Update

.gitignore

@@ -12,6 +12,10 @@ OUTPUT/
 *.pdf
 Dataset/
 GumTreeInput/
+GumTreeInput1/
+GumTreeOutput1/
+GumTreeResults/
+
 *TestParser.java
 src/main/java/edu/lu/uni/serval/FixPatternParser/TestParser.java
 # Package Files #

pom.xml

@@ -16,7 +16,7 @@
 	</properties>
 
 	<dependencies>
-		<dependency>
+		<!-- <dependency>
 			<groupId>edu.lu.uni.serval</groupId>
 			<artifactId>MyCluster</artifactId>
 			<version>0.0.1-SNAPSHOT</version>
@@ -26,7 +26,7 @@
 			<groupId>edu.lu.uni.serval</groupId>
 			<artifactId>MyFeatureLearner</artifactId>
 			<version>0.0.1-SNAPSHOT</version>
-		</dependency>
+		</dependency> -->
 		
 		<dependency>
 			<groupId>edu.lu.uni</groupId>

src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchHunkParser.java

@@ -36,9 +36,9 @@ public class CommitPatchHunkParser extends CommitPatchParser {
 			List<DiffEntryHunk> diffentryHunks = new DiffEntryReader().readHunks(diffEntryFile);
 			//Filter out the modify actions, which are not in the DiffEntry hunks.
 			HunkActionFilter hunkFilter = new HunkActionFilter();
-			List<HunkFixPattern> allHunkFixPatternss = hunkFilter.filterActionsByDiffEntryHunk2(diffentryHunks, actionSets, revFile, prevFile);
+			List<HunkFixPattern> allHunkFixPatterns = hunkFilter.filterActionsByDiffEntryHunk2(diffentryHunks, actionSets, revFile, prevFile);
 			
-			for (HunkFixPattern hunkFixPattern : allHunkFixPatternss) {
+			for (HunkFixPattern hunkFixPattern : allHunkFixPatterns) {
 				// Range of buggy source code
 				int startLine = 0;
 				int endLine = 0;

src/main/java/edu/lu/uni/serval/FixPatternParser/patch/CommitPatchSingleStatementParser.java

@@ -37,6 +37,12 @@ public class CommitPatchSingleStatementParser extends CommitPatchParser {
 		if (actionSets.size() > 0) {
 			// DiffEntry Hunks: filter out big hunks.
 			List<DiffEntryHunk> 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;
@@ -80,31 +86,21 @@ public class CommitPatchSingleStatementParser extends CommitPatchParser {
 							endPosition2 = startPosition2 + newNode.getLength();
 						}
 					}
-				} else {// DEL actions and MOV actions: we don't need these
+				} else {// DEL actions and MOV actions: we don't need these actions, as for now.
-						// actions, as for now.
 					continue;
 				}
 				if (startPosition == 0 || startPosition2 == 0) {
 					continue;
 				}
 
-				CUCreator cuCreator = new CUCreator();
-				CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-				CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-				if (prevUnit == null || revUnit == null) {
-					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
+				if (endLine - startLine >= Configuration.HUNK_SIZE - 2 || endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2)
-						|| endLine2 - startLine2 >= Configuration.HUNK_SIZE - 2)
 					continue;
-				// Filter out the modify actions, which are not in the DiffEntry
+				// Filter out the modify actions, which are not in the DiffEntry hunks.
-				// hunks.
 				DiffEntryHunk hunk = matchHunk(startLine, endLine, startLine2, endLine2, actionStr, diffentryHunks);
 				if (hunk == null) {
 					continue;
@@ -117,8 +113,7 @@ public class CommitPatchSingleStatementParser extends CommitPatchParser {
 				SimplifyTree abstractIdentifier = new SimplifyTree();
 				abstractIdentifier.abstractTree(actionSet);
 				SimpleTree simpleTree = actionSet.getSimpleTree();
-				if (simpleTree == null) { // Failed to get the simple tree for
+				if (simpleTree == null) { // Failed to get the simple tree for INS actions.
-											// INS actions.
 					continue;
 				}
 
@@ -142,12 +137,12 @@ public class CommitPatchSingleStatementParser extends CommitPatchParser {
 				this.patchesSourceCode += Configuration.PATCH_SIGNAL + "\n" + patchSourceCode + "\n";
 				this.sizes += size + "\n";
 				this.astEditScripts += astEditScripts + "\n";
-				// 2. source code: raw tokens
+//				// 2. source code: raw tokens
-				String rawTokenEditScripts = getRawTokenEditScripts(actionSet);
+//				String rawTokenEditScripts = getRawTokenEditScripts(actionSet);
-				// 3. abstract identifiers:
+//				// 3. abstract identifiers:
-				String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet);
+//				String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet);
-				// 4. semi-source code:
+//				// 4. semi-source code:
-				String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet);
+//				String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet);
 
 				// this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" +
 				// simpleTree.toString() + "\n";

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationHunkParser.java

@@ -12,7 +12,6 @@ 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.regroup.ActionFilter;
 import edu.lu.uni.serval.gumtree.regroup.HierarchicalActionSet;
 import edu.lu.uni.serval.gumtree.regroup.HunkActionFilter;
 import edu.lu.uni.serval.gumtree.regroup.HunkFixPattern;
@@ -21,7 +20,7 @@ import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
 import edu.lu.uni.serval.utils.MapSorter;
 
 /**
- * Parse fix patterns with GumTree.
+ * Parse fix violations with GumTree.
  * 
  * @author kui.liu
  *
@@ -29,36 +28,44 @@ import edu.lu.uni.serval.utils.MapSorter;
 public class FixedViolationHunkParser extends FixedViolationParser {
 	
 	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File positionsFile) {
+	public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) {
 		
 		// GumTree results
 		List<HierarchicalActionSet> actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile);
 		
 		if (actionSets.size() > 0) {
-			Map<Integer, Integer> positions = readPositions(positionsFile);
+			Map<Integer, Integer> positions = readPositions();
 			if (positions.size() > 1) {
 				MapSorter<Integer, Integer> sorter = new MapSorter<>();
 				positions = sorter.sortByKeyAscending(positions);
 			}
 			
+			List<DiffEntryHunk> diffentryHunks1 = new DiffEntryReader().readHunks(diffentryFile);
+			int index = 0;
+			int hunkListSize = diffentryHunks1.size();
+//			Map<Integer, DiffEntryHunk> diffentryHunks = new HashMap<>();
+			// Select hunks by positions of violations.
+			List<DiffEntryHunk> diffentryHunks = new ArrayList<>();
 			for (Map.Entry<Integer, Integer> entry : positions.entrySet()) {
-				// only statements
+				int startRange = entry.getKey();
-				for (HierarchicalActionSet actionSet : actionSets) {
+				int endRange = entry.getValue();
-					String astNodeType = actionSet.getAstNodeType();
+				for (; index < hunkListSize; index ++) {
-					if (astNodeType.endsWith("Statement") || "FieldDeclaration".equals(astNodeType)) {
+					DiffEntryHunk hunk = diffentryHunks1.get(index);
-						
+					int startLine = hunk.getBugLineStartNum();
-					}
+					int range = hunk.getBugRange();
+					if (startRange > startLine + range) continue;
+					if (endRange < startLine) break;
+					// startRange and endRange
+//					diffentryHunks.put(startRange, hunk);
+					diffentryHunks.add(hunk);
 				}
 			}
 			
-			ActionFilter filter = new ActionFilter();
-			// DiffEntry size: filter out big hunks.
-			List<DiffEntryHunk> diffentryHunks = new DiffEntryReader().readHunks(positionsFile);
 			//Filter out the modify actions, which are not in the DiffEntry hunks.
 			HunkActionFilter hunkFilter = new HunkActionFilter();
-			List<HunkFixPattern> allHunkFixPatternss = hunkFilter.filterActionsByDiffEntryHunk2(diffentryHunks, actionSets, revFile, prevFile);
+			List<HunkFixPattern> allHunkFixPatterns = hunkFilter.filterActionsByDiffEntryHunk2(diffentryHunks, actionSets, revFile, prevFile);
 						
-			for (HunkFixPattern hunkFixPattern : allHunkFixPatternss) {
+			for (HunkFixPattern hunkFixPattern : allHunkFixPatterns) {
 				// Range of buggy source code
 				int startLine = 0;
 				int endLine = 0;

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationParser.java

@@ -18,8 +18,14 @@ import edu.lu.uni.serval.utils.FileHelper;
  */
 public class FixedViolationParser extends Parser {
 	
+	File positionFile = null;
+	
+	public void setPositionFile(File positionFile) {
+		this.positionFile = positionFile;
+	}
+	
 	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File positionFile) {
+	public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) {
 	}
 	
 	protected boolean inPositions(int startLine, int endLine, Map<Integer, Integer> positions) {
@@ -31,7 +37,7 @@ public class FixedViolationParser extends Parser {
 		return false;
 	}
 
-	protected Map<Integer, Integer> readPositions(File positionFile) {
+	protected Map<Integer, Integer> readPositions() {
 		Map<Integer, Integer> positions = new HashMap<>();
 		String fileContent = FileHelper.readFile(positionFile);
 		BufferedReader reader = null;

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/FixedViolationSingleStatementParser.java

@@ -19,7 +19,7 @@ import edu.lu.uni.serval.gumtree.regroup.SimpleTree;
 import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
 
 /**
- * Parse fix patterns with GumTree.
+ * Parse fixed violations with GumTree.
  * 
  * @author kui.liu
  *
@@ -27,13 +27,20 @@ import edu.lu.uni.serval.gumtree.regroup.SimplifyTree;
 public class FixedViolationSingleStatementParser extends FixedViolationParser {
 	
 	@Override
-	public void parseFixPatterns(File prevFile, File revFile, File positionFile) {
+	public void parseFixPatterns(File prevFile, File revFile, File diffentryFile) {
 		// GumTree results
 		List<HierarchicalActionSet> actionSets = parseChangedSourceCodeWithGumTree(prevFile, revFile);
 		
 		if (actionSets.size() > 0) {
-			// DiffEntry Hunks: filter out big hunks.
+			CUCreator cuCreator = new CUCreator();
-			Map<Integer, Integer> positions = readPositions(positionFile);
+			CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
+			CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
+			if (prevUnit == null || revUnit == null) {
+				return;
+			}
+			
+			// Read the positions of checked violations
+			Map<Integer, Integer> positions = readPositions();
 			for (HierarchicalActionSet actionSet : actionSets) {
 				// position of buggy statements
 				int startPosition = 0;
@@ -76,29 +83,13 @@ public class FixedViolationSingleStatementParser extends FixedViolationParser {
 							endPosition2 = startPosition2 + newNode.getLength();
 						}
 					}
-				}  else if (actionStr.startsWith("MOV")) {// DEL actions and MOV actions: we don't need these actions, as for now.
+				}  else {// DEL actions and MOV actions: we don't need these actions, as for now.
-					continue;
-//					startPosition = actionSet.getStartPosition();
-//					endPosition = startPosition + actionSet.getLength();
-//					ITree node = actionSet.getNode().getParent();
-//					startPosition2 = node.getPos();
-//					endPosition2 = startPosition2 + node.getLength();
-				} else {
-					startPosition = actionSet.getStartPosition();
-					endPosition = startPosition + actionSet.getLength();
 					continue;
 				}
 				if (startPosition == 0 || startPosition2 == 0) {
 					continue;
 				}
 				
-				CUCreator cuCreator = new CUCreator();
-				CompilationUnit prevUnit = cuCreator.createCompilationUnit(prevFile);
-				CompilationUnit revUnit = cuCreator.createCompilationUnit(revFile);
-				if (prevUnit == null || revUnit == null) {
-					continue;
-				}
-				
 				// Get line numbers.
 				int startLine = prevUnit.getLineNumber(startPosition);
 				int endLine = prevUnit.getLineNumber(endPosition);
@@ -138,11 +129,11 @@ public class FixedViolationSingleStatementParser extends FixedViolationParser {
 				this.sizes += size + "\n";
 				this.astEditScripts += astEditScripts + "\n";
 				// 2. source code: raw tokens
-				String rawTokenEditScripts = getRawTokenEditScripts(actionSet);
+//				String rawTokenEditScripts = getRawTokenEditScripts(actionSet);
-				// 3. abstract identifiers: 
+//				// 3. abstract identifiers: 
-				String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet);
+//				String abstractIdentifiersEditScripts = getAbstractIdentifiersEditScripts(actionSet);
-				// 4. semi-source code: 
+//				// 4. semi-source code: 
-				String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet);
+//				String semiSourceCodeEditScripts = getSemiSourceCodeEditScripts(actionSet);
 				
 //				this.buggyTrees += Configuration.BUGGY_TREE_TOKEN + "\n" + simpleTree.toString() + "\n";
 				this.tokensOfSourceCode += Tokenizer.getTokensDeepFirst(simpleTree).trim() + "\n";

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/AkkaParser.java

@@ -55,10 +55,10 @@ public class AkkaParser {
 		List<MessageFile> msgFiles = new ArrayList<>();
 		
 		for (File file : files) {
+			if (!file.isDirectory()) continue;
 			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

src/main/java/edu/lu/uni/serval/MultipleThreadsParser/MessageFile.java

@@ -7,6 +7,7 @@ public class MessageFile {
 	private File revFile;
 	private File prevFile;
 	private File diffEntryFile;
+	private File positionFile;
 	
 	public MessageFile(File revFile, File prevFile, File diffEntryFile) {
 		super();
@@ -27,4 +28,12 @@ public class MessageFile {
 		return diffEntryFile;
 	}
 
+	public File getPositionFile() {
+		return positionFile;
+	}
+
+	public void setPositionFile(File positionFile) {
+		this.positionFile = positionFile;
+	}
+	
 }

src/main/java/edu/lu/uni/serval/diffentry/DiffEntryReader.java

@@ -77,4 +77,76 @@ public class DiffEntryReader {
 		return diffentryHunks;
 	}
 
+	/**
+	 * Read all hunks without considering their sizes.
+	 * 
+	 * @param diffentryFile
+	 * @return
+	 */
+	public List<DiffEntryHunk> readHunks2(File diffentryFile) {
+		List<DiffEntryHunk> 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();
+			
+			while ((line = reader.readLine()) != null) {
+				if (RegExp.filterSignal(line.trim())) {
+					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;
+				}
+				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;
+	}
+
 }