpleTree originalTree) { - this.originalTree = originalTree; - } - - public int getBugEndPosition() { - return bugEndPosition; - } public void setBugEndPosition(int bugEndPosition) { this.bugEndPosition = bugEndPosition; } - public int getFixEndPosition() { - return fixEndPosition; - } + public void setFixEndPosition(int fixEndPosition) { this.fixEndPosition = fixEndPosition; @@ -197,10 +165,7 @@ public class HierarchicalActionSet implements Comparable, @Override public int compareTo(HierarchicalActionSet o) { -// int result = this.startPosition.compareTo(o.startPosition); -// if (result == 0) { -// result = this.length >= o.length ? -1 : 1; -// } + return this.startPosition.compareTo(o.startPosition);//this.action.compareTo(o.action); } @@ -238,28 +203,5 @@ public class HierarchicalActionSet implements Comparable, return str; } - public String toASTNodeLevelAction() { - if (strList.size() == 0) { - toString(); - } - String astNodeStr = ""; - for (String str : strList) { - astNodeStr += str.substring(0, str.indexOf("@@")) + "\n"; - } - return astNodeStr; - } - - public String toRawCodeLevelAction() { - if (strList.size() == 0) { - toString(); - } - String astNodeStr = ""; - for (String str : strList) { - str = str.substring(0, str.indexOf(" @AT@")) + "\n"; - int index1 = str.indexOf(" ") + 1; - int index2 = str.indexOf("@@") + 2; - astNodeStr += str.substring(0, index1) + str.substring(index2); - } - return astNodeStr; - } + } diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java index c00f09e..db1e1db 100644 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java +++ b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouper.java @@ -1,22 +1,13 @@ package edu.lu.uni.serval.gumtree.regroup; -import java.io.File; +import com.github.gumtreediff.actions.model.*; +import com.github.gumtreediff.tree.ITree; +import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; +import edu.lu.uni.serval.utils.ListSorter; + import java.util.ArrayList; import java.util.List; -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.actions.model.Addition; -import com.github.gumtreediff.actions.model.Delete; -import com.github.gumtreediff.actions.model.Insert; -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.actions.model.Update; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.gumtree.GumTreeComparer; -import edu.lu.uni.serval.utils.ListSorter; - /** * Regroup GumTree results to a hierarchical construction. * @@ -209,11 +200,6 @@ public class HierarchicalRegrouper { } -// } else if (parent.getType() == 31) { // method declaration -// int type = action.getNode().getType(); -// if (Checker.isStatement(type)) {// statements -// return null; -// } } for (Action act : actions) { diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java deleted file mode 100644 index 23df400..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HierarchicalRegrouperForC.java +++ /dev/null @@ -1,300 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.util.ArrayList; -import java.util.List; - -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.actions.model.Addition; -import com.github.gumtreediff.actions.model.Delete; -import com.github.gumtreediff.actions.model.Insert; -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.actions.model.Update; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.CNodeMap; -import edu.lu.uni.serval.utils.ListSorter; - -/** - * Regroup GumTree results to a hierarchical construction. - * - * @author kui.liu - * - */ -public class HierarchicalRegrouperForC { - -// public static void main(String[] args) { -// GumTreeComparer com = new GumTreeComparer(); -// File cFile1 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/prevFiles/prev_0a3d00_b404bc_drivers#pci#iov.c"); -// File cFile2 = new File("/Users/anilkoyuncu/bugStudy/dataset/GumTreeInput/linux-stable/revFiles/0a3d00_b404bc_drivers#pci#iov.c"); -// List action = com.compareTwoFilesWithGumTreeForCCode(cFile1, cFile2); -// List actionSet = new HierarchicalRegrouperForC().regroupGumTreeResults(action); -// System.out.println(actionSet); -// } - - List actionSets = new ArrayList<>(); - - public List regroupGumTreeResults(List actions) { - /* - * First, sort actions by their positions. - */ -// List actions = new ListSorter(actionsArgu).sortAscending(); -// if (actions == null) { -// actions = actionsArgu; -// } - - /* - * Second, group actions by their positions. - */ - HierarchicalActionSet actionSet = null; - for(Action act : actions){ - Action parentAct = findParentAction(act, actions); - - if (parentAct == null) { - actionSet = createActionSet(act, parentAct, null); - actionSets.add(actionSet); - } else { - if (!addToAactionSet(act, parentAct, actionSets)) { - // The index of the parent action in the actions' list is larger than the index of this action. - actionSet = createActionSet(act, parentAct, null); - actionSets.add(actionSet); - } - } - } - - /* - * Third, add the subActionSet to its parent ActionSet. - */ - List reActionSets = new ArrayList<>(); - for (HierarchicalActionSet actSet : actionSets) { - Action parentAct = actSet.getParentAction(); - if (parentAct != null) { - addToActionSets(actSet, parentAct, actionSets); - } else { - // TypeDeclaration, FieldDeclaration, MethodDeclaration, Statement. - // CatchClause, ConstructorInvocation, SuperConstructorInvocation, SwitchCase -// String astNodeType = actSet.getAstNodeType(); -// if (astNodeType.endsWith("TypeDeclaration") || astNodeType.endsWith("FieldDeclaration") || astNodeType.endsWith("EnumDeclaration") || -// astNodeType.endsWith("MethodDeclaration") || astNodeType.endsWith("Statement") || -// astNodeType.endsWith("ConstructorInvocation") || astNodeType.endsWith("CatchClause") || astNodeType.endsWith("SwitchCase")) { - reActionSets.add(actSet); -// } - } - } - return reActionSets; - } - - private HierarchicalActionSet createActionSet(Action act, Action parentAct, HierarchicalActionSet parent) { - HierarchicalActionSet actionSet = new HierarchicalActionSet(); - actionSet.setAction(act); - String actStr = parseAction(act.toString()); - actionSet.setActionString(actStr); - actionSet.setParentAction(parentAct); - actionSet.setNode(act.getNode()); - actionSet.setParent(parent); - - int bugStartLineNum = 0; - int bugEndLineNum = 0; - int fixStartLineNum = 0; - int fixEndLineNum = 0; - if (actStr.startsWith("INS")) { - Insert insert = (Insert) act; -// int pos = insert.getPos();//index position of the new node in the children array list of its corresponding old parent node. - ITree newTree = insert.getNode(); - fixStartLineNum = newTree.getPos(); - fixEndLineNum = newTree.getLength(); - } else { - ITree tree = act.getNode(); - bugStartLineNum = tree.getPos(); - bugEndLineNum = tree.getLength(); - if (actStr.startsWith("UPD")) { - Update update = (Update) act; - ITree newTree = update.getNewNode(); - fixStartLineNum = newTree.getPos(); - fixEndLineNum = newTree.getLength(); - } else if (actStr.startsWith("MOV")) { - Move update = (Move) act; - ITree newTree = update.getNewNode(); - fixStartLineNum = newTree.getPos(); - fixEndLineNum = newTree.getLength(); - } - } - actionSet.setBugStartLineNum(bugStartLineNum); - actionSet.setBugEndLineNum(bugEndLineNum); - actionSet.setFixStartLineNum(fixStartLineNum); - actionSet.setFixEndLineNum(fixEndLineNum); - return actionSet; - } - - private String parseAction(String actStr1) { - // UPD 25@@!a from !a to isTrue(a) at 69 - String[] actStrArrays = actStr1.split("@@"); - String actStr = ""; - int length = actStrArrays.length; - for (int i =0; i < length - 1; i ++) { - String actStrFrag = actStrArrays[i]; - int index = actStrFrag.lastIndexOf(" ") + 1; - String nodeType = actStrFrag.substring(index); - if (!"".equals(nodeType)) { - if (Character.isDigit(nodeType.charAt(0)) || (nodeType.startsWith("-") && Character.isDigit(nodeType.charAt(1)))) { - try { - int typeInt = Integer.parseInt(nodeType); - if (CNodeMap.map.containsKey(typeInt)) { - String type = CNodeMap.map.get(Integer.parseInt(nodeType)); - nodeType = type; - } - } catch (NumberFormatException e) { - nodeType = actStrFrag.substring(index); - } - } - } - actStrFrag = actStrFrag.substring(0, index) + nodeType + "@@"; - actStr += actStrFrag; - } - actStr += actStrArrays[length - 1]; - return actStr; - } - - private void addToActionSets(HierarchicalActionSet actionSet, Action parentAct, List actionSets) { - Action act = actionSet.getAction(); - for (HierarchicalActionSet actSet : actionSets) { - if (actSet.equals(actionSet)) continue; - Action action = actSet.getAction(); - - if (!areRelatedActions(action, act)) continue; - if (action.equals(parentAct)) { // actSet is the parent of actionSet. - actionSet.setParent(actSet); - actSet.getSubActions().add(actionSet); - sortSubActions(actSet); - break; - } else { - if (isPossibileSubAction(action, act)) { - // SubAction range： startPosition2 <= startPosition && length <= length2 - addToActionSets(actionSet, parentAct, actSet.getSubActions()); - } - } - } - } - - private boolean isPossibileSubAction(Action parent, Action child) { - if ((parent instanceof Update && !(child instanceof Addition)) - || (parent instanceof Delete && child instanceof Delete) - || (parent instanceof Insert && (child instanceof Insert))) { - int startPosition = child.getPosition(); - int length = child.getLength(); - int startPosition2 = parent.getPosition(); - int length2 = parent.getLength(); - - if (!(startPosition2 <= startPosition && length <= length2)) { - // when act is not the sub-set of action. - return false; - } - } - return true; - } - - private void sortSubActions(HierarchicalActionSet actionSet) { - ListSorter sorter = new ListSorter(actionSet.getSubActions()); - List subActions = sorter.sortAscending(); - if (subActions != null) { - actionSet.setSubActions(subActions); - } - } - - private boolean addToAactionSet(Action act, Action parentAct, List actionSets) { - for(HierarchicalActionSet actionSet : actionSets) { - Action action = actionSet.getAction(); - - if (!areRelatedActions(action, act)) continue; - - if (action.equals(parentAct)) { // actionSet is the parent of actSet. - HierarchicalActionSet actSet = createActionSet(act, actionSet.getAction(), actionSet); - actionSet.getSubActions().add(actSet); - sortSubActions(actionSet); - return true; - } else { - if (isPossibileSubAction(action, act)) { - // SubAction range: startPosition2 <= startPosition && startPosition + length <= startP + length2 - List subActionSets = actionSet.getSubActions(); - if (subActionSets.size() > 0) { - boolean added = addToAactionSet(act, parentAct, subActionSets); - if (added) { - return true; - } else { - continue; - } - } - } - } - } - return false; - } - - List newParentActions = new ArrayList<>(); - private Action findParentAction(Action action, List actions) { - - ITree parent = action.getNode().getParent(); - if (parent == null) return null; - if (action instanceof Addition) { - parent = ((Addition) action).getParent(); // parent in the fixed source code tree - } - - for (Action act : actions) { - if (act.getNode().equals(parent)) { - if (areRelatedActions(act, action)) { - return act; - } - } - } - for (Action act : newParentActions) { - if (act.getNode().equals(parent)) { - if (areRelatedActions(act, action)) { - return act; - } - } - } - - ITree tree = action.getNode(); - Action parentAction = null; - if (!isStatement(tree)) { - parentAction = new Update(parent, action.getNode().getParent()); - newParentActions.add(parentAction); - - Action higherParentAct = findParentAction(parentAction, actions); - HierarchicalActionSet actionSet = null; - if (higherParentAct == null) { - actionSet = createActionSet(parentAction, higherParentAct, null); - actionSets.add(actionSet); - } else { - if (!addToAactionSet(parentAction, higherParentAct, actionSets)) { - // The index of the parent action in the actions' list is larger than the index of this action. - actionSet = createActionSet(parentAction, higherParentAct, null); - actionSets.add(actionSet); - } - } - } - return parentAction; - } - - private boolean isStatement(ITree tree) { - int nodeType = tree.getType(); - if (nodeType == 280002 || nodeType == 280001 || nodeType == 310200 || nodeType == 280100 - || nodeType == 300100 || nodeType == 280003 || nodeType == 310100 || nodeType == 310300 - || 260300 == nodeType || nodeType == 460000) {// TODO - return true; - } - return false; - } - - private boolean areRelatedActions(Action parent, Action child) { - if (parent instanceof Move && !(child instanceof Move)) {// If action is MOV, its children must be MOV. - return false; - } - if (parent instanceof Delete && !(child instanceof Delete)) {// If action is DEL, its children must be DEL. - return false; - } - if (parent instanceof Insert && !(child instanceof Addition)) {// If action is INS, its children must be MOV or INS. - return false; - } - return true; - } -} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java deleted file mode 100644 index f986f33..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkActionFilter.java +++ /dev/null @@ -1,625 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import org.eclipse.jdt.core.dom.CompilationUnit; - -import com.github.gumtreediff.actions.model.Move; -import com.github.gumtreediff.actions.model.Update; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.FixPatternParser.CUCreator; -import edu.lu.uni.serval.FixPatternParser.violations.Violation; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; - -public class HunkActionFilter { - - /** - * Filter out the modify actions, which are not in the DiffEntry hunks, without considering the same parent node. - * - * @param hunks - * @param actionSets - * @return - */ - public List filterActionsByDiffEntryHunk(List hunks, - List actionSets, File revFile, File prevFile) { - List uselessActions = new ArrayList<>(); - - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return uselessActions; - } - - for (HierarchicalActionSet actionSet : actionSets) { - // position of buggy statements - int startPosition = 0; - int endPosition = 0; - int startLine = 0; - int endLine = 0; - // position of fixed statements - int startPosition2 = 0; - int endPosition2 = 0; - int startLine2 = 0; - int endLine2 = 0; - - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { - startPosition2 = actionSet.getStartPosition(); - endPosition2 = startPosition2 + actionSet.getLength(); - - List firstAndLastMov = getFirstAndLastMoveAction(actionSet); - if (firstAndLastMov != null) { - startPosition = firstAndLastMov.get(0).getNode().getPos(); - ITree lastTree = firstAndLastMov.get(1).getNode(); - endPosition = lastTree.getPos() + lastTree.getLength(); - } - } else { - startPosition = actionSet.getStartPosition(); // range of actions - endPosition = startPosition + actionSet.getLength(); - if (actionStr.startsWith("UPD")) { - Update update = (Update) actionSet.getAction(); - ITree newNode = update.getNewNode(); - startPosition2 = newNode.getPos(); - endPosition2 = startPosition2 + newNode.getLength(); - } - } - startLine = startPosition == 0 ? 0 : prevUnit.getLineNumber(startPosition); - endLine = endPosition == 0 ? 0 : prevUnit.getLineNumber(endPosition); - startLine2 = startPosition2 == 0 ? 0 : revUnit.getLineNumber(startPosition2); - endLine2 = endPosition2 == 0 ? 0 : revUnit.getLineNumber(endPosition2); - - for (DiffEntryHunk hunk : hunks) { - int bugStartLine = hunk.getBugLineStartNum(); - int bugRange = hunk.getBugRange(); - int fixStartLine = hunk.getFixLineStartNum(); - int fixRange = hunk.getFixRange(); - - if (actionStr.startsWith("INS")) { - if (fixStartLine + fixRange < startLine2) { - continue; - } - if (endLine2 < fixStartLine ) { - uselessActions.add(actionSet); - } - } else { - if (bugStartLine + bugRange < startLine) { - continue; - } - if (endLine < bugStartLine ) { - uselessActions.add(actionSet); - } - break; - } - } - actionSet.setBugStartLineNum(startLine); - actionSet.setBugEndLineNum(endLine); - actionSet.setFixStartLineNum(startLine2); - actionSet.setFixEndLineNum(endLine2); - } - - actionSets.removeAll(uselessActions); - uselessActions.clear(); - return actionSets; - } - - /** - * Filter out the modify actions, which are not in the DiffEntry hunks, with considering the same parent node. - * - * @param hunks - * @param actionSets - * @return - */ - public List filterActionsByDiffEntryHunk2(List hunks, - List actionSets, File revFile, File prevFile) { - List allHunkFixPatterns = new ArrayList<>(); - - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return allHunkFixPatterns; - } - - int i = 0; - int size = actionSets.size(); - for (DiffEntryHunk hunk : hunks) { - int hunkBugStartLine = hunk.getBugLineStartNum(); - int hunkBugRange = hunk.getBugRange(); - int hunkFixStartLine = hunk.getFixLineStartNum(); - int hunkFixRange = hunk.getFixRange(); - - for (; i < size; i ++) { - HierarchicalActionSet actionSet = actionSets.get(i); - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - int actionBugEndLine = actionSet.getBugEndLineNum(); - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - - String actionStr = actionSet.getActionString(); - ITree previousParent = null; - List hunkActionSets = new ArrayList<>(); - - if (actionStr.startsWith("INS")) { - if (hunkFixStartLine + hunkFixRange < actionFixStartLine) { - addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk);// save the previous non-null hunkFixPattern. - break; - } - if (actionFixEndLine >= hunkFixStartLine ) { - ITree parent = addToHunkActionSets(actionSet, hunkActionSets, allHunkFixPatterns, previousParent, hunk); - if (parent != null) { - if (parent != previousParent) { - hunkActionSets = new ArrayList<>(); - } - hunkActionSets.add(actionSet); - } else if (hunkActionSets.size() > 0) { - hunkActionSets = new ArrayList<>(); - } - previousParent = parent; - } - } else { // UPD, DEL, MOV - if (hunkBugStartLine + hunkBugRange < actionBugStartLine) { - addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk);// save the previous non-null hunkFixPattern. - break; - } - if (actionBugEndLine >= hunkBugStartLine ) { - ITree parent = addToHunkActionSets(actionSet, hunkActionSets, allHunkFixPatterns, previousParent, hunk); - if (parent != null) { // same parent - if (parent != previousParent) { - hunkActionSets = new ArrayList<>(); - } - hunkActionSets.add(actionSet); - } else if (hunkActionSets.size() > 0) { - hunkActionSets = new ArrayList<>(); - } - previousParent = parent; - } - } - addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk); - } - } - - return allHunkFixPatterns; - } - - private int getEndPosition(List children) { - int endPosition = 0; - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - int type = child.getType(); - if (Checker.isStatement2(type)) { - if ( i > 0) { - child = children.get(i - 1); - endPosition = child.getPos() + child.getLength(); - } else { - endPosition = child.getPos() - 1; - } - break; - } - } - return endPosition; - } - - private void addHunkActionSets(List hunkActionSets, List allHunkFixPatterns, DiffEntryHunk hunk) { - if (hunkActionSets.size() > 0) { - HunkFixPattern hunkFixPattern = new HunkFixPattern(hunk, hunkActionSets); - allHunkFixPatterns.add(hunkFixPattern); - } - } - - private ITree addToHunkActionSets(HierarchicalActionSet actionSet, List hunkActionSets, - List allHunkFixPatterns, ITree previousParent, DiffEntryHunk hunk) { - String astNodeType = actionSet.getAstNodeType(); - if ("FieldDeclaration".equals(astNodeType)) { - addHunkActionSets(hunkActionSets, allHunkFixPatterns, hunk); - hunkActionSets = new ArrayList<>(); - hunkActionSets.add(actionSet); - HunkFixPattern hunkFixPattern = new HunkFixPattern(hunk, hunkActionSets); - allHunkFixPatterns.add(hunkFixPattern); - return null; - } else { - ITree currentParent = actionSet.getNode().getParent(); - if (previousParent == null) { - previousParent = currentParent; - } else { - if (!previousParent.equals(currentParent)) { - HunkFixPattern hunkFixPattern = new HunkFixPattern(hunk, hunkActionSets); - allHunkFixPatterns.add(hunkFixPattern); - previousParent = currentParent; - } - } - return previousParent; - } - } - - private List getFirstAndLastMoveAction(HierarchicalActionSet gumTreeResult) { - List firstAndLastMoveActions = new ArrayList<>(); - List actions = new ArrayList<>(); - actions.addAll(gumTreeResult.getSubActions()); - if (actions.size() == 0) { - return null; - } - Move firstMoveAction = null; - Move lastMoveAction = null; - while (actions.size() > 0) { - List subActions = new ArrayList<>(); - for (HierarchicalActionSet action : actions) { - subActions.addAll(action.getSubActions()); - if (action.toString().startsWith("MOV")) { - if (firstMoveAction == null) { - firstMoveAction = (Move) action.getAction(); - lastMoveAction = (Move) action.getAction(); - } else { - int startPosition = action.getStartPosition(); - int length = action.getLength(); - int startPositionFirst = firstMoveAction.getPosition(); - int startPositionLast = lastMoveAction.getPosition(); - int lengthLast = lastMoveAction.getNode().getLength(); - if (startPosition < startPositionFirst || (startPosition == startPositionFirst && length > firstMoveAction.getLength())) { - firstMoveAction = (Move) action.getAction(); - } - if ((startPosition + length) > (startPositionLast + lengthLast)) { - lastMoveAction = (Move) action.getAction(); - } - } - } - } - - actions.clear(); - actions.addAll(subActions); - } - if (firstMoveAction == null) { - return null; - } - firstAndLastMoveActions.add(firstMoveAction); - firstAndLastMoveActions.add(lastMoveAction); - return firstAndLastMoveActions; - } - - /** - * Filter out the modify actions, which are not in the DiffEntry hunks, without considering the same parent node. - * - * @param violations - * @param actionSets - * @param revFile - * @param prevFile - * @return - */ - public List filterActionsByModifiedRange(List violations, - List actionSets, File revFile, File prevFile) { - - List selectedViolations = new ArrayList<>(); - - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return selectedViolations; - } - - for (Violation violation : violations) { - int startLine = violation.getStartLineNum(); - int endLine = violation.getEndLineNum(); - int bugStartLine = violation.getBugStartLineNum(); - int bugEndLine = violation.getBugEndLineNum(); - int fixStartLine = violation.getFixStartLineNum(); - int fixEndLine = violation.getFixEndLineNum(); - - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - int actionBugEndLine = actionSet.getBugEndLineNum(); - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { - if (fixStartLine <= actionFixStartLine && actionFixEndLine <= fixEndLine) { - if (actionBugStartLine != 0) { - if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) { - violation.getActionSets().add(actionSet); - } - } else { - - violation.getActionSets().add(actionSet); - } - } - } else { -// if (bugEndLine < actionBugStartLine) { -// break; -// } - if (bugStartLine <= actionBugStartLine && actionBugEndLine <= bugEndLine) { - if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) { - violation.getActionSets().add(actionSet); - } - } - } - } - - if (violation.getActionSets().size() > 0) { - selectedViolations.add(violation); - } - } - return selectedViolations; - } - - /** - * Match hierarchical actions with code change diffs for C code. - * - * @param diffentryHunks - * @param actionSets - * @param revFile - * @param prevFile - * @return - */ - public List matchActionsByDiffEntryForC(List diffentryHunks, List actionSets) { - - List selectedViolations = new ArrayList<>(); - - for (DiffEntryHunk diffentryHunk : diffentryHunks) { - int bugHunkStartLine = diffentryHunk.getBugLineStartNum(); - int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1; - int fixHunkStartLine = diffentryHunk.getFixLineStartNum(); - int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1; - - for (HierarchicalActionSet actionSet : actionSets) { - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - if (fixHunkStartLine <= actionFixEndLine && actionFixStartLine <= fixHunkEndLine ) { - diffentryHunk.getActionSets().add(actionSet); - } - } else { - int actionBugStartLine = actionSet.getBugStartLineNum(); - int actionBugEndLine = actionSet.getBugEndLineNum(); - - if (bugHunkStartLine <= actionBugEndLine && actionBugStartLine <= bugHunkEndLine) { - diffentryHunk.getActionSets().add(actionSet); - } - } - } - - if (diffentryHunk.getActionSets().size() > 0) { - selectedViolations.add(diffentryHunk); - } - } - return selectedViolations; - } - - - /** - * Filter out the modify actions, which are not in the DiffEntry hunks, with considering the same parent node. - * - * @param violations - * @param actionSets - * @param revFile - * @param prevFile - * @return - */ - public List filterActionsByModifiedRange2(List diffentryHunks, - List actionSets, File revFile, File prevFile) { - - List selectedViolations = new ArrayList<>(); - - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return selectedViolations; - } - - for (DiffEntryHunk diffentryHunk : diffentryHunks) { -// int violationEndLine = violationStartLine + diffentryHunk.getBugRange(); - int bugHunkStartLine = diffentryHunk.getBugLineStartNum(); - int bugHunkEndLine = bugHunkStartLine + diffentryHunk.getBugRange() - 1; - int fixHunkStartLine = diffentryHunk.getFixLineStartNum(); - int fixHunkEndLine = fixHunkStartLine + diffentryHunk.getFixedHunkSize() - 1; - - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getBugStartLineNum(); - if (actionBugStartLine == 0) { - actionBugStartLine = setLineNumbers(actionSet, prevUnit, revUnit); - } - int actionBugEndLine = actionSet.getBugEndLineNum(); - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { - if (fixHunkStartLine <= actionFixEndLine && fixHunkEndLine >= actionFixStartLine ) { - if (actionBugStartLine != 0) { - diffentryHunk.getActionSets().add(actionSet); - } - } - } else { - if (bugHunkStartLine <= actionBugEndLine && bugHunkEndLine >= actionBugStartLine) { - diffentryHunk.getActionSets().add(actionSet); - } - } - } - - - if (diffentryHunk.getActionSets().size() > 0) { - selectedViolations.add(diffentryHunk); - } - } - return selectedViolations; - } - - - /** - * Filter out the modify actions, which are not in the DiffEntry hunks, without considering DiffEntry hunks. - * - * @param violations - * @param actionSets - * @param revFile - * @param prevFile - * @return - */ - public List filterActionsByModifiedRange3(List violations, - List actionSets, File revFile, File prevFile) { - - List selectedViolations = new ArrayList<>(); - - CUCreator cuCreator = new CUCreator(); - CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile); - CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile); - if (prevUnit == null || revUnit == null) { - return selectedViolations; - } - - for (Violation violation : violations) { - int startLine = violation.getStartLineNum(); - int endLine = violation.getEndLineNum(); - -// ITree parent = null; -// List actionSetsWithSameParent = new ArrayList<>(); //TODO - for (HierarchicalActionSet actionSet : actionSets) { - int actionBugStartLine = actionSet.getStartPosition(); - int actionBugEndLine = actionSet.getLength(); - int actionFixStartLine = actionSet.getFixStartLineNum(); - int actionFixEndLine = actionSet.getFixEndLineNum(); - - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { // FIXME It is impossible to locate the INS action by the buggy line range. - if (startLine <= actionFixStartLine && actionFixEndLine <= endLine) { - if (actionBugStartLine != 0) { - if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) { - violation.getActionSets().add(actionSet); - } - } else { - violation.getActionSets().add(actionSet); - } - } - } else { -// if (endLine < actionBugStartLine) { -// break; -// } - if (startLine <= actionBugStartLine && actionBugEndLine <= endLine) { - if (startLine <= actionBugEndLine && endLine >= actionBugStartLine) { - violation.getActionSets().add(actionSet); - } - } - } - } - - if (violation.getActionSets().size() > 0) { - selectedViolations.add(violation); - } - } - return selectedViolations; - } - - private int setLineNumbers(HierarchicalActionSet actionSet, CompilationUnit prevUnit, CompilationUnit revUnit) { - int actionBugStartLine; - int actionBugEndLine; - int actionFixStartLine; - int actionFixEndLine; - - // position of buggy statements - int bugStartPosition = 0; - int bugEndPosition = 0; - // position of fixed statements - int fixStartPosition = 0; - int fixEndPosition = 0; - - String actionStr = actionSet.getActionString(); - if (actionStr.startsWith("INS")) { - fixStartPosition = actionSet.getStartPosition(); - fixEndPosition = fixStartPosition + actionSet.getLength(); - - List firstAndLastMov = getFirstAndLastMoveAction(actionSet); - if (firstAndLastMov != null) { - bugStartPosition = firstAndLastMov.get(0).getNode().getPos(); - ITree lastTree = firstAndLastMov.get(1).getNode(); - bugEndPosition = lastTree.getPos() + lastTree.getLength(); - } - } else { - bugStartPosition = actionSet.getStartPosition(); // range of actions - bugEndPosition = bugStartPosition + actionSet.getLength(); - if (actionStr.startsWith("UPD")) { - Update update = (Update) actionSet.getAction(); - ITree newNode = update.getNewNode(); - fixStartPosition = newNode.getPos(); - fixEndPosition = fixStartPosition + newNode.getLength(); - - String astNodeType = actionSet.getAstNodeType(); -// if (Checker.withBlockStatement(newNode.getType())) { -//// List children = update.getNode().getChildren(); -//// bugEndPosition = getEndPosition(children); -//// List newChildren = newNode.getChildren(); -//// fixEndPosition = getEndPosition(newChildren); -// } else - if ("TypeDeclaration".equals(astNodeType)) { - bugEndPosition = getClassBodyStartPosition(update.getNode()); - fixEndPosition = getClassBodyStartPosition(newNode); - } else if ("MethodDeclaration".equals(astNodeType)) { - List children = update.getNode().getChildren(); - bugEndPosition = getEndPosition(children); - List newChildren = newNode.getChildren(); - fixEndPosition = getEndPosition(newChildren); - } - if (fixEndPosition == 0) { - fixEndPosition = fixStartPosition + newNode.getLength(); - } - } else if (actionStr.startsWith("DEL")) { - ITree buggyTree = actionSet.getNode(); - int type = buggyTree.getType(); - if (type == 55) { // TypeDeclaration - bugEndPosition = getClassBodyStartPosition(buggyTree); - } else if (type == 31 || Checker.withBlockStatement(type)) {//MethodDeclaration && Block-Statements - List children = buggyTree.getChildren(); - bugEndPosition = getEndPosition(children); - } - } - if (bugEndPosition == 0) { - bugEndPosition = bugStartPosition + actionSet.getLength(); - } - } - actionBugStartLine = bugStartPosition == 0 ? 0 : prevUnit.getLineNumber(bugStartPosition); - actionBugEndLine = bugEndPosition == 0 ? 0 : prevUnit.getLineNumber(bugEndPosition); - actionFixStartLine = fixStartPosition == 0 ? 0 : revUnit.getLineNumber(fixStartPosition); - actionFixEndLine = fixEndPosition == 0 ? 0 : revUnit.getLineNumber(fixEndPosition); - actionSet.setBugStartLineNum(actionBugStartLine); - actionSet.setBugEndLineNum(actionBugEndLine); - actionSet.setFixStartLineNum(actionFixStartLine); - actionSet.setFixEndLineNum(actionFixEndLine); - actionSet.setBugEndPosition(bugEndPosition); - actionSet.setFixEndPosition(fixEndPosition); - - return actionBugStartLine; - } - - private int getClassBodyStartPosition(ITree tree) { - List children = tree.getChildren(); - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - int type = child.getType(); - // Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation - if (type != 83 && type != 77 && type != 78 && type != 79 - && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 - && type != 76 && type != 84 && type != 87 && type != 88 && type != 42) { - // ArrayType, PrimitiveType, SimpleType, ParameterizedType, - // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType, SimpleName - if (i > 0) { - child = children.get(i - 1); - return child.getPos() + child.getLength() + 1; - } else { - return child.getPos() - 1; - } - } - } - return 0; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkFixPattern.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkFixPattern.java deleted file mode 100644 index 3bd89fe..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/HunkFixPattern.java +++ /dev/null @@ -1,27 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.util.List; - -import edu.lu.uni.serval.diffentry.DiffEntryHunk; - -public class HunkFixPattern { - - private DiffEntryHunk hunk; - - private List hunkActionSets; - - public HunkFixPattern(DiffEntryHunk hunk, List hunkActionSets) { - super(); - this.hunk = hunk; - this.hunkActionSets = hunkActionSets; - } - - public DiffEntryHunk getHunk() { - return hunk; - } - - public List getHunkActionSets() { - return hunkActionSets; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimpleTree.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimpleTree.java deleted file mode 100644 index 0900b7a..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimpleTree.java +++ /dev/null @@ -1,68 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.util.ArrayList; -import java.util.List; - -public class SimpleTree { - - private String nodeType; - private String label; - private SimpleTree parent; - private List children = new ArrayList<>(); - - public String getNodeType() { - return nodeType; - } - - public void setNodeType(String nodeType) { - this.nodeType = nodeType; - } - - public String getLabel() { - return label; - } - - public void setLabel(String label) { - this.label = label; - } - - public SimpleTree getParent() { - return parent; - } - - public void setParent(SimpleTree parent) { - this.parent = parent; - } - - public List getChildren() { - return children; - } - - public void setChildren(List children) { - this.children = children; - } - - private List strList = new ArrayList<>(); - - @Override - public String toString() { - String str = this.nodeType + "@@" + this.label; - if (strList.size() == 0) { - strList.add(str); - for (SimpleTree child : children) { - child.toString(); - List strList1 = child.strList; - for (String str1 : strList1) { - strList.add("------" + str1); - } - } - } - - str = ""; - for (String str1 : strList) { - str += str1 + "\n"; - } - - return str; - } -} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java deleted file mode 100644 index 317bf18..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/SimplifyTree.java +++ /dev/null @@ -1,902 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import com.github.gumtreediff.actions.model.Action; -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; -import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.utils.ListSorter; - -/** - * Simplify the ITree of source code into a simple tree. - * - * @author kui.liu - * - */ -public class SimplifyTree { - - private static final String ABSTRACT_TYPE = "T"; - private static final String ABSTRACT_NAME = "N"; - private static final String ABSTRACT_METHOD = "m"; - private static final String ABSTRACT_VARIABLE = "v"; - - private Map abstractTypeIdentifiers = new HashMap<>(); - private Map abstractMethodIdentifiers = new HashMap<>(); - private Map abstractNameIdentifiers = new HashMap<>(); - private Map abstractVariableIdentifiers = new HashMap<>(); - - /** - * Convert ITree to a source code simple tree, an abstract identifier simple tree, and a semi-source code simple tree. - * - * @param actionSet - */ - public void abstractTree(HierarchicalActionSet actionSet) { - SimpleTree sourceCodeSimpleTree = null; // source code tree and AST node type tree - SimpleTree abstractIdentifierTree = null; // abstract identifier tree - SimpleTree abstractSimpleTree = null; // semi-source code tree. and AST node type tree - SimpleTree simpleTree = null; // source code tree with canonical variable names. - - if (actionSet.getActionString().startsWith("INS")) { - List allMoveActions = getAllMoveActions(actionSet); - if (allMoveActions != null) { - List actions = new ArrayList<>(); - for (Action action : allMoveActions) { - boolean hasParent = false; - ITree parent = action.getNode().getParent(); - for (Action act : allMoveActions) { - if (act == action) continue; - ITree actNode = act.getNode(); - if (actNode.equals(parent)) { - hasParent = true; - break; - } - } - if (!hasParent) { - actions.add(action); - } - } -// sourceCodeSimpleTree = sourceCodeTree(actions); - simpleTree = canonicalizeSourceCodeTree(actions, null); - } - } else { - ITree tree = actionSet.getNode(); - String astNodeType = actionSet.getAstNodeType(); - if (Checker.containsBodyBlock(astNodeType)) { - // delete the body block. - List children = tree.getChildren(); - List newChildren = new ArrayList<>(); - for (ITree child : children) { - if (!child.getLabel().endsWith("Body")) { - newChildren.add(child); - } - } - tree.setChildren(newChildren); - } -// sourceCodeSimpleTree = originalSourceCodeTree(tree, null); -// abstractIdentifierTree = abstractIdentifierTree(actionSet, tree, null); -// abstractSimpleTree = semiSourceCodeTree(actionSet, tree, null); - simpleTree = canonicalizeSourceCodeTree(tree, null); - } - - actionSet.setAbstractSimpleTree(abstractSimpleTree); - actionSet.setAbstractIdentifierTree(abstractIdentifierTree); - actionSet.setSimpleTree(simpleTree); - actionSet.setOriginalTree(sourceCodeSimpleTree); - } - - /** - * Convert ITree to a source code simple tree, an abstract identifier simple tree, and a semi-source code simple tree. - * - * @param actionSet - */ - public void abstractTree(HierarchicalActionSet actionSet, int bugEndPosition) { - SimpleTree sourceCodeSimpleTree = null; // source code tree and AST node type tree - SimpleTree abstractIdentifierTree = null; // abstract identifier tree - SimpleTree abstractSimpleTree = null; // semi-source code tree. and AST node type tree - SimpleTree simpleTree = null; // source code tree with canonical variable names. - - if (actionSet.getActionString().startsWith("INS")) { - List allMoveActions = getAllMoveActions(actionSet); - if (allMoveActions != null) { - List actions = new ArrayList<>(); - for (Action action : allMoveActions) { - boolean hasParent = false; - ITree parent = action.getNode().getParent(); - for (Action act : allMoveActions) { - if (act == action) continue; - ITree actNode = act.getNode(); - if (actNode.equals(parent)) { - hasParent = true; - break; - } - } - if (!hasParent) { - actions.add(action); - } - } -// sourceCodeSimpleTree = sourceCodeTree(actions); - simpleTree = canonicalizeSourceCodeTree(actions, null); - } - } else { - ITree tree = actionSet.getNode(); -// String astNodeType = actionSet.getAstNodeType(); -// if (Checker.containsBodyBlock(astNodeType)) { -// // delete the body block. -// List children = tree.getChildren(); -// List newChildren = new ArrayList<>(); -// for (ITree child : children) { -// if (!child.getLabel().endsWith("Body")) { -// newChildren.add(child); -// } -// } -// tree.setChildren(newChildren); -// } -// sourceCodeSimpleTree = originalSourceCodeTree(tree, null); -// abstractIdentifierTree = abstractIdentifierTree(actionSet, tree, null); -// abstractSimpleTree = semiSourceCodeTree(actionSet, tree, null); -// if (actionSet.getActionString().startsWith("UPD")) { -// simpleTree = canonicalizeSourceCodeTree(tree, null, bugEndPosition); -// } else { -// simpleTree = canonicalizeSourceCodeTree(tree, null); -// } - simpleTree = canonicalizeSourceCodeTree(tree, null, bugEndPosition); - } - - actionSet.setAbstractSimpleTree(abstractSimpleTree); - actionSet.setAbstractIdentifierTree(abstractIdentifierTree); - actionSet.setSimpleTree(simpleTree); - actionSet.setOriginalTree(sourceCodeSimpleTree); - } - - private SimpleTree canonicalizeSourceCodeTree(List actions, SimpleTree parent) { - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - simpleTree.setParent(parent); - List children = new ArrayList<>(); - for (Action action : actions) { - ITree node = action.getNode(); - children.add(canonicalizeSourceCodeTree(node, simpleTree)); - } - simpleTree.setChildren(children); - return simpleTree; - } - - public SimpleTree canonicalizeSourceCodeTree(ITree tree, SimpleTree parent) { - SimpleTree simpleTree = new SimpleTree(); - - String label = tree.getLabel(); - String astNode = ASTNodeMap.map.get(tree.getType()); - - List children = tree.getChildren(); - if (children.size() > 0) { - simpleTree.setNodeType(astNode); - if (astNode.endsWith("Type")) { - simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", "")); - } else { - if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) { - if (label.startsWith("MethodName:")) { - simpleTree.setNodeType("MethodName"); - label = label.substring(11); - int argusIndex = label.indexOf(":["); - if (argusIndex > 0) { - label = label.substring(0, argusIndex); - } - } else if (label.startsWith("ClassName:")) { - simpleTree.setNodeType("ClassName"); - label = label.substring(10); - } - simpleTree.setLabel(label); - } else { - simpleTree.setLabel(astNode); - } - List subTrees = new ArrayList<>(); - for (ITree child : children) { - subTrees.add(canonicalizeSourceCodeTree(child, simpleTree)); - } - simpleTree.setChildren(subTrees); - } - } else { - if (astNode.endsWith("Name")) { - // variableName, methodName, QualifiedName - if (label.startsWith("MethodName:")) { // - simpleTree.setNodeType("MethodName"); - label = label.substring(11); - int argusIndex = label.indexOf(":["); - if (argusIndex > 0) { - label = label.substring(0, argusIndex); - } - simpleTree.setLabel(label); - } else if (label.startsWith("ClassName:")) { - simpleTree.setNodeType("ClassName"); - label = label.substring(10); - simpleTree.setLabel(label); - } else if (label.startsWith("Name:")) { - label = label.substring(5); - char firstChar = label.charAt(0); - if (Character.isUpperCase(firstChar)) { - simpleTree.setNodeType("Name"); - simpleTree.setLabel(label); - } else {// variableName: - simpleTree.setNodeType("VariableName"); - simpleTree.setLabel(canonicalVariableName(label, tree)); - } - } else {// variableName: - simpleTree.setNodeType("VariableName"); - simpleTree.setLabel(canonicalVariableName(label, tree)); - } - } else { - simpleTree.setNodeType(astNode); - if (astNode.endsWith("Type")) { - simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", "")); - } else if (astNode.startsWith("Type")) { - simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", "")); - } else if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation")) && label.startsWith("MethodName:")) { - simpleTree.setNodeType("MethodName"); - label = label.substring(11); - int argusIndex = label.indexOf(":["); - if (argusIndex > 0) { - label = label.substring(0, argusIndex); - } - simpleTree.setLabel(label); - } else { - simpleTree.setLabel(label.replaceAll(" ", "")); - } - } - } - - simpleTree.setParent(parent); - return simpleTree; - } - - public void canonicalizeSourceCodeTree(ITree tree) { - String label = tree.getLabel(); - String astNode = ASTNodeMap.map.get(tree.getType()); - - List children = tree.getChildren(); - if (children.size() > 0) { - if (astNode.endsWith("Type")) { - } else { - if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) { - if (label.startsWith("MethodName:")) { - } else if (label.startsWith("ClassName:")) { - } - } else { - } - for (ITree child : children) { - canonicalizeSourceCodeTree(child); - } - } - } else { - if (astNode.endsWith("Name")) { - // variableName, methodName, QualifiedName - if (label.startsWith("MethodName:")) { // - } else if (label.startsWith("ClassName:")) { - } else if (label.startsWith("Name:")) { - label = label.substring(5); - char firstChar = label.charAt(0); - if (Character.isUpperCase(firstChar)) { -// simpleTree.setNodeType("Name"); - } else {// variableName: - canonicalVariableName(label, tree); - } - } else {// variableName: - canonicalVariableName(label, tree); - } - } - } - } - - public SimpleTree canonicalizeSourceCodeTree(ITree tree, SimpleTree parent, int bugEndPosition) { - SimpleTree simpleTree = new SimpleTree(); - - String label = tree.getLabel(); - String astNode = ASTNodeMap.map.get(tree.getType()); - - List children = tree.getChildren(); - if (children.size() > 0) { - simpleTree.setNodeType(astNode); - if (astNode.endsWith("Type")) { - simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", "")); - } else { - if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation"))) { - if (label.startsWith("MethodName:")) { - simpleTree.setNodeType("MethodName"); - label = label.substring(11); - int argusIndex = label.indexOf(":["); - if (argusIndex > 0) { - label = label.substring(0, argusIndex); - } - } else if (label.startsWith("ClassName:")) { - simpleTree.setNodeType("ClassName"); - label = label.substring(10); - } - simpleTree.setLabel(label); - } else { - simpleTree.setLabel(astNode); - } - List subTrees = new ArrayList<>(); - for (ITree child : children) { - if (child.getPos() > bugEndPosition) continue; - subTrees.add(canonicalizeSourceCodeTree(child, simpleTree)); - } - simpleTree.setChildren(subTrees); - } - } else { - if (astNode.endsWith("Name")) { - // variableName, methodName, QualifiedName - if (label.startsWith("MethodName:")) { // - simpleTree.setNodeType("MethodName"); - label = label.substring(11); - int argusIndex = label.indexOf(":["); - if (argusIndex > 0) { - label = label.substring(0, argusIndex); - } - simpleTree.setLabel(label); - } else if (label.startsWith("ClassName:")) { - simpleTree.setNodeType("ClassName"); - label = label.substring(10); - simpleTree.setLabel(label); - } else if (label.startsWith("Name:")) { - label = label.substring(5); - char firstChar = label.charAt(0); - if (Character.isUpperCase(firstChar)) { - simpleTree.setNodeType("Name"); - simpleTree.setLabel(label); - } else {// variableName: - simpleTree.setNodeType("VariableName"); - simpleTree.setLabel(canonicalVariableName(label, tree)); - } - } else {// variableName: - simpleTree.setNodeType("VariableName"); - simpleTree.setLabel(canonicalVariableName(label, tree)); - } - } else { - simpleTree.setNodeType(astNode); - if (astNode.endsWith("Type")) { - simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", "")); - } else if (astNode.startsWith("Type")) { - simpleTree.setLabel(canonicalizeTypeStr(label).replaceAll(" ", "")); - } else if ((astNode.equals("SimpleName") || astNode.equals("MethodInvocation")) && label.startsWith("MethodName:")) { - simpleTree.setNodeType("MethodName"); - label = label.substring(11); - int argusIndex = label.indexOf(":["); - if (argusIndex > 0) { - label = label.substring(0, argusIndex); - } - simpleTree.setLabel(label); - } else { - simpleTree.setLabel(label.replaceAll(" ", "")); - } - } - } - - simpleTree.setParent(parent); - return simpleTree; - } - - public String canonicalVariableName(String label, ITree tree) { - ITree parent = tree.getParent(); - if (parent == null) { - return label; - } else { - String matchStr = null; - int parentType = parent.getType(); - if (parentType == 44) { // SingleVariableDeclaration - matchStr = matchSingleVariableDeclaration(parent, label); - } else if (parentType == 23 || parentType == 58 || parentType == 60) { - //FieldDeclaration, VariableDeclarationExpression, VariableDeclarationStatement - matchStr = matchVariableDeclarationExpression(parent, label); - } else if (parentType == 31) { // MethodDeclaration - List children = parent.getChildren(); - int index = children.indexOf(tree); - for (int i = index - 1; i >=0; i --) { - ITree child = children.get(i); - int childType = child.getType(); - if (childType == 60) { // VariableDeclarationStatement - matchStr = matchVariableDeclarationExpression(child, label); - } else if (childType == 44) { // SingleVariableDeclaration - matchStr = matchSingleVariableDeclaration(child, label); - } - if (matchStr != null) break; - } - } else if (parentType ==70 || parentType == 24 ||parentType == 12 || parentType == 54) { - // EnhancedForStatement, ForStatement, CatchClause, TryStatement - matchStr = matchStatements(parentType, parent, label); - } else if (parentType == 55) { // TypeDeclaration: Class Declaration - List children = parent.getChildren(); - int index = children.indexOf(tree); - for (int i = index - 1; i >=0; i --) { - ITree child = children.get(i); - if (child.getType() == 23) { // FieldDeclaration - matchStr = matchVariableDeclarationExpression(child, label); - if (matchStr != null) break; - } - } - } else if (parentType == 8) { // Block body - List children = parent.getChildren(); - int index = children.indexOf(tree); - for (int i = index - 1; i >=0; i --) { - ITree child = children.get(i); - if (child.getType() == 60) { // VariableDeclarationStatement - matchStr = matchVariableDeclarationExpression(child, label); - if (matchStr != null) break; - } - } - } - - if (matchStr != null) { - return matchStr; - } else { - return canonicalVariableName(label, parent); - } - } - } - - private String matchStatements(int typeInt, ITree tree, String label) { - String matchStr = null; - if (typeInt == 70) { // EnhancedForStatement - matchStr = matchSingleVariableDeclaration(tree.getChild(0), label); - } else if (typeInt == 24) { // ForStatement - List children = tree.getChildren(); - for (ITree child : children) { - if (child.getType() == 58) { - matchStr = matchVariableDeclarationExpression(child, label); - if (matchStr != null) break; - } else { - break; - } - } - } else if (typeInt == 12) { // CatchClause - matchStr = matchSingleVariableDeclaration(tree.getChild(0), label); - } else if (typeInt == 54) { // TryStatement - List children = tree.getChildren(); - for (ITree child : children) { - if (child.getType() == 58) { //VariableDeclarationExpression - matchStr = matchVariableDeclarationExpression(tree, label); - if (matchStr != null) break; - } else { - break; - } - } - } - return null; - } - - public Map canonicalVariableMap = new HashMap<>(); - public Map canonicalVariables = new HashMap<>(); - - private String matchVariableDeclarationExpression(ITree variable, String label) { - List children = variable.getChildren(); - ITree type = null; - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - if (child.getType() == 59) {// VariableDeclarationFragment - if (type == null) { - type = children.get(i - 1); - } - ITree simpleName = child.getChild(0); - if (simpleName.getLabel().equals(label)) { - String typeStr = canonicalizeTypeStr(type.getLabel()); - return canonicalizeVariable(label, typeStr); - } - } - } - return null; - } - - private String matchSingleVariableDeclaration(ITree singleVariable, String label) { - List children = singleVariable.getChildren(); - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - if (child.getType() == 42) { // SimpleName - if (child.getLabel().equals(label)) { - ITree type = children.get(i - 1); - String typeStr = canonicalizeTypeStr(type.getLabel()); - return canonicalizeVariable(label, typeStr); - } - break; - } - } - return null; - } - - private String canonicalizeVariable(String label, String typeStr) { - String key = label + ":" + typeStr; - if (canonicalVariableMap.containsKey(key)) { - label = canonicalVariableMap.get(key); - } else { - label = typeStr.toLowerCase() + "Var"; - Integer num = canonicalVariables.get(label); - if (num == null) { - num = 0; - } - num ++; - canonicalVariables.put(label, num); - label += "" + num; - canonicalVariableMap.put(key, label); - } - return label; - } - - private String canonicalizeTypeStr(String label) { - String typeStr = label; - int index1 = typeStr.indexOf("<"); - if (index1 != -1) { - typeStr = typeStr.substring(0, index1); - } - index1 = typeStr.lastIndexOf("."); - if (index1 != -1) { - typeStr = typeStr.substring(index1 + 1); - } - return typeStr; - } - -// public static String addPrefixByType(Type type) { -// String newName = ""; -// if (type instanceof PrimitiveType) { -// // byte,short,char,int,long,float,double,boolean,void -// newName = type.toString().toLowerCase(); -// } else if (type instanceof ArrayType) { -// // Type [ ] -// ArrayType at = (ArrayType) type; -// type = at.getElementType(); -// if (type instanceof SimpleType || type instanceof PrimitiveType) { -// newName = getNewName(type); -// } else { -// newName = addPrefixByType(type); -// } -// } else if (type instanceof SimpleType) { -// // TypeName -// if (type.toString().equals("Integer")) { -// newName = "int"; -// } else { -// newName = getNewName(type); -// } -// } else if (type instanceof QualifiedType) { -// // Type.SimpleName -// newName = ((QualifiedType) type).getName().toString().toLowerCase(); -// } else if (type instanceof ParameterizedType) { -// // Type < Type { , Type } > 泛型 -// ParameterizedType t = (ParameterizedType) type; -// newName = getNewName(t.getType()); -// } else if (type instanceof WildcardType) { -// newName = "object"; -// } -// return newName; -// } -// -// private static String getNewName(Type type) { -// String newName = ""; -// String typeName = type.toString(); -// int dot = typeName.lastIndexOf("."); -// if (dot > 0) { -// newName = typeName.substring(dot + 1).toString().toLowerCase(); -// } else { -// newName = typeName.toString().toLowerCase(); -// } -// return newName; -// } - - /** - * Convert the Move actions of an INS action into a simple tree with AST nodes and leaf labels. - * - * @param actions - * @return - */ - private SimpleTree sourceCodeTree(List actions) { - if (actions.size() > 0) { - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setNodeType("Block"); - simpleTree.setLabel("Block"); - simpleTree.setParent(null); - List subTrees = new ArrayList<>(); - for (Action action : actions) { - ITree node = action.getNode(); - subTrees.add(sourceCodeTree(node, simpleTree)); - } - simpleTree.setChildren(subTrees); - - return simpleTree; - } - return null; - } - - /** - * Convert a Move action into a simple tree with AST nodes and leaf labels. - * - * @param tree - * @param parent - * @return - */ - private SimpleTree sourceCodeTree(ITree tree, SimpleTree parent) { - SimpleTree simpleTree = new SimpleTree(); - String astNode = ASTNodeMap.map.get(tree.getType()); - do { - if (astNode.endsWith("Statement") || astNode.equals("FieldDeclaration")) break; - - tree = tree.getParent(); - astNode = ASTNodeMap.map.get(tree.getType());// FIXME if the ASTNode is a method declaration or class declaration? - } while (!astNode.endsWith("Statement") && !astNode.equals("FieldDeclaration")); - - String label = tree.getLabel(); - List children = tree.getChildren(); - if (children.size() > 0) { - List subTrees = new ArrayList<>(); - for (ITree child : children) { - subTrees.add(sourceCodeTree(child, simpleTree)); - } - simpleTree.setChildren(subTrees); - simpleTree.setLabel(astNode); - } else { - simpleTree.setLabel(label); - } - simpleTree.setNodeType(astNode); - simpleTree.setParent(parent); - return simpleTree; - } - - /** - * Convert an UPD/DEL/MOV action into a simple tree with AST nodes and leaf labels. - * - * @param tree - * @param parent - * @return - */ - private SimpleTree originalSourceCodeTree(ITree tree, SimpleTree parent) { - SimpleTree simpleTree = new SimpleTree(); - - String label = tree.getLabel(); - String astNode = ASTNodeMap.map.get(tree.getType()); - - simpleTree.setNodeType(astNode); - List children = tree.getChildren(); - if (children.size() > 0) { - List subTrees = new ArrayList<>(); - for (ITree child : children) { - subTrees.add(originalSourceCodeTree(child, simpleTree)); - } - simpleTree.setChildren(subTrees); - simpleTree.setLabel(astNode); - } else { - simpleTree.setLabel(label); - } - - simpleTree.setParent(parent); - return simpleTree; - } - - /** - * Convert an UPD/DEL/MOV action into a simple tree with abstract identifiers of AST nodes and abstract identifiers of leaf labels. - * - * @param actionSet - * @param tree - * @param parent - * @return - */ - private SimpleTree abstractIdentifierTree(ITree tree, SimpleTree parent) { - SimpleTree simpleTree = new SimpleTree(); - - String label = tree.getLabel(); - String astNode = ASTNodeMap.map.get(tree.getType()); - - simpleTree.setNodeType(astNode); - List children = tree.getChildren(); - if (children.size() > 0) { - if (astNode.endsWith("Type")) { - simpleTree.setNodeType("Type"); - simpleTree.setLabel(getAbstractLabel(abstractTypeIdentifiers, label, ABSTRACT_TYPE)); // abstract Type identifier - } else { - List subTrees = new ArrayList<>(); - for (ITree child : children) { - subTrees.add(abstractIdentifierTree(child, simpleTree)); - } - simpleTree.setChildren(subTrees); - simpleTree.setLabel(astNode); - } - } else { - if (astNode.endsWith("Type")) { - simpleTree.setNodeType("Type"); - if (astNode.equals("WildcardType")) { - simpleTree.setLabel("?"); - } else { - simpleTree.setLabel(getAbstractLabel(abstractTypeIdentifiers, label, ABSTRACT_TYPE)); // abstract Type identifier - } - } else if (astNode.endsWith("Name")) { - // variableName, methodName, QualifiedName - if (label.startsWith("MethodName:")) { // - label = label.substring(11); - simpleTree.setNodeType("Method"); - simpleTree.setLabel(getAbstractLabel(abstractMethodIdentifiers, label, ABSTRACT_METHOD)); // abstract method identifier - } else if (label.startsWith("Name:")) { - label = label.substring(5); - String firstChar = label.substring(0, 1); - if (firstChar.equals(firstChar.toUpperCase())) { - simpleTree.setNodeType("Name"); - simpleTree.setLabel(getAbstractLabel(abstractNameIdentifiers, label, ABSTRACT_NAME)); // abstract Name identifier - } else {// variableName: - simpleTree.setNodeType("Variable"); - simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE));// abstract Variable identifier - } - } else {// variableName: - simpleTree.setNodeType("Variable"); - simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE));// abstract Variable identifier - } - } else if (astNode.equals("BooleanLiteral") || astNode.equals("CharacterLiteral") || astNode.equals("NullLiteral") - || astNode.equals("NumberLiteral") || astNode.equals("StringLiteral") || astNode.equals("ThisExpression") - || astNode.equals("Modifier") || astNode.equals("Operator")) { - simpleTree.setNodeType(astNode); - simpleTree.setLabel(label); - } - } - - simpleTree.setParent(parent); - return simpleTree; - } - - /** - * Convert an UPD/DEL/MOV action into a semi-source code simple tree by abstracting the non-buggy code. - * - * @param actionSet - * @param tree - * @param parent - * @return - */ - private SimpleTree semiSourceCodeTree(HierarchicalActionSet actionSet, ITree tree, SimpleTree parent) { - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setParent(parent); - // deep first - abstractBuggyTreeDeepFirst(actionSet, tree, simpleTree); - - return simpleTree; - } - - private void abstractBuggyTreeDeepFirst(HierarchicalActionSet actionSet, ITree tree, SimpleTree simpleTree) { - List children = tree.getChildren(); - HierarchicalActionSet modifyAction = findHierarchicalActionSet(tree.getPos(), tree.getLength(), actionSet); - String label = tree.getLabel(); - String astNode = ASTNodeMap.map.get(tree.getType()); - - if (Checker.isExpressionType(astNode)) { - if (modifyAction == null || !modifyAction.getActionString().contains("@@" + label)) { - simpleTree.setNodeType("Expression"); - simpleTree.setLabel("EXP"); // astNode - } - } else { - if (astNode.endsWith("Type")) { // TODO: sub Type - simpleTree.setNodeType("Type"); - // simpleTree.setLabel("?"); - if (astNode.equals("WildcardType")) { - simpleTree.setLabel("?"); - } else { // ArrayType, PrimitiveType, SimpleType, ParameterizedType, QualifiedType, WildcardType, UnionType,NameQualifiedType, IntersectionType - simpleTree.setLabel(astNode + "@@" + label); - } - } else if (astNode.endsWith("Name")) { // variableName, methodName, QualifiedName - if (label.startsWith("MethodName:")) { // - label = label.substring(11); - simpleTree.setNodeType("Method"); - simpleTree.setLabel(label); - } else if (label.startsWith("Name:")) { - label = label.substring(5); - String firstChar = label.substring(0, 1); - if (firstChar.equals(firstChar.toUpperCase())) { - simpleTree.setNodeType("Name"); - simpleTree.setLabel(label); // - } else {// variableName: - simpleTree.setNodeType("Variable"); - simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE)); - } - } else {// variableName: - simpleTree.setNodeType("Variable"); - simpleTree.setLabel(getAbstractLabel(abstractVariableIdentifiers, label, ABSTRACT_VARIABLE)); - } - } else if (astNode.equals("BooleanLiteral") ||astNode.equals("CharacterLiteral") || astNode.equals("ThisExpression") - || astNode.equals("NullLiteral") || astNode.equals("NumberLiteral") || astNode.equals("StringLiteral") - || astNode.equals("Modifier") || astNode.equals("Operator")) { - simpleTree.setNodeType(astNode); - simpleTree.setLabel(label); - } else { - simpleTree.setNodeType(astNode); - simpleTree.setLabel(astNode); - } - } - - List simpleChildren = new ArrayList<>(); - if (children != null && !astNode.endsWith("Type")) { - for (ITree child : children) { - simpleChildren.add(semiSourceCodeTree(actionSet, child, simpleTree)); - } - } - simpleTree.setChildren(simpleChildren); - } - - private List getAllMoveActions(HierarchicalActionSet actionSet) { - String astNodeType = actionSet.getAstNodeType(); - if (Checker.containsBodyBlock(astNodeType)) { - List allMoveActions = getAllMoveActions2(actionSet); - if (allMoveActions != null && allMoveActions.size() > 0) { - ListSorter sorter = new ListSorter(allMoveActions); - List moveActions = sorter.sortAscending(); - if (moveActions != null) { - allMoveActions = moveActions; - } - return allMoveActions; - } else {// FIXME: pure INS actions. - return null; - } - } else {// FIXME: pure INS actions. - return null; - } - /** - * Variables, non-new and used in the inserted statements, could be selected to localize buggy code - */ - } - - private List getAllMoveActions2(HierarchicalActionSet actionSet) { - List allMoveActions = new ArrayList<>(); - List actions = new ArrayList<>(); - actions.addAll(actionSet.getSubActions()); - if (actions.size() == 0) { - return null; - } - while (actions.size() > 0) { - List subActions = new ArrayList<>(); - for (HierarchicalActionSet action : actions) { - subActions.addAll(action.getSubActions()); - if (action.toString().startsWith("MOV")) { - allMoveActions.add(action.getAction()); - } - } - - actions.clear(); - actions.addAll(subActions); - } - return allMoveActions; - } - - private String getAbstractLabel(Map map, String label, String nameType) { - if (map.containsKey(label)) { - return map.get(label); - } else { - String name = nameType + map.size(); - map.put(label, name); - return name; - } - } - - private HierarchicalActionSet findHierarchicalActionSet(int position, int length, HierarchicalActionSet actionSet) { - if (actionSet.getStartPosition() == position && actionSet.getLength() == length && !actionSet.getActionString().startsWith("INS")) { - return actionSet; - } else { - for (HierarchicalActionSet subActionSet : actionSet.getSubActions()) { - HierarchicalActionSet actSet = findHierarchicalActionSet(position, length, subActionSet); - if (actSet != null) { - return actSet; - } - } - } - return null; - } - - public Map getAbstractTypeIdentifiers() { - return abstractTypeIdentifiers; - } - - public Map getAbstractMethodIdentifiers() { - return abstractMethodIdentifiers; - } - - public Map getAbstractNameIdentifiers() { - return abstractNameIdentifiers; - } - - public Map getAbstractVariableIdentifiers() { - return abstractVariableIdentifiers; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/gumtree/regroup/Traveler.java b/src/main/java/edu/lu/uni/serval/gumtree/regroup/Traveler.java deleted file mode 100644 index 451086d..0000000 --- a/src/main/java/edu/lu/uni/serval/gumtree/regroup/Traveler.java +++ /dev/null @@ -1,140 +0,0 @@ -package edu.lu.uni.serval.gumtree.regroup; - -import java.util.ArrayList; -import java.util.List; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.ASTNodeMap; - -/** - * A traveler to travel a tree-constructed object. - * - * @author kui.liu - * - */ -public class Traveler { - - public List> list = new ArrayList<>(); - - /** - * Get all action string by traveling HierarchicalActionSet in a deep-first way. - * - * @param actionSet - * @param astNodeTypeActionQueue - */ - public void travelActionSetDeepFirstToASTNodeQueue(HierarchicalActionSet actionSet, List astNodeTypeActionQueue) { - if (actionSet == null) { - System.err.println("Null Action set!"); - } else { - if (astNodeTypeActionQueue == null) { - astNodeTypeActionQueue = new ArrayList<>(); - } - - String actionStr = actionSet.getActionString(); - actionStr = actionStr.substring(0, actionStr.indexOf("@@")); - astNodeTypeActionQueue.add(actionStr); // RawToken: TODO - - if (actionStr.startsWith("DEL")) { - list.add(astNodeTypeActionQueue); // FIXME BUG: Change AST node type 1 to AST node type 2. Solve method: a list is one pattern. - } else { - List subActionSet = actionSet.getSubActions(); - int size = subActionSet.size(); - if (size > 0) { - for (HierarchicalActionSet subAction : subActionSet) { - List astNodeTypeActionQueue_ = new ArrayList<>(); - astNodeTypeActionQueue_.addAll(astNodeTypeActionQueue); - travelActionSetDeepFirstToASTNodeQueue(subAction, astNodeTypeActionQueue_); - } - } else { - list.add(astNodeTypeActionQueue); - } - } - } - } - - /** - * Get all AST node types of a root tree by traveling the root tree in a deep-first way. - * - * @param root - * @return - */ - public static List travelTreeDeepFirstToASTNodeQueue(ITree root) { - if (root == null) { - System.err.println("Null tree!"); - return null; - } - - List astNodeTypeQueue = new ArrayList<>(); - astNodeTypeQueue.add(ASTNodeMap.map.get(root.getType())); // RawToken: root.getLabel(); - - List childrenTreeList = root.getChildren(); - - if (childrenTreeList != null && childrenTreeList.size() > 0) { - for (ITree childTree : childrenTreeList) { - astNodeTypeQueue.addAll(travelTreeDeepFirstToASTNodeQueue(childTree)); - } - } - return astNodeTypeQueue; - } - - /** - * Get all AST node types of a root tree by traveling the root tree in a breadth-first way. - * - * @param root - * @return - */ - public static List travelTreeBreadthFirstToASTNodeQueue(ITree root) { - if (root == null) { - System.err.println("Null tree."); - return null; - } - - List astNodeTypeQueue = new ArrayList<>(); - astNodeTypeQueue.add(ASTNodeMap.map.get(root.getType())); // RawToken: root.getLabel(); - - List treeList = new ArrayList<>(); - treeList.add(root); - while (!treeList.isEmpty()) { - List childrenTreeList = new ArrayList<>(); - for (ITree tree : treeList) { - astNodeTypeQueue.addAll(travelTreeBreadthFirstToASTNodeQueue(tree)); - childrenTreeList.addAll(tree.getChildren()); - } - - treeList.clear(); - treeList.addAll(childrenTreeList); - } - return astNodeTypeQueue; - } - - /** - * Convert a root ITree into a SimpleTree by traveling the root tree in a deep-first way. - * - * SimpleTree node label is root.toShortString(). - * - * @param root - * @param parent - * @return - */ - public static SimpleTree travelITreeDeepFirstToSimpleTree(ITree root, SimpleTree parent) { - if (root == null) { - System.err.println("Null tree!"); - return null; - } - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setLabel(root.toShortString()); - simpleTree.setParent(parent); - List children = new ArrayList<>(); - - List childrenTreeList = root.getChildren(); - if (childrenTreeList != null && childrenTreeList.size() > 0) { - for (ITree childTree : childrenTreeList) { - children.add(travelITreeDeepFirstToSimpleTree(childTree, simpleTree)); - } - } - simpleTree.setChildren(children); - return simpleTree; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/livestudy/Alarm.java b/src/main/java/edu/lu/uni/serval/livestudy/Alarm.java deleted file mode 100644 index a49ef12..0000000 --- a/src/main/java/edu/lu/uni/serval/livestudy/Alarm.java +++ /dev/null @@ -1,33 +0,0 @@ -package edu.lu.uni.serval.livestudy; - -public class Alarm { - private String alarmType; - private String fileName; - private int startLine; - private int endLine; - - public String getAlarmType() { - return alarmType; - } - - public String getFileName() { - return fileName; - } - - public int getStartLine() { - return startLine; - } - - public int getEndLine() { - return endLine; - } - - public Alarm(String alarmType, String fileName, int startLine, int endLine) { - super(); - this.alarmType = alarmType; - this.fileName = fileName; - this.startLine = startLine; - this.endLine = endLine; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/livestudy/ParseViolations.java b/src/main/java/edu/lu/uni/serval/livestudy/ParseViolations.java deleted file mode 100644 index 8e0d4ae..0000000 --- a/src/main/java/edu/lu/uni/serval/livestudy/ParseViolations.java +++ /dev/null @@ -1,212 +0,0 @@ -package edu.lu.uni.serval.livestudy; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.utils.FileHelper; - -public class ParseViolations { - - private static final String OUTPUT_PATH = Configuration.ROOT_PATH + "LiveStudy/BugsInfo/"; - private static int i = 0; - private static int j = 0; - - public static void main(String[] args) { - // output path -// FileHelper.deleteDirectory(OUTPUT_PATH); - List projects = new ArrayList<>(); - File[] files = new File(OUTPUT_PATH).listFiles(); - for (File file : files) { - if (file.isDirectory()) { - projects.add(file.getName()); - } - } - String projectsPath = Configuration.ROOT_PATH + "LiveStudy/projects/"; - String bugsListPath = Configuration.ROOT_PATH + "LiveStudy/BugsList/"; - List bugsListFiles = FileHelper.getAllFiles(bugsListPath, ".list"); - for (File bugsListFile : bugsListFiles) { - String fileName = FileHelper.getFileNameWithoutExtension(bugsListFile); - if (projects.contains(fileName)) continue; - ParseViolations parser = new ParseViolations(); - Map violations = new HashMap<>(); // , Violation: >. - violations = parser.readViolations(bugsListFile); - parser.parseViolationToTokens(violations, projectsPath); - } - - System.out.println(i); - System.out.println(j); - } - - /** - * Get the source code tokens of all violation instances by visiting each java project. - * - * @param violations - * @param projectsPath - */ - public void parseViolationToTokens(Map violations, String projectsPath) { - for (Map.Entry entry : violations.entrySet()) { - String projectName = entry.getKey(); - List alarms = entry.getValue().getAlarms(); - List javaFiles = FileHelper.getAllFiles(projectsPath + projectName, ".java"); - - //Each violation: commons-math : DLS_DEAD_LOCAL_STORE : org/apache/commons/math4/dfp/Dfp.java : 2049 : 2049 - /** - * @ProjectName - * @ViolationType - * @FileName - * @LineNumber - * @SourceCode - * @Tokens - * @NumberOfTokens - */ - // sizes file, tokens file, and bugs-info file - StringBuilder sizesBuilder = new StringBuilder(); - StringBuilder tokensBuilder = new StringBuilder(); - StringBuilder bugsInfoBuilder = new StringBuilder(); - for (Alarm alarm : alarms) { - String fileName = alarm.getFileName(); -// if (fileName.toLowerCase(Locale.ENGLISH).contains("test")) continue; - - File sourceCodeFile = locateSourceCodeFile(javaFiles, fileName); - if (sourceCodeFile == null) { - j ++; - continue; - } - - Parser parser = new Parser(alarm, sourceCodeFile); - parser.parse(); - SimpleTree simpleTree = parser.getSimpleTree(); - - if (simpleTree != null) { - int finalStartLine = parser.getFinalStartLine(); - int finalEndLine = parser.getFinalEndLine(); - String violationType = alarm.getAlarmType(); - - String tokens = Tokenizer.getTokensDeepFirst(simpleTree); - String[] tokensArray = tokens.split(" "); - int length = tokensArray.length; - StringBuilder sourceCode = readSourceCode(sourceCodeFile, finalStartLine, finalEndLine); - - sizesBuilder.append(length).append("\n"); - tokensBuilder.append(tokens).append("\n"); - bugsInfoBuilder.append("###BugInstance###\n##Info:"); - bugsInfoBuilder.append(violationType).append(":"); - bugsInfoBuilder.append(projectName).append(":"); - bugsInfoBuilder.append(fileName).append(":"); - bugsInfoBuilder.append(finalStartLine).append(":"); - bugsInfoBuilder.append(finalEndLine).append("\n"); - bugsInfoBuilder.append(sourceCode).append("\n"); - i ++; - } else { - j ++; - } - } - - FileHelper.outputToFile(OUTPUT_PATH + "sizes.list", sizesBuilder, true); - FileHelper.outputToFile(OUTPUT_PATH + "tokens.list", tokensBuilder, true); - FileHelper.outputToFile(OUTPUT_PATH + "bugsInfo.list", bugsInfoBuilder, true); - } - } - - private StringBuilder readSourceCode(File javaFile, int startLine, int endLine) { - StringBuilder sourceCode = new StringBuilder("##Source_Code:\n"); - FileInputStream fis = null; - Scanner scanner = null; - - try { - fis = new FileInputStream(javaFile); - scanner = new Scanner(fis); - int counter = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - counter ++; - if (startLine <= counter && counter <= endLine) { - sourceCode.append(line + "\n"); - } - if (counter == endLine) break; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return sourceCode; - } - - private File locateSourceCodeFile(List javaFiles, String fileName) { - for (File javaFile : javaFiles) { - if (javaFile.getPath().endsWith(fileName)) return javaFile; - } - return null; - } - - public Map readViolations(String violationFile) { - return readViolations(new File(violationFile)); - } - - public Map readViolations(File violationFile) { - Map violations = new HashMap<>(); - - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(violationFile); - scanner = new Scanner(fis); - - while (scanner.hasNextLine()) { - //commons-math : DLS_DEAD_LOCAL_STORE : org/apache/commons/math4/dfp/Dfp.java : 2049 : 2049 - String line = scanner.nextLine(); - String[] elements = line.split(" : "); - String projectName = elements[0]; - String alarmType = elements[1]; - String fileName = elements[2]; - int startLine = Integer.parseInt(elements[3]); - int endLine = Integer.parseInt(elements[4]); - - Alarm alarm = new Alarm(alarmType, fileName, startLine, endLine); - addAlarmToViolations(projectName, alarm, violations); - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return violations; - } - - private void addAlarmToViolations(String projectName, Alarm alarm, Map violations) { - Violation violation = null; - if (violations.containsKey(projectName)) { - violation = violations.get(projectName); - } else { - violation = new Violation(projectName); - violations.put(projectName, violation); - } - - List alarms = violation.getAlarms(); - alarms.add(alarm); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/livestudy/Parser.java b/src/main/java/edu/lu/uni/serval/livestudy/Parser.java deleted file mode 100644 index 93d1d30..0000000 --- a/src/main/java/edu/lu/uni/serval/livestudy/Parser.java +++ /dev/null @@ -1,84 +0,0 @@ -package edu.lu.uni.serval.livestudy; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; -import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; - -public class Parser { - // input - private Alarm alarm; - private File sourceCodeFile; - - // output - private int finalStartLine = 0; - private int finalEndLine = 0; - private SimpleTree simpleTree = null; - - public Parser(Alarm alarm, File sourceCodeFile) { - this.alarm = alarm; - this.sourceCodeFile = sourceCodeFile; - } - - public int getFinalStartLine() { - return finalStartLine; - } - - public int getFinalEndLine() { - return finalEndLine; - } - - public SimpleTree getSimpleTree() { - return simpleTree; - } - - public void parse() { - int startLine = this.alarm.getStartLine(); - int endLine = this.alarm.getEndLine(); - - String violationType = this.alarm.getAlarmType(); - - ViolationSourceCodeTree treeParser = new ViolationSourceCodeTree(this.sourceCodeFile, startLine, endLine); - - if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(violationType)|| "HE_EQUALS_USE_HASHCODE".equals(violationType) - || "HE_INHERITS_EQUALS_USE_HASHCODE".equals(violationType)|| "SE_NO_SUITABLE_CONSTRUCTOR".equals(violationType) - || "RI_REDUNDANT_INTERFACES".equals(violationType) || "CN_IDIOM".equals(violationType) - || "SE_NO_SERIALVERSIONID".equals(violationType) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(violationType)) { - // Class name level, tokens - // classStartP <= vS <= vE <= classEndP - ITree classNameTree = treeParser.getClassNameTokens(); - if (classNameTree != null) { - this.simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(classNameTree, null); - } else { - System.err.println("#Null_Violation_Hunk: " + this.alarm.getAlarmType() + ":" + this.sourceCodeFile.getPath() + ":" + startLine + ":" + endLine); - } - } else { - treeParser.extract(); - List matchedTrees = treeParser.getViolationSourceCodeTrees(); - if (matchedTrees.size() == 0) { - System.err.println("#Null_Violation_Hunk: " + this.alarm.getAlarmType() + ":" + this.sourceCodeFile.getPath() + ":" + startLine + ":" + endLine); - } else { - this.simpleTree = new SimpleTree(); - this.simpleTree.setLabel("Block"); - this.simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, this.simpleTree); - children.add(simpleT); - } - this.simpleTree.setChildren(children); - } - } - - if (this.simpleTree != null) { - this.finalStartLine = treeParser.getViolationFinalStartLine(); - this.finalEndLine = treeParser.getViolationFinalEndLine(); - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/livestudy/README.md b/src/main/java/edu/lu/uni/serval/livestudy/README.md deleted file mode 100644 index bdda18e..0000000 --- a/src/main/java/edu/lu/uni/serval/livestudy/README.md +++ /dev/null @@ -1,6 +0,0 @@ -## Parse the violations of Live Study ## - -1. Localize bugs with FindBugs. -2. Parse results of FindBugs. (bug-type project.) - -3. Parse source code of violations. (ParseViolation.java) \ No newline at end of file diff --git a/src/main/java/edu/lu/uni/serval/livestudy/Violation.java b/src/main/java/edu/lu/uni/serval/livestudy/Violation.java deleted file mode 100644 index e6eaa2d..0000000 --- a/src/main/java/edu/lu/uni/serval/livestudy/Violation.java +++ /dev/null @@ -1,25 +0,0 @@ -package edu.lu.uni.serval.livestudy; - -import java.util.ArrayList; -import java.util.List; - -public class Violation { - - private String project; - private List alarms; - - public String getProject() { - return project; - } - - public List getAlarms() { - return alarms; - } - - public Violation(String project) { - super(); - this.project = project; - this.alarms = new ArrayList<>(); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/parameters/ParseAlarms.java b/src/main/java/edu/lu/uni/serval/parameters/ParseAlarms.java deleted file mode 100644 index fe174b6..0000000 --- a/src/main/java/edu/lu/uni/serval/parameters/ParseAlarms.java +++ /dev/null @@ -1,145 +0,0 @@ -package edu.lu.uni.serval.parameters; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.FixPatternParser.violations.Violation; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.violation.code.parser.ViolationSourceCodeTree; - -/** - * Prepare data for tuning parameters of deep learning models. - * - * @author kui.liu - * - */ -public class ParseAlarms { - - public static void main(String[] args) { - ParseAlarms parser = new ParseAlarms(); - - String outputPath = Configuration.ROOT_PATH + "TuneParameters/fixedAlarmTokens.list"; - String outputPath2 = Configuration.ROOT_PATH + "TuneParameters/EmptyStatement/fixedAlarmTokens.list"; - FileHelper.deleteFile(outputPath); - FileHelper.deleteFile(outputPath2); - int subIndex = 5; - String fixedAlarmFilesPath = Configuration.GUM_TREE_INPUT + "prevFiles/"; - String positionsFilePath = Configuration.GUM_TREE_INPUT + "positions/"; - parser.dataPreparation(fixedAlarmFilesPath, positionsFilePath, subIndex, outputPath, outputPath2); - - outputPath = Configuration.ROOT_PATH + "TuneParameters/unfixedAlarmTokens.list"; - outputPath2 = Configuration.ROOT_PATH + "TuneParameters/EmptyStatement/unfixedAlarmTokens.list"; - FileHelper.deleteFile(outputPath); - FileHelper.deleteFile(outputPath2); - subIndex = 8; - String unfixedAlarmFilesPath = Configuration.GUM_TREE_INPUT + "unfixAlarms/"; - String unfixedPositionsFilePath = Configuration.GUM_TREE_INPUT + "un_positions/"; - parser.dataPreparation(unfixedAlarmFilesPath, unfixedPositionsFilePath, subIndex, outputPath, outputPath2); - } - - public void dataPreparation(String sourceCodeFilePath, String positionFilePath, int subIndex, String outputPath, String outputPath2) { - StringBuilder tokensBuilder = new StringBuilder(); - List javaFiles = FileHelper.getAllFilesInCurrentDiectory(sourceCodeFilePath, ".java"); - int counter = 0; - int a = 0; - StringBuilder emptyStatements = new StringBuilder(); - StringBuilder sizes = new StringBuilder(); - for (File javaFile : javaFiles) { - String fileName = javaFile.getName().replace(".java", ".txt"); - fileName = fileName.substring(subIndex); - -// if (fileName.endsWith("apache-commons-configuration_8c42aa_8b26e6src#java#org#apache#commons#configuration#plist#XMLPropertyListConfiguration.txt")) { -// System.out.println(); -// } - - List violations = readViolations(positionFilePath + fileName); - - for (Violation violation : violations) { - int startLine = violation.getStartLineNum(); - int endLine = violation.getEndLineNum(); - String alarmType = violation.getViolationType(); - - if (endLine > startLine + 5) continue; - - ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(javaFile, startLine, endLine); - alarmTree.extract(alarmType); - List matchedTrees = alarmTree.getViolationSourceCodeTrees(); - if (matchedTrees.size() == 0) { - emptyStatements.append(alarmType + "," + fileName + "," + startLine + "," + endLine + "\n"); - a ++; - continue; - } - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, null); - children.add(simpleT); - } - simpleTree.setChildren(children); - - String tokens = Tokenizer.getTokensDeepFirst(simpleTree); - String[] tokensArray = tokens.split(" "); - int length = tokensArray.length; - sizes.append(length + "\n"); - tokensBuilder.append(alarmType + ":" + fileName + ":" + alarmTree.getViolationFinalStartLine() + ":" + alarmTree.getViolationFinalEndLine() + ":" + tokens + "\n"); - - counter ++; - if (counter % 10000 == 0) { - FileHelper.outputToFile(outputPath, tokensBuilder, true); - tokensBuilder.setLength(0); - } - } - } - - System.out.println("Volidated Instances: " + counter); - System.out.println("Empty Instances: " + a); - FileHelper.outputToFile(outputPath2, emptyStatements, false); - FileHelper.outputToFile(outputPath.replace(".list", "Sizes.csv"), sizes, false); - FileHelper.outputToFile(outputPath, tokensBuilder, true); - } - - private List readViolations(String file) { - List violations = new ArrayList<>(); - - String fileContent = FileHelper.readFile(file); - BufferedReader reader = null; - reader = new BufferedReader(new StringReader(fileContent)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - String[] positionStr = line.split(":"); - int startLine = Integer.parseInt(positionStr[1]); - int endLine = Integer.parseInt(positionStr[2]); - - if (startLine == -1 || endLine == -1) { - continue; - } - String alarmType = positionStr[0]; - Violation violation = new Violation(startLine, endLine, alarmType); - violations.add(violation); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return violations; - } -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/.Rapp.history b/src/main/java/edu/lu/uni/serval/statistics/.Rapp.history deleted file mode 100644 index e69de29..0000000 diff --git a/src/main/java/edu/lu/uni/serval/statistics/Categories.java b/src/main/java/edu/lu/uni/serval/statistics/Categories.java deleted file mode 100644 index 0eea731..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/Categories.java +++ /dev/null @@ -1,75 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -public class Categories { - - public static void main(String[] args) throws IOException { - String content = FileHelper.readFile(Configuration.ROOT_PATH + "RQ1/Quantity-per-Fixed_1.0V-Type.csv");//"RQ1/Quantity-per-V-Type.csv"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = reader.readLine(); - int counter = 0; -// int size = 400; - Map map = new HashMap<>(); - map.put("Dodgy code", 0); - map.put("Experimental", 0); - map.put("Internationalization", 0); - map.put("Multithreaded correctness", 0); - map.put("Malicious code vulnerability", 0); - map.put("Performance", 0); - map.put("Correctness", 0); - map.put("Security", 0); - map.put("Bad practice", 0); - map.put("Other", 0); -// List list = new ArrayList<>(); - Map> map2 = new HashMap<>(); - map2.put("Dodgy code", new ArrayList()); - map2.put("Experimental", new ArrayList()); - map2.put("Internationalization", new ArrayList()); - map2.put("Multithreaded correctness", new ArrayList()); - map2.put("Malicious code vulnerability", new ArrayList()); - map2.put("Performance", new ArrayList()); - map2.put("Correctness", new ArrayList()); - map2.put("Security", new ArrayList()); - map2.put("Bad practice", new ArrayList()); - map2.put("Other", new ArrayList()); - while ((line = reader.readLine()) != null) { - String type = line.substring(line.lastIndexOf(",") + 1); - counter ++; - if (map.containsKey(type)) { - map.put(type, map.get(type) + 1); - } else { - map.put(type, 1); - } - if (counter % 10 == 0) { - for (Map.Entry> entry : map2.entrySet()) { - String type2 = entry.getKey(); - Integer integ = map.get(type2); - if (integ == null) { - map2.get(type2).add(0); - } else { - map2.get(type2).add(integ); - } - } -// System.out.println(); - } - } - reader.close(); - for (Map.Entry entry : map.entrySet()) { - System.out.println(entry.getKey() + "," + entry.getValue()); - } - for (Map.Entry> entry : map2.entrySet()) { - System.out.println(entry.getKey() + "," + entry.getValue()); - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/FixedProjects.java b/src/main/java/edu/lu/uni/serval/statistics/FixedProjects.java deleted file mode 100644 index 122cfab..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/FixedProjects.java +++ /dev/null @@ -1,26 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.StringReader; - -import edu.lu.uni.serval.utils.FileHelper; - -public class FixedProjects { - - public static void main(String[] args) throws IOException { - String content = FileHelper.readFile("../FPM_Violations/RQ1/Quantity-per-FixedProj.csv"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = reader.readLine(); - StringBuilder builder = new StringBuilder(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); -// String projectName = elements[0]; - builder.append(elements[0] + "\n"); - } - reader.close(); - - FileHelper.outputToFile("../FPM_Violations/RQ1/fixedProjects.list", builder, false); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/FixedVilations.java b/src/main/java/edu/lu/uni/serval/statistics/FixedVilations.java deleted file mode 100644 index 95c8023..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/FixedVilations.java +++ /dev/null @@ -1,47 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.FileInputStream; -import java.io.IOException; -import java.util.HashMap; -import java.util.Map; -import java.util.Scanner; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -public class FixedVilations { - - public static void main(String[] args) throws IOException { - // projectName,ViolationType,Number. - FileInputStream fis = new FileInputStream(Configuration.ROOT_PATH + "RQ1/fixed-alarms-v1.0.list"); - Scanner scanner = new Scanner(fis); - Map map = new HashMap<>(); - int counter = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - String[] elements = line.split(":"); -// String violationType = elements[0]; -// String projectName = elements[1]; - String key = elements[1] + "," + elements[0]; - if (map.containsKey(key)) { - map.put(key, map.get(key)+ 1); - } else { - map.put(key, 1); - } - counter ++; - } - - scanner.close(); - fis.close(); - - System.out.println(counter); - StringBuilder builder = new StringBuilder(); - for (Map.Entry entry : map.entrySet()) { - builder.append(entry.getKey()).append(",").append(entry.getValue()).append("\n"); - counter -= entry.getValue(); - } - FileHelper.outputToFile(Configuration.ROOT_PATH + "RQ1/fixedViolations-v-1.0.csv", builder, false); - System.out.println(counter); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/HunkSizeComputer.java b/src/main/java/edu/lu/uni/serval/statistics/HunkSizeComputer.java deleted file mode 100644 index ca5f4b5..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/HunkSizeComputer.java +++ /dev/null @@ -1,106 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; - -public class HunkSizeComputer { - - public static void main(String[] args) throws IOException { - String violationsFilePath = Configuration.ROOT_PATH + "unFixedInstances/"; - sizes(violationsFilePath, ".list"); - } - - public static void sizes(String filePath, String fileType) throws NumberFormatException, IOException { - List unfixedAlarmFiles = FileHelper.getAllFilesInCurrentDiectory(filePath, fileType); - System.out.println(unfixedAlarmFiles.size()); - StringBuilder builder = new StringBuilder(); - int counter = 0; - int size = 0; - int i = 0; - List sizes = new ArrayList<>(); - Map map = new HashMap<>();// - for (File file : unfixedAlarmFiles) { - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - int startLine = Integer.parseInt(elements[4]); - int endLine = Integer.parseInt(elements[5]); - i ++; - if (startLine == -1 || endLine == -1) continue; - - int range = endLine - startLine + 1; - builder.append(range + "\n"); - if (range != 1) { - counter ++; - } - size ++; - sizes.add(range); - if (map.containsKey(range)) { - map.put(range, map.get(range) + 1); - } else { - map.put(range, 1); - } - } - reader.close(); - } - System.out.println(i); - - String content = FileHelper.readFile("Dataset/fixed-alarms-v1.0.list"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - int arrowIndex = line.indexOf("=>"); - String buggyInfo = line.substring(0, arrowIndex); - String[] buggyElements = buggyInfo.split(":"); - - int startLine = Integer.parseInt(buggyElements[4]); - int endLine = Integer.parseInt(buggyElements[5]); - - if (startLine == -1 || endLine == -1) continue; - - int range = endLine - startLine + 1; - if (range != 1) { - counter ++; - } - builder.append(range + "\n"); - size ++; - sizes.add(range); - if (map.containsKey(range)) { - map.put(range, map.get(range) + 1); - } else { - map.put(range, 1); - } - } - reader.close(); - - FileHelper.outputToFile("Dataset/sizes.csv", builder, false); - - System.out.println(size); - System.out.println(counter); - ListSorter sorter = new ListSorter<>(sizes); - sizes = sorter.sortAscending(); - System.out.println(sizes.get((int) (sizes.size() * 0.7))); - System.out.println(sizes.get((int) (sizes.size() * 0.8))); - System.out.println(sizes.get((int) (sizes.size() * 0.9))); - System.out.println(sizes.get((int) (sizes.size() * 0.95))); - - int sum = 0; - for (i = 1; i <= 100; i ++) { - sum += map.get(i); - System.out.println(i + "," + String.format("%.2f", ((double) sum / size * 100))); - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/NumberOfFilesAndCodeLines.java b/src/main/java/edu/lu/uni/serval/statistics/NumberOfFilesAndCodeLines.java deleted file mode 100644 index 8a9fe38..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/NumberOfFilesAndCodeLines.java +++ /dev/null @@ -1,74 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.List; -import java.util.Locale; -import java.util.Scanner; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -/** - * Statistics of files and code lines of projects in Live Study. - * - * @author kui.liu - * - */ -public class NumberOfFilesAndCodeLines { - - public static void main(String[] args) { - String projectsPath = Configuration.ROOT_PATH + "LiveStudy/BugsInfo/"; - File[] projects = new File(projectsPath).listFiles(); - for (File project : projects) { - if (project.isDirectory()) { - if (project.getName().equals("poi")) - new NumberOfFilesAndCodeLines().statistic(project.getName()); - } - } - } - - public void statistic(String project) { - List javaFiles = FileHelper.getAllFiles(Configuration.ROOT_PATH + "LiveStudy/projects/" + project, ".java"); - int numberOfFiles = 0; - int LOC = 0; - for (File javaFile : javaFiles) { - if (!javaFile.getPath().toLowerCase(Locale.ENGLISH).contains("test")) { - numberOfFiles ++; - LOC += readLinesOfCode(javaFile); - } -// numberOfFiles ++; -// LOC += readLinesOfCode(javaFile); - } - System.out.println(project + " : Files = " + numberOfFiles + ", LOC = " + LOC); - } - - private int readLinesOfCode(File javaFile) { - int LOC = 0; - Scanner scanner = null; - FileInputStream fis = null; - try { - fis = new FileInputStream(javaFile); - scanner = new Scanner(fis); - - while (scanner.hasNextLine()) { - scanner.nextLine(); - LOC ++; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return LOC; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/ReadSpearmanResults.java b/src/main/java/edu/lu/uni/serval/statistics/ReadSpearmanResults.java deleted file mode 100644 index 9763c70..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/ReadSpearmanResults.java +++ /dev/null @@ -1,104 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.StringReader; - -import edu.lu.uni.serval.utils.FileHelper; - -public class ReadSpearmanResults { - - public static void main(String[] args) throws IOException { - String fileName = "../FPM_Violations/RQ1/SpearmanResults.list"; - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - String str1 = "1"; - String str2 = "2"; - String str3 = "3"; - String str4 = "4"; - String str5 = "5"; - String str6 = "6"; - String str7 = "7"; - String str8 = "8"; - String str9 = "9"; - String str10 = "10"; - int counter = 0; - while ((line = reader.readLine()) != null) { -// String[] elements = line.split(""); - - counter ++; - - if ((counter / 10 == 2 || counter / 10 == 4) && counter % 10 == 1) { - str1 += "@@@@1"; - str2 += "@@@@2"; - str3 += "@@@@3"; - str4 += "@@@@4"; - str5 += "@@@@5"; - str6 += "@@@@6"; - str7 += "@@@@7"; - str8 += "@@@@8"; - str9 += "@@@@9"; - str10 += "@@@@10"; - } - - - int n = counter % 10; - switch (n) { - case 1: - str1 += "@" + line; - break; - case 2: - str2 += "@" + line; - break; - case 3: - str3 += "@" + line; - break; - case 4: - str4 += "@" + line; - break; - case 5: - str5 += "@" + line; - break; - case 6: - str6 += "@" + line; - break; - case 7: - str7 += "@" + line; - break; - case 8: - str8 += "@" + line; - break; - case 9: - str9 += "@" + line; - break; - case 0: - str10 += "@" + line; - break; - } - } - reader.close(); - - str1 = str1.replace(".", ","); - str2 = str2.replace(".", ","); - str3 = str3.replace(".", ","); - str4 = str4.replace(".", ","); - str5 = str5.replace(".", ","); - str6 = str6.replace(".", ","); - str7 = str7.replace(".", ","); - str8 = str8.replace(".", ","); - str9 = str9.replace(".", ","); - str10 = str10.replace(".", ","); - System.out.println(str1); - System.out.println(str2); - System.out.println(str3); - System.out.println(str4); - System.out.println(str5); - System.out.println(str6); - System.out.println(str7); - System.out.println(str8); - System.out.println(str9); - System.out.println(str10); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/Spearman.R b/src/main/java/edu/lu/uni/serval/statistics/Spearman.R deleted file mode 100644 index 549ad42..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/Spearman.R +++ /dev/null @@ -1,362 +0,0 @@ -a <- read.csv("~/Public/git/FPM_Violations/RQ1/TenFolds-Q/Ten-fold-all-fixed-violation-type1-70.csv", header=T) -d<-cor.test( ~ X0 + X0.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = FALSE, sep = "@") - -d<-cor.test( ~ X1 + X1.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X2 + X2.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X3 + X3.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X4 + X4.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X5 + X5.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X6 + X6.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X7 + X7.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X8 + X8.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X9 + X9.T, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X0.R + X0.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X1.R + X1.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X2.R + X2.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X3.R + X3.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X4.R + X4.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X5.R + X5.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X6.R + X6.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X7.R + X7.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X8.R + X8.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X9.R + X9.T.R, - data=a, method = "spearman", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X0 + X0.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X1 + X1.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X2 + X2.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X3 + X3.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X4 + X4.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X5 + X5.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X6 + X6.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X7 + X7.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X8 + X8.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X9 + X9.T, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X0.R + X0.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X1.R + X1.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X2.R + X2.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X3.R + X3.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X4.R + X4.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X5.R + X5.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X6.R + X6.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X7.R + X7.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X8.R + X8.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X9.R + X9.T.R, - data=a, method = "pearson", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X0 + X0.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X1 + X1.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X2 + X2.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X3 + X3.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X4 + X4.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X5 + X5.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X6 + X6.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X7 + X7.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X8 + X8.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X9 + X9.T, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X0.R + X0.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X1.R + X1.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X2.R + X2.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X3.R + X3.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X4.R + X4.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X5.R + X5.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X6.R + X6.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X7.R + X7.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X8.R + X8.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -d<-cor.test( ~ X9.R + X9.T.R, - data=a, method = "kendall", - continuity = FALSE, - conf.level = 0.95) -write(c(d$estimate, d$p.value), file = "~/Public/git/FPM_Violations/RQ1/SpearmanResults.list",append = TRUE, sep = "@") - -a=1 diff --git a/src/main/java/edu/lu/uni/serval/statistics/SpearmanCodeGenerator.java b/src/main/java/edu/lu/uni/serval/statistics/SpearmanCodeGenerator.java deleted file mode 100644 index 055e522..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/SpearmanCodeGenerator.java +++ /dev/null @@ -1,81 +0,0 @@ -package edu.lu.uni.serval.statistics; - - -public class SpearmanCodeGenerator { - - public static void main(String[] args) { - generateSpearmanCode(); - } - - public static void generateSpearmanCode() { - for (int i = 0; i < 10; i ++) { - String s = "d<-cor.test( ~ X" + i + " + X" + i + ".T, \n"; - s += " data=a,"; - s += " method = \"spearman\",\n"; - s += " continuity = FALSE,\n"; - s += " conf.level = 0.95)\n"; - if (i == 0) { - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = FALSE, sep = \"@\")\n"; - } else { - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = TRUE, sep = \"@\")\n"; - } - - System.out.println(s); - } - for (int i = 0; i < 10; i ++) { - String s = "d<-cor.test( ~ X" + i + ".R + X" + i + ".T.R, \n"; - s += " data=a,"; - s += " method = \"spearman\",\n"; - s += " continuity = FALSE,\n"; - s += " conf.level = 0.95)\n"; - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = TRUE, sep = \"@\")\n"; - System.out.println(s); - } - - for (int i = 0; i < 10; i ++) { - String s = "d<-cor.test( ~ X" + i + " + X" + i + ".T, \n"; - s += " data=a,"; - s += " method = \"pearson\",\n"; - s += " continuity = FALSE,\n"; - s += " conf.level = 0.95)\n"; - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = TRUE, sep = \"@\")\n"; - System.out.println(s); - } - for (int i = 0; i < 10; i ++) { - String s = "d<-cor.test( ~ X" + i + ".R + X" + i + ".T.R, \n"; - s += " data=a,"; - s += " method = \"pearson\",\n"; - s += " continuity = FALSE,\n"; - s += " conf.level = 0.95)\n"; - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = TRUE, sep = \"@\")\n"; - System.out.println(s); - } - - for (int i = 0; i < 10; i ++) { - String s = "d<-cor.test( ~ X" + i + " + X" + i + ".T, \n"; - s += " data=a,"; - s += " method = \"kendall\",\n"; - s += " continuity = FALSE,\n"; - s += " conf.level = 0.95)\n"; - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = TRUE, sep = \"@\")\n"; - System.out.println(s); - } - for (int i = 0; i < 10; i ++) { - String s = "d<-cor.test( ~ X" + i + ".R + X" + i + ".T.R, \n"; - s += " data=a,"; - s += " method = \"kendall\",\n"; - s += " continuity = FALSE,\n"; - s += " conf.level = 0.95)\n"; - s += "write(c(d$estimate, d$p.value), file = \"~/Public/git/FPM_Violations/RQ1/SpearmanResults.list\"," + - "append = TRUE, sep = \"@\")\n"; - System.out.println(s); - } - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/Statistic.java b/src/main/java/edu/lu/uni/serval/statistics/Statistic.java deleted file mode 100644 index f1f1aae..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/Statistic.java +++ /dev/null @@ -1,947 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; -import edu.lu.uni.serval.utils.MapSorter; - -public class Statistic { - private static Map map1 = new HashMap(); - private static Map map2 = new HashMap<>(); - - public static void main(String[] args) throws IOException { - /* - * DM_DEFAULT_ENCODING - * NP_NONNULL_RETURN_VIOLATION - * NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE - * NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE - * ODR_OPEN_DATABASE_RESOURCE - * PZLA_PREFER_ZERO_LENGTH_ARRAYS - * RI_REDUNDANT_INTERFACES - * RV_RETURN_VALUE_IGNORED_BAD_PRACTICE - * RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT - * SE_NO_SERIALVERSIONID - * SF_SWITCH_NO_DEFAULT - * SIC_INNER_SHOULD_BE_STATIC - * SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING - * UC_USELESS_CONDITION - * UC_USELESS_OBJECT - * UCF_USELESS_CONTROL_FLOW - * WMI_WRONG_MAP_ITERATOR - */ -// /* -// * Quantities' distribution of all violation types. -// */ -// quantityOfEachViolationType(); -// /* -// * Widespread of each violation type. -// */ -// widespreadOfEachViolationType(); -// /* -// * Statistics of categories of all violation types. -// */ -// statisticWithCategories(); -// -// /* -// * Quantity of each violation type in each project. -// */ -// reloadData(); -// -// /* -// * Quantities' distribution of all fixed violation types. -// * Widespread of each fixed violation type. -// * Statistics of categories of all fixed violation types. -// * Quantity of each fixed violation type in each project. -// */ -// statisticOfFixedViolations(); -// fixedVSunfixed(); - - /** - * Do statistics from two files: - */ - statistics("../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv", "", map1, 16918530, 730); -// statistics("../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv", "Fixed"); - statistics("../FPM_Violations/RQ1/fixedViolations-v-1.0.csv", "Fixed_1.0", map2, 88927, 548); -// fixedVSunfixed(); - StringBuilder builder = new StringBuilder(); - for (Map.Entry entry : map1.entrySet()) { - String key = entry.getKey(); - builder.append(key + "," + entry.getValue() + "," + (map2.containsKey(key) ? map2.get(key) : 0) + "\n"); - } - FileHelper.outputToFile(Configuration.ROOT_PATH + "RQ2/quantity-ratios.csv", builder, false); - -// statisticsOfFixedViolations(); - - //rsync -avP gaia-cluster:/work/users/kliu/FixPattern/FPM_Violations/UnfixedViolations/BC_UNCONFIRMED_CAST/Sizes.list Sizes/Sizes1.list -// String s = "rsync -avP gaia-cluster:/work/users/kliu/FixPattern/FPM_Violations/UnfixedViolations_RQ3/"; -// File[] files = new File(Configuration.ROOT_PATH + "RQ3_1/UnfixedInstances/").listFiles(); -// int i = 0; -// for (File file : files) { -// if (file.getName().endsWith(".list")) { -// i ++; -// System.out.println(s + FileHelper.getFileNameWithoutExtension(file) + "/Sizes.list Sizes/Sizes" + i + ".list"); -// } -// } -// tokenSizes(); - } - - public static void tokenSizes() { - List sizes = new ArrayList<>(); - List files = FileHelper.getAllFilesInCurrentDiectory(Configuration.ROOT_PATH + "RQ3_1/Sizes/", ".list"); - StringBuilder builder = new StringBuilder(); - for (File file : files) { - try { - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - sizes.add(Integer.parseInt(line)); - builder.append("1,").append(line).append("\n"); - } - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - System.out.println(sizes.size()); - FileHelper.outputToFile(Configuration.ROOT_PATH + "RQ3_1/Sizes.csv", builder, false); - } - - public static void statisticsOfFixedViolations() { - String statistic = "../FPM_Violations/OUTPUT3/"; - List files = FileHelper.getAllFiles(statistic, ".list"); - - int positions = 0; - int numV = 0; - int testAlarms = 0; - int nullGumTreeResults = 0; - int nullMappingGumTreeResults = 0; - int pureDeletion = 0; - int timeout = 0; - int noSourceCodeChagnes = 0; - int largeHunk = 0; - int nullSourceCode = 0; - int noStatementChanges = 0; - int nullDiffentry = 0; - int TestingInfo = 0; - int i = 0; - Map types1 = new HashMap<>(); - for (File file : files) { - if (file.getName().startsWith("statistic")) { - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - i ++; - try { - while ((line = reader.readLine()) != null) { - if (line.startsWith("Positions")) { - positions += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NumViolations")) { - numV += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else - if (line.startsWith("TestViolations")) { - testAlarms += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NullGumTreeResults")) { - nullGumTreeResults += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NoSourceCodeChanges")) { - noSourceCodeChagnes += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NoStatementChanges")) { - noStatementChanges += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NullDiffEntry")) { - nullDiffentry += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NullMatchedGumTreeResults")) { - nullMappingGumTreeResults += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("PureDeletion")) { - pureDeletion += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("LargeHunk")) { - largeHunk += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("NullSourceCode")) { - nullSourceCode += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("Timeout")) { - timeout += Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } else if (line.startsWith("TestingInfo")) { - TestingInfo +=Integer.parseInt(line.substring(line.lastIndexOf(":") + 1).trim()); - } - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - } - - - if (file.getName().startsWith("UnfixedV")) { - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - try { - while ((line = reader.readLine()) != null) { -// types1 - if (line.startsWith("## OAR [")) break; - String type = line.substring(0, line.indexOf(":")); - if (types1.containsKey(type)) { - types1.put(type, types1.get(type) + 1); - } else { - types1.put(type, 1); - } - if (line.startsWith("#NullSourceCode:")) { - System.out.println(line); - } - } - } catch(IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - } - } - - Map types = new HashMap<>(); -// FileInputStream fis = new FileInputStream("../FPM_Violations/OAR.FPM.4222208.stderr"); -// Scanner scanner = new Scanner(fis); -// while (scanner.hasNextLine()) { -// String line = scanner.nextLine(); -// if (line.startsWith("## OAR [")) break; -// String type = line.substring(0, line.indexOf(":")); -// if (types.containsKey(type)) { -// types.put(type, types.get(type) + 1); -// } else { -// types.put(type, 1); -// } -// } -// scanner.close(); -// fis.close(); -// int sum = 0; -// int sum2 = 0; -// for (Map.Entry entry : types.entrySet()) { -// System.out.println(entry.getKey() + ": " + entry.getValue()); -// if (!entry.getKey().startsWith("#PureDeletion")) { -// if (!entry.getKey().startsWith("#Timeout") && !entry.getKey().startsWith("#TestViolation")) -// sum += entry.getValue(); -// else sum2 += entry.getValue(); -// } -// } - int sum3 = 0; - int sum4 = 0; - int sum5 = 0; - for (Map.Entry entry : types1.entrySet()) { - System.out.println(entry.getKey() + ": " + entry.getValue()); - if (!entry.getKey().startsWith("#PureDeletion")) { - if (!entry.getKey().startsWith("#Timeout") && !entry.getKey().startsWith("#TestViolation")) - sum3 += entry.getValue(); - else sum4 += entry.getValue(); - sum5+= entry.getValue(); - } - } - System.out.println(sum5); - - System.out.println(i); - System.out.println("\n\nStatistics:\nPositions: " + positions); - System.out.println("NumViolations: " + numV); - System.out.println("\nTestViolation: " + testAlarms + " :: " + types.get("#TestViolation") + " :: " + types1.get("#TestViolation")); - System.out.println("NullGumTreeResults: " + nullGumTreeResults + " :: " + types.get("#NullGumTreeResults") + " :: " + types1.get("#NullGumTreeResults")); - System.out.println("NoSourceCodeChange: " + noSourceCodeChagnes + " :: " + types.get("#NoSourceCodeChange") + " :: " + types1.get("#NoSourceCodeChange")); - System.out.println("NoStatementChange: " + noStatementChanges + " :: " + types.get("#NoStatementChange") + " :: " + types1.get("#NoStatementChange")); - System.out.println("NullDiffEntry: " + nullDiffentry + " :: " + types.get("#NullDiffEntry") + " :: " + types1.get("#NullDiffEntry")); - System.out.println("NullMatchedGumTreeResult: " + nullMappingGumTreeResults + " :: " + types.get("#NullMatchedGumTreeResult") + " :: " + types1.get("#NullMatchedGumTreeResult")); - System.out.println("PureDeletion: " + pureDeletion + " :: " + types.get("#PureDeletion") + " :: " + types1.get("#PureDeletion")); - System.out.println("LargeHunk: " + largeHunk + " :: " + types.get("#LargeHunk") + " :: " + types1.get("#LargeHunk")); - System.out.println("NullSourceCode: " + nullSourceCode + " :: " + types.get("#NullSourceCode") + " :: " + types1.get("#NullSourceCode")); - System.out.println("Timeout: " + timeout + " :: " + types.get("#Timeout") + " :: " + types1.get("#Timeout")); - System.out.println("TestingInfo: " + TestingInfo + " :: " + types.get("#TestingInfo") + " :: " + types1.get("#TestingInfo")); -// System.out.println("A: " + (positions + testAlarms + timeout)); -// System.out.println("B: " + (numV + testAlarms + timeout)); - System.out.println(testAlarms + nullGumTreeResults + noSourceCodeChagnes + noStatementChanges + - nullDiffentry + nullMappingGumTreeResults + nullSourceCode + timeout + TestingInfo); -// System.out.println(nullGumTreeResults + noSourceCodeChagnes + noStatementChanges + -// nullDiffentry + nullMappingGumTreeResults + nullSourceCode + TestingInfo); -// System.out.println(testAlarms + timeout); -// System.out.println(sum); -// System.out.println(sum2); - System.out.println(sum3); - System.out.println(sum4); - System.out.println(types1); - /*32690 56237 ,, 88927 31782 - * Statistics: - -TestViolation: 4682 :: null :: null -NullGumTreeResults: 0 :: null :: null -NoSourceCodeChange: 7010 :: null :: 6984 -NoStatementChange: 163 :: null :: 163 -NullDiffEntry: 6943 :: null :: 6943 -NullMatchedGumTreeResult: 25747 :: null :: 25747 -PureDeletion: 10815 :: null :: 10815 -LargeHunk: 6318 :: null :: 6318 -NullSourceCode: 1025 :: null :: 1025 -Timeout: 0 :: null :: null -TestingInfo: 0 :: null :: null -A: 4682 -B: 4682 -51888 -47206 -4682 -47180 -0 - */ - } - - public static void statistics(String fileName, String type, Map map, int totalQ, int totalS) throws IOException { - FileInputStream fis = new FileInputStream(fileName); - Scanner scanner = new Scanner(fis); - - Map violationTypesMap = new HashMap<>(); - Map projectsMap = new HashMap<>(); - Map perVperProjMap = new HashMap<>(); - Map> perVProjs = new HashMap<>(); - Map> widespreadViolationsMap = new HashMap<>(); - - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - String[] elements = line.split(","); - String projectName = elements[0]; - String violationType = elements[1]; - int quantity = Integer.parseInt(elements[2]); - - addToMap(projectsMap, projectName, quantity); - addToMap(violationTypesMap, violationType, quantity); - addToMap(perVperProjMap, projectName + "," + violationType, quantity); - - if (widespreadViolationsMap.containsKey(violationType)) { - List projectList = widespreadViolationsMap.get(violationType); - if (!projectList.contains(projectName)) { - projectList.add(projectName); - } - } else { - List projectList = new ArrayList<>(); - projectList.add(projectName); - widespreadViolationsMap.put(violationType, projectList); - } - - if (perVProjs.containsKey(violationType)) { - perVProjs.get(violationType).add(projectName); - } else { - List projs = new ArrayList<>(); - projs.add(projectName); - perVProjs.put(violationType, projs); - } - } - - scanner.close(); - fis.close(); - - - // Category - MapSorter sorter = new MapSorter(); - violationTypesMap = sorter.sortByValueDescending(violationTypesMap); - projectsMap = sorter.sortByValueDescending(projectsMap); - - Map categories = new HashMap<>(); - Map> categoryVList = new HashMap<>(); - String content = FileHelper.readFile("../FPM_Violations/RQ1/ViolationCategory.list"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split("@@"); - categories.put(elements[1], elements[0]); // Violation type, category - } - reader.close(); - - // Sort Violation types by widespread. - Map widespreadOfAllViolations = new HashMap<>(); - for (Map.Entry> entry : widespreadViolationsMap.entrySet()) { - widespreadOfAllViolations.put(entry.getKey(), entry.getValue().size()); - } - widespreadOfAllViolations = sorter.sortByValueDescending(widespreadOfAllViolations); - StringBuilder wbuilder = new StringBuilder("Type,Identifier,Quantity,Category\n"); - int identifier1 = 0; - for (Map.Entry entry : widespreadOfAllViolations.entrySet()) { - identifier1 ++; - String violationType = entry.getKey(); - String category = categories.get(violationType); - if (category == null || category.equals("null")) { - category = "Other"; - } - wbuilder.append(violationType + "," + identifier1 + "," + entry.getValue() + "," + category + "\n"); - - if (categoryVList.containsKey(category)) { - categoryVList.get(category).add(violationType); - } else { - List list = new ArrayList<>(); - list.add(violationType); - categoryVList.put(category, list); - } - } - - FileHelper.outputToFile("../FPM_Violations/RQ1/Widespread-per-" + type + "V-Type.csv", wbuilder, false); - - // output statistics - List sortedViolationTypes = new ArrayList<>(); - - Map quantityOfCategory = new HashMap<>(); - Map> violationTypesOfCategory = new HashMap<>(); - Map> projectsOfCategory = new HashMap<>(); - StringBuilder violationsBuilder = new StringBuilder("Type,Identifier,Quantity,Ratio,Widespread,Ratio2, Categories\n"); - int identifier = 0; - for (Map.Entry entry : violationTypesMap.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - identifier ++; - String category = categories.get(violationType); - if (category == null || category.equals("null")) { - category = "Other"; - } - int spread = widespreadViolationsMap.get(violationType).size(); - violationsBuilder.append(violationType + "," + identifier + "," + quantity + "," + ((double) quantity / totalQ * 100) + "," - + spread + "," + ((double) spread / totalS * 100) + "," + category + "\n"); - - if (quantityOfCategory.containsKey(category)) { - quantityOfCategory.put(category, quantityOfCategory.get(category) + quantity); - } else { - quantityOfCategory.put(category, quantity); - } - - if (violationTypesOfCategory.containsKey(category)) { - List violationTypes = violationTypesOfCategory.get(category); - if (!violationTypes.contains(violationType)) { - violationTypes.add(violationType); - } - } else { - List violationTypes = new ArrayList<>(); - violationTypes.add(violationType); - violationTypesOfCategory.put(category, violationTypes); - } - - if (projectsOfCategory.containsKey(category)) { - List projs = projectsOfCategory.get(category); - List projs2 = perVProjs.get(violationType); - for (String proj : projs2) { - if (!projs.contains(proj)) { - projs.add(proj); - } - } - } else { - projectsOfCategory.put(category, perVProjs.get(violationType)); - } - - sortedViolationTypes.add(violationType); - - map.put(violationType, quantity); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-" + type + "V-Type.csv", violationsBuilder, false); - - StringBuilder pBuilder = new StringBuilder("Project,Quantity\n"); - List projectNames = new ArrayList<>(); - for (Map.Entry entry : projectsMap.entrySet()) { - String project = entry.getKey(); - pBuilder.append(project + "," + entry.getValue() + "\n"); - projectNames.add(project); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-" + type + "Proj.csv", pBuilder, false); - - StringBuilder categoryBuilder = new StringBuilder("Category,Quantity,Types,Projects\n"); - for (Map.Entry entry : quantityOfCategory.entrySet()) { - String key = entry.getKey(); - categoryBuilder.append(key + "," + entry.getValue() + "," + violationTypesOfCategory.get(key).size() + "," + projectsOfCategory.get(key).size() + "\n"); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-" + type + "Category.csv", categoryBuilder, false); - - StringBuilder builder = new StringBuilder("Projects"); - String a = ""; - String b = ""; - for (int i = 0; i < sortedViolationTypes.size(); i ++) { - builder.append("," + sortedViolationTypes.get(i)); - if (i < 50) { - a += "a$" + sortedViolationTypes.get(i) + ","; - b += "'" + (i + 1) + "',"; - } - } - builder.append("\n"); - System.out.println(a); - System.out.println(b); -// for (int i = 0; i < sortedViolationTypes.size(); i ++) { -// builder.append("," + i); -// } -// builder.append("\n"); - StringBuilder bui = new StringBuilder(); - for (int i = 0; i < projectNames.size(); i++) { - String projectName = projectNames.get(i); - builder.append(projectName); - - for (int j = 0; j < sortedViolationTypes.size(); j ++) { - String violationType = sortedViolationTypes.get(j); - String key = projectName + "," + violationType; - Integer value = perVperProjMap.get(key); - if (value == null) { - value = 0; - } else { - bui.append(projectName).append(",").append(violationType).append(",").append(value).append(",").append(categories.get(violationType) == null ? "Other" : categories.get(violationType)).append("\n"); - } - builder.append("," + value); - } - builder.append("\n"); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type.csv", builder, false); - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type___.csv", bui, false); - - StringBuilder ssbuilder = new StringBuilder("Type, Identifier, Quantity, Category\n"); - Map perTypePerProj = new HashMap<>(); - Map> categoryProjects = new HashMap<>(); - - List others = new ArrayList<>(); - for (int j = 0; j < sortedViolationTypes.size(); j ++) { - String violationType = sortedViolationTypes.get(j); - List projs = new ArrayList<>(); - - for (int i = 0; i < projectNames.size(); i++) { - String projectName = projectNames.get(i); - String key = projectName + "," + violationType; - Integer value = perVperProjMap.get(key); - - if (value != null) { - String category = categories.get(violationType); - if (category == null || category.equals("null")) { - category = "Other"; - if (!others.contains(violationType)) { - others.add(violationType); - } - } - ssbuilder.append(violationType + "," + (j + 1) + "," + value + "," + category + "\n"); - - projs.add(value); - - if (categoryProjects.containsKey(category)) { - List projects = categoryProjects.get(category); - if (!projects.contains(projectName)) { - projects.add(projectName); - } - } else { - List projects = new ArrayList<>(); - projects.add(projectName); - categoryProjects.put(category, projects); - } - } - } - ListSorter sorter2 = new ListSorter(projs); - projs = sorter2.sortAscending(); - int index = projs.size() % 2 == 0 ? projs.size() / 2 - 1 : projs.size() / 2; - perTypePerProj.put(violationType, projs.get(index)); - } - - System.out.println(others); - - for (Map.Entry> entry : categoryVList.entrySet()) { - System.out.println(entry.getKey() + ":" + entry.getValue().size() + ":" + categoryProjects.get(entry.getKey()).size()); - } - - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type2.csv", ssbuilder, false); - StringBuilder ssbuilder2 = new StringBuilder("Type, Identifier, Quantity, Category\n"); - perTypePerProj = sorter.sortByValueDescending(perTypePerProj); - int j = 0; - for (Map.Entry entry : perTypePerProj.entrySet()) { - String violationType = entry.getKey(); -// System.out.println(entry.getValue()); - j ++; - for (int i = 0; i < projectNames.size(); i++) { - String projectName = projectNames.get(i); - String key = projectName + "," + violationType; - Integer value = perVperProjMap.get(key); - - if (value != null) { - String category = categories.get(violationType); - if (category == null || category.equals("null")) { - category = "Other"; - } - ssbuilder2.append(violationType + "," + j + "," + value + "," + category + "\n"); - } - } - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-" + type + "type3.csv", ssbuilder2, false); -// StringBuilder pVpPBuilder = new StringBuilder(); -// for (Map.Entry entry : perVperProjMap.entrySet()) { -// pVpPBuilder.append(entry.getKey() + "," + entry.getValue() + "\n"); -// } -// FileHelper.outputToFile("../FPM_Violations/RQ1/Per-project-per-" + type + "type.csv", pVpPBuilder, false); - } - - private static void addToMap(Map map, String key, int value) { - if (map.containsKey(key)) { - map.put(key, map.get(key) + value); - } else { - map.put(key, value); - } - } - - public static void quantityOfEachViolationType() { - Map violationQuantities = readTypeQuantityMap("../FPM_Violations/RQ1/distinct-per-vtype.csv"); - - Map violationWidespread = readWidespread("../FPM_Violations/RQ1/distinct-per-project-vtype.csv"); - - StringBuilder buidler = new StringBuilder("Violation Type, Identifier, Quantity, Quantity of Projects, Ratio\n"); - int identifier = 0; - double totality = 15961605d; - int sum = 0; - for (Map.Entry entry : violationQuantities.entrySet()) { - String key = entry.getKey(); - identifier ++; - int quantity = entry.getValue(); - sum += quantity; - buidler.append(key + "," + identifier + "," + quantity + "," + violationWidespread.get(key) + "," + (sum / totality) + "\n"); -// if (identifier >= 50) break; - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-V-type.csv", buidler, false); - } - - public static void widespreadOfEachViolationType() { - Map violationWidespread = readWidespread("../FPM_Violations/RQ1/distinct-per-project-vtype.csv"); - System.out.println("Violation types: " + violationWidespread.size()); - - StringBuilder buidler = new StringBuilder("Violation Type, Identifier, Quantity of Projects\n"); - int identifier = 0; - for (Map.Entry entry : violationWidespread.entrySet()) { - identifier ++; - buidler.append(entry.getKey() + "," + identifier + "," + entry.getValue() + "\n"); -// if (identifier >= 50) break; - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Widespread-per-V-type.csv", buidler, false); - } - - public static void statisticWithCategories() throws IOException { - Map categories = new HashMap<>(); - String content = FileHelper.readFile("../FPM_Violations/RQ1/ViolationCategory.list"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split("@@"); - categories.put(elements[1], elements[0]); // Violation type, category - } - reader.close(); - - Map quantityOfCategory = new HashMap<>(); - - String content2 = FileHelper.readFile("../FPM_Violations/RQ1/distinct-per-vtype.csv"); - reader = new BufferedReader(new StringReader(content2)); - line = reader.readLine(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - String violationType = elements[0]; - int quantity = Integer.parseInt(elements[1]); - String category = categories.get(violationType); - if (quantityOfCategory.containsKey(category)) { - quantityOfCategory.put(category, quantityOfCategory.get(category) + quantity); - } else { - quantityOfCategory.put(category, quantity); - } - } - reader.close(); - - String categoryQuantity = "Category Type, Quantity\n"; - for (Map.Entry entry : quantityOfCategory.entrySet()) { - categoryQuantity += entry.getKey() + "," + entry.getValue() + "\n"; - } - - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-Category.csv", categoryQuantity, false); - } - - public static void reloadData() { - // ordered projects by quantity of violations - Map projectQuantities = readTypeQuantityMap("../FPM_Violations/RQ1/distinct-per-project.csv"); - List projectNames = new ArrayList<>(); - for (Map.Entry entry : projectQuantities.entrySet()) { - projectNames.add(entry.getKey()); - } - - // get ordered types by quantity of violations. - Map violations = readTypeQuantityMap("../FPM_Violations/RQ1/distinct-per-vtype.csv"); - List violationTypes = new ArrayList<>(); - for (Map.Entry entry : violations.entrySet()) { - violationTypes.add(entry.getKey()); - } - - Map perVperProjs = readData("../FPM_Violations/RQ1/distinct-per-project-vtype.csv"); - - StringBuilder builder = new StringBuilder("Projects"); - for (int i = 0; i < violationTypes.size(); i ++) { - builder.append("," + violationTypes.get(i)); - } - builder.append("\n"); - for (int i = 0; i < projectNames.size(); i++) { - String projectName = projectNames.get(i); - builder.append(projectName); - for (int j = 0; j < violationTypes.size(); j ++) { - String violationType = violationTypes.get(j); - String key = projectName + "," + violationType; - String value = perVperProjs.get(key); - if (value == null) { - value = "0"; - } - builder.append("," + value); - - } - builder.append("\n"); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-type.csv", builder, false); - } - - public static void statisticOfFixedViolations() throws IOException { - String fileName = "../FPM_Violations/RQ1/fixed-alarms-v1.0.list"; - FileInputStream fis = new FileInputStream(fileName); - Scanner scanner = new Scanner(fis); - - Map violations = new HashMap<>(); - Map projects = new HashMap<>(); - Map perVperPro = new HashMap<>(); - Map> widespreadFixedV = new HashMap<>(); - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - String[] elements = line.split(":"); - String violationType = elements[0]; - String projectName = elements[1]; - - if (violations.containsKey(violationType)) { - violations.put(violationType, violations.get(violationType) + 1); - } else { - violations.put(violationType, 1); - } - - if (projects.containsKey(projectName)) { - projects.put(projectName, projects.get(projectName) + 1); - } else { - projects.put(projectName, 1); - } - - String perVperProj = projectName + "," + violationType; - if (perVperPro.containsKey(perVperProj)) { - perVperPro.put(perVperProj, perVperPro.get(perVperProj) + 1); - } else { - perVperPro.put(perVperProj, 1); - } - - if (widespreadFixedV.containsKey(violationType)) { - List projectList = widespreadFixedV.get(violationType); - if (!projectList.contains(projectName)) { - projectList.add(projectName); - } - } else { - List projectList = new ArrayList<>(); - projectList.add(projectName); - widespreadFixedV.put(violationType, projectList); - } - } - - scanner.close(); - fis.close(); - - MapSorter sorter = new MapSorter(); - violations = sorter.sortByValueDescending(violations); - projects = sorter.sortByValueDescending(projects); - - Map categories = new HashMap<>(); - String content = FileHelper.readFile("../FPM_Violations/RQ1/ViolationCategory.list"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split("@@"); - categories.put(elements[1], elements[0]); // Violation type, category - } - reader.close(); - - List violationTypes = new ArrayList<>(); - - Map quantityOfCategory = new HashMap<>(); - StringBuilder violationsBuilder = new StringBuilder(); - for (Map.Entry entry : violations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - - violationsBuilder.append(violationType + "," + quantity + "," + widespreadFixedV.get(violationType).size() + "\n"); - - String category = categories.get(violationType); - if (quantityOfCategory.containsKey(category)) { - quantityOfCategory.put(category, quantityOfCategory.get(category) + quantity); - } else { - quantityOfCategory.put(category, quantity); - } - - violationTypes.add(violationType); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-FixedV-Type.csv", violationsBuilder, false); - - StringBuilder pBuilder = new StringBuilder(); - List projectNames = new ArrayList<>(); - for (Map.Entry entry : projects.entrySet()) { - String project = entry.getKey(); - pBuilder.append(project + "," + entry.getValue() + "\n"); - projectNames.add(project); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-FixedV-Proj.csv", pBuilder, false); - - StringBuilder categoryBuilder = new StringBuilder(); - for (Map.Entry entry : quantityOfCategory.entrySet()) { - categoryBuilder.append(entry.getKey() + "," + entry.getValue() + "\n"); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Quantity-per-Fixed-Category.csv", categoryBuilder, false); - - StringBuilder builder = new StringBuilder("Projects"); - for (int i = 0; i < violationTypes.size(); i ++) { - builder.append("," + violationTypes.get(i)); - if (i < 500) { - } - } - builder.append("\n"); - for (int i = 0; i < projectNames.size(); i++) { - String projectName = projectNames.get(i); - builder.append(projectName); - for (int j = 0; j < violationTypes.size(); j ++) { - String violationType = violationTypes.get(j); - String key = projectName + "," + violationType; - Integer value = perVperPro.get(key); - if (value == null) { - value = 0; - } - builder.append("," + value); - } - builder.append("\n"); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-project-per-Fixed-type.csv", builder, false); - - StringBuilder pVpPBuilder = new StringBuilder(); - for (Map.Entry entry : perVperPro.entrySet()) { - pVpPBuilder.append(entry.getKey() + "," + entry.getValue() + "\n"); - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Per-project-per-Fixed-type.csv", pVpPBuilder, false); - } - - public static void fixedVSunfixed() throws IOException { - String fileName = "../FPM_Violations/RQ1/Quantity-per-V-type.csv"; // all violations - Map allViolations = readTypeQuantityMap(fileName); - String file = "../FPM_Violations/RQ1/Quantity-per-FixedV-Type.csv"; // fixed violations - Map fixedViolations = readTypeQuantityMap(file); - - MapSorter sorter = new MapSorter<>(); - allViolations = sorter.sortByValueDescending(allViolations); - StringBuilder builder = new StringBuilder("Type,fixed,unfixed,all,fixed Ratio,unfixed Ratio\n"); - for (Map.Entry entry : allViolations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - Integer fixedQuantity = fixedViolations.get(violationType); - if (fixedQuantity == null) { - builder.append(violationType + "," + 0 + "," + quantity + "," + quantity + ",0.0,1\n"); - } else { - builder.append(violationType + "," + fixedQuantity + "," + (quantity) - + "," + quantity + "," + ((double)fixedQuantity) / ((double) quantity) - + "," + ((double)(quantity)) / ((double) quantity) + "\n"); - } - } - FileHelper.outputToFile("../FPM_Violations/RQ1/Distribution-per-Fixed-type-VS-per-unFixed-type.csv", builder, false); - } - - private static Map readData(String fileName) { - Map perVperPros = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(fileName); - scanner = new Scanner(fis); - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - String[] elements = line.split(","); - String key = elements[0] + "," + elements[1]; - String value = elements[2]; - perVperPros.put(key, value); - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return perVperPros; - } - - private static Map readTypeQuantityMap(String fileName) { - Map map = new HashMap<>(); - String fileContent = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(fileContent)); - - try { - String line= reader.readLine(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - map.put(elements[0], Integer.valueOf(elements[2])); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - MapSorter sorter = new MapSorter<>(); - map = sorter.sortByValueDescending(map); - return map; - } - - private static Map readWidespread(String fileName) { - Map violationWidespread = new HashMap(); - - String fileContent = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(fileContent)); - - try { - String line = null; - while ((line = reader.readLine()) != null) { - String[] strArray = line.split(","); - String key = strArray[1]; - if (violationWidespread.containsKey(key)) { - violationWidespread.put(key, violationWidespread.get(key) + 1); - } else { - violationWidespread.put(key, 1); - } - -// String[] elements = line.split(","); -// violationWidespread.put(elements[0], Integer.valueOf(elements[1])); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - MapSorter sorter = new MapSorter<>(); - violationWidespread = sorter.sortByValueDescending(violationWidespread); - return violationWidespread; - } -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities.java b/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities.java deleted file mode 100644 index 58b276a..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities.java +++ /dev/null @@ -1,243 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.MapSorter; - -public class TenFoldPossibilities { - - public static void main(String[] args) throws IOException { - rankingInTenFolds("../FPM_Violations/RQ1/TenFolds/", "../FPM_Violations/RQ1/Quantity-per-V-type.csv", "TenFolds"); // ten folds of all projects. - rankingInTenFolds("../FPM_Violations/RQ1/FixedTenFolds-1/", "../FPM_Violations/RQ1/Quantity-per-FixedV-Type.csv", "FixedTenFolds-1");// all fixed violation types are contained. - } - - public static void rankingInTenFolds(String tenFoldFiles, String typeFile, String outputPath) throws NumberFormatException, IOException { - List files = FileHelper.getAllFilesInCurrentDiectory(tenFoldFiles, ".list"); - - Map> tenFoldsOfAllViolationTypes = new HashMap<>(); - Map> tenFoldsOfAllFixedViolationTypes1 = new HashMap<>(); - Map> tenFoldsOfAllFixedViolationTypes2 = new HashMap<>(); - Map> testingTenFoldsOfAllViolationTypes = new HashMap<>(); - Map> testingTenFoldsOfAllFixedViolationTypes1 = new HashMap<>(); - Map> testingTenFoldsOfAllFixedViolationTypes2 = new HashMap<>(); - for (int i = 0; i < 10; i ++) { - List projects = selectPorjects(files, i); - - // the distribution of all violation types in these 9 sub-sets. - Map violations = new HashMap<>(); - int quantityOfAllViolations = readViolationsPerProject(violations, projects, "../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv"); - // the distribution of all fixed violation types in these 9 sub-sets. - Map fixedViolations = new HashMap<>(); - int quantityOfAllFixedViolations = readViolationsPerProject(fixedViolations, projects, "../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv"); - - // Ratio of each violation type in all violations. - Map ratioOfEachViolationType = new HashMap<>(); // ratio of each violation type - Map ratioOfEachFixedViolationType1 = new HashMap<>(); // quantity of each fixed violation type / quantity of each violation type. - Map ratioOfEachFixedViolationType2 = new HashMap<>(); // quantity of each fixed violation type / quantityOfAllFixedViolations - - for (Map.Entry entry : violations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - double ratio = (double) quantity / quantityOfAllViolations; - ratioOfEachViolationType.put(violationType, ratio); - - if (fixedViolations.containsKey(violationType)) { - int quantity1 = fixedViolations.get(violationType); - double ratio1 = (double)quantity1 / quantity; - double ratio2 = (double)quantity1 / quantityOfAllFixedViolations; - ratioOfEachFixedViolationType1.put(violationType, ratio1); - ratioOfEachFixedViolationType2.put(violationType, ratio2); - } else { - ratioOfEachFixedViolationType1.put(violationType, 0d); - } - } - - tenFoldsOfAllViolationTypes.put(i, ratioOfEachViolationType); - tenFoldsOfAllFixedViolationTypes1.put(i, ratioOfEachFixedViolationType1); - tenFoldsOfAllFixedViolationTypes2.put(i, ratioOfEachFixedViolationType2); - - - // Testing Data - List testingProjects = readList(files.get(i)); - Map testingViolations = new HashMap<>(); - int testingQuantitifOfAllViolations = readViolationsPerProject(testingViolations, testingProjects, "../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv"); - Map testingFixedViolations = new HashMap<>(); - int testingQuantityOfAllFixedViolations = readViolationsPerProject(testingFixedViolations, testingProjects, "../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv"); - - Map testingRatioOfEachViolationType = new HashMap<>(); - Map testingRatioOfEachFixedViolationType1 = new HashMap<>(); - Map testingRatioOfEachFixedViolationType2 = new HashMap<>(); - - for (Map.Entry entry : testingViolations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - double ratio = (double) quantity / testingQuantitifOfAllViolations; - - testingRatioOfEachViolationType.put(violationType, ratio); - if (testingFixedViolations.containsKey(violationType)) { - int quantity1 = testingFixedViolations.get(violationType); - testingRatioOfEachFixedViolationType1.put(violationType, (double)quantity1 / quantity); - testingRatioOfEachFixedViolationType2.put(violationType, (double)quantity1 / testingQuantityOfAllFixedViolations); - } else { - testingRatioOfEachFixedViolationType1.put(violationType, 0d); - } - } - testingTenFoldsOfAllViolationTypes.put(i, testingRatioOfEachViolationType); - testingTenFoldsOfAllFixedViolationTypes1.put(i, testingRatioOfEachFixedViolationType1); - testingTenFoldsOfAllFixedViolationTypes2.put(i, testingRatioOfEachFixedViolationType2); - } - - List violationTypes = readTypes(typeFile); - outputTenFolds(tenFoldsOfAllViolationTypes, testingTenFoldsOfAllViolationTypes, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-violation-type.csv"); - outputTenFolds(tenFoldsOfAllFixedViolationTypes1, testingTenFoldsOfAllFixedViolationTypes1, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-fixed-violation-type1.csv"); - outputTenFolds(tenFoldsOfAllFixedViolationTypes2, testingTenFoldsOfAllFixedViolationTypes2, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-fixed-violation-type2.csv"); - } - - private static List readTypes(String fileName) throws IOException { - List violationTypes = new ArrayList<>(); - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = reader.readLine(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - violationTypes.add(elements[0]); - } - reader.close(); - return violationTypes; - } - - private static void outputTenFolds(Map> ratiosMap, Map> testingMap, List violationTypes, String fileName) { - StringBuilder builder = new StringBuilder("Violatype, 0, 0-R, 0-T, 0-T-R, 1, 1-R, 1-T, 1-T-R, 2, 2-R, 2-T, 2-T-R, 3, 3-R, 3-T, 3-T-R, 4, 4-R, 4-T, 4-T-R, 5, 5-R, 5-T, 5-T-R, 6, 6-R, 6-T, 6-T-R, 7, 7-R, 7-T, 7-T-R, 8, 8-R, 8-T, 8-T-R, 9, 9-R, 9-T, 9-T-R\n"); - - Map> ratiosRankingMap = new HashMap<>(); - Map> testingDataRankingMap = new HashMap<>(); - - for (String type : violationTypes) { - builder.append(type); - for (int i = 0; i < 10; i ++) { - Map ratios = ratiosMap.get(i); - Map testingData = testingMap.get(i); - - Map ratiosRanking; - Map testingDataRanking; - if (!ratiosRankingMap.containsKey(i)) { - ratiosRanking = rankAlarmTypes(ratios); - testingDataRanking = rankAlarmTypes(testingData); - } else { - ratiosRanking = ratiosRankingMap.get(i); - testingDataRanking = testingDataRankingMap.get(i); - } - - - if (ratios.containsKey(type)) { - builder.append(", " + ratios.get(type));//.toString().replace(".", ",") - } else { - builder.append(", 0.0"); - } - if (ratiosRanking.containsKey(type)) { - builder.append(", " + ratiosRanking.get(type)); - } else { - builder.append(", " + (ratiosRanking.size() + 1)); - } - if (testingData.containsKey(type)) { - builder.append(", " + testingData.get(type)); - } else { - builder.append(", 0.0"); - } - if (testingDataRanking.containsKey(type)) { - builder.append(", " + testingDataRanking.get(type)); - } else { - builder.append(", " + (testingDataRanking.size() + 1)); - } - } - builder.append("\n"); - } - FileHelper.outputToFile(fileName, builder, false); - } - - private static Map rankAlarmTypes(Map possibilityMap) { - MapSorter sorter = new MapSorter<>(); - possibilityMap = sorter.sortByValueDescending(possibilityMap); - Map ranking = new HashMap<>(); - int ranker = 0; - double possibility = 0; - for (Map.Entry entry : possibilityMap.entrySet()) { - String alarmType = entry.getKey(); - double value = entry.getValue(); - if (possibility != value) { - ranker = ranking.size() + 1; - } - ranking.put(alarmType, ranker); - } - return ranking; - } - - private static int readViolationsPerProject(Map violations, List projects, String fileName) throws NumberFormatException, IOException { - int quantityOfAllViolations = 0; - - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - String projectName = elements[0]; - if (projects.contains(projectName)) { - String alarmType = elements[1]; - int quantity = Integer.parseInt(elements[2]); - - quantityOfAllViolations += quantity; - if (violations.containsKey(alarmType)) { - violations.put(alarmType, violations.get(alarmType) + quantity); - } else { - violations.put(alarmType, quantity); - } - } - } - reader.close(); - return quantityOfAllViolations; - } - - private static List selectPorjects(List files, int i) { - List projects = new ArrayList<>(); - for (File file : files) { - if (file.getName().equals("Fold_" + i + ".list")) { - continue; - } - - projects.addAll(readList(file)); - } - return projects; - } - - private static List readList(File file) { - List projects = new ArrayList<>(); - - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - projects.add(line); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return projects; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities2.java b/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities2.java deleted file mode 100644 index 96ba1b6..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities2.java +++ /dev/null @@ -1,256 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.MapSorter; - -/** - * Fixed violation types are selected by their widespread. - * - * @author kui.liu - * - */ -public class TenFoldPossibilities2 { - - public static void main(String[] args) throws IOException { - rankingInTenFolds("../FPM_Violations/RQ1/FixedTenFolds-W/", "../FPM_Violations/RQ1/Widespread-per-FixedV-Type.csv", "FixedTenFolds-W"); - } - - public static void rankingInTenFolds(String tenFoldFiles, String typeFile, String outputPath) throws NumberFormatException, IOException { - int topNumber = 10; - List violationTypes = readTypes(typeFile, topNumber); - - List files = FileHelper.getAllFilesInCurrentDiectory(tenFoldFiles, ".list"); - - Map> tenFoldsOfAllViolationTypes = new HashMap<>(); - Map> tenFoldsOfAllFixedViolationTypes1 = new HashMap<>(); - Map> tenFoldsOfAllFixedViolationTypes2 = new HashMap<>(); - Map> testingTenFoldsOfAllViolationTypes = new HashMap<>(); - Map> testingTenFoldsOfAllFixedViolationTypes1 = new HashMap<>(); - Map> testingTenFoldsOfAllFixedViolationTypes2 = new HashMap<>(); - for (int i = 0; i < 10; i ++) { - List projects = selectPorjects(files, i); - - // all violations in these 9 sub-sets. - Map violations = new HashMap<>(); - int quantityOfAllViolations = readViolationsPerProject(violationTypes, violations, projects, "../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv"); - Map fixedViolations = new HashMap<>(); - int quantityOfAllFixedViolations = readViolationsPerProject(violationTypes, fixedViolations, projects, "../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv"); - - // Ratio of each violation type in all violations. - Map ratioOfEachViolationType = new HashMap<>(); // ratio of each violation type - Map ratioOfEachFixedViolationType1 = new HashMap<>(); // quantity of each fixed violation type / quantity of each violation type. - Map ratioOfEachFixedViolationType2 = new HashMap<>(); // quantity of each fixed violation type / quantityOfAllFixedViolations - - for (Map.Entry entry : violations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - double ratio = (double) quantity / quantityOfAllViolations; - ratioOfEachViolationType.put(violationType, ratio); - - if (fixedViolations.containsKey(violationType)) { - int quantity1 = fixedViolations.get(violationType); - double ratio1 = (double)quantity1 / quantity; - double ratio2 = (double)quantity1 / quantityOfAllFixedViolations; - ratioOfEachFixedViolationType1.put(violationType, ratio1); - ratioOfEachFixedViolationType2.put(violationType, ratio2); - } else { - ratioOfEachFixedViolationType1.put(violationType, 0d); - } - } - - tenFoldsOfAllViolationTypes.put(i, ratioOfEachViolationType); - tenFoldsOfAllFixedViolationTypes1.put(i, ratioOfEachFixedViolationType1); - tenFoldsOfAllFixedViolationTypes2.put(i, ratioOfEachFixedViolationType2); - - - // Testing Data - List testingProjects = readList(files.get(i)); - Map testingViolations = new HashMap<>(); - int testingQuantitifOfAllViolations = readViolationsPerProject(violationTypes, testingViolations, testingProjects, "../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv"); - Map testingFixedViolations = new HashMap<>(); - int testingQuantityOfAllFixedViolations = readViolationsPerProject(violationTypes, testingFixedViolations, testingProjects, "../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv"); - - Map testingRatioOfEachViolationType = new HashMap<>(); - Map testingRatioOfEachFixedViolationType1 = new HashMap<>(); - Map testingRatioOfEachFixedViolationType2 = new HashMap<>(); - - for (Map.Entry entry : testingViolations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - double ratio = (double) quantity / testingQuantitifOfAllViolations; - - testingRatioOfEachViolationType.put(violationType, ratio); - if (testingFixedViolations.containsKey(violationType)) { - int quantity1 = testingFixedViolations.get(violationType); - testingRatioOfEachFixedViolationType1.put(violationType, (double)quantity1 / quantity); - testingRatioOfEachFixedViolationType2.put(violationType, (double)quantity1 / testingQuantityOfAllFixedViolations); - } else { - testingRatioOfEachFixedViolationType1.put(violationType, 0d); - } - } - testingTenFoldsOfAllViolationTypes.put(i, testingRatioOfEachViolationType); - testingTenFoldsOfAllFixedViolationTypes1.put(i, testingRatioOfEachFixedViolationType1); - testingTenFoldsOfAllFixedViolationTypes2.put(i, testingRatioOfEachFixedViolationType2); - } - - outputTenFolds(tenFoldsOfAllViolationTypes, testingTenFoldsOfAllViolationTypes, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-violation-type-" + topNumber + ".csv"); - outputTenFolds(tenFoldsOfAllFixedViolationTypes1, testingTenFoldsOfAllFixedViolationTypes1, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-fixed-violation-type1-" + topNumber + ".csv"); - outputTenFolds(tenFoldsOfAllFixedViolationTypes2, testingTenFoldsOfAllFixedViolationTypes2, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-fixed-violation-type2-" + topNumber + ".csv"); - } - - private static List readTypes(String fileName, int number) throws IOException { - List violationTypes = new ArrayList<>(); - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = reader.readLine(); - int counter = 0; - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - violationTypes.add(elements[0]); - - if (++counter == number) break; - } - reader.close(); - return violationTypes; - } - - private static void outputTenFolds(Map> ratiosMap, Map> testingMap, List violationTypes, String fileName) { - StringBuilder builder = new StringBuilder("Violatype, 0, 0-R, 0-T, 0-T-R, 1, 1-R, 1-T, 1-T-R, 2, 2-R, 2-T, 2-T-R, 3, 3-R, 3-T, 3-T-R, 4, 4-R, 4-T, 4-T-R, 5, 5-R, 5-T, 5-T-R, 6, 6-R, 6-T, 6-T-R, 7, 7-R, 7-T, 7-T-R, 8, 8-R, 8-T, 8-T-R, 9, 9-R, 9-T, 9-T-R\n"); - - Map> ratiosRankingMap = new HashMap<>(); - Map> testingDataRankingMap = new HashMap<>(); - - for (String type : violationTypes) { - builder.append(type); - for (int i = 0; i < 10; i ++) { - Map ratios = ratiosMap.get(i); - Map testingData = testingMap.get(i); - - Map ratiosRanking; - Map testingDataRanking; - if (!ratiosRankingMap.containsKey(i)) { - ratiosRanking = rankAlarmTypes(ratios); - testingDataRanking = rankAlarmTypes(testingData); - } else { - ratiosRanking = ratiosRankingMap.get(i); - testingDataRanking = testingDataRankingMap.get(i); - } - - - if (ratios.containsKey(type)) { - builder.append(", " + ratios.get(type));//.toString().replace(".", ",") - } else { - builder.append(", 0.0"); - } - if (ratiosRanking.containsKey(type)) { - builder.append(", " + ratiosRanking.get(type)); - } else { - builder.append(", " + (ratiosRanking.size() + 1)); - } - if (testingData.containsKey(type)) { - builder.append(", " + testingData.get(type)); - } else { - builder.append(", 0.0"); - } - if (testingDataRanking.containsKey(type)) { - builder.append(", " + testingDataRanking.get(type)); - } else { - builder.append(", " + (testingDataRanking.size() + 1)); - } - } - builder.append("\n"); - } - FileHelper.outputToFile(fileName, builder, false); - } - - private static Map rankAlarmTypes(Map possibilityMap) { - MapSorter sorter = new MapSorter<>(); - possibilityMap = sorter.sortByValueDescending(possibilityMap); - Map ranking = new HashMap<>(); - int ranker = 0; - double possibility = 0; - for (Map.Entry entry : possibilityMap.entrySet()) { - String alarmType = entry.getKey(); - double value = entry.getValue(); - if (possibility != value) { - ranker = ranking.size() + 1; - } - ranking.put(alarmType, ranker); - } - return ranking; - } - - private static int readViolationsPerProject(List violationTypes, Map violations, List projects, String fileName) throws NumberFormatException, IOException { - int quantityOfAllViolations = 0; - - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - String projectName = elements[0]; - if (projects.contains(projectName)) { - String alarmType = elements[1]; - - if (violationTypes.contains(alarmType)) { - int quantity = Integer.parseInt(elements[2]); - - quantityOfAllViolations += quantity; - if (violations.containsKey(alarmType)) { - violations.put(alarmType, violations.get(alarmType) + quantity); - } else { - violations.put(alarmType, quantity); - } - } - - } - } - reader.close(); - return quantityOfAllViolations; - } - - private static List selectPorjects(List files, int i) { - List projects = new ArrayList<>(); - for (File file : files) { - if (file.getName().equals("Fold_" + i + ".list")) { - continue; - } - - projects.addAll(readList(file)); - } - return projects; - } - - private static List readList(File file) { - List projects = new ArrayList<>(); - - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - projects.add(line); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return projects; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities3.java b/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities3.java deleted file mode 100644 index 3aabe88..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/TenFoldPossibilities3.java +++ /dev/null @@ -1,256 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.MapSorter; - -/** - * Fixed violation types are selected by their quantities. - * - * @author kui.liu - * - */ -public class TenFoldPossibilities3 { - - public static void main(String[] args) throws IOException { - rankingInTenFolds("../FPM_Violations/RQ1/TenFolds/", "../FPM_Violations/RQ1/Quantity-per-V-type.csv", "TenFolds-Q"); // ten folds of all projects. -// rankingInTenFolds("../FPM_Violations/RQ1/FixedTenFolds-Q/", "../FPM_Violations/RQ1/Quantity-per-FixedV-Type.csv", "FixedTenFolds-Q"); - } - - public static void rankingInTenFolds(String tenFoldFiles, String typeFile, String outputPath) throws NumberFormatException, IOException { - int topNumber = 70; - List violationTypes = readTypes(typeFile, topNumber); - - List files = FileHelper.getAllFilesInCurrentDiectory(tenFoldFiles, ".list"); - - Map> tenFoldsOfAllViolationTypes = new HashMap<>(); - Map> tenFoldsOfAllFixedViolationTypes1 = new HashMap<>(); - Map> tenFoldsOfAllFixedViolationTypes2 = new HashMap<>(); - Map> testingTenFoldsOfAllViolationTypes = new HashMap<>(); - Map> testingTenFoldsOfAllFixedViolationTypes1 = new HashMap<>(); - Map> testingTenFoldsOfAllFixedViolationTypes2 = new HashMap<>(); - for (int i = 0; i < 10; i ++) { - List projects = selectPorjects(files, i); - - // all violations in these 9 sub-sets. - Map violations = new HashMap<>(); - int quantityOfAllViolations = readViolationsPerProject(violationTypes, violations, projects, "../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv"); - Map fixedViolations = new HashMap<>(); - int quantityOfAllFixedViolations = readViolationsPerProject(violationTypes, fixedViolations, projects, "../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv"); - - // Ratio of each violation type in all violations. - Map ratioOfEachViolationType = new HashMap<>(); // ratio of each violation type - Map ratioOfEachFixedViolationType1 = new HashMap<>(); // quantity of each fixed violation type / quantity of each violation type. - Map ratioOfEachFixedViolationType2 = new HashMap<>(); // quantity of each fixed violation type / quantityOfAllFixedViolations - - for (Map.Entry entry : violations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - double ratio = (double) quantity / quantityOfAllViolations; - ratioOfEachViolationType.put(violationType, ratio); - - if (fixedViolations.containsKey(violationType)) { - int quantity1 = fixedViolations.get(violationType); - double ratio1 = (double)quantity1 / quantity; - double ratio2 = (double)quantity1 / quantityOfAllFixedViolations; - ratioOfEachFixedViolationType1.put(violationType, ratio1); - ratioOfEachFixedViolationType2.put(violationType, ratio2); - } else { - ratioOfEachFixedViolationType1.put(violationType, 0d); - } - } - - tenFoldsOfAllViolationTypes.put(i, ratioOfEachViolationType); - tenFoldsOfAllFixedViolationTypes1.put(i, ratioOfEachFixedViolationType1); - tenFoldsOfAllFixedViolationTypes2.put(i, ratioOfEachFixedViolationType2); - - - // Testing Data - List testingProjects = readList(files.get(i)); - Map testingViolations = new HashMap<>(); - int testingQuantitifOfAllViolations = readViolationsPerProject(violationTypes, testingViolations, testingProjects, "../FPM_Violations/RQ1/all-leafnodes-per-project-vtype.csv"); - Map testingFixedViolations = new HashMap<>(); - int testingQuantityOfAllFixedViolations = readViolationsPerProject(violationTypes, testingFixedViolations, testingProjects, "../FPM_Violations/RQ1/distinct-fixed-summary-per-project-vtype.csv"); - - Map testingRatioOfEachViolationType = new HashMap<>(); - Map testingRatioOfEachFixedViolationType1 = new HashMap<>(); - Map testingRatioOfEachFixedViolationType2 = new HashMap<>(); - - for (Map.Entry entry : testingViolations.entrySet()) { - String violationType = entry.getKey(); - int quantity = entry.getValue(); - double ratio = (double) quantity / testingQuantitifOfAllViolations; - - testingRatioOfEachViolationType.put(violationType, ratio); - if (testingFixedViolations.containsKey(violationType)) { - int quantity1 = testingFixedViolations.get(violationType); - testingRatioOfEachFixedViolationType1.put(violationType, (double)quantity1 / quantity); - testingRatioOfEachFixedViolationType2.put(violationType, (double)quantity1 / testingQuantityOfAllFixedViolations); - } else { - testingRatioOfEachFixedViolationType1.put(violationType, 0d); - } - } - testingTenFoldsOfAllViolationTypes.put(i, testingRatioOfEachViolationType); - testingTenFoldsOfAllFixedViolationTypes1.put(i, testingRatioOfEachFixedViolationType1); - testingTenFoldsOfAllFixedViolationTypes2.put(i, testingRatioOfEachFixedViolationType2); - } - - outputTenFolds(tenFoldsOfAllViolationTypes, testingTenFoldsOfAllViolationTypes, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-violation-type" + topNumber + ".csv"); - outputTenFolds(tenFoldsOfAllFixedViolationTypes1, testingTenFoldsOfAllFixedViolationTypes1, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-fixed-violation-type1-" + topNumber + ".csv"); - outputTenFolds(tenFoldsOfAllFixedViolationTypes2, testingTenFoldsOfAllFixedViolationTypes2, violationTypes, "../FPM_Violations/RQ1/" + outputPath + "/Ten-fold-all-fixed-violation-type2-" + topNumber + ".csv"); - } - - private static List readTypes(String fileName, int number) throws IOException { - List violationTypes = new ArrayList<>(); - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = reader.readLine(); - int counter = 0; - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - violationTypes.add(elements[0]); - - if(++ counter == number) break; - } - reader.close(); - return violationTypes; - } - - private static void outputTenFolds(Map> ratiosMap, Map> testingMap, List violationTypes, String fileName) { - StringBuilder builder = new StringBuilder("Violatype, 0, 0-R, 0-T, 0-T-R, 1, 1-R, 1-T, 1-T-R, 2, 2-R, 2-T, 2-T-R, 3, 3-R, 3-T, 3-T-R, 4, 4-R, 4-T, 4-T-R, 5, 5-R, 5-T, 5-T-R, 6, 6-R, 6-T, 6-T-R, 7, 7-R, 7-T, 7-T-R, 8, 8-R, 8-T, 8-T-R, 9, 9-R, 9-T, 9-T-R\n"); - - Map> ratiosRankingMap = new HashMap<>(); - Map> testingDataRankingMap = new HashMap<>(); - - for (String type : violationTypes) { - builder.append(type); - for (int i = 0; i < 10; i ++) { - Map ratios = ratiosMap.get(i); - Map testingData = testingMap.get(i); - - Map ratiosRanking; - Map testingDataRanking; - if (!ratiosRankingMap.containsKey(i)) { - ratiosRanking = rankAlarmTypes(ratios); - testingDataRanking = rankAlarmTypes(testingData); - } else { - ratiosRanking = ratiosRankingMap.get(i); - testingDataRanking = testingDataRankingMap.get(i); - } - - - if (ratios.containsKey(type)) { - builder.append(", " + ratios.get(type));//.toString().replace(".", ",") - } else { - builder.append(", 0.0"); - } - if (ratiosRanking.containsKey(type)) { - builder.append(", " + ratiosRanking.get(type)); - } else { - builder.append(", " + (ratiosRanking.size() + 1)); - } - if (testingData.containsKey(type)) { - builder.append(", " + testingData.get(type)); - } else { - builder.append(", 0.0"); - } - if (testingDataRanking.containsKey(type)) { - builder.append(", " + testingDataRanking.get(type)); - } else { - builder.append(", " + (testingDataRanking.size() + 1)); - } - } - builder.append("\n"); - } - FileHelper.outputToFile(fileName, builder, false); - } - - private static Map rankAlarmTypes(Map possibilityMap) { - MapSorter sorter = new MapSorter<>(); - possibilityMap = sorter.sortByValueDescending(possibilityMap); - Map ranking = new HashMap<>(); - int ranker = 0; - double possibility = 0; - for (Map.Entry entry : possibilityMap.entrySet()) { - String alarmType = entry.getKey(); - double value = entry.getValue(); - if (possibility != value) { - ranker = ranking.size() + 1; - } - ranking.put(alarmType, ranker); - } - return ranking; - } - - private static int readViolationsPerProject(List violationTypes, Map violations, List projects, String fileName) throws NumberFormatException, IOException { - int quantityOfAllViolations = 0; - - String content = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - String projectName = elements[0]; - if (projects.contains(projectName)) { - String alarmType = elements[1]; - if (violationTypes.contains(alarmType)) { - int quantity = Integer.parseInt(elements[2]); - - quantityOfAllViolations += quantity; - if (violations.containsKey(alarmType)) { - violations.put(alarmType, violations.get(alarmType) + quantity); - } else { - violations.put(alarmType, quantity); - } - } - - } - } - reader.close(); - return quantityOfAllViolations; - } - - private static List selectPorjects(List files, int i) { - List projects = new ArrayList<>(); - for (File file : files) { - if (file.getName().equals("Fold_" + i + ".list")) { - continue; - } - - projects.addAll(readList(file)); - } - return projects; - } - - private static List readList(File file) { - List projects = new ArrayList<>(); - - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - projects.add(line); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return projects; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/TenFoldProjs.java b/src/main/java/edu/lu/uni/serval/statistics/TenFoldProjs.java deleted file mode 100644 index f697a47..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/TenFoldProjs.java +++ /dev/null @@ -1,121 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Random; - -import edu.lu.uni.serval.utils.FileHelper; - -public class TenFoldProjs { - - public static void main(String[] args) { - List allProjects = readList("../FPM_Violations/RQ1/Quantity-per-Proj.csv"); - randomSeparateProjects(allProjects, "../FPM_Violations/RQ1/TenFolds/"); - List allFixedProjects = readList("../FPM_Violations/RQ1/Quantity-per-FixedProj.csv"); - randomSeparateProjects(allFixedProjects, "../FPM_Violations/RQ1/FixedTenFolds-1/"); - - List selectedProjects = selectFixedProjects("../FPM_Violations/RQ1/Quantity-per-FixedProj.csv"); - randomSeparateProjects(selectedProjects, "../FPM_Violations/RQ1/FixedTenFolds-2/"); - } - - private static void randomSeparateProjects(List projectNames, String outputPath) { - List selectedIndexes = new ArrayList<>(); - - int number = projectNames.size(); - int number2 = (int) Math.round((double) number / 10); - - - Map> map = new HashMap<>(); - - for (int i = 0; i < 9; i ++) { - int counter = 0; - List value = new ArrayList<>(); - - while (counter < number2) { - Random random = new Random(); - int index = random.nextInt(number); - if (!selectedIndexes.contains(index)) { - counter ++; - value.add(projectNames.get(index)); - selectedIndexes.add(index); - - if (selectedIndexes.size() == number) break; - } - } - - map.put(i, value); - } - - List value = new ArrayList<>(); - for (int i = 0; i < number; i ++) { - if (!selectedIndexes.contains(i)) { - value.add(projectNames.get(i)); - } - } - map.put(9, value); - - for (Map.Entry> entry : map.entrySet()) { - int key = entry.getKey(); - List projects = entry.getValue(); - System.out.println(projects.size()); - String pojectsStr = ""; - for (String project : projects) { - pojectsStr += project + "\n"; - } - FileHelper.outputToFile(outputPath + "Fold_" + key + ".list", pojectsStr, false); - } - } - - private static List selectFixedProjects(String fileName) { - List list = new ArrayList<>(); - String fileContent = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(fileContent)); - String line= null; - try { - line = reader.readLine(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(","); - list.add(elements[0]); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return list; - } - - private static List readList(String fileName) { - List list = new ArrayList<>(); - String fileContent = FileHelper.readFile(fileName); - BufferedReader reader = new BufferedReader(new StringReader(fileContent)); - String line= null; - try { - line = reader.readLine(); - while ((line = reader.readLine()) != null) { - list.add(line.split(",")[0]);; - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return list; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/UnhappenedTypesLiveStudy.java b/src/main/java/edu/lu/uni/serval/statistics/UnhappenedTypesLiveStudy.java deleted file mode 100644 index 12ea075..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/UnhappenedTypesLiveStudy.java +++ /dev/null @@ -1,73 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.MapSorter; - -public class UnhappenedTypesLiveStudy { - - public static void main(String[] args) throws IOException { - List top50Types = readTypes(); - String path = Configuration.ROOT_PATH + "RQ3_3/LiveStudy/BugsInfo/"; - File[] projects = new File(path).listFiles(); - Map map = new HashMap<>(); - int i = 0; - for (File project : projects) { - if (project.isDirectory()) { - File[] types = project.listFiles(); - List top50TypesCopy = new ArrayList<>(); - top50TypesCopy.addAll(top50Types); - for (File type :types) { - if (type.isDirectory()) { - String typeStr = type.getName(); - top50TypesCopy.remove(typeStr); - } - } - - System.out.println(project.getName() + "::"); - for (String type : top50TypesCopy) { - System.out.println(type); - if (map.containsKey(type)) { - map.put(type, map.get(type) + 1); - } else { - map.put(type, 1); - } - } - i ++; - if (i == 10) break; - } - } - - MapSorter sorter = new MapSorter<>(); - map = sorter.sortByValueDescending(map); - for (Map.Entry entry : map.entrySet()) { - System.out.println(entry.getKey() + "==" + entry.getValue()); - } - } - - private static List readTypes() throws IOException { - List types = new ArrayList<>(); - String content = FileHelper.readFile(Configuration.ROOT_PATH + "RQ1/Quantity-per-Fixed_1.0V-Type.csv"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - int i = 0; - while ((line = reader.readLine()) != null) { - String type = line.substring(0, line.indexOf(",")); - types.add(type); - i ++; - if (i == 51) break; - } - - return types; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/statistics/UnparsedFiles.java b/src/main/java/edu/lu/uni/serval/statistics/UnparsedFiles.java deleted file mode 100644 index a139fb0..0000000 --- a/src/main/java/edu/lu/uni/serval/statistics/UnparsedFiles.java +++ /dev/null @@ -1,55 +0,0 @@ -package edu.lu.uni.serval.statistics; - -import java.io.FileInputStream; -import java.io.IOException; -import java.util.ArrayList; -import java.util.List; -import java.util.Scanner; - -import edu.lu.uni.serval.FixPatternParser.violations.Violation; -import edu.lu.uni.serval.utils.FileHelper; - -public class UnparsedFiles { - - public static void main(String[] args) throws IOException { - FileInputStream fis = new FileInputStream("../FPM_Violations/OAR.FPM.4221129.stderr"); - Scanner scanner = new Scanner(fis); - List vList = new ArrayList<>(); - String test1 = ""; - String test2 = ""; - String test3 = ""; - int i = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - String[] elements = line.split(":"); - Violation v = new Violation(Integer.parseInt(elements[2]), Integer.parseInt(elements[3]), elements[4]); - v.setFileName(elements[1]); - if (vList.contains(v)) { - i ++; -// System.out.println(elements[0]); - } else { - vList.add(v); - } - if (line.startsWith("#TestViolation:")) { -// System.out.println(line); - if (elements[1].toLowerCase().contains("/test/")) { - test1 += elements[1] + "\n"; - } else if (elements[1].toLowerCase().contains("tests/")) { - test2 += elements[1] + "\n"; - } else { - test3 += elements[1] + "\n"; - } - } - } - - scanner.close(); - fis.close(); - - System.out.println(vList.size()); - System.out.println(i); - FileHelper.outputToFile("logs/test1.txt", test1, false); - FileHelper.outputToFile("logs/test2.txt", test2, false); - FileHelper.outputToFile("logs/test3.txt", test3, false); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/Alarm.java b/src/main/java/edu/lu/uni/serval/violation/Alarm.java deleted file mode 100644 index e566658..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/Alarm.java +++ /dev/null @@ -1,82 +0,0 @@ -package edu.lu.uni.serval.violation; - -import java.util.List; -import java.util.Map; - -public class Alarm { - - private String buggyCommitId; - private String buggyFileName; - private String fixedCommitId; - private String fixedFileName; - @Deprecated - private Map alarmTypes; - @Deprecated - private Map positions; - private List alarmTypesAndPositions; - - public Alarm(String buggyCommitId, String buggyFileName, String fixedCommitId, String fixedFileName) { - super(); - this.buggyCommitId = buggyCommitId; - this.buggyFileName = buggyFileName; - this.fixedCommitId = fixedCommitId; - this.fixedFileName = fixedFileName; - } - - public String getBuggyCommitId() { - return buggyCommitId; - } - - public String getBuggyFileName() { - return buggyFileName; - } - - public String getFixedCommitId() { - return fixedCommitId; - } - - public String getFixedFileName() { - return fixedFileName; - } - - @Deprecated - public Map getAlarmTypes() { - return alarmTypes; - } - - @Deprecated - public void setAlarmTypes(Map alarmTypes) { - this.alarmTypes = alarmTypes; - } - - @Deprecated - public Map getPositions() { - return positions; - } - - @Deprecated - public void setPositions(Map positions) { - this.positions = positions; - } - - public List getAlarmTypesAndPositions() { - return alarmTypesAndPositions; - } - - public void setAlarmTypesAndPositions(List alarmTypesAndPositions) { - this.alarmTypesAndPositions = alarmTypesAndPositions; - } - - @Override - public boolean equals(Object obj) { - if (obj instanceof Alarm) { - Alarm alarm = (Alarm) obj; - if (alarm.buggyCommitId.equals(this.buggyCommitId) && alarm.buggyFileName.equals(this.buggyFileName) - && alarm.fixedCommitId.equals(this.fixedCommitId) && alarm.fixedFileName.equals(this.fixedFileName)) { - return true; - } - } - return false; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/Violation.java b/src/main/java/edu/lu/uni/serval/violation/Violation.java deleted file mode 100644 index 27fb771..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/Violation.java +++ /dev/null @@ -1,31 +0,0 @@ -package edu.lu.uni.serval.violation; - -import java.util.ArrayList; -import java.util.List; - -/** - * Violation: all alarms identified by FindBugs in one java project. - * - * @author kui.liu - * - */ -public class Violation { - - private String project; - private List alarms; - - public Violation(String project) { - this.project = project; - this.alarms = new ArrayList<>(); - } - - public String getProject() { - return project; - } - - public List getAlarms() { - return alarms; - } - - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/code/parser/Test.java b/src/main/java/edu/lu/uni/serval/violation/code/parser/Test.java deleted file mode 100644 index e848b11..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/code/parser/Test.java +++ /dev/null @@ -1,223 +0,0 @@ -package edu.lu.uni.serval.violation.code.parser; - -import java.io.BufferedReader; -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.diffentry.DiffEntryHunk; -import edu.lu.uni.serval.diffentry.DiffEntryReader; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.ListSorter; - -public class Test { - - public static void main(String[] args) throws IOException { -// testV1(); -// testV2(); -// testV3("../FPM_Violations/OAR.FPM.4225346.stderr", "OUTPUT/unparsedviolations.txt"); -// testV4("../FPM_Violations/OAR.FPM.4222208.stderr"); - } - - public static void testV4(String inputFile) throws IOException { - FileInputStream fis = new FileInputStream(inputFile); - Scanner scanner = new Scanner(fis); - StringBuilder builder = new StringBuilder(); - -// boolean isDiff = false; - - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - if (line.startsWith("## OAR")) break; -// if (line.startsWith("#NullDiffEntry")) { -// isDiff = true; -// continue; -// } else if (line.startsWith("#")) { -// isDiff = false; -// continue; -// } -// if (!isDiff) continue; - - String[] elements = line.trim().split(":"); - String type = elements[0]; - - - if (type.equals("#NullDiffEntry")) { - List diffentryHunks = new DiffEntryReader().readHunks2(new File("/Users/kui.liu/Public/git/FPM_Violations/GumTreeInput/diffentries/" + elements[1].replace(".java", ".txt").trim())); - int startLine = Integer.parseInt(elements[2].trim()); - int endLine = Integer.parseInt(elements[3].trim()); - for (DiffEntryHunk hunk : diffentryHunks) { - int hunkStart = hunk.getBugLineStartNum(); - int hunkEnd = hunk.getBugRange() + hunkStart - 1; - - if (startLine <= hunkEnd && hunkStart <= endLine) { - builder.append("vi " + elements[1].replace(".java", ".txt") + "\n : " + elements[2] + " : " + elements[3] + " : " + elements[4] + "\n"); - } - } - } -// List diffentryHunks = new DiffEntryReader().readHunks2(new File("/Users/kui.liu/Public/git/FPM_Violations/GumTreeInput/diffentries/" + elements[0].replace(".java", ".txt").trim())); -// int startLine = Integer.parseInt(elements[1].trim()); -// int endLine = Integer.parseInt(elements[2].trim()); -// for (DiffEntryHunk hunk : diffentryHunks) { -// int hunkStart = hunk.getBugLineStartNum(); -// int hunkEnd = hunk.getBugRange() + hunkStart - 1; -// -// if (startLine <= hunkEnd && hunkStart <= endLine) { -// builder.append("vi " + elements[0].replace(".java", ".txt") + "\n : " + elements[1] + " : " + elements[2] + "\n"); //+ " : " + elements[4] -// } -// } - } - scanner.close(); - fis.close(); - - FileHelper.outputToFile("Dataset/a.txt", builder, false); - } - - public static void testV3(String inputFile, String outputFile) throws IOException { - FileInputStream fis = new FileInputStream(inputFile); - Scanner scanner = new Scanner(fis); - - Map> types = new HashMap<>(); - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - if (line.startsWith("## OAR")) break; - String[] elements = line.split(":"); - String type = elements[0]; - - if (types.containsKey(type)) { - String info = elements[1] + " : " + elements[2] + " : " + elements[3] + " : " + elements[4]; - if (!types.get(type).contains(info)) { - types.get(type).add(info); - } - } else { - List files = new ArrayList<>(); - files.add(elements[1] + " : " + elements[2] + " : " + elements[3] + " : " + elements[4]); - types.put(type, files); - } - } - scanner.close(); - fis.close(); - - StringBuilder builder = new StringBuilder(); - for (Map.Entry> entry : types.entrySet()) { - System.out.println(entry.getKey()); - if (entry.getKey().equals("#NoStatementChange")) { - // --- /dev/null - builder.append(entry.getKey() + "\n"); - List files = entry.getValue(); - for (String file : files) { - builder.append(" " + file + "\n"); - String fileName = Configuration.GUM_TREE_INPUT + "diffentries/" + file.substring(0, file.indexOf(".java")) + ".txt"; - String content = FileHelper.readFile(fileName); - if (!content.contains("--- /dev/null")) { - System.out.println(file.substring(0, file.indexOf(".java")) + ".txt"); - } - } - } - } - FileHelper.outputToFile(outputFile, builder, false); - } - - public static void testV2() throws IOException { - String content = FileHelper.readFile("logs/testV2.txt"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - Map> types = new HashMap<>(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(" : "); - String type = elements[0]; - - if (types.containsKey(type)) { - types.get(type).add(elements[1] + " : " + elements[2] + " : " + elements[3]); - } else { - List files = new ArrayList<>(); - files.add(elements[1] + " : " + elements[2] + " : " + elements[3]); - types.put(type, files); - } - } - reader.close(); - - StringBuilder builder = new StringBuilder(); - for (Map.Entry> entry : types.entrySet()) { - System.out.println(entry.getKey()); - builder.append(entry.getKey() + "\n"); - List files = entry.getValue(); - for (String file : files) { - builder.append(file + "\n"); - } - } - FileHelper.outputToFile("logs/MultiV.txt", builder, false); - } - - public static void testV1() throws IOException { - Map>> map = new HashMap<>(); - String content = FileHelper.readFile("OUTPUT/list-1.txt"); - BufferedReader reader = new BufferedReader(new StringReader(content)); - String line = null; - List types1 = new ArrayList<>(); - List types2 = new ArrayList<>(); - while ((line = reader.readLine()) != null) { - String[] elements = line.split(":"); - String type = elements[0]; - String startLine = elements[2]; - if (!"-1".equals(startLine)) { - startLine = "1"; - if (!types1.contains(type)) { - types1.add(type); - } - } else { - if (!types2.contains(type)) { - types2.add(type); - } - } - if (map.containsKey(startLine)) { - Map> types = map.get(startLine); - if (types.containsKey(type)) { - List files = types.get(type); - files.add(elements[1] + "\n" + elements[2] + " : " + elements[3]); - } else { - List files = new ArrayList<>(); - files.add(elements[1] + "\n" + elements[2] + " : " + elements[3]); - types.put(type, files); - } - } else { - Map> types = new HashMap<>(); - List files = new ArrayList<>(); - files.add(elements[1] + "\n" + elements[2] + " : " + elements[3]); - types.put(type, files); - map.put(startLine, types); - } - } - reader.close(); - - StringBuilder builder = new StringBuilder(); - for (Map.Entry>> entry : map.entrySet()) { - builder.append(entry.getKey() + "\n"); - List tList = null; - if (entry.getKey().equals("1")) { - tList = types1; - } else { - tList = types2; - } - ListSorter sorter = new ListSorter(tList); - tList = sorter.sortAscending(); - Map> types = entry.getValue(); - for (String type : tList) { - builder.append(" " + type + "\n"); - List files = types.get(type); - for (String file : files) { - builder.append(file + "\n"); - } - } - } - FileHelper.outputToFile("OUTPUT/NullV.txt", builder, false); - } - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolatePositionReader.java b/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolatePositionReader.java deleted file mode 100644 index 68bacd7..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolatePositionReader.java +++ /dev/null @@ -1,138 +0,0 @@ -package edu.lu.uni.serval.violation.code.parser; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import edu.lu.uni.serval.MultipleThreadsParser.MessageFile; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -/** - * Read violations' positions. - * - * Class name part, - * Field declaration, - * Initializer, - * Method name, - * Method body, - * Inner class, - * Anonymous class. - * - * @author kui.liu - * - */ -public class ViolatePositionReader { - /* - -0 : 1280 --1 : 15 -1 : 505 AnonymousClassDeclaration -23 : 7108 FieldDeclaration -71 : 310 EnumDeclaration -55 : 640 TypeDeclaration -72 : 87 EnumConstantDeclaration -28 : 1022 Initializer -31 : 77960 MethodDeclaration - - */ - public static void main(String[] args) throws NumberFormatException, IOException { - List msgFiles = getMessageFiles(Configuration.GUM_TREE_INPUT); - - Map map1 = new HashMap<>(); - Map> map2 = new HashMap<>(); - - StringBuilder zeorBuilder = new StringBuilder(); - StringBuilder minusOneBuilder = new StringBuilder(); - for (MessageFile file : msgFiles) { - -// if (!file.getPrevFile().getName().equals( -//"prev_ovgu-ccd-jchess_c3f4a0_bdca7bjchess#util#PixelCoordinateNotOnBoardException.java")) continue; - - String fileContent = FileHelper.readFile(file.getPositionFile()); - BufferedReader reader = null; - reader = new BufferedReader(new StringReader(fileContent)); - String line = null; - - while ((line = reader.readLine()) != null) { - String[] positionStr = line.split(":"); - int startLine = Integer.parseInt(positionStr[1]); - int endLine = Integer.parseInt(positionStr[2]); - String violationType = positionStr[0]; - - int range; - if (startLine != -1) { - ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(file.getPrevFile(), startLine, endLine); - alarmTree.locateParentNode(); - range = alarmTree.getViolationFinalStartLine(); - } else { - range = 0; - } - - if (map1.containsKey(range)) { - map1.put(range, map1.get(range) + 1); - } else { - map1.put(range, 1); - } - - if (map2.containsKey(violationType)) { - Map map = map2.get(violationType); - if (map.containsKey(range)) { - map.put(range, map.get(range) + 1); - } else { - map.put(range, 1); - } - } else { - Map map = new HashMap<>(); - map.put(range, 1); - map2.put(violationType, map); - } - - if (range == 0) { - zeorBuilder.append(line + ":" + file.getPrevFile().getName() + "\n"); - } else if (range == -1) { - minusOneBuilder.append(line + ":" + file.getPrevFile().getName() + "\n"); - } - } - - reader.close(); - } - for (Map.Entry entry : map1.entrySet()) { - System.out.println(entry.getKey() + " : " + entry.getValue()); - } - FileHelper.outputToFile("Dataset/0.list", zeorBuilder, false); - FileHelper.outputToFile("Dataset/1.list", minusOneBuilder, false); - } - - /** - * Get violation-related files. - * - * @param gumTreeInput - * @return - */ - public static List getMessageFiles(String gumTreeInput) { - String inputPath = gumTreeInput; // prevFiles revFiles diffentryFile positionsFile - File revFilesPath = new File(inputPath + "revFiles/"); - File[] revFiles = revFilesPath.listFiles(); // project folders - List msgFiles = new ArrayList<>(); - - for (File revFile : revFiles) { - if (revFile.getName().endsWith(".java")) { - String fileName = revFile.getName(); - File prevFile = new File(gumTreeInput + "prevFiles/prev_" + fileName);// previous file - fileName = fileName.replace(".java", ".txt"); - File positionFile = new File(gumTreeInput + "positions/" + fileName); // position file - MessageFile msgFile = new MessageFile(null, prevFile, null); - msgFile.setPositionFile(positionFile); - msgFiles.add(msgFile); - } - } - - return msgFiles; - } -} diff --git a/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationCodeParser.java b/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationCodeParser.java deleted file mode 100644 index 5f01175..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationCodeParser.java +++ /dev/null @@ -1,282 +0,0 @@ -package edu.lu.uni.serval.violation.code.parser; - -import java.io.BufferedReader; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; -import java.util.Scanner; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPatternParser.Tokenizer; -import edu.lu.uni.serval.FixPatternParser.violations.Violation; -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.gumtree.regroup.SimpleTree; -import edu.lu.uni.serval.gumtree.regroup.SimplifyTree; -import edu.lu.uni.serval.utils.FileHelper; - -public class ViolationCodeParser { - - private static Logger log = LoggerFactory.getLogger(ViolationCodeParser.class); - - public static void main(String[] args) { - /* - * Fixed violations: - * Violation code files. - * Position files. - */ -// String fixedViolationFilesPath = Configuration.GUM_TREE_INPUT + "prevFiles/"; -// String positionsFilePath = Configuration.GUM_TREE_INPUT + "positions/"; -// int subIndex = 5; -// String outputPath = Configuration.ROOT_PATH + "Alarms_tokens/fixedAlarms.list"; -// FileHelper.deleteFile(outputPath); -// new ViolationCodeParser().parse(fixedViolationFilesPath, positionsFilePath, subIndex, outputPath); - - /* - * UnFixed violations: - * Violation code files. - * Position files. - */ - String unfixedViolationFilesPath = Configuration.GUM_TREE_INPUT + "unfixAlarms/"; - String un_positionsFilePath = Configuration.GUM_TREE_INPUT + "un_positions/"; - int subIndex2 = 8; - String outputPath2 = Configuration.ROOT_PATH + "Alarms_tokens/unfixedAlarms.list"; - FileHelper.deleteFile(outputPath2); - new ViolationCodeParser().parse(unfixedViolationFilesPath, un_positionsFilePath, subIndex2, outputPath2); - } - - public void parse(String alarmFilesPath, String positionFilesPath, int subIndex, String outputPath) { - StringBuilder tokensBuilder = new StringBuilder(); - List javaFiles = FileHelper.getAllFilesInCurrentDiectory(alarmFilesPath, ".java"); - int counter = 0; - int a = 0; - int maxLength = 0; - for (File javaFile : javaFiles) { - String fileName = javaFile.getName().replace(".java", ".txt"); - fileName = fileName.substring(subIndex); - - List violations = readViolationInfo(positionFilesPath + fileName); - - for (Violation violation : violations) { - int startLine = violation.getStartLineNum(); - int endLine = violation.getEndLineNum(); - String alarmType = violation.getViolationType(); - -// if (endLine > startLine + 5) { -// log.warn("#Large_Violation_Hunk: " + fileName.replace("#", "/").replace(".txt", ".java") + ":" + startLine + ":" + endLine + ":" + alarmType); -// continue; -// } - - ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(javaFile, startLine, endLine); - alarmTree.extract(); - List matchedTrees = alarmTree.getViolationSourceCodeTrees(); - if (matchedTrees.size() == 0) { - System.out.println(fileName + " == " + startLine + " : " + endLine); - a ++; - log.warn("#Null_Violation_Hunk: " + fileName.replace("#", "/").replace(".txt", ".java") + ":" + startLine + ":" + endLine + ":" + alarmType); - continue; - } - SimpleTree simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, null); - children.add(simpleT); - } - simpleTree.setChildren(children); - - String tokens = Tokenizer.getTokensDeepFirst(simpleTree); - String[] tokensArray = tokens.split(" "); - int length = tokensArray.length; - if (length > maxLength) maxLength = length; - tokensBuilder.append(alarmType + ":" + fileName + ":" + alarmTree.getViolationFinalStartLine() + ":" + alarmTree.getViolationFinalEndLine() + ":" + tokens + "\n"); - counter ++; - if (counter % 5000 == 0) { - FileHelper.outputToFile(outputPath, tokensBuilder, true); - tokensBuilder.setLength(0); - } - } - } - - System.out.println(counter); - System.out.println(a); - System.out.println("MaxLength: " + maxLength); - FileHelper.outputToFile(outputPath, tokensBuilder, true); - tokensBuilder.setLength(0); - } - - public String sourceCode = ""; - public String tokens = ""; - public String sizes = ""; - - public void parse(File javaFile, File positionFile) { - - List violations = readViolationInfo(positionFile); - for (Violation violation : violations) { - int startLine = violation.getStartLineNum(); - int endLine = violation.getEndLineNum(); - - String type = violation.getViolationType(); - -// if (violationTypes != null && violationTypes.contains(type)) { -//// if (endLine > startLine + 5) { -////// log.warn("#Large_Violation_Hunk: " + javaFile.getName() + ":" + startLine + ":" + endLine + ":" + alarmType); -//// continue; -//// } -// } - SimpleTree simpleTree = null; - if ("EQ_DOESNT_OVERRIDE_EQUALS".equals(type)|| "HE_EQUALS_USE_HASHCODE".equals(type) || "HE_INHERITS_EQUALS_USE_HASHCODE".equals(type)|| - "SE_NO_SUITABLE_CONSTRUCTOR".equals(type) || "RI_REDUNDANT_INTERFACES".equals(type) - ||"CN_IDIOM".equals(type)||"SE_NO_SERIALVERSIONID".equals(type) || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(type)) { - ViolationSourceCodeTree parser = new ViolationSourceCodeTree(javaFile, violation.getStartLineNum(), violation.getEndLineNum()); - ITree classNameTree = parser.getClassNameTokens(); - simpleTree = new SimplifyTree().canonicalizeSourceCodeTree(classNameTree, null); - - startLine = parser.getViolationFinalStartLine(); - endLine = parser.getViolationFinalEndLine(); - } else { - ViolationSourceCodeTree alarmTree = new ViolationSourceCodeTree(javaFile, startLine, endLine); - alarmTree.extract(); - List matchedTrees = alarmTree.getViolationSourceCodeTrees(); - if (matchedTrees.size() == 0) { - System.err.println("#Null_Violation_Hunk: " + javaFile.getName() + ":" + startLine + ":" + endLine); - continue; - } - simpleTree = new SimpleTree(); - simpleTree.setLabel("Block"); - simpleTree.setNodeType("Block"); - List children = new ArrayList<>(); - - for (ITree matchedTree : matchedTrees) { - SimpleTree simpleT = new SimplifyTree().canonicalizeSourceCodeTree(matchedTree, null); - children.add(simpleT); - } - simpleTree.setChildren(children); - - startLine = alarmTree.getViolationFinalStartLine(); - endLine = alarmTree.getViolationFinalEndLine(); - } - String tokens = Tokenizer.getTokensDeepFirst(simpleTree); - String[] tokensArray = tokens.split(" "); - int length = tokensArray.length; - sizes += length + "\n"; - this.tokens += tokens + "\n"; - String sourceCode = readSourceCode(javaFile, startLine, endLine, violation.getViolationType()); - this.sourceCode += sourceCode + "\n"; - } - } - - private String readSourceCode(File javaFile, int startLine, int endLine, String violationType) { - StringBuilder sourceCode = new StringBuilder("##Source_Code:\n"); - sourceCode.append(violationType).append("\n"); - sourceCode.append(javaFile.getName().replaceAll("#", "/")).append("\nPosition: ").append(startLine).append(" : ").append(endLine).append("\n"); - FileInputStream fis = null; - Scanner scanner = null; - - try { - fis = new FileInputStream(javaFile); - scanner = new Scanner(fis); - int counter = 0; - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - counter ++; - if (startLine <= counter && counter <= endLine) { - sourceCode.append(line + "\n"); - } - if (counter == endLine) break; - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - return sourceCode.toString(); - } - - private List readViolationInfo(String file) { - List violations = new ArrayList<>(); - - String fileContent = FileHelper.readFile(file); - BufferedReader reader = null; - reader = new BufferedReader(new StringReader(fileContent)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - String[] positionStr = line.split(":"); - int startLine = Integer.parseInt(positionStr[1]); - int endLine = Integer.parseInt(positionStr[2]); - String alarmType = positionStr[0]; - - if (startLine == -1 || endLine == -1) { - log.warn("#Illegal_Line_Position: " + FileHelper.getFileName(file).replace("#", "/").replace(".txt", ".java") + ":" + startLine + ":" + endLine + ":" + alarmType); - continue; - } - - Violation violation = new Violation(startLine, endLine, alarmType); - violations.add(violation); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return violations; - } - - private List readViolationInfo(File file) { - List violations = new ArrayList<>(); - - String fileContent = FileHelper.readFile(file); - BufferedReader reader = null; - reader = new BufferedReader(new StringReader(fileContent)); - String line = null; - try { - while ((line = reader.readLine()) != null) { - String[] positionStr = line.split(":"); - int startLine = Integer.parseInt(positionStr[1]); - int endLine = Integer.parseInt(positionStr[2]); - String alarmType = positionStr[0]; - - if (startLine == -1 || endLine == -1) { - continue; - } - - Violation violation = new Violation(startLine, endLine, alarmType); - violations.add(violation); - } - } catch (IOException e) { - e.printStackTrace(); - } finally { - try { - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - return violations; - } - - public void setTypes(List violationTypes) { - this.violationTypes = violationTypes; - } - private List violationTypes = null; -} diff --git a/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationSourceCodeTree.java b/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationSourceCodeTree.java deleted file mode 100644 index d48173a..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/code/parser/ViolationSourceCodeTree.java +++ /dev/null @@ -1,785 +0,0 @@ -package edu.lu.uni.serval.violation.code.parser; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import org.eclipse.jdt.core.dom.CompilationUnit; - -import com.github.gumtreediff.tree.ITree; - -import edu.lu.uni.serval.FixPattern.utils.Checker; -import edu.lu.uni.serval.FixPatternParser.CUCreator; -import edu.lu.uni.serval.gumtree.GumTreeGenerator; -import edu.lu.uni.serval.gumtree.GumTreeGenerator.GumTreeType; - -public class ViolationSourceCodeTree { - - private File file; - private int violationStartLine; - private int violationEndLine; - private CompilationUnit cUnit; - - private int violationFinalStartLine = 0; - private int violationFinalEndLine; - - private List matchedTrees = new ArrayList<>(); - - public ViolationSourceCodeTree(File file, int violationStartLine, int violationEndLine) { - super(); - this.file = file; - this.violationStartLine = violationStartLine; - this.violationEndLine = violationEndLine; - - CUCreator cuCreator = new CUCreator(); - this.cUnit = cuCreator.createCompilationUnit(this.file); - } - - public ViolationSourceCodeTree(String fileName, int violationStartLine, int violationEndLine) { - this(new File(fileName), violationStartLine, violationEndLine); - } - - public List getViolationSourceCodeTrees() { - return this.matchedTrees; - } - - public int getViolationFinalStartLine() { - return violationFinalStartLine; - } - - public int getViolationFinalEndLine() { - return violationFinalEndLine; - } - - /** - * extract source code of violations in method body or field body. - */ - public void extract() { - ITree rootTree = new GumTreeGenerator().generateITreeForJavaFile(file, GumTreeType.EXP_JDT); - - List trees = rootTree.getChildren(); - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition - 1); - if (endLine < violationStartLine) continue; - - // FIXME the violation occurred in the Class Name - matchTrees(tree.getChildren()); - } - - int size = matchedTrees.size(); - if (size > 0) { - this.violationFinalStartLine = cUnit.getLineNumber(this.matchedTrees.get(0).getPos()); - ITree lastTree = matchedTrees.get(size - 1); - this.violationFinalEndLine = cUnit.getLineNumber(lastTree.getPos() + lastTree.getLength()); - } else { - System.err.println(this.file.getName() + " : " + this.violationStartLine + " : " + this.violationEndLine); - } - - } - - public void extract(String type) { - ITree rootTree = new GumTreeGenerator().generateITreeForJavaFile(file, GumTreeType.EXP_JDT); - - List trees = rootTree.getChildren(); - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition - 1); - if (endLine < violationStartLine) continue; - /* - violationT || - violationType.equals("UC_USELESS_CONDITION") - */ - if (type.equals("SE_NO_SERIALVERSIONID")) { - - } - // FIXME the violation occurred in the Class Name - matchTrees(tree.getChildren()); - } - - int size = matchedTrees.size(); - if (size > 0) { - this.violationFinalStartLine = cUnit.getLineNumber(this.matchedTrees.get(0).getPos()); - ITree lastTree = matchedTrees.get(size - 1); - this.violationFinalEndLine = cUnit.getLineNumber(lastTree.getPos() + lastTree.getLength()); - } else { - System.err.println(type + " : " + this.file.getName() + " : " + this.violationStartLine + " : " + this.violationEndLine); - } - - } - - private void matchTrees(List trees) { - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition); - if (endLine < violationStartLine) continue; - - if (endLine == violationEndLine) { - if (tree.getType() == 31) { // MethodDeclaration - matchTrees(tree.getChildren()); - } else if (isStatement(tree)) { - addToMatchedTrees(tree); - } else { - ITree parent = getParentStatement(tree); - if (parent == null) { - if (tree.getType() == 8) { // 8: Block - matchTrees(tree.getChildren()); - } - continue; - } - addToMatchedTrees(parent); - } - continue; - } - - if (startLine >= violationStartLine) { - if (isStatement(tree)) { - addToMatchedTrees(tree); - } else { - ITree parent = getParentStatement(tree); - if (parent == null) { - if (tree.getType() == 8) { - matchTrees(tree.getChildren()); - } - continue; - } - addToMatchedTrees(parent); - } - } else { -// if (tree.getType() == 14) { -// ITree parent = getParentStatement(tree); -// if (parent == null) { -// matchTrees(tree.getChildren()); -// } else { -// addToMatchedTrees(parent); -// } -// } else { -// matchTrees(tree.getChildren()); -// } - matchTrees(tree.getChildren()); - } - } - } - - private void addToMatchedTrees(ITree tree) { - if (!matchedTrees.contains(tree)) { - /* - * TODO with the same parent, or the sub trees. - * In the same method body. - */ - matchedTrees.add(tree); - } - int type = tree.getType(); - if (type == 8 || type == 12 || Checker.withBlockStatement(type)) { - int endLine = cUnit.getLineNumber(tree.getPos() + tree.getLength()); - if (endLine > violationEndLine) { - tree = removeBlock(tree); - } - } - } - - private ITree removeBlock(ITree tree) { - List oldChildren = tree.getChildren(); - List newChildren = new ArrayList<>(); - for (ITree child : oldChildren) { - int startPosition = child.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - int endPosition = startPosition + child.getLength(); - int endLine = cUnit.getLineNumber(endPosition); - if (endLine > this.violationEndLine) { - int type = child.getType(); - if (type == 8 || type == 12 || Checker.withBlockStatement(type)) { // 8: Block, CatchClause - child = removeBlock(child); - if (child.getChildren().size() == 0) { - continue; - } - } - } - newChildren.add(child); - } - tree.setChildren(newChildren); - return tree; - } - - private ITree getParentStatement(ITree tree) { - ITree parent = tree; - int type = parent.getType(); - do { - parent = parent.getParent(); - if (parent == null) { - return null; - } - - type = parent.getType(); - if (type == 1 || type == 31 || type == 55 || type == 71) { - // AnonymousClassDeclaration - // MethodDeclaration Initializer (type == 28) - // TypeDeclaration - // EnumDeclaration - return null; - } - } while (!isStatement(parent)); - - return parent; - } - - private boolean isStatement(ITree tree) { - int type = tree.getType(); // 8 Block - if (type == 12) return true; // catchClause - if (type == 23) return true; // FieldDeclaration - if (Checker.isStatement(type)) return true; - return false; - } - - public void locateParentNode(String type) { - ITree rootTree = new GumTreeGenerator().generateITreeForJavaFile(file, GumTreeType.EXP_JDT); - - List trees = rootTree.getChildren(); - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition - 1); - if (endLine < violationStartLine) continue; - - if (startLine == this.violationStartLine || endLine == this.violationEndLine) { - this.violationFinalStartLine = startLine; - this.violationFinalEndLine = endLine; - } - locateParentNode(tree.getChildren(), type); - } - } - - private void locateParentNode(List trees, String type) { - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition); - if (endLine < violationStartLine) { - continue; - } - - if (endLine < violationEndLine) { - if ("NM_SAME_SIMPLE_NAME_AS_INTERFACE".equals(type) || "NM_SAME_SIMPLE_NAME_AS_SUPERCLASS".equals(type) || "NM_CLASS_NAMING_CONVENTION".equals(type) - || "NM_CLASS_NOT_EXCEPTION".equals(type) || "RI_REDUNDANT_INTERFACES".equals(type) - // inner class - || "SE_INNER_CLASS".equals(type) || "SE_BAD_FIELD_INNER_CLASS".equals(type) || "SIC_INNER_SHOULD_BE_STATIC_ANON".equals(type) - || "SIC_INNER_SHOULD_BE_STATIC".equals(type) || "SIC_INNER_SHOULD_BE_STATIC_NEEDS_THIS".equals(type)) { - if (tree.getType() != 55) { - ITree parent = getParentTypeDeclaration(tree); - if (parent == null) { - this.violationFinalStartLine = -1; - break; - } - tree = parent; - } - startPosition = tree.getPos(); - this.violationFinalStartLine = cUnit.getLineNumber(startPosition); - endPosition = getClassBodyStartPosition(tree); - if (endPosition == 0) { - endPosition = startPosition + tree.getLength(); - } - this.violationFinalEndLine = cUnit.getLineNumber(endPosition); - } else if ("NM_METHOD_NAMING_CONVENTION".equals(type)){ - // method name level - if (tree.getType() != 31) { - ITree parent = getParentMethodDeclaration(tree); - if (parent == null) { - this.violationFinalStartLine = -1; - break; - } - tree = parent; - } - startPosition = tree.getPos(); - this.violationFinalStartLine = cUnit.getLineNumber(startPosition); - endPosition = getMethodBodyStartPosition(tree); - if (endPosition == 0) { - endPosition = startPosition + tree.getLength(); - } - this.violationFinalEndLine = cUnit.getLineNumber(endPosition); -// } else if ("SE_NO_SUITABLE_CONSTRUCTOR".equals(type) || "CN_IDIOM".equals(type) -// || "SE_NO_SERIALVERSIONID".equals(type) || "SE_NO_SUITABLE_CONSTRUCTOR_FOR_EXTERNALIZATION".equals(type) -// || "SE_COMPARATOR_SHOULD_BE_SERIALIZABLE".equals(type)) { -// this.violationFinalStartLine = -1; - } else { - this.violationFinalStartLine = -1; - } -// FileHelper.outputToFile("logs/testV2.txt", type + " : " + this.file.getName() + " : " + this.violationStartLine + " : " + this.violationEndLine + "\n", true); - break; - } - - int astNodeType = tree.getType(); - // Class Name(super class etc.), Field, initializer, EnumDeclaration, EnumConstantDeclaration, Method Name, method body, - if (astNodeType == 31 || astNodeType == 23 || astNodeType == 28 || astNodeType == 71 || astNodeType == 72 - || astNodeType == 1 || astNodeType == 55) {// inner class - // MethodDeclaration, FieldDeclaration, Initializer, EnumDeclaration, EnumConstantDeclaration, AnonymousClassDeclaration - this.violationFinalStartLine = startLine; - this.violationFinalEndLine = endLine; - break; - } else { - locateParentNode(tree.getChildren(), type); - } - } - } - - private int getMethodBodyStartPosition(ITree tree) { - List children = tree.getChildren(); - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - int type = child.getType(); - if (Checker.isStatement2(type)) { - if ( i > 0) { - child = children.get(i - 1); - return child.getPos() + child.getLength(); - } else { - return child.getPos() - 1; - } - } - } - return 0; - } - - private ITree getParentMethodDeclaration(ITree tree) { - ITree parent = tree; - int type = 0; - do { - parent = parent.getParent(); - if (parent == null) { - return null; - } - type = parent.getType(); - } while (type != 31); - return parent; - } - - private int getClassBodyStartPosition(ITree tree) { - List children = tree.getChildren(); - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - int type = child.getType(); - // Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation - if (type != 83 && type != 77 && type != 78 && type != 79 - && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 - && type != 76 && type != 84 && type != 87 && type != 88) { - // ArrayType, PrimitiveType, SimpleType, ParameterizedType, - // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType - if (type == 42 && child.getLabel().startsWith("ClassName:")) { - continue; - } - if (i > 0) { - child = children.get(i - 1); - return child.getPos() + child.getLength() + 1; - } else { - return child.getPos() - 1; - } - } - } - return 0; - } - - private ITree getParentTypeDeclaration(ITree tree) { - ITree parent = tree; - int type = 0; - do { - parent = parent.getParent(); - if (parent == null) { - return null; - } - type = parent.getType(); - } while (type != 55); - return parent; - } - - public void locateParentNode() { - ITree rootTree = new GumTreeGenerator().generateITreeForJavaFile(file, GumTreeType.EXP_JDT); - - List trees = rootTree.getChildren(); - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition - 1); - if (endLine < violationStartLine) continue; - - int type = tree.getType(); - switch (type) { - case 55: - this.classNamePosition = 1; - break; - case 71: - this.enumPosition = 1; - break; - case 72: - this.enumConsP = 1; - break; - default : - break; - } - locateParentNode(tree.getChildren()); - } - -// if (this.violationFinalStartLine == 0) { -// FileHelper.outputToFile("logs/testV1.txt", type + " : " + this.file.getName() + " : " + this.violationStartLine + " : " + this.violationEndLine + "\n", true); -// } - } - int methodPosition = 0; - int classNamePosition = 0; - int fieldPosition = 0; - int initializerP = 0; - int anonymousPosition = 0; - int enumPosition = 0; - int enumConsP = 0; - private void locateParentNode(List trees) { - boolean isBigRange = false; - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition); - if (endLine < violationStartLine) { - continue; - } - - int type = tree.getType(); - if (isBigRange) { - if (type == 31 || type == 55 || type == 23 || type == 28 || type == 71 || type == 72 - || type == 81 || type == 82|| type == 1) { - this.violationFinalStartLine = -1; - break; - } - } - - - if (endLine < violationEndLine) { - if (this.violationFinalStartLine == 0) { - this.violationFinalStartLine = type; - isBigRange = true; - continue; - } - } - - // Class Name(super class etc.), Method Name, - if (type == 31) { //MethodDeclaration - this.violationFinalStartLine = type; - this.methodPosition = 1; - locateParentNode(tree.getChildren()); - break; - } else if (type == 55) {// TypeDeclaration, inner class - this.violationFinalStartLine = type; - this.classNamePosition = 1; - locateParentNode(tree.getChildren()); - break; - } else if (type == 1) {// AnonymousClassDeclaration - this.violationFinalStartLine = type; - this.anonymousPosition = 1; - locateParentNode(tree.getChildren()); - break; - } else if (type == 23) {// FieldDeclaration - this.violationFinalStartLine = type; - this.fieldPosition = 1; - locateParentNode(tree.getChildren()); - break; - } else if (type == 28) {// Initializer - this.violationFinalStartLine = type; - this.initializerP = 1; - locateParentNode(tree.getChildren()); - break; - } else if (type == 71) {// EnumDeclaration - this.violationFinalStartLine = type; - this.enumPosition = 1; - locateParentNode(tree.getChildren()); - break; - } else if (type == 72) {// EnumConstantDeclaration - this.violationFinalStartLine = tree.getType(); - this.enumConsP = 1; - locateParentNode(tree.getChildren()); - break; - } else { - locateParentNode(tree.getChildren()); - } - } - } - - /** - * extract source code of violations. - */ - public void extract2() { - ITree rootTree = new GumTreeGenerator().generateITreeForJavaFile(file, GumTreeType.EXP_JDT); - - List trees = rootTree.getChildren(); - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition - 1); - if (endLine < violationStartLine) continue; - - matchTrees2(tree.getChildren()); - } - - int size = matchedTrees.size(); - if (size > 0) { - if (this.violationFinalStartLine != 0) { - this.violationFinalStartLine = cUnit.getLineNumber(this.matchedTrees.get(0).getPos()); - ITree lastTree = matchedTrees.get(size - 1); - this.violationFinalEndLine = cUnit.getLineNumber(lastTree.getPos() + lastTree.getLength()); - } - } else { - System.err.println(this.file.getName() + "===" + this.violationStartLine + ":" + this.violationEndLine); - } - - } - - private void matchTrees2(List trees) { - for (ITree tree : trees) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationEndLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition); - if (endLine < violationStartLine) continue; - - if (endLine == violationEndLine) { - if (tree.getType() == 31) { // MethodDeclaration - if (startLine == violationStartLine) { - int finalEndPosition = getMethodDeclarationWithoutBody(tree); - addToMatchedTrees(tree); - this.violationFinalStartLine = cUnit.getLineNumber(tree.getPos()); - this.violationFinalEndLine = cUnit.getLineNumber(finalEndPosition); - } else { - matchTrees(tree.getChildren()); - } - } else if (isStatement(tree)) { - addToMatchedTrees(tree); - } else { - ITree parent = getParentStatement2(tree); - if (parent == null) { - if (tree.getType() == 8) { // 8: Block - matchTrees(tree.getChildren()); - } - continue; - } else if (parent.getType() == 31) { // method name - if (startLine == violationStartLine || endLine < violationEndLine) { - int finalEndPosition = getMethodDeclarationWithoutBody(parent); - addToMatchedTrees(parent); - this.violationFinalStartLine = cUnit.getLineNumber(parent.getPos()); - this.violationFinalEndLine = cUnit.getLineNumber(finalEndPosition); - } - break; - } else if (parent.getType() == 55) { // class name - if (startLine == violationStartLine || endLine < violationEndLine) { - int finalEndPosition = getClassDecalrationWithoutBody(parent); - addToMatchedTrees(parent); - this.violationFinalStartLine = cUnit.getLineNumber(parent.getPos()); - this.violationFinalEndLine = cUnit.getLineNumber(finalEndPosition); - } - break; - } - addToMatchedTrees(parent); - } - continue; - } - - if (startLine >= violationStartLine) { - if (isStatement(tree)) { - addToMatchedTrees(tree); - } else { - ITree parent = getParentStatement2(tree); - if (parent == null) { - if (tree.getType() == 8) { - matchTrees(tree.getChildren()); - } - continue; - } else if (parent.getType() == 31) { // method name - if (startLine == violationStartLine || endLine < violationEndLine) { - int finalEndPosition = getMethodDeclarationWithoutBody(parent); - addToMatchedTrees(parent); - this.violationFinalStartLine = cUnit.getLineNumber(parent.getPos()); - this.violationFinalEndLine = cUnit.getLineNumber(finalEndPosition); - } - break; - } else if (parent.getType() == 55) { // class name - if (startLine == violationStartLine || endLine < violationEndLine) { - int finalEndPosition = getClassDecalrationWithoutBody(parent); - addToMatchedTrees(parent); - this.violationFinalStartLine = cUnit.getLineNumber(parent.getPos()); - this.violationFinalEndLine = cUnit.getLineNumber(finalEndPosition); - } - break; - } - addToMatchedTrees(parent); - } - } else { - matchTrees(tree.getChildren()); - } - } - } - - private int getMethodDeclarationWithoutBody(ITree tree) { - List children = tree.getChildren(); - List newChildren = new ArrayList<>(); - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - int type = child.getType(); - if (Checker.isStatement2(type)) { - if (i > 0) { - child = children.get(i - 1); - return child.getPos() + child.getLength() + 1; - } else { - return child.getPos() - 1; - } - } else { - newChildren.add(child); - } - } - tree.setChildren(newChildren); - return 0; - } - - private int getClassDecalrationWithoutBody(ITree tree) { - List children = tree.getChildren(); - List newChildren = new ArrayList<>(); - for (int i = 0, size = children.size(); i < size; i ++) { - ITree child = children.get(i); - int type = child.getType(); - // Modifier, NormalAnnotation, MarkerAnnotation, SingleMemberAnnotation - if (type != 83 && type != 77 && type != 78 && type != 79 - && type != 5 && type != 39 && type != 43 && type != 74 && type != 75 - && type != 76 && type != 84 && type != 87 && type != 88) { - // ArrayType, PrimitiveType, SimpleType, ParameterizedType, - // QualifiedType, WildcardType, UnionType, IntersectionType, NameQualifiedType - if (type == 42 && child.getLabel().startsWith("ClassName:")) { - newChildren.add(child); - continue; - } - if (i > 0) { - child = children.get(i - 1); - tree.setChildren(newChildren); - return child.getPos() + child.getLength() + 1; - } else { - tree.setChildren(newChildren); - return child.getPos() - 1; - } - } else { - newChildren.add(child); - } - } - tree.setChildren(newChildren); - return 0; - } - - private ITree getParentStatement2(ITree tree) { - ITree parent = tree; - do { - parent = parent.getParent(); - if (parent == null) { - return null; - } - - int type = parent.getType(); - if (type == 31 || type == 55) { - // MethodDeclaration - // TypeDeclaration - return parent; - } else if (type == 1 || type == 71) { - // AnonymousClassDeclaration - // EnumDeclaration - return null; - } - } while (!isStatement(parent)); - - return parent; - } - - public ITree getClassNameTokens() { - ITree classNameTree = null; - - ITree rootTree = new GumTreeGenerator().generateITreeForJavaFile(file, GumTreeType.EXP_JDT); - List trees = rootTree.getChildren(); - for (ITree tree : trees) { - int type = tree.getType(); - if (type == 55 || type == 71) { - classNameTree = tree; - ITree classNameTree2 = getClassNameTokens(tree.getChildren()); - if (classNameTree2 != null) { - classNameTree = classNameTree2; - } - } - } - - if (classNameTree != null) { - int finalEndPosition = getClassDecalrationWithoutBody(classNameTree); - int finalStartPosition = classNameTree.getPos(); - this.violationFinalStartLine = this.cUnit.getLineNumber(finalStartPosition); - this.violationFinalEndLine = this.cUnit.getLineNumber(finalEndPosition); - } - return classNameTree; - } - - private ITree getClassNameTokens(List children) { - ITree classNameTree = null; - for (ITree tree : children) { - int startPosition = tree.getPos(); - int startLine = cUnit.getLineNumber(startPosition); - if (startLine > violationStartLine) { - break; - } - - int endPosition = startPosition + tree.getLength(); - int endLine = cUnit.getLineNumber(endPosition - 1); - if (endLine < violationStartLine) continue; - - int type = tree.getType(); - if (type == 55 || type == 71) { - classNameTree = tree; - break; - } - } - return classNameTree; - } -} diff --git a/src/main/java/edu/lu/uni/serval/violation/parse/AlarmsReader.java b/src/main/java/edu/lu/uni/serval/violation/parse/AlarmsReader.java deleted file mode 100644 index bebe02e..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/parse/AlarmsReader.java +++ /dev/null @@ -1,197 +0,0 @@ -package edu.lu.uni.serval.violation.parse; - -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import edu.lu.uni.serval.violation.Alarm; -import edu.lu.uni.serval.violation.Violation; - -public class AlarmsReader { - - @SuppressWarnings("unused") - private static Logger log = LoggerFactory.getLogger(AlarmsReader.class); - - int counter = 0; - - public Map readAlarmsList(String fileName) { -// StringBuilder builder = new StringBuilder(); - Map violationsMap = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(fileName); - scanner = new Scanner(fis); - - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); - int arrowIndex = line.indexOf("=>"); - String buggyInfo = line.substring(0, arrowIndex); - String fixedInfo = line.substring(arrowIndex + 2); - String[] buggyElements = buggyInfo.split(":"); - String[] fixedElements = fixedInfo.split(":"); - -// String alarmType = buggyElements[0]; - String projectName = buggyElements[1]; - String buggyCommitId = buggyElements[2]; - String buggyFile = buggyElements[3]; -// int startLine = Integer.parseInt(buggyElements[4]); -// int endLine = Integer.parseInt(buggyElements[5]); - String fixCommitId = fixedElements[1]; - String fixedFile = fixedElements[2]; - -// if (startLine == -1 || endLine == -1 || endLine == 1) { -//// log.error("FIXED ALARM WRONG_POSITION: " + line); -// builder.append(line + "\n"); -// continue; -// } - - Alarm alarm = new Alarm(buggyCommitId, buggyFile, fixCommitId, fixedFile); -// String alarmTypeAndPosition = buggyElements[0] + ":" + startLine + ":" + endLine; - String alarmTypeAndPosition = buggyElements[0] + ":" + buggyElements[4] + ":" + buggyElements[5]; - - Violation violation; - if (violationsMap.containsKey(projectName)) { - violation = violationsMap.get(projectName); - } else { - violation = new Violation(projectName); - violationsMap.put(projectName, violation); - } - List alarms = violation.getAlarms(); - int index = alarms.indexOf(alarm); - if (index >= 0) { - Alarm tempAlarm = alarms.get(index); -// Map positions = tempAlarm.getPositions(); -// if (positions.containsKey(startLine)) { -// int end = positions.get(startLine); -// if (endLine < end) { -// positions.put(startLine, endLine); -// tempAlarm.getAlarmTypes().put(startLine, alarmType); -// } -// } else { -// positions.put(startLine, endLine); -// tempAlarm.getAlarmTypes().put(startLine, alarmType); - counter ++; -// } - tempAlarm.getAlarmTypesAndPositions().add(alarmTypeAndPosition); - } else { -// Map alarmTypes = new HashMap<>(); -// alarmTypes.put(startLine, alarmType); -// alarm.setAlarmTypes(alarmTypes); -// Map positions = new HashMap<>(); -// positions.put(startLine, endLine); -// alarm.setPositions(positions); - List alarmTypesAndPositions = new ArrayList<>(); - alarmTypesAndPositions.add(alarmTypeAndPosition); - alarm.setAlarmTypesAndPositions(alarmTypesAndPositions); - alarms.add(alarm); - counter ++; - } - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - System.out.println(counter); -// FileHelper.outputToFile("../FPM_Violations/TuneParameters/WrongPosition/FixedAlarm.list", builder, false); - return violationsMap; - } - - public Map readAlarmsList2(String fileName) { -// StringBuilder builder = new StringBuilder(); - Map violationsMap = new HashMap<>(); - FileInputStream fis = null; - Scanner scanner = null; - try { - fis = new FileInputStream(fileName); - scanner = new Scanner(fis); - - while (scanner.hasNextLine()) { - String line = scanner.nextLine(); -// int arrowIndex = line.indexOf("=>"); -// String alarmInfo = arrowIndex > 0 ? line.substring(0, arrowIndex) : line; -// String[] buggyElements = alarmInfo.split(","); - String[] buggyElements = line.split(","); - - String projectName = buggyElements[1]; - String buggyCommitId = buggyElements[2]; - String buggyFile = buggyElements[3]; -// if (startLine == -1 || endLine == -1 || endLine == 1) { -//// log.error("UNFIXED ALARM WRONG_POSITION: " + line); -// builder.append(line + "\n"); -// continue; -// } - String alarmTypeAndPosition = buggyElements[0] + ":" + buggyElements[4] + ":" + buggyElements[5]; // Alarm type : start line : end line. - - Alarm alarm = new Alarm(buggyCommitId, buggyFile, "", ""); - - Violation violation; - if (violationsMap.containsKey(projectName)) { - violation = violationsMap.get(projectName); - } else { - violation = new Violation(projectName); - violationsMap.put(projectName, violation); - } - List alarms = violation.getAlarms(); - int index = alarms.indexOf(alarm); - if (index >= 0) { - Alarm tempAlarm = alarms.get(index); -// Map positions = tempAlarm.getPositions(); -// if (positions.containsKey(startLine)) { -// int end = positions.get(startLine); -// if (endLine < end) { -// positions.put(startLine, endLine); -// tempAlarm.getAlarmTypes().put(startLine, alarmType); -// } -// } else { -// positions.put(startLine, endLine); -// tempAlarm.getAlarmTypes().put(startLine, alarmType); - counter ++; -// } - tempAlarm.getAlarmTypesAndPositions().add(alarmTypeAndPosition); - } else { -// Map alarmTypes = new HashMap<>(); -// alarmTypes.put(startLine, alarmType); -// alarm.setAlarmTypes(alarmTypes); -// Map positions = new HashMap<>(); -// positions.put(startLine, endLine); -// alarm.setPositions(positions); - List alarmTypesAndPositions = new ArrayList<>(); - alarmTypesAndPositions.add(alarmTypeAndPosition); - alarm.setAlarmTypesAndPositions(alarmTypesAndPositions); - alarms.add(alarm); - counter ++; - } - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - try { - scanner.close(); - fis.close(); - } catch (IOException e) { - e.printStackTrace(); - } - } - - System.out.println(counter); -// FileHelper.outputToFile("../FPM_Violations/TuneParameters/WrongPosition/UnFixedAlarm.list", builder, true); - return violationsMap; - } - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/parse/Test.java b/src/main/java/edu/lu/uni/serval/violation/parse/Test.java deleted file mode 100644 index 294ceb2..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/parse/Test.java +++ /dev/null @@ -1,83 +0,0 @@ -package edu.lu.uni.serval.violation.parse; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.StringReader; -import java.util.List; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -public class Test { - - public static void main(String[] args) throws IOException { -// String filePath = Configuration.GUM_TREE_INPUT + "un_positions/"; -// List files = FileHelper.getAllFiles(filePath, ".txt"); -// System.out.println(files.size()); -// List projects = new ArrayList<>(); -// int unfixedI = 0; -// for (File file : files) { -// String fileName = file.getName(); -// fileName = fileName.substring(0, fileName.indexOf("#")); -// fileName = fileName.substring(0, fileName.lastIndexOf("_")); -// fileName = fileName.substring(0, fileName.lastIndexOf("_")); -// if (!projects.contains(fileName)) { -// projects.add(fileName); -// } -// String content = FileHelper.readFile(file); -// BufferedReader reader = new BufferedReader(new StringReader(content)); -// while (reader.readLine() != null) { -// unfixedI ++; -// } -// reader.close(); -// } -// -// for (String str : projects) { -// System.out.println(str); -// } -// System.out.println("Unfixed: " + unfixedI); - - String positionFath = Configuration.GUM_TREE_INPUT + "positions/"; - List files = FileHelper.getAllFilesInCurrentDiectory(positionFath, ".txt"); - System.out.println("File Path: " + positionFath); - System.out.println(files.size()); - int i = 0; - for (File file : files) { - String content = FileHelper.readFile(file); - BufferedReader reader = new BufferedReader(new StringReader(content)); - while (reader.readLine() != null) { - i ++; - } - reader.close(); - } - - System.out.println("Fixed: " + i); - - -// String unfixedAlarmFile = "Dataset/Unfixed-Alarms/"; -// List unfixedAlarmFiles = FileHelper.getAllFilesInCurrentDiectory(unfixedAlarmFile, ".csv"); -// int a = 0; -// for (File file : unfixedAlarmFiles) { -// String content = FileHelper.readFile(file); -// BufferedReader reader = new BufferedReader(new StringReader(content)); -// while (reader.readLine() != null) { -// a ++; -// } -// reader.close(); -// } -// System.out.println("unfixed: " + a); - - String fixedAlarmFile = "Dataset/fixed-alarms-v1.0.list"; - int b = 0; - String content = FileHelper.readFile(fixedAlarmFile); - BufferedReader reader = new BufferedReader(new StringReader(content)); - while (reader.readLine() != null) { - b ++; - } - reader.close(); - System.out.println(b); - - } - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/parse/TestViolationParser.java b/src/main/java/edu/lu/uni/serval/violation/parse/TestViolationParser.java deleted file mode 100644 index 42a7431..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/parse/TestViolationParser.java +++ /dev/null @@ -1,94 +0,0 @@ -package edu.lu.uni.serval.violation.parse; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.List; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.utils.FileHelper; - -public class TestViolationParser { - - private static final String REPO_PATH = "../../repos/";//"/Volumes/MacBook/repos/"; - - public static void main(String[] args) throws IOException { - List repositoriesList = new ArrayList<>(); - File repositories = new File(REPO_PATH); - File[] subFiles = repositories.listFiles(); - for (File subFile : subFiles) { - if (subFile.isDirectory()) { - File[] repos = subFile.listFiles(); - for (File repo : repos) { - if (repo.isDirectory()) { - repositoriesList.add(repo); - } - } - } - } - - List violationTypes = new ArrayList<>(); - /* - * DM_DEFAULT_ENCODING - */ - violationTypes.add("NP_NONNULL_RETURN_VIOLATION"); - violationTypes.add("NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE"); - violationTypes.add("NP_PARAMETER_MUST_BE_NONNULL_BUT_MARKED_AS_NULLABLE"); - violationTypes.add("ODR_OPEN_DATABASE_RESOURCE"); - violationTypes.add("PZLA_PREFER_ZERO_LENGTH_ARRAYS"); - violationTypes.add("RI_REDUNDANT_INTERFACES"); - violationTypes.add("RV_RETURN_VALUE_IGNORED_BAD_PRACTICE"); - violationTypes.add("RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT"); - violationTypes.add("SE_NO_SERIALVERSIONID"); - violationTypes.add("SF_SWITCH_NO_DEFAULT"); - violationTypes.add("SIC_INNER_SHOULD_BE_STATIC"); - violationTypes.add("SQL_PREPARED_STATEMENT_GENERATED_FROM_NONCONSTANT_STRING"); - violationTypes.add("UC_USELESS_CONDITION"); - violationTypes.add("UC_USELESS_OBJECT"); - violationTypes.add("UCF_USELESS_CONTROL_FLOW"); - violationTypes.add("WMI_WRONG_MAP_ITERATOR"); - - // Violation instances of single violation type - String unfixedViolations = "../FPM_Violations/unFixedInstances/"; - String unfixedFilesPath = Configuration.GUM_TREE_INPUT + "UnfixedViolations/"; - String unfixedPositionsFilePath = Configuration.GUM_TREE_INPUT + "UnFV_positions/"; - List unfixedAlarmFiles = FileHelper.getAllFilesInCurrentDiectory(unfixedViolations, ".list"); - for (File file : unfixedAlarmFiles) { - String fileName = FileHelper.getFileNameWithoutExtension(file); -// if (!violationTypes.contains(fileName)) continue; - if (!fileName.equals("DM_DEFAULT_ENCODING")) continue; - FileHelper.createDirectory(unfixedFilesPath + fileName + "/"); - FileHelper.createDirectory(unfixedPositionsFilePath + fileName + "/"); - ViolationParser parser = new ViolationParser(); - parser.parseViolations(file, repositoriesList, unfixedFilesPath + fileName + "/", unfixedPositionsFilePath + fileName + "/"); - } - -// String unfixedAlarmFile = "Dataset/Unfixed-Alarms/"; -// final String unfixedFilesPath = Configuration.GUM_TREE_INPUT + "unfixAlarms/"; -// final String unfixedOositionsFilePath = Configuration.GUM_TREE_INPUT + "un_positions/"; -// FileHelper.createDirectory(unfixedFilesPath); -// FileHelper.createDirectory(unfixedOositionsFilePath); -// -// List unfixedAlarmFiles = FileHelper.getAllFilesInCurrentDiectory(unfixedAlarmFile, ".csv"); -// -// for (File file : unfixedAlarmFiles) { -// ViolationParser parser = new ViolationParser(); -// parser.parseViolations(file, repositoriesList, unfixedFilesPath, unfixedOositionsFilePath); -// } - -// String fixedAlarmFile = "Dataset/fixed-alarms-v1.0.list"; -// final String previousFilesPath = Configuration.GUM_TREE_INPUT + "prevFiles/"; -// final String revisedFilesPath = Configuration.GUM_TREE_INPUT + "revFiles/"; -// final String positionsFilePath = Configuration.GUM_TREE_INPUT + "positions/"; -// final String diffentryFilePath = Configuration.GUM_TREE_INPUT + "diffentries/"; -// FileHelper.createDirectory(previousFilesPath); -// FileHelper.createDirectory(revisedFilesPath); -// FileHelper.createDirectory(positionsFilePath); -// FileHelper.createDirectory(diffentryFilePath); -// -// ViolationParser parser = new ViolationParser(); -// parser.parseViolations(fixedAlarmFile, repositoriesList, previousFilesPath, revisedFilesPath, positionsFilePath, diffentryFilePath); - - } - -} diff --git a/src/main/java/edu/lu/uni/serval/violation/parse/ViolationParser.java b/src/main/java/edu/lu/uni/serval/violation/parse/ViolationParser.java deleted file mode 100644 index 481c56a..0000000 --- a/src/main/java/edu/lu/uni/serval/violation/parse/ViolationParser.java +++ /dev/null @@ -1,274 +0,0 @@ -package edu.lu.uni.serval.violation.parse; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.eclipse.jgit.errors.RevisionSyntaxException; - -import edu.lu.uni.serval.config.Configuration; -import edu.lu.uni.serval.git.exception.GitRepositoryNotFoundException; -import edu.lu.uni.serval.git.exception.NotValidGitRepositoryException; -import edu.lu.uni.serval.git.travel.GitRepository; -import edu.lu.uni.serval.utils.Exporter; -import edu.lu.uni.serval.utils.FileHelper; -import edu.lu.uni.serval.utils.MapSorter; -import edu.lu.uni.serval.violation.Alarm; -import edu.lu.uni.serval.violation.Violation; - -/** - * - * @author kui.liu - * - */ -public class ViolationParser { - - Map alarmTypesCounter = new HashMap<>(); - - /** - * Travel Git repositories to get the violation-localized java files, violation-removed java files, and violation types and positions. - * - * @param fixedAlarmFile - * @param repos - * @param previousFilesPath - * @param revisedFilesPath - * @param positionsFilePath - * @param diffentryFilePath - */ - public void parseViolations(String fixedAlarmFile, List repos, String previousFilesPath, String revisedFilesPath, String positionsFilePath, String diffentryFilePath) { - AlarmsReader reader = new AlarmsReader(); - Map violations = reader.readAlarmsList(fixedAlarmFile); - List throwExpProjs = new ArrayList<>(); - int a = 0; - int exceptionsCounter = 0; - int violationsAmount = 0; -// System.out.println(violations.size()); - for (Map.Entry entry : violations.entrySet()) { - String projectName = entry.getKey(); - String repoName = ""; - for (File repo : repos) { - if (repo.getName().equals(projectName)) { - repoName = repo.getPath() + "/"; - break; - } - } - if ("".equals(repoName)) { - a ++; - System.out.println(projectName); - continue; - } - Violation violation = entry.getValue(); - List alarms = violation.getAlarms(); - - String repoPath = repoName + "/.git"; - GitRepository gitRepo = new GitRepository(repoPath, revisedFilesPath, previousFilesPath); - try { - gitRepo.open(); - for (Alarm alarm : alarms) { - String buggyCommitId = alarm.getBuggyCommitId(); - String buggyFileName = alarm.getBuggyFileName(); - String buggyFileContent = gitRepo.getFileContentByCommitIdAndFileName(buggyCommitId, buggyFileName); - if (buggyFileContent == null || "".equals(buggyFileContent)) { -// System.out.println(projectName); - throwExpProjs.add(projectName); - exceptionsCounter ++; - continue; - } - - String fixedCommitId = alarm.getFixedCommitId(); - String fixedFileName = alarm.getFixedFileName(); - String fixedFileContent = gitRepo.getFileContentByCommitIdAndFileName(fixedCommitId, fixedFileName); - if (fixedFileContent == null || "".equals(fixedFileContent)) { -// System.out.println(projectName); - throwExpProjs.add(projectName); - exceptionsCounter ++; - continue; - } - - String diffentry = gitRepo.getDiffentryByTwoCommitIds(buggyCommitId, fixedCommitId, fixedFileName); - if (diffentry == null) { -// System.out.println(projectName); - throwExpProjs.add(projectName); - exceptionsCounter ++; - continue; - } - - String commitId = buggyCommitId.substring(0, 6) + "_" + fixedCommitId.substring(0, 6); - String fileName = fixedFileName.replaceAll("/", "#"); - fileName = projectName + "_" + commitId + fileName; - if (fileName.length() > 240) { - List files = FileHelper.getAllFilesInCurrentDiectory(revisedFilesPath, ".java"); - fileName = files.size() + "TooLongFileName.java"; - } - String buggyFile = previousFilesPath + "prev_" + fileName; - String fixedFile = revisedFilesPath + fileName; - fileName = fileName.replace(".java", ".txt"); - String positionFile = positionsFilePath + fileName; - String diffentryFile = diffentryFilePath + fileName; - FileHelper.outputToFile(buggyFile, buggyFileContent, false); - FileHelper.outputToFile(fixedFile, fixedFileContent, false); -// FileHelper.outputToFile(positionFile, readPosition(alarm.getPositions(), alarm.getAlarmTypes()), false); - FileHelper.outputToFile(positionFile, readAlarmTypeAndPosition(alarm.getAlarmTypesAndPositions()), false); - FileHelper.outputToFile(diffentryFile, diffentry, false); - - violationsAmount += counter(alarm); - } - } catch (GitRepositoryNotFoundException e) { - System.out.println("Exception: " + projectName); - exceptionsCounter ++; - e.printStackTrace(); - } catch (NotValidGitRepositoryException e) { - System.out.println("Exception: " + projectName); - exceptionsCounter ++; - e.printStackTrace(); - } catch (IOException e) { - System.out.println("Exception: " + projectName); - exceptionsCounter ++; - e.printStackTrace(); - } catch (RevisionSyntaxException e) { - System.out.println("Exception: " + projectName); - exceptionsCounter ++; - e.printStackTrace(); - } finally { - gitRepo.close(); - } - } - System.out.println(a); - System.out.println(exceptionsCounter); - System.out.println(throwExpProjs.size()); - System.out.println(throwExpProjs); - - System.out.println("### Violations amount: " + violationsAmount); - - MapSorter sorter = new MapSorter(); - alarmTypesCounter = sorter.sortByKeyAscending(alarmTypesCounter); - String[] columns = { "Alarm Type", "amount" }; - Exporter.exportOutliers(alarmTypesCounter, new File(Configuration.GUM_TREE_INPUT + "FixedAlarmTypes.xls"), 1, columns); - } - - private int counter(Alarm alarm) { - int counter = 0; -// Map alarmTypes = alarm.getAlarmTypes(); -// counter += alarmTypes.size(); -// for (Map.Entry entry : alarmTypes.entrySet()) { -// String type = entry.getValue(); -// if (this.alarmTypesCounter.containsKey(entry.getValue())) { -// this.alarmTypesCounter.put(type, this.alarmTypesCounter.get(type) + 1); -// } else { -// this.alarmTypesCounter.put(type, 1); -// } -// } - - List alarmTypesAndPositions = alarm.getAlarmTypesAndPositions(); - for (String alarmTypeAndPosition : alarmTypesAndPositions) { - String[] elements = alarmTypeAndPosition.split(":"); - String alarmType = elements[0]; - if (this.alarmTypesCounter.containsKey(alarmType)) { - this.alarmTypesCounter.put(alarmType, this.alarmTypesCounter.get(alarmType) + 1); - } else { - this.alarmTypesCounter.put(alarmType, 1); - } - } - counter += alarmTypesAndPositions.size(); - return counter; - } - - /** - * Output data in terms of alarm types. - * - * @param alarmsInfo - * @param repos - * @param previousFilesPath - * @param revisedFilesPath - * @param positionsFilePath - * @param diffentryFilePath - */ - public void parseViolations(File alarmsInfo, List repos, String violationFilesPath, String positionsFilePath) { - AlarmsReader reader = new AlarmsReader(); - Map violations = reader.readAlarmsList2(alarmsInfo.getPath()); - int a = 0; - for (Map.Entry entry : violations.entrySet()) { - String projectName = entry.getKey(); - String repoName = ""; - for (File repo : repos) { - if (repo.getName().equals(projectName)) { - repoName = repo.getPath() + "/"; - break; - } - } - if ("".equals(repoName)) { - a ++; - System.out.println(projectName); - continue; - } - Violation violation = entry.getValue(); - List alarms = violation.getAlarms(); - - String repoPath = repoName + "/.git"; - GitRepository gitRepo = new GitRepository(repoPath, "", ""); - try { - gitRepo.open(); - for (Alarm alarm : alarms) { - String buggyCommitId = alarm.getBuggyCommitId(); - String buggyFileName = alarm.getBuggyFileName(); - String buggyFileContent = gitRepo.getFileContentByCommitIdAndFileName(buggyCommitId, buggyFileName); - if (buggyFileContent == null || "".equals(buggyFileContent)) { - System.out.println(projectName); - continue; - } - - String commitId = buggyCommitId.substring(0, 6) + "_"; - String fileName = buggyFileName.replaceAll("/", "#"); - fileName = projectName + "_" + commitId + fileName; - if (fileName.length() > 240) { - List files = FileHelper.getAllFilesInCurrentDiectory(violationFilesPath, ".java"); - fileName = files.size() + "TooLongFileName.java"; - } - String buggyFile = violationFilesPath + "unfixed_" + fileName; - fileName = fileName.replace(".java", ".txt"); - String positionFile = positionsFilePath + fileName; - FileHelper.outputToFile(buggyFile, buggyFileContent, false); - FileHelper.outputToFile(positionFile, readAlarmTypeAndPosition(alarm.getAlarmTypesAndPositions()), false); - } - } catch (GitRepositoryNotFoundException e) { - System.out.println("Exception: " + projectName); - e.printStackTrace(); - } catch (NotValidGitRepositoryException e) { - System.out.println("Exception: " + projectName); - e.printStackTrace(); - } catch (IOException e) { - System.out.println("Exception: " + projectName); - e.printStackTrace(); - } catch (RevisionSyntaxException e) { - System.out.println("Exception: " + projectName); - e.printStackTrace(); - } finally { - gitRepo.close(); - } - } - System.out.println(a); - } - - private String readAlarmTypeAndPosition(List alarmTypesAndPositions) { - String positionsStr = ""; - for (String element : alarmTypesAndPositions) { - positionsStr += element + "\n"; - } - return positionsStr; - } - - @SuppressWarnings("unused") - @Deprecated - private String readAlarmTypeAndPosition(Map positions, Map alarmTypes) { - String positionsStr = ""; - for (Map.Entry entry : alarmTypes.entrySet()) { - int key = entry.getKey(); - positionsStr += key + ":" + positions.get(key) + ":" + entry.getValue() + "\n"; - } - return positionsStr; - } - -}