java miner test cases

gumtree/gen.jdt/src/main/java/com/github/gumtreediff/gen/jdt/AbstractJdtVisitor.java

@@ -56,6 +56,7 @@ public abstract class AbstractJdtVisitor extends ASTVisitor {
     }
 
     protected void push(int type, String typeName, String label, int startPosition, int length) {
+//        label = label.replace("\n","");
         ITree t = context.createTree(type, label, typeName);
         t.setPos(startPosition);
         t.setLength(length);

gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gen/jdt/exp/ExpJdtVisitor.java

@@ -985,7 +985,13 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     private void visitList(List<?> list) {
         for (Object obj : list) {
         	ASTNode node = (ASTNode) obj;
-            (node).accept(this);
+			if (node instanceof Block) {
+				List<?> statements = ((Block) node).statements();
+				visitList(statements);
+			} else {
+				node.accept(this);
+			}
+//            (node).accept(this);
         }
     }
     ///////////////////
@@ -995,12 +1001,12 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     
     @Override
     public boolean visit(CatchClause node) {
-        pushNode(node, node.getException().toString());
+        pushNode(node, node.toString().replace("\n",""));
         SingleVariableDeclaration exc = node.getException();
         exc.accept(this);
         Statement body = node.getBody();
         if (body != null) {
-//        	push(8, "Block", "CatchBody", body.getStartPosition(), body.getLength());
+//        	push(8, "Block", "CatchBody:"+body.toString().replace("\n",""), body.getStartPosition(), body.getLength());
         	visitBody(body);
 //        	popNode();
         }
@@ -1046,7 +1052,8 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     @Override
     public boolean visit(DoStatement node) {
     	Expression exp = node.getExpression();
-        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+//        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+        pushNode(node, node.toString().replace("\n",""));
         Statement body = node.getBody();
         if (body != null) {
 //        	push(8, "Block", "DoBody", body.getStartPosition(), body.getLength());
@@ -1070,7 +1077,8 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     public boolean visit(EnhancedForStatement node) {
     	SingleVariableDeclaration parameter = node.getParameter();
     	Expression exp = node.getExpression();
-        pushNode(node, parameter.toString() + ", " + exp.getClass().getSimpleName() + COLON + exp.toString());
+//        pushNode(node, parameter.toString() + ", " + exp.getClass().getSimpleName() + COLON + exp.toString());
+        pushNode(node, node.toString().replace("\n",""));
         parameter.accept(this);
         exp.accept(this);
         Statement body = node.getBody();
@@ -1103,7 +1111,8 @@ public class ExpJdtVisitor extends CdJdtVisitor {
 		}
 		value += update.toString();
         
-        pushNode(node, value);
+//        pushNode(node, value);
+        pushNode(node, node.toString().replace("\n",""));
 		visitList(init);
 		if (exp != null) {
 			exp.accept(this);
@@ -1123,27 +1132,29 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     @Override
     public boolean visit(IfStatement node) {
         Expression exp = node.getExpression();
-        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+//        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+        pushNode(node, node.toString().replace("\n",""));
         exp.accept(this);
         Statement stmt = node.getThenStatement();
         if (stmt != null) {
-//        	push(8, "Block", "ThenBody", stmt.getStartPosition(), stmt.getLength());
+        	push(8, "Block", "ThenBody:"+stmt.toString().replace("\n",""), stmt.getStartPosition(), stmt.getLength());
             visitBody(stmt);
-//            popNode();
+            popNode();
         }
 
         stmt = node.getElseStatement();
         if (stmt != null) {
-//        	push(8, "Block", "ElseBody", stmt.getStartPosition(), stmt.getLength());
+        	push(8, "Block", "ElseBody:"+stmt.toString().replace("\n",""), stmt.getStartPosition(), stmt.getLength());
             visitBody(stmt);
-//            popNode();
+            popNode();
         }
         return false;
     }
     
     @Override
     public boolean visit(LabeledStatement node) {
-        pushNode(node, node.getLabel().getFullyQualifiedName());
+//        pushNode(node, node.getLabel().getFullyQualifiedName());
+        pushNode(node,node.toString().replace("\n",""));
         Statement body = node.getBody();
         if (body != null) {
 //        	push(8, "Block", "LabelBody", body.getStartPosition(), body.getLength());
@@ -1179,7 +1190,8 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     public boolean visit(SwitchCase node) {
     	Expression exp = node.getExpression();
     	if (exp != null) {
-    		pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+//    		pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+    		pushNode(node, node.toString().replace("\n",""));
     		exp.accept(this);
     	} else {
     		pushNode(node, "default");
@@ -1190,7 +1202,8 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     @Override
     public boolean visit(SwitchStatement node) {
     	Expression exp = node.getExpression();
-        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+//        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+        pushNode(node, node.toString().replace("\n",""));
         exp.accept(this);
 //        int startPosition = exp.getStartPosition();
 //        int length1 = exp.getLength();
@@ -1204,13 +1217,14 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     @Override
     public boolean visit(SynchronizedStatement node) {
     	Expression exp = node.getExpression();
-        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+//        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+        pushNode(node, node.toString().replace("\n",""));
         exp.accept(this);
         Statement body = node.getBody();
         if (body != null) {
-//        	push(8, "Block", "SyncBody", body.getStartPosition(), body.getLength());
+        	push(8, "Block", "SyncBody:"+body.toString().replace("\n",""), body.getStartPosition(), body.getLength());
         	visitBody(body);
-//        	popNode();
+        	popNode();
         }
 //        visitBody(node.getBody());
         return false;
@@ -1227,7 +1241,8 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     @Override
     public boolean visit(TryStatement node) {
     	List<?> resources = node.resources();
-    	pushNode(node, "try:" + resources.toString());
+//    	pushNode(node, "try:" + resources.toString());
+    	pushNode(node,  node.toString().replace("\n",""));
 		visitList(resources);
 
 		Statement body = node.getBody();
@@ -1242,7 +1257,7 @@ public class ExpJdtVisitor extends CdJdtVisitor {
 
         Statement stmt = node.getFinally();
         if (stmt != null) {
-        	push(8, "Block", "FinallyBody", stmt.getStartPosition(), stmt.getLength());
+        	push(8, "Block", "FinallyBody:"+stmt.toString().replace("\n",""), stmt.getStartPosition(), stmt.getLength());
             visitBody(stmt);
             popNode();
         }
@@ -1272,14 +1287,15 @@ public class ExpJdtVisitor extends CdJdtVisitor {
     @Override
     public boolean visit(WhileStatement node) {
     	Expression exp = node.getExpression();
-        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+//        pushNode(node, exp.getClass().getSimpleName() + COLON + exp.toString());
+        pushNode(node, node.toString().replace("\n",""));
         exp.accept(this);
         
         Statement body = node.getBody();
         if (body != null) {
-//        	push(8, "Block", "WhileBody", body.getStartPosition(), body.getLength());
+        	push(8, "Block", "WhileBody:"+body.toString().replace("\n",""), body.getStartPosition(), body.getLength());
         	visitBody(body);
-//        	popNode();
+        	popNode();
         }
         return false;
     }

gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeComparer.java

@@ -31,9 +31,12 @@ public class GumTreeComparer {
 		} catch (Exception e) {
 			if (oldTree == null) {
 				log.info("Null GumTree of Previous File: " + prevFile.getPath());
+				throw new NullPointerException(prevFile.getPath());
 			} else if (newTree == null) {
 				log.info("Null GumTree of Revised File: " + revFile.getPath());
+				throw new NullPointerException(revFile.getPath());
 			}
+
 		}
 		if (oldTree != null && newTree != null) {
 			Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);

gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeGenerator.java

@@ -18,7 +18,7 @@ public class GumTreeGenerator {
 		RAW_TOKEN,
 	}
 	
-	public ITree generateITreeForJavaFile(File javaFile, GumTreeType type) {
+	public ITree generateITreeForJavaFile(File javaFile, GumTreeType type) throws IOException {
 		ITree gumTree = null;
 		try {
 			TreeContext tc = null;
@@ -37,7 +37,8 @@ public class GumTreeGenerator {
 				gumTree = tc.getRoot();
 			}
 		} catch (IOException e) {
-			e.printStackTrace();
+			throw new IOException(e);
+//			e.printStackTrace();
 		}
 		return gumTree;
 	}

python/abstractPatch.py

@@ -104,7 +104,7 @@ def getMapping(pathMapping,x):
 
 
 
-def cluster(clusterPath,pairsPath, level,rootType):
+def cluster(clusterPath,pairsPath, level):
 
         try:
             # logging.info('Parameters: \ninputPath %s \nclusterPath %s \nport %s \nmatchesName %s \nthreshold %s \n%indexFile',inputPath,clusterPath,str(port),matchesName,str(threshold),indexFile)

python/common/commons.py

@@ -178,22 +178,22 @@ def getRun():
 
 
 
-# def shellCallTemplate(cmd,enc='utf-8'):
-#     process = subprocess.Popen(cmd,
-#                                stdout=subprocess.PIPE,stderr=PIPE, shell=True,encoding=enc,
-#                                universal_newlines=True)
-#
-#     while True:
-#         output = process.stdout.readline()
-#         print(output.strip())
-#         # Do something else
-#         return_code = process.poll()
-#         if return_code is not None:
-#             print('RETURN CODE', return_code)
-#             # Process has finished, read rest of the output
-#             for output in process.stdout.readlines():
-#                 print(output.strip())
-#             break
+def shellCallTemplate4jar(cmd,enc='utf-8'):
+    process = subprocess.Popen(cmd,
+                               stdout=subprocess.PIPE,stderr=PIPE, shell=True,encoding=enc,
+                               universal_newlines=True)
+
+    while True:
+        output = process.stdout.readline()
+        print(output.strip())
+        # Do something else
+        return_code = process.poll()
+        if return_code is not None:
+            print('RETURN CODE', return_code)
+            # Process has finished, read rest of the output
+            for output in process.stdout.readlines():
+                print(output.strip())
+            break
 
 def shellCallTemplate(cmd,enc='utf-8'):
     try:

python/main.py

@@ -15,7 +15,7 @@ if __name__ == '__main__':
         setEnv(args)
 
         job = args.job
-        job = "cluster"
+        # job = "cluster"
         ROOT_DIR = os.environ["ROOT_DIR"]
         REPO_PATH = os.environ["REPO_PATH"]
         CODE_PATH = os.environ["CODE_PATH"]
@@ -32,7 +32,7 @@ if __name__ == '__main__':
 
 
         # subject = 'ALL'
-        rootType = 'if'
+        # rootType = 'if'
 
         print(job)
 
@@ -46,7 +46,7 @@ if __name__ == '__main__':
         elif job =='dataset4c':
             from otherDatasets import core
             core()
-        elif job =='richEditScript':
+        elif job =='richedit':
             dbDir = join(DATA_PATH, 'redis')
             stopDB(dbDir, REDIS_PORT)
             cmd = "JAVA_HOME='" + jdk8 + "' java  -jar " + join(Path(ROOT_DIR).parent, 'target','FixPatternMiner-1.0.0-jar-with-dependencies.jar') + " " + args.prop + " RICHEDITSCRIPT "
@@ -71,7 +71,7 @@ if __name__ == '__main__':
         elif job =='compare':
              # cmd = "mvn exec:java -f '/data/fixminer_source/' -Dexec.mainClass='edu.lu.uni.serval.richedit.akka.compare.CompareTrees' -Dexec.args='"+ " shape " + join(DATA_PATH,"redis") +" ALLdumps-gumInput.rdb " + "clusterl0-gumInputALL.rdb /data/richedit-core/python/data/richEditScript'"
             cmd = "JAVA_HOME='" + jdk8 + "' java  -jar " + join(Path(ROOT_DIR).parent, 'target','FixPatternMiner-1.0.0-jar-with-dependencies.jar') + " " + args.prop + " COMPARE "
-            output = shellCallTemplate(cmd)
+            output = shellCallTemplate4jar(cmd)
             logging.info(output)
 
         # elif job == 'clusterAdditional':
@@ -83,7 +83,7 @@ if __name__ == '__main__':
 
             dbDir = join(DATA_PATH, 'redis')
             startDB(dbDir, "6399", PROJECT_TYPE)
-            cluster(join(DATA_PATH,'shapes'),join(DATA_PATH, 'pairs'),'shapes',rootType)
+            cluster(join(DATA_PATH,'shapes'),join(DATA_PATH, 'pairs'),'shapes')
 
         # elif job =='actionSI':
         #     from pairs import actionPairs

richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffParser.java

@@ -69,11 +69,11 @@ public class EDiffParser extends Parser {
 			if (isJava){
 				allActionSets = new HierarchicalRegrouper().regroupGumTreeResults(gumTreeResults);
 			}else{
-				HashSet<Integer> removeType = new HashSet<Integer>(Arrays.asList(171,172,99,100,101,102));
-				boolean b = gumTreeResults.stream().anyMatch(p -> removeType.contains(p.getNode().getType()));
-				if(b){
-					return actionSets;
-				}
+//				HashSet<Integer> removeType = new HashSet<Integer>(Arrays.asList(171,172,99,100,101,102));
+//				boolean b = gumTreeResults.stream().anyMatch(p -> removeType.contains(p.getNode().getType()));
+//				if(b){
+//					return actionSets;
+//				}
 				allActionSets = new HierarchicalRegrouperForC().regroupGumTreeResults(gumTreeResults);
 			}
 

richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouper.java

@@ -8,6 +8,8 @@ import edu.lu.uni.serval.utils.ListSorter;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.function.Predicate;
+import java.util.stream.Collectors;
 
 /**
  * Regroup GumTree results to a hierarchical construction.
@@ -21,10 +23,8 @@ public class HierarchicalRegrouper {
 		/*
 		 * First, sort actions by their positions.
 		 */
-//		List<Action> actions = new ListSorter<Action>(actionsArgu).sortAscending();
-//		if (actions == null) {
-//			actions = actionsArgu;
-//		}
+		actions = new ListSorter<Action>(actions).sortAscending();
+
 		
 		/*
 		 * Second, group actions by their positions.
@@ -65,9 +65,111 @@ public class HierarchicalRegrouper {
 			}
 		}
 
-		return reActionSets;
+		List<HierarchicalActionSet> reActionSets1 = new ArrayList<>();
+
+		ITree movDelNode = null;
+
+		for(HierarchicalActionSet a:reActionSets){
+			a = removeBlocks(a);
+
+			HierarchicalActionSet hierarchicalActionSet1 = postOrder(a).stream().collect(Collectors.toList()).get(0);
+			Action action = hierarchicalActionSet1.getAction();
+			if (hierarchicalActionSet1.getSubActions().size() == 0 && action instanceof Update){
+				List<ITree> collect = hierarchicalActionSet1.getNode().getChildren().stream().filter(x -> x.getType() == 14).collect(Collectors.toList());
+//				if(hierarchicalActionSet1.getNode().getChildren().size() == 1){
+				if(collect.size() == 1){
+//					if(hierarchicalActionSet1.getNode().getChild(0).getType() == 14){
+					if(collect.get(0).getType() == 14){
+						continue;
+					}
+				}
+			}
+			else{
+				Predicate<HierarchicalActionSet> predicate = x->x.getAction() instanceof Move;
+				List<HierarchicalActionSet> collect = postOrder(a).stream().filter(predicate).collect(Collectors.toList());
+				if(collect.size() == 1){
+					HierarchicalActionSet hierarchicalActionSet = collect.get(0);
+					movDelNode = hierarchicalActionSet.getNode().getParent();
+					reActionSets1.add(a);
+					continue;
 				}
 
+			}
+			if( movDelNode != null){
+				if(a.getNode().equals(movDelNode)){
+					continue;
+				}
+			}
+			reActionSets1.add(a);
+
+		}
+
+
+
+		return reActionSets1;
+//		return reActionSets;
+	}
+
+
+	private boolean isStatement(HierarchicalActionSet actSet){
+		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")) {
+			return true;
+		}
+		return false;
+	}
+	Predicate<HierarchicalActionSet> predicate = x-> isStatement(x);
+
+	private HierarchicalActionSet removeBlocks(HierarchicalActionSet actionSet){
+		List<HierarchicalActionSet> subActions = actionSet.getSubActions();
+
+
+
+		Action action = actionSet.getAction();
+		if (subActions.size() == 1){
+			HierarchicalActionSet subaction = subActions.get(0);
+
+			List<HierarchicalActionSet> collect = postOrder(subaction).stream().filter(predicate).collect(Collectors.toList());
+			if(collect.size() == 0){
+				return actionSet;
+			}
+			boolean b = collect.stream().anyMatch(p -> p.getAction().getName().equals(subActions.get(0).getAction().getName()));
+			if(!b){
+				return actionSet;
+			}
+			Action action1 = subaction.getAction();
+			if(action.getClass().equals(action1.getClass()) && action.getName().equals("UPD")) {
+				subaction.setParent(null);
+				return removeBlocks(subaction);
+
+			}
+		}
+		return actionSet;
+
+	}
+
+	public List<HierarchicalActionSet> postOrder(HierarchicalActionSet a) {
+		List<HierarchicalActionSet> trees = new ArrayList<>();
+		getAllSubActions(a, trees);
+		return trees;
+	}
+	private void getAllSubActions(HierarchicalActionSet a,List<HierarchicalActionSet> as) {
+
+		List<HierarchicalActionSet> subActions = a.getSubActions();
+		if (subActions.size() != 0){
+			for (HierarchicalActionSet s : subActions) {
+				getAllSubActions(s, as);
+			}
+
+		}
+		as.add(a);
+//		List<HierarchicalActionSet> b = new ArrayList<HierarchicalActionSet>();
+//		for (HierarchicalActionSet child: this.getSubActions())
+//			b.add(child);
+//		return b;
+	}
 	private HierarchicalActionSet createActionSet(Action act, Action parentAct, HierarchicalActionSet parent) {
 		HierarchicalActionSet actionSet = new HierarchicalActionSet();
 		actionSet.setAction(act);
@@ -129,19 +231,19 @@ public class HierarchicalRegrouper {
 	}
 
 	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;
-				}
-		}
+//		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;
 	}
 
@@ -214,9 +316,9 @@ public class HierarchicalRegrouper {
 	}
 	
 	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 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;
 		}

richedit/src/main/resource/config.yml

@@ -0,0 +1,28 @@
+java:
+    8home:  /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
+spinfer:
+    home:   /Users/anilkoyuncu/projects/fixminer/spinfer/spinfer.native
+coccinelle:
+    home:   /Users/anilkoyuncu/projects/fixminer/spinfer/statics
+
+dataset:
+#    home:   /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux
+    inputPath : /Users/anilkoyuncu/projects/test/fixminer-data/patches
+    repo:   /Users/anilkoyuncu/projects/test/fixminer-data/datasets
+
+fixminer:
+    projectType : java
+    datapath: /Users/anilkoyuncu/projects/test/fixminer-data/
+
+
+    pjName : patches
+    portDumps : 6399
+    numOfWorkers : 14
+    hostname : localhost
+    hunkLimit : 2
+    patchSize : 50
+
+    projectList : spring-shell,fuse,metadata,commons-codec,commons-collections,commons-compress,commons-configuration,commons-crypto,commons-csv
+    inputPath : /Users/anilkoyuncu/projects/test/fixminer-data/patches
+    redisPath : /Users/anilkoyuncu/projects/release/test/fixminer_source/python/data/redis
+    srcMLPath :  /usr/local/bin/srcml

richedit/src/main/resource/testFiles/commons-codec/prevFiles/prev_55a865_ecec1c_src#main#java#org#apache#commons#codec#StringEncoderComparator.java

@@ -0,0 +1,87 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.codec;
+
+import java.util.Comparator;
+
+/**
+ * Compares Strings using a {@link StringEncoder}. This comparator is used to sort Strings by an encoding scheme such as
+ * Soundex, Metaphone, etc. This class can come in handy if one need to sort Strings by an encoded form of a name such
+ * as Soundex.
+ *
+ * <p>This class is immutable and thread-safe.</p>
+ *
+ * @version $Id$
+ */
+public class StringEncoderComparator implements Comparator {
+
+    /**
+     * Internal encoder instance.
+     */
+    private final StringEncoder stringEncoder;
+
+    /**
+     * Constructs a new instance.
+     *
+     * @deprecated Creating an instance without a {@link StringEncoder} leads to a {@link NullPointerException}. Will be
+     *             removed in 2.0.
+     */
+    @Deprecated
+    public StringEncoderComparator() {
+        this.stringEncoder = null; // Trying to use this will cause things to break
+    }
+
+    /**
+     * Constructs a new instance with the given algorithm.
+     *
+     * @param stringEncoder
+     *            the StringEncoder used for comparisons.
+     */
+    public StringEncoderComparator(final StringEncoder stringEncoder) {
+        this.stringEncoder = stringEncoder;
+    }
+
+    /**
+     * Compares two strings based not on the strings themselves, but on an encoding of the two strings using the
+     * StringEncoder this Comparator was created with.
+     *
+     * If an {@link EncoderException} is encountered, return <code>0</code>.
+     *
+     * @param o1
+     *            the object to compare
+     * @param o2
+     *            the object to compare to
+     * @return the Comparable.compareTo() return code or 0 if an encoding error was caught.
+     * @see Comparable
+     */
+    @Override
+    public int compare(final Object o1, final Object o2) {
+
+        int compareCode = 0;
+
+        try {
+            final Comparable s1 = (Comparable) this.stringEncoder.encode(o1);
+            final Comparable s2 = (Comparable) this.stringEncoder.encode(o2);
+            compareCode = s1.compareTo(s2);
+        } catch (final EncoderException ee) {
+            compareCode = 0;
+        }
+        return compareCode;
+    }
+
+}

richedit/src/main/resource/testFiles/commons-codec/revFiles/55a865_ecec1c_src#main#java#org#apache#commons#codec#StringEncoderComparator.java

@@ -0,0 +1,89 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.codec;
+
+import java.util.Comparator;
+
+/**
+ * Compares Strings using a {@link StringEncoder}. This comparator is used to sort Strings by an encoding scheme such as
+ * Soundex, Metaphone, etc. This class can come in handy if one need to sort Strings by an encoded form of a name such
+ * as Soundex.
+ *
+ * <p>This class is immutable and thread-safe.</p>
+ *
+ * @version $Id$
+ */
+@SuppressWarnings("rawtypes")
+public class StringEncoderComparator implements Comparator {
+
+    /**
+     * Internal encoder instance.
+     */
+    private final StringEncoder stringEncoder;
+
+    /**
+     * Constructs a new instance.
+     *
+     * @deprecated Creating an instance without a {@link StringEncoder} leads to a {@link NullPointerException}. Will be
+     *             removed in 2.0.
+     */
+    @Deprecated
+    public StringEncoderComparator() {
+        this.stringEncoder = null; // Trying to use this will cause things to break
+    }
+
+    /**
+     * Constructs a new instance with the given algorithm.
+     *
+     * @param stringEncoder
+     *            the StringEncoder used for comparisons.
+     */
+    public StringEncoderComparator(final StringEncoder stringEncoder) {
+        this.stringEncoder = stringEncoder;
+    }
+
+    /**
+     * Compares two strings based not on the strings themselves, but on an encoding of the two strings using the
+     * StringEncoder this Comparator was created with.
+     *
+     * If an {@link EncoderException} is encountered, return <code>0</code>.
+     *
+     * @param o1
+     *            the object to compare
+     * @param o2
+     *            the object to compare to
+     * @return the Comparable.compareTo() return code or 0 if an encoding error was caught.
+     * @see Comparable
+     */
+    @SuppressWarnings("unchecked")
+    @Override
+    public int compare(final Object o1, final Object o2) {
+
+        int compareCode = 0;
+
+        try {
+            final Comparable s1 = (Comparable) this.stringEncoder.encode(o1);
+            final Comparable s2 = (Comparable) this.stringEncoder.encode(o2);
+            compareCode = s1.compareTo(s2);
+        } catch (final EncoderException ee) {
+            compareCode = 0;
+        }
+        return compareCode;
+    }
+
+}

richedit/src/main/resource/testFiles/commons-collections/prevFiles/prev_05b6c7_eedfe8_src#java#org#apache#commons#collections#BeanMap.java

@@ -0,0 +1,841 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/BeanMap.java,v 1.25 2003/12/05 20:23:57 scolebourne Exp $
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 2001-2003 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowledgement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowledgement may appear in the software itself,
+ *    if and wherever such third-party acknowledgements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Software Foundation.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+package org.apache.commons.collections;
+
+import java.beans.BeanInfo;
+import java.beans.IntrospectionException;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.AbstractMap;
+import java.util.AbstractSet;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Set;
+
+import org.apache.commons.collections.list.UnmodifiableList;
+import org.apache.commons.collections.keyvalue.AbstractMapEntry;
+import org.apache.commons.collections.set.UnmodifiableSet;
+
+/** 
+ * An implementation of Map for JavaBeans which uses introspection to
+ * get and put properties in the bean.
+ * <p>
+ * If an exception occurs during attempts to get or set a property then the
+ * property is considered non existent in the Map
+ *
+ * @since Commons Collections 1.0
+ * @version $Revision: 1.25 $ $Date: 2003/12/05 20:23:57 $
+ * 
+ * @author James Strachan
+ * @author Stephen Colebourne
+ */
+public class BeanMap extends AbstractMap implements Cloneable {
+
+    private transient Object bean;
+
+    private transient HashMap readMethods = new HashMap();
+    private transient HashMap writeMethods = new HashMap();
+    private transient HashMap types = new HashMap();
+
+    /**
+     * An empty array.  Used to invoke accessors via reflection.
+     */
+    public static final Object[] NULL_ARGUMENTS = {};
+
+    /**
+     * Maps primitive Class types to transformers.  The transformer
+     * transform strings into the appropriate primitive wrapper.
+     */
+    public static HashMap defaultTransformers = new HashMap();
+    
+    static {
+        defaultTransformers.put( 
+            Boolean.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Boolean.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Character.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return new Character( input.toString().charAt( 0 ) );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Byte.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Byte.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Short.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Short.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Integer.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Integer.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Long.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Long.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Float.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Float.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Double.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Double.valueOf( input.toString() );
+                }
+            }
+        );
+    }
+    
+    
+    // Constructors
+    //-------------------------------------------------------------------------
+
+    /**
+     * Constructs a new empty <code>BeanMap</code>.
+     */
+    public BeanMap() {
+    }
+
+    /**
+     * Constructs a new <code>BeanMap</code> that operates on the 
+     * specified bean.  If the given bean is <code>null</code>, then
+     * this map will be empty.
+     *
+     * @param bean  the bean for this map to operate on
+     */
+    public BeanMap(Object bean) {
+        this.bean = bean;
+        initialise();
+    }
+
+    // Map interface
+    //-------------------------------------------------------------------------
+
+    public String toString() {
+        return "BeanMap<" + String.valueOf(bean) + ">";
+    }
+    
+    /**
+     * Clone this bean map using the following process: 
+     *
+     * <ul>
+     * <li>If there is no underlying bean, return a cloned BeanMap without a
+     * bean.
+     *
+     * <li>Since there is an underlying bean, try to instantiate a new bean of
+     * the same type using Class.newInstance().
+     * 
+     * <li>If the instantiation fails, throw a CloneNotSupportedException
+     *
+     * <li>Clone the bean map and set the newly instantiated bean as the
+     * underlying bean for the bean map.
+     *
+     * <li>Copy each property that is both readable and writable from the
+     * existing object to a cloned bean map.  
+     *
+     * <li>If anything fails along the way, throw a
+     * CloneNotSupportedException.
+     *
+     * <ul>
+     */
+    public Object clone() throws CloneNotSupportedException {
+        BeanMap newMap = (BeanMap)super.clone();
+
+        if(bean == null) {
+            // no bean, just an empty bean map at the moment.  return a newly
+            // cloned and empty bean map.
+            return newMap;
+        }
+
+        Object newBean = null;            
+        Class beanClass = null;
+        try {
+            beanClass = bean.getClass();
+            newBean = beanClass.newInstance();
+        } catch (Exception e) {
+            // unable to instantiate
+            throw new CloneNotSupportedException
+                ("Unable to instantiate the underlying bean \"" +
+                 beanClass.getName() + "\": " + e);
+        }
+            
+        try {
+            newMap.setBean(newBean);
+        } catch (Exception exception) {
+            throw new CloneNotSupportedException
+                ("Unable to set bean in the cloned bean map: " + 
+                 exception);
+        }
+            
+        try {
+            // copy only properties that are readable and writable.  If its
+            // not readable, we can't get the value from the old map.  If
+            // its not writable, we can't write a value into the new map.
+            Iterator readableKeys = readMethods.keySet().iterator();
+            while(readableKeys.hasNext()) {
+                Object key = readableKeys.next();
+                if(getWriteMethod(key) != null) {
+                    newMap.put(key, get(key));
+                }
+            }
+        } catch (Exception exception) {
+            throw new CloneNotSupportedException
+                ("Unable to copy bean values to cloned bean map: " +
+                 exception);
+        }
+
+        return newMap;
+    }
+
+    /**
+     * Puts all of the writeable properties from the given BeanMap into this
+     * BeanMap. Read-only and Write-only properties will be ignored.
+     *
+     * @param map  the BeanMap whose properties to put
+     */
+    public void putAllWriteable(BeanMap map) {
+        Iterator readableKeys = map.readMethods.keySet().iterator();
+        while (readableKeys.hasNext()) {
+            Object key = readableKeys.next();
+            if (getWriteMethod(key) != null) {
+                this.put(key, map.get(key));
+            }
+        }
+    }
+
+
+    /**
+     * This method reinitializes the bean map to have default values for the
+     * bean's properties.  This is accomplished by constructing a new instance
+     * of the bean which the map uses as its underlying data source.  This
+     * behavior for <code>clear()</code> differs from the Map contract in that
+     * the mappings are not actually removed from the map (the mappings for a
+     * BeanMap are fixed).
+     */
+    public void clear() {
+        if(bean == null) return;
+
+        Class beanClass = null;
+        try {
+            beanClass = bean.getClass();
+            bean = beanClass.newInstance();
+        }
+        catch (Exception e) {
+            throw new UnsupportedOperationException( "Could not create new instance of class: " + beanClass );
+        }
+    }
+
+    /**
+     * Returns true if the bean defines a property with the given name.
+     * <p>
+     * The given name must be a <code>String</code>; if not, this method
+     * returns false. This method will also return false if the bean
+     * does not define a property with that name.
+     * <p>
+     * Write-only properties will not be matched as the test operates against
+     * property read methods.
+     *
+     * @param name  the name of the property to check
+     * @return false if the given name is null or is not a <code>String</code>;
+     *   false if the bean does not define a property with that name; or
+     *   true if the bean does define a property with that name
+     */
+    public boolean containsKey(Object name) {
+        Method method = getReadMethod(name);
+        return method != null;
+    }
+
+    /**
+     * Returns true if the bean defines a property whose current value is
+     * the given object.
+     *
+     * @param value  the value to check
+     * @return false  true if the bean has at least one property whose 
+     *   current value is that object, false otherwise
+     */
+    public boolean containsValue(Object value) {
+        // use default implementation
+        return super.containsValue(value);
+    }
+
+    /**
+     * Returns the value of the bean's property with the given name.
+     * <p>
+     * The given name must be a {@link String} and must not be 
+     * null; otherwise, this method returns <code>null</code>.
+     * If the bean defines a property with the given name, the value of
+     * that property is returned.  Otherwise, <code>null</code> is 
+     * returned.
+     * <p>
+     * Write-only properties will not be matched as the test operates against
+     * property read methods.
+     *
+     * @param name  the name of the property whose value to return
+     * @return  the value of the property with that name
+     */
+    public Object get(Object name) {
+        if ( bean != null ) {
+            Method method = getReadMethod( name );
+            if ( method != null ) {
+                try {
+                    return method.invoke( bean, NULL_ARGUMENTS );
+                }
+                catch (  IllegalAccessException e ) {
+                    logWarn( e );
+                }
+                catch ( IllegalArgumentException e ) {
+                    logWarn(  e );
+                }
+                catch ( InvocationTargetException e ) {
+                    logWarn(  e );
+                }
+                catch ( NullPointerException e ) {
+                    logWarn(  e );
+                }
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Sets the bean property with the given name to the given value.
+     *
+     * @param name  the name of the property to set
+     * @param value  the value to set that property to
+     * @return  the previous value of that property
+     * @throws IllegalArgumentException  if the given name is null;
+     *   if the given name is not a {@link String}; if the bean doesn't
+     *   define a property with that name; or if the bean property with
+     *   that name is read-only
+     */
+    public Object put(Object name, Object value) throws IllegalArgumentException, ClassCastException {
+        if ( bean != null ) {
+            Object oldValue = get( name );
+            Method method = getWriteMethod( name );
+            if ( method == null ) {
+                throw new IllegalArgumentException( "The bean of type: "+ bean.getClass().getName() + " has no property called: " + name );
+            }
+            try {
+                Object[] arguments = createWriteMethodArguments( method, value );
+                method.invoke( bean, arguments );
+
+                Object newValue = get( name );
+                firePropertyChange( name, oldValue, newValue );
+            }
+            catch ( InvocationTargetException e ) {
+                logInfo( e );
+                throw new IllegalArgumentException( e.getMessage() );
+            }
+            catch ( IllegalAccessException e ) {
+                logInfo( e );
+                throw new IllegalArgumentException( e.getMessage() );
+            }
+            return oldValue;
+        }
+        return null;
+    }
+                    
+    /**
+     * Returns the number of properties defined by the bean.
+     *
+     * @return  the number of properties defined by the bean
+     */
+    public int size() {
+        return readMethods.size();
+    }
+
+    
+    /**
+     * Get the keys for this BeanMap.
+     * <p>
+     * Write-only properties are <b>not</b> included in the returned set of
+     * property names, although it is possible to set their value and to get 
+     * their type.
+     * 
+     * @return BeanMap keys.  The Set returned by this method is not
+     *        modifiable.
+     */
+    public Set keySet() {
+        return UnmodifiableSet.decorate(readMethods.keySet());
+    }
+
+    /**
+     * Gets a Set of MapEntry objects that are the mappings for this BeanMap.
+     * <p>
+     * Each MapEntry can be set but not removed.
+     * 
+     * @return the unmodifiable set of mappings
+     */
+    public Set entrySet() {
+        return UnmodifiableSet.decorate(new AbstractSet() {
+            public Iterator iterator() {
+                return entryIterator();
+            }
+            public int size() {
+              return BeanMap.this.readMethods.size();
+            }
+        });
+    }
+
+    /**
+     * Returns the values for the BeanMap.
+     * 
+     * @return values for the BeanMap.  The returned collection is not
+     *        modifiable.
+     */
+    public Collection values() {
+        ArrayList answer = new ArrayList( readMethods.size() );
+        for ( Iterator iter = valueIterator(); iter.hasNext(); ) {
+            answer.add( iter.next() );
+        }
+        return UnmodifiableList.decorate(answer);
+    }
+
+
+    // Helper methods
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns the type of the property with the given name.
+     *
+     * @param name  the name of the property
+     * @return  the type of the property, or <code>null</code> if no such
+     *  property exists
+     */
+    public Class getType(String name) {
+        return (Class) types.get( name );
+    }
+
+    /**
+     * Convenience method for getting an iterator over the keys.
+     * <p>
+     * Write-only properties will not be returned in the iterator.
+     *
+     * @return an iterator over the keys
+     */
+    public Iterator keyIterator() {
+        return readMethods.keySet().iterator();
+    }
+
+    /**
+     * Convenience method for getting an iterator over the values.
+     *
+     * @return an iterator over the values
+     */
+    public Iterator valueIterator() {
+        final Iterator iter = keyIterator();
+        return new Iterator() {            
+            public boolean hasNext() {
+                return iter.hasNext();
+            }
+            public Object next() {
+                Object key = iter.next();
+                return get( (String) key );
+            }
+            public void remove() {
+                throw new UnsupportedOperationException( "remove() not supported for BeanMap" );
+            }
+        };
+    }
+
+    /**
+     * Convenience method for getting an iterator over the entries.
+     *
+     * @return an iterator over the entries
+     */
+    public Iterator entryIterator() {
+        final Iterator iter = keyIterator();
+        return new Iterator() {            
+            public boolean hasNext() {
+                return iter.hasNext();
+            }            
+            public Object next() {
+                Object key = iter.next();
+                Object value = get(key);
+                return new MyMapEntry( BeanMap.this, key, value );
+            }            
+            public void remove() {
+                throw new UnsupportedOperationException( "remove() not supported for BeanMap" );
+            }
+        };
+    }
+
+
+    // Properties
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns the bean currently being operated on.  The return value may
+     * be null if this map is empty.
+     *
+     * @return the bean being operated on by this map
+     */
+    public Object getBean() {
+        return bean;
+    }
+
+    /**
+     * Sets the bean to be operated on by this map.  The given value may
+     * be null, in which case this map will be empty.
+     *
+     * @param newBean  the new bean to operate on
+     */
+    public void setBean( Object newBean ) {
+        bean = newBean;
+        reinitialise();
+    }
+
+    /**
+     * Returns the accessor for the property with the given name.
+     *
+     * @param name  the name of the property 
+     * @return the accessor method for the property, or null
+     */
+    public Method getReadMethod(String name) {
+        return (Method) readMethods.get(name);
+    }
+
+    /**
+     * Returns the mutator for the property with the given name.
+     *
+     * @param name  the name of the property
+     * @return the mutator method for the property, or null
+     */
+    public Method getWriteMethod(String name) {
+        return (Method) writeMethods.get(name);
+    }
+
+
+    // Implementation methods
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns the accessor for the property with the given name.
+     *
+     * @param name  the name of the property 
+     * @return null if the name is null; null if the name is not a 
+     * {@link String}; null if no such property exists; or the accessor
+     *  method for that property
+     */
+    protected Method getReadMethod( Object name ) {
+        return (Method) readMethods.get( name );
+    }
+
+    /**
+     * Returns the mutator for the property with the given name.
+     *
+     * @param name  the name of the 
+     * @return null if the name is null; null if the name is not a 
+     * {@link String}; null if no such property exists; null if the 
+     * property is read-only; or the mutator method for that property
+     */
+    protected Method getWriteMethod( Object name ) {
+        return (Method) writeMethods.get( name );
+    }
+
+    /**
+     * Reinitializes this bean.  Called during {@link #setBean(Object)}.
+     * Does introspection to find properties.
+     */
+    protected void reinitialise() {
+        readMethods.clear();
+        writeMethods.clear();
+        types.clear();
+        initialise();
+    }
+
+    private void initialise() {
+        if(getBean() == null) return;
+
+        Class  beanClass = getBean().getClass();
+        try {
+            //BeanInfo beanInfo = Introspector.getBeanInfo( bean, null );
+            BeanInfo beanInfo = Introspector.getBeanInfo( beanClass );
+            PropertyDescriptor[] propertyDescriptors = beanInfo.getPropertyDescriptors();
+            if ( propertyDescriptors != null ) {
+                for ( int i = 0; i < propertyDescriptors.length; i++ ) {
+                    PropertyDescriptor propertyDescriptor = propertyDescriptors[i];
+                    if ( propertyDescriptor != null ) {
+                        String name = propertyDescriptor.getName();
+                        Method readMethod = propertyDescriptor.getReadMethod();
+                        Method writeMethod = propertyDescriptor.getWriteMethod();
+                        Class aType = propertyDescriptor.getPropertyType();
+
+                        if ( readMethod != null ) {
+                            readMethods.put( name, readMethod );
+                        }
+                        if ( writeMethods != null ) {
+                            writeMethods.put( name, writeMethod );
+                        }
+                        types.put( name, aType );
+                    }
+                }
+            }
+        }
+        catch ( IntrospectionException e ) {
+            logWarn(  e );
+        }
+    }
+
+    /**
+     * Called during a successful {@link #put(Object,Object)} operation.
+     * Default implementation does nothing.  Override to be notified of
+     * property changes in the bean caused by this map.
+     *
+     * @param key  the name of the property that changed
+     * @param oldValue  the old value for that property
+     * @param newValue  the new value for that property
+     */
+    protected void firePropertyChange( Object key, Object oldValue, Object newValue ) {
+    }
+
+    // Implementation classes
+    //-------------------------------------------------------------------------
+
+    /**
+     * Map entry used by {@link BeanMap}.
+     */
+    protected static class MyMapEntry extends AbstractMapEntry {        
+        private BeanMap owner;
+        
+        /**
+         * Constructs a new <code>MyMapEntry</code>.
+         *
+         * @param owner  the BeanMap this entry belongs to
+         * @param key  the key for this entry
+         * @param value  the value for this entry
+         */
+        protected MyMapEntry( BeanMap owner, Object key, Object value ) {
+            super( key, value );
+            this.owner = owner;
+        }
+
+        /**
+         * Sets the value.
+         *
+         * @param value  the new value for the entry
+         * @return the old value for the entry
+         */
+        public Object setValue(Object value) {
+            Object key = getKey();
+            Object oldValue = owner.get( key );
+
+            owner.put( key, value );
+            Object newValue = owner.get( key );
+            super.setValue( newValue );
+            return oldValue;
+        }
+    }
+
+    /**
+     * Creates an array of parameters to pass to the given mutator method.
+     * If the given object is not the right type to pass to the method 
+     * directly, it will be converted using {@link #convertType(Class,Object)}.
+     *
+     * @param method  the mutator method
+     * @param value  the value to pass to the mutator method
+     * @return an array containing one object that is either the given value
+     *   or a transformed value
+     * @throws IllegalAccessException if {@link #convertType(Class,Object)}
+     *   raises it
+     * @throws IllegalArgumentException if any other exception is raised
+     *   by {@link #convertType(Class,Object)}
+     */
+    protected Object[] createWriteMethodArguments( Method method, Object value ) throws IllegalAccessException, ClassCastException {            
+        try {
+            if ( value != null ) {
+                Class[] types = method.getParameterTypes();
+                if ( types != null && types.length > 0 ) {
+                    Class paramType = types[0];
+                    if ( ! paramType.isAssignableFrom( value.getClass() ) ) {
+                        value = convertType( paramType, value );
+                    }
+                }
+            }
+            Object[] answer = { value };
+            return answer;
+        }
+        catch ( InvocationTargetException e ) {
+            logInfo( e );
+            throw new IllegalArgumentException( e.getMessage() );
+        }
+        catch ( InstantiationException e ) {
+            logInfo( e );
+            throw new IllegalArgumentException( e.getMessage() );
+        }
+    }
+
+    /**
+     * Converts the given value to the given type.  First, reflection is
+     * is used to find a public constructor declared by the given class 
+     * that takes one argument, which must be the precise type of the 
+     * given value.  If such a constructor is found, a new object is
+     * created by passing the given value to that constructor, and the
+     * newly constructed object is returned.<P>
+     *
+     * If no such constructor exists, and the given type is a primitive
+     * type, then the given value is converted to a string using its 
+     * {@link Object#toString() toString()} method, and that string is
+     * parsed into the correct primitve type using, for instance, 
+     * {@link Integer#valueOf(String)} to convert the string into an
+     * <code>int</code>.<P>
+     *
+     * If no special constructor exists and the given type is not a 
+     * primitive type, this method returns the original value.
+     *
+     * @param newType  the type to convert the value to
+     * @param value  the value to convert
+     * @return the converted value
+     * @throws NumberFormatException if newType is a primitive type, and 
+     *  the string representation of the given value cannot be converted
+     *  to that type
+     * @throws InstantiationException  if the constructor found with 
+     *  reflection raises it
+     * @throws InvocationTargetExcetpion  if the constructor found with
+     *  reflection raises it
+     * @throws IllegalAccessException  never
+     * @throws IllegalArgumentException  never
+     */
+    protected Object convertType( Class newType, Object value ) 
+        throws InstantiationException, IllegalAccessException, IllegalArgumentException, InvocationTargetException {
+        
+        // try call constructor
+        Class[] types = { value.getClass() };
+        try {
+            Constructor constructor = newType.getConstructor( types );        
+            Object[] arguments = { value };
+            return constructor.newInstance( arguments );
+        }
+        catch ( NoSuchMethodException e ) {
+            // try using the transformers
+            Transformer transformer = getTypeTransformer( newType );
+            if ( transformer != null ) {
+                return transformer.transform( value );
+            }
+            return value;
+        }
+    }
+
+    /**
+     * Returns a transformer for the given primitive type.
+     *
+     * @param aType  the primitive type whose transformer to return
+     * @return a transformer that will convert strings into that type,
+     *  or null if the given type is not a primitive type
+     */
+    protected Transformer getTypeTransformer( Class aType ) {
+        return (Transformer) defaultTransformers.get( aType );
+    }
+
+    /**
+     * Logs the given exception to <code>System.out</code>.  Used to display
+     * warnings while accessing/mutating the bean.
+     *
+     * @param ex  the exception to log
+     */
+    protected void logInfo(Exception ex) {
+        // Deliberately do not use LOG4J or Commons Logging to avoid dependencies
+        System.out.println( "INFO: Exception: " + ex );
+    }
+
+    /**
+     * Logs the given exception to <code>System.err</code>.  Used to display
+     * errors while accessing/mutating the bean.
+     *
+     * @param ex  the exception to log
+     */
+    protected void logWarn(Exception ex) {
+        // Deliberately do not use LOG4J or Commons Logging to avoid dependencies
+        System.out.println( "WARN: Exception: " + ex );
+        ex.printStackTrace();
+    }
+}

richedit/src/main/resource/testFiles/commons-collections/prevFiles/prev_2d2aef_fb3daa_src#java#org#apache#commons#collections#map#TransformedMap.java

@@ -0,0 +1,242 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.collections.map;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+import java.util.Map;
+
+import org.apache.commons.collections.IterableMap;
+import org.apache.commons.collections.Transformer;
+
+/**
+ * Decorates another <code>Map</code> to transform objects that are added.
+ * <p>
+ * The Map put methods and Map.Entry setValue method are affected by this class.
+ * Thus objects must be removed or searched for using their transformed form.
+ * For example, if the transformation converts Strings to Integers, you must
+ * use the Integer form to remove objects.
+ * <p>
+ * <strong>Note that TransformedMap is not synchronized and is not thread-safe.</strong>
+ * If you wish to use this map from multiple threads concurrently, you must use
+ * appropriate synchronization. The simplest approach is to wrap this map
+ * using {@link java.util.Collections#synchronizedMap(Map)}. This class may throw
+ * exceptions when accessed by concurrent threads without synchronization.
+ * <p>
+ * This class is Serializable from Commons Collections 3.1.
+ * <p>
+ * @see org.apache.commons.collections.splitmap.TransformedMap
+ *
+ * @since Commons Collections 3.0
+ * @version $Revision$ $Date$
+ *
+ * @author Stephen Colebourne
+ */
+public class TransformedMap<K, V>
+        extends AbstractInputCheckedMapDecorator<K, V>
+        implements Serializable {
+
+    /** Serialization version */
+    private static final long serialVersionUID = 7023152376788900464L;
+
+    /** The transformer to use for the key */
+    protected final Transformer<? super K, ? extends K> keyTransformer;
+    /** The transformer to use for the value */
+    protected final Transformer<? super V, ? extends V> valueTransformer;
+
+    /**
+     * Factory method to create a transforming map.
+     * <p>
+     * If there are any elements already in the map being decorated, they
+     * are NOT transformed.
+     * Contrast this with {@link #decorateTransform}.
+     *
+     * @param map  the map to decorate, must not be null
+     * @param keyTransformer  the transformer to use for key conversion, null means no transformation
+     * @param valueTransformer  the transformer to use for value conversion, null means no transformation
+     * @throws IllegalArgumentException if map is null
+     */
+    public static <K, V> IterableMap<K, V> decorate(Map<K, V> map,
+            Transformer<? super K, ? extends K> keyTransformer,
+            Transformer<? super V, ? extends V> valueTransformer) {
+        return new TransformedMap<K, V>(map, keyTransformer, valueTransformer);
+    }
+
+    /**
+     * Factory method to create a transforming map that will transform
+     * existing contents of the specified map.
+     * <p>
+     * If there are any elements already in the map being decorated, they
+     * will be transformed by this method.
+     * Contrast this with {@link #decorate}.
+     *
+     * @param map  the map to decorate, must not be null
+     * @param keyTransformer  the transformer to use for key conversion, null means no transformation
+     * @param valueTransformer  the transformer to use for value conversion, null means no transformation
+     * @throws IllegalArgumentException if map is null
+     * @since Commons Collections 3.2
+     */
+    public static <K, V> Map<K, V> decorateTransform(Map<K, V> map,
+            Transformer<? super K, ? extends K> keyTransformer,
+            Transformer<? super V, ? extends V> valueTransformer) {
+        TransformedMap<K, V> decorated = new TransformedMap<K, V>(map, keyTransformer, valueTransformer);
+        if (map.size() > 0) {
+            Map<K, V> transformed = decorated.transformMap(map);
+            decorated.clear();
+            decorated.decorated().putAll(transformed);  // avoids double transformation
+        }
+        return decorated;
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Constructor that wraps (not copies).
+     * <p>
+     * If there are any elements already in the collection being decorated, they
+     * are NOT transformed.
+     *
+     * @param map  the map to decorate, must not be null
+     * @param keyTransformer  the transformer to use for key conversion, null means no conversion
+     * @param valueTransformer  the transformer to use for value conversion, null means no conversion
+     * @throws IllegalArgumentException if map is null
+     */
+    protected TransformedMap(Map<K, V> map, Transformer<? super K, ? extends K> keyTransformer,
+            Transformer<? super V, ? extends V> valueTransformer) {
+        super(map);
+        this.keyTransformer = keyTransformer;
+        this.valueTransformer = valueTransformer;
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Write the map out using a custom routine.
+     *
+     * @param out  the output stream
+     * @throws IOException
+     * @since Commons Collections 3.1
+     */
+    private void writeObject(ObjectOutputStream out) throws IOException {
+        out.defaultWriteObject();
+        out.writeObject(map);
+    }
+
+    /**
+     * Read the map in using a custom routine.
+     *
+     * @param in  the input stream
+     * @throws IOException
+     * @throws ClassNotFoundException
+     * @since Commons Collections 3.1
+     */
+    @SuppressWarnings("unchecked")
+    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
+        in.defaultReadObject();
+        map = (Map) in.readObject();
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Transforms a key.
+     * <p>
+     * The transformer itself may throw an exception if necessary.
+     *
+     * @param object  the object to transform
+     * @throws the transformed object
+     */
+    protected K transformKey(K object) {
+        if (keyTransformer == null) {
+            return object;
+        }
+        return keyTransformer.transform(object);
+    }
+
+    /**
+     * Transforms a value.
+     * <p>
+     * The transformer itself may throw an exception if necessary.
+     *
+     * @param object  the object to transform
+     * @throws the transformed object
+     */
+    protected V transformValue(V object) {
+        if (valueTransformer == null) {
+            return object;
+        }
+        return valueTransformer.transform(object);
+    }
+
+    /**
+     * Transforms a map.
+     * <p>
+     * The transformer itself may throw an exception if necessary.
+     *
+     * @param map  the map to transform
+     * @throws the transformed object
+     */
+    @SuppressWarnings("unchecked")
+    protected Map<K, V> transformMap(Map<? extends K, ? extends V> map) {
+        if (map.isEmpty()) {
+            return (Map<K, V>) map;
+        }
+        Map<K, V> result = new LinkedMap<K, V>(map.size());
+
+        for (Map.Entry<? extends K, ? extends V> entry : map.entrySet()) {
+            result.put((K) transformKey(entry.getKey()), transformValue(entry.getValue()));
+        }
+        return result;
+    }
+
+    /**
+     * Override to transform the value when using <code>setValue</code>.
+     *
+     * @param value  the value to transform
+     * @return the transformed value
+     * @since Commons Collections 3.1
+     */
+    @Override
+    protected V checkSetValue(V value) {
+        return valueTransformer.transform(value);
+    }
+
+    /**
+     * Override to only return true when there is a value transformer.
+     *
+     * @return true if a value transformer is in use
+     * @since Commons Collections 3.1
+     */
+    @Override
+    protected boolean isSetValueChecking() {
+        return (valueTransformer != null);
+    }
+
+    //-----------------------------------------------------------------------
+    @Override
+    public V put(K key, V value) {
+        key = transformKey(key);
+        value = transformValue(value);
+        return decorated().put(key, value);
+    }
+
+    @Override
+    public void putAll(Map<? extends K, ? extends V> mapToCopy) {
+        mapToCopy = transformMap(mapToCopy);
+        decorated().putAll(mapToCopy);
+    }
+
+}

richedit/src/main/resource/testFiles/commons-collections/prevFiles/prev_3761b5_3639ab_src#java#org#apache#commons#collections#FastHashMap.java

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+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/FastHashMap.java,v 1.2 2001/04/21 12:19:57 craigmcc Exp $
+ * $Revision: 1.2 $
+ * $Date: 2001/04/21 12:19:57 $
+ *
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 1999-2001 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowlegement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowlegement may appear in the software itself,
+ *    if and wherever such third-party acknowlegements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Group.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+
+
+package org.apache.commons.collections;
+
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+
+/**
+ * <p>A customized implementation of <code>java.util.HashMap</code> designed
+ * to operate in a multithreaded environment where the large majority of
+ * method calls are read-only, instead of structural changes.  When operating
+ * in "fast" mode, read calls are non-synchronized and write calls perform the
+ * following steps:</p>
+ * <ul>
+ * <li>Clone the existing collection
+ * <li>Perform the modification on the clone
+ * <li>Replace the existing collection with the (modified) clone
+ * </ul>
+ * <p>When first created, objects of this class default to "slow" mode, where
+ * all accesses of any type are synchronized but no cloning takes place.  This
+ * is appropriate for initially populating the collection, followed by a switch
+ * to "fast" mode (by calling <code>setFast(true)</code>) after initialization
+ * is complete.</p>
+ *
+ * <p><strong>NOTE</strong>: If you are creating and accessing a
+ * <code>HashMap</code> only within a single thread, you should use
+ * <code>java.util.HashMap</code> directly (with no synchronization), for
+ * maximum performance.</p>
+ *
+ * @author Craig R. McClanahan
+ * @version $Revision: 1.2 $ $Date: 2001/04/21 12:19:57 $
+ */
+
+public class FastHashMap extends HashMap {
+
+
+    // ----------------------------------------------------------- Constructors
+
+
+    /**
+     * Construct a an empty map.
+     */
+    public FastHashMap() {
+
+        super();
+        this.map = new HashMap();
+
+    }
+
+
+    /**
+     * Construct an empty map with the specified capacity.
+     *
+     * @param capacity The initial capacity of the empty map
+     */
+    public FastHashMap(int capacity) {
+
+        super();
+        this.map = new HashMap(capacity);
+
+    }
+
+
+    /**
+     * Construct an empty map with the specified capacity and load factor.
+     *
+     * @param capacity The initial capacity of the empty map
+     * @param factor The load factor of the new map
+     */
+    public FastHashMap(int capacity, float factor) {
+
+        super();
+        this.map = new HashMap(capacity, factor);
+
+    }
+
+
+    /**
+     * Construct a new map with the same mappings as the specified map.
+     *
+     * @param map The map whose mappings are to be copied
+     */
+    public FastHashMap(Map map) {
+
+        super();
+        this.map = new HashMap(map);
+
+    }
+
+
+    // ----------------------------------------------------- Instance Variables
+
+
+    /**
+     * The underlying map we are managing.
+     */
+    protected HashMap map = null;
+
+
+    // ------------------------------------------------------------- Properties
+
+
+    /**
+     * Are we operating in "fast" mode?
+     */
+    protected boolean fast = false;
+
+    public boolean getFast() {
+        return (this.fast);
+    }
+
+    public void setFast(boolean fast) {
+        this.fast = fast;
+    }
+
+
+    // --------------------------------------------------------- Public Methods
+
+
+    /**
+     * Remove all mappings from this map.
+     */
+    public void clear() {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                temp.clear();
+                map = temp;
+            }
+        } else {
+            synchronized (map) {
+                map.clear();
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a shallow copy of this <code>FastHashMap</code> instance.
+     * The keys and values themselves are not copied.
+     */
+    public Object clone() {
+
+        FastHashMap results = null;
+        if (fast) {
+            results = new FastHashMap(map);
+        } else {
+            synchronized (map) {
+                results = new FastHashMap(map);
+            }
+        }
+        results.setFast(getFast());
+        return (results);
+
+    }
+
+
+    /**
+     * Return <code>true</code> if this map contains a mapping for the
+     * specified key.
+     *
+     * @param key Key to be searched for
+     */
+    public boolean containsKey(Object key) {
+
+        if (fast) {
+            return (map.containsKey(key));
+        } else {
+            synchronized (map) {
+                return (map.containsKey(key));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return <code>true</code> if this map contains one or more keys mapping
+     * to the specified value.
+     *
+     * @param value Value to be searched for
+     */
+    public boolean containsValue(Object value) {
+
+        if (fast) {
+            return (map.containsValue(value));
+        } else {
+            synchronized (map) {
+                return (map.containsValue(value));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a collection view of the mappings contained in this map.  Each
+     * element in the returned collection is a <code>Map.Entry</code>.
+     */
+    public Set entrySet() {
+
+        if (fast) {
+            return (map.entrySet());
+        } else {
+            synchronized (map) {
+                return (map.entrySet());
+            }
+        }
+
+    }
+
+
+    /**
+     * Compare the specified object with this list for equality.  This
+     * implementation uses exactly the code that is used to define the
+     * list equals function in the documentation for the
+     * <code>Map.equals</code> method.
+     *
+     * @param o Object to be compared to this list
+     */
+    public boolean equals(Object o) {
+
+        // Simple tests that require no synchronization
+        if (o == this)
+            return (true);
+        else if (!(o instanceof Map))
+            return (false);
+        Map mo = (Map) o;
+
+        // Compare the two maps for equality
+        if (fast) {
+            if (mo.size() != map.size())
+                return (false);
+            Iterator i = map.entrySet().iterator();
+            while (i.hasNext()) {
+                Entry e = (Entry) i.next();
+                Object key = e.getKey();
+                Object value = e.getValue();
+                if (value == null) {
+                    if (!(mo.get(key) == null && mo.containsKey(key)))
+                        return (false);
+                } else {
+                    if (!value.equals(mo.get(key)))
+                        return (false);
+                }
+            }
+            return (true);
+        } else {
+            synchronized (map) {
+                if (mo.size() != map.size())
+                    return (false);
+                Iterator i = map.entrySet().iterator();
+                while (i.hasNext()) {
+                    Entry e = (Entry) i.next();
+                    Object key = e.getKey();
+                    Object value = e.getValue();
+                    if (value == null) {
+                        if (!(mo.get(key) == null && mo.containsKey(key)))
+                            return (false);
+                    } else {
+                        if (!value.equals(mo.get(key)))
+                            return (false);
+                    }
+                }
+                return (true);
+            }
+        }
+
+    }
+
+
+    /**
+     * Return the value to which this map maps the specified key.  Returns
+     * <code>null</code> if the map contains no mapping for this key, or if
+     * there is a mapping with a value of <code>null</code>.  Use the
+     * <code>containsKey()</code> method to disambiguate these cases.
+     *
+     * @param key Key whose value is to be returned
+     */
+    public Object get(Object key) {
+
+        if (fast) {
+            return (map.get(key));
+        } else {
+            synchronized (map) {
+                return (map.get(key));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return the hash code value for this map.  This implementation uses
+     * exactly the code that is used to define the list hash function in the
+     * documentation for the <code>Map.hashCode</code> method.
+     */
+    public int hashCode() {
+
+        if (fast) {
+            int h = 0;
+            Iterator i = map.entrySet().iterator();
+            while (i.hasNext())
+                h += i.next().hashCode();
+            return (h);
+        } else {
+            synchronized (map) {
+                int h = 0;
+                Iterator i = map.entrySet().iterator();
+                while (i.hasNext())
+                    h += i.next().hashCode();
+                return (h);
+            }
+        }
+
+    }
+
+
+    /**
+     * Return <code>true</code> if this map contains no mappings.
+     */
+    public boolean isEmpty() {
+
+        if (fast) {
+            return (map.isEmpty());
+        } else {
+            synchronized (map) {
+                return (map.isEmpty());
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a set view of the keys contained in this map.
+     */
+    public Set keySet() {
+
+        if (fast) {
+            return (map.keySet());
+        } else {
+            synchronized (map) {
+                return (map.keySet());
+            }
+        }
+
+    }
+
+
+    /**
+     * Associate the specified value with the specified key in this map.
+     * If the map previously contained a mapping for this key, the old
+     * value is replaced and returned.
+     *
+     * @param key The key with which the value is to be associated
+     * @param value The value to be associated with this key
+     */
+    public Object put(Object key, Object value) {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                Object result = temp.put(key, value);
+                map = temp;
+                return (result);
+            }
+        } else {
+            synchronized (map) {
+                return (map.put(key, value));
+            }
+        }
+
+    }
+
+
+    /**
+     * Copy all of the mappings from the specified map to this one, replacing
+     * any mappings with the same keys.
+     *
+     * @param in Map whose mappings are to be copied
+     */
+    public void putAll(Map in) {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                temp.putAll(in);
+                map = temp;
+            }
+        } else {
+            synchronized (map) {
+                map.putAll(in);
+            }
+        }
+
+    }
+
+
+    /**
+     * Remove any mapping for this key, and return any previously
+     * mapped value.
+     *
+     * @param key Key whose mapping is to be removed
+     */
+    public Object remove(Object key) {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                Object result = temp.remove(key);
+                map = temp;
+                return (result);
+            }
+        } else {
+            synchronized (map) {
+                return (map.remove(key));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return the number of key-value mappings in this map.
+     */
+    public int size() {
+
+        if (fast) {
+            return (map.size());
+        } else {
+            synchronized (map) {
+                return (map.size());
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a collection view of the values contained in this map.
+     */
+    public Collection values() {
+
+        if (fast) {
+            return (map.values());
+        } else {
+            synchronized (map) {
+                return (map.values());
+            }
+        }
+
+    }
+
+
+}

richedit/src/main/resource/testFiles/commons-collections/prevFiles/prev_51c9ef_d65e29_src#java#org#apache#commons#collections#iterators#IteratorChain.java

@@ -0,0 +1,288 @@
+/*
+ *  Copyright 1999-2004 The Apache Software Foundation
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+package org.apache.commons.collections.iterators;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.collections.list.UnmodifiableList;
+
+/**
+ * An IteratorChain is an Iterator that wraps a number of Iterators.
+ * <p>
+ * This class makes multiple iterators look like one to the caller
+ * When any method from the Iterator interface is called, the IteratorChain
+ * will delegate to a single underlying Iterator. The IteratorChain will
+ * invoke the Iterators in sequence until all Iterators are exhausted.
+ * <p>
+ * Under many circumstances, linking Iterators together in this manner is
+ * more efficient (and convenient) than reading out the contents of each
+ * Iterator into a List and creating a new Iterator.
+ * <p>
+ * Calling a method that adds new Iterator<i>after a method in the Iterator
+ * interface has been called</i> will result in an UnsupportedOperationException.
+ * Subclasses should <i>take care</i> to not alter the underlying List of Iterators.
+ * <p>
+ * NOTE: As from version 3.0, the IteratorChain may contain no
+ * iterators. In this case the class will function as an empty iterator.
+ * 
+ * @since Commons Collections 2.1
+ * @version $Revision$ $Date$
+ * 
+ * @author Morgan Delagrange
+ * @author Stephen Colebourne
+ */
+public class IteratorChain implements Iterator {
+
+	/** The chain of iterators */
+    protected final List iteratorChain = new ArrayList();
+    /** The index of the current iterator */
+    protected int currentIteratorIndex = 0;
+    /** The current iterator */
+    protected Iterator currentIterator = null;
+    /**
+     * The "last used" Iterator is the Iterator upon which
+     * next() or hasNext() was most recently called
+     * used for the remove() operation only
+     */
+    protected Iterator lastUsedIterator = null;
+    /**
+     * ComparatorChain is "locked" after the first time
+     * compare(Object,Object) is called
+     */
+    protected boolean isLocked = false;
+
+    //-----------------------------------------------------------------------
+    /**
+     * Construct an IteratorChain with no Iterators.
+     * <p>
+     * You will normally use {@link #addIterator(Iterator)} to add
+     * some iterators after using this constructor.
+     */
+    public IteratorChain() {
+        super();
+    }
+
+    /**
+     * Construct an IteratorChain with a single Iterator.
+     * 
+     * @param iterator first Iterator in the IteratorChain
+     * @throws NullPointerException if the iterator is null
+     */
+    public IteratorChain(Iterator iterator) {
+        super();
+        addIterator(iterator);
+    }
+
+    /**
+     * Constructs a new <code>IteratorChain</code> over the two
+     * given iterators.
+     *
+     * @param a  the first child iterator
+     * @param b  the second child iterator
+     * @throws NullPointerException if either iterator is null
+     */
+    public IteratorChain(Iterator a, Iterator b) {
+        super();
+        addIterator(a);
+        addIterator(b);
+    }
+
+    /**
+     * Constructs a new <code>IteratorChain</code> over the array
+     * of iterators.
+     *
+     * @param iterators  the array of iterators
+     * @throws NullPointerException if iterators array is or contains null
+     */
+    public IteratorChain(Iterator[] iterators) {
+        super();
+        for (int i = 0; i < iterators.length; i++) {
+            addIterator(iterators[i]);
+        }
+    }
+
+    /**
+     * Constructs a new <code>IteratorChain</code> over the collection
+     * of iterators.
+     *
+     * @param iterators  the collection of iterators
+     * @throws NullPointerException if iterators collection is or contains null
+     * @throws ClassCastException if iterators collection doesn't contain an iterator
+     */
+    public IteratorChain(Collection iterators) {
+        super();
+        for (Iterator it = iterators.iterator(); it.hasNext();) {
+            Iterator item = (Iterator) it.next();
+            addIterator(item);
+        }
+    }
+    
+    //-----------------------------------------------------------------------
+    /**
+     * Add an Iterator to the end of the chain 
+     * 
+     * @param iterator Iterator to add
+     * @throws IllegalStateException if I've already started iterating
+     * @throws NullPointerException if the iterator is null
+     */
+    public void addIterator(Iterator iterator) {
+        checkLocked();
+        if (iterator == null) {
+            throw new NullPointerException("Iterator must not be null");
+        }
+        iteratorChain.add(iterator);
+    }
+
+    /**
+     * Set the Iterator at the given index     
+     * 
+     * @param index      index of the Iterator to replace
+     * @param iterator   Iterator to place at the given index
+     * @throws IndexOutOfBoundsException if index &lt; 0 or index &gt; size()
+     * @throws IllegalStateException if I've already started iterating
+     * @throws NullPointerException if the iterator is null
+     */
+    public void setIterator(int index, Iterator iterator) throws IndexOutOfBoundsException {
+        checkLocked();
+        if (iterator == null) {
+            throw new NullPointerException("Iterator must not be null");
+        }
+        iteratorChain.set(index, iterator);
+    }
+
+    /**
+     * Get the list of Iterators (unmodifiable)
+     * 
+     * @return the unmodifiable list of iterators added
+     */
+    public List getIterators() {
+        return UnmodifiableList.decorate(iteratorChain);
+    }
+
+    /**
+     * Number of Iterators in the current IteratorChain.
+     * 
+     * @return Iterator count
+     */
+    public int size() {
+        return iteratorChain.size();
+    }
+
+    /**
+     * Determine if modifications can still be made to the IteratorChain.
+     * IteratorChains cannot be modified once they have executed a method
+     * from the Iterator interface.
+     * 
+     * @return true if IteratorChain cannot be modified, false if it can 
+     */
+    public boolean isLocked() {
+        return isLocked;
+    }
+
+    /**
+     * Checks whether the iterator chain is now locked and in use.
+     */
+    private void checkLocked() {
+        if (isLocked == true) {
+            throw new UnsupportedOperationException("IteratorChain cannot be changed after the first use of a method from the Iterator interface");
+        }
+    }
+
+    /**
+     * Lock the chain so no more iterators can be added.
+     * This must be called from all Iterator interface methods.
+     */
+    private void lockChain() {
+        if (isLocked == false) {
+            isLocked = true;
+        }
+    }
+
+    /**
+     * Updates the current iterator field to ensure that the current Iterator
+     * is not exhausted
+     */
+    protected void updateCurrentIterator() {
+        if (currentIterator == null) {
+            if (iteratorChain.isEmpty()) {
+                currentIterator = EmptyIterator.INSTANCE;
+            } else {
+                currentIterator = (Iterator) iteratorChain.get(0);
+            }
+            // set last used iterator here, in case the user calls remove
+            // before calling hasNext() or next() (although they shouldn't)
+            lastUsedIterator = currentIterator;
+        }
+
+        while (currentIterator.hasNext() == false && currentIteratorIndex < iteratorChain.size() - 1) {
+            currentIteratorIndex++;
+            currentIterator = (Iterator) iteratorChain.get(currentIteratorIndex);
+        }
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Return true if any Iterator in the IteratorChain has a remaining element.
+     * 
+     * @return true if elements remain
+     */
+    public boolean hasNext() {
+        lockChain();
+        updateCurrentIterator();
+        lastUsedIterator = currentIterator;
+
+        return currentIterator.hasNext();
+    }
+
+    /**
+     * Returns the next Object of the current Iterator
+     * 
+     * @return Object from the current Iterator
+     * @throws java.util.NoSuchElementException if all the Iterators are exhausted
+     */
+    public Object next() {
+        lockChain();
+        updateCurrentIterator();
+        lastUsedIterator = currentIterator;
+
+        return currentIterator.next();
+    }
+
+    /**
+     * Removes from the underlying collection the last element 
+     * returned by the Iterator.  As with next() and hasNext(),
+     * this method calls remove() on the underlying Iterator.
+     * Therefore, this method may throw an 
+     * UnsupportedOperationException if the underlying
+     * Iterator does not support this method. 
+     * 
+     * @throws UnsupportedOperationException
+     *   if the remove operator is not supported by the underlying Iterator
+     * @throws IllegalStateException
+     *   if the next method has not yet been called, or the remove method has
+     *   already been called after the last call to the next method.
+     */
+    public void remove() {
+        lockChain();
+        updateCurrentIterator();
+
+        lastUsedIterator.remove();
+    }
+
+}

richedit/src/main/resource/testFiles/commons-collections/prevFiles/prev_906468_31bc59_src#java#org#apache#commons#collections#SequencedHashMap.java

@@ -0,0 +1,888 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/SequencedHashMap.java,v 1.3 2002/02/18 20:34:57 morgand Exp $
+ * $Revision: 1.3 $
+ * $Date: 2002/02/18 20:34:57 $
+ *
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 1999-2002 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowlegement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowlegement may appear in the software itself,
+ *    if and wherever such third-party acknowlegements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Group.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+package org.apache.commons.collections;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.AbstractCollection;
+import java.util.AbstractMap;
+import java.util.AbstractSet;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.NoSuchElementException;
+
+/**
+ *  A map of objects whose mapping entries are sequenced based on the order in
+ *  which they were added.  This data structure has fast <I>O(1)</I> search
+ *  time, deletion time, and insertion time.
+ *
+ *  This class inherits from {@link java.util.HashMap} purely for backwards
+ *  compatibility.  It should really be inheriting from {@link
+ *  java.util.AbstractMap}, or with a tiny extra bit of work, implement the
+ *  full map interface on its own. APIs should not rely on this class being an
+ *  actual {@link java.util.HashMap}, and instead should recognize it only as a
+ *  generic {@link java.util.Map} (unless, of course, you need the sequencing
+ *  functionality, but even in that case, this class should not be referred to
+ *  as a java.util.HashMap).
+ *
+ *  <P>Although this map is sequenced, it cannot implement {@link
+ *  java.util.List} because of incompatible interface definitions.  The remove
+ *  methods in List and Map have different return values (see: {@link
+ *  java.util.List#remove(Object)} and {@link java.util.Map#remove(Object)}).
+ *
+ *  <P>This class is not thread safe.  When a thread safe implementation is
+ *  required, use {@link Collections#synchronizedMap(Map)} as it is documented,
+ *  or use explicit synchronization controls.
+ *
+ *  @author <a href="mailto:michael@iammichael.org">Michael A. Smith</A>
+ * @author <a href="mailto:dlr@collab.net">Daniel Rall</a>
+ * @author <a href="mailto:hps@intermeta.de">Henning P. Schmiedehausen</a>
+ */
+public class SequencedHashMap extends HashMap {
+
+  /**
+   *  {@link java.util.Map.Entry} that doubles as a node in the linked list
+   *  of sequenced mappings.  
+   **/
+  private static class Entry implements Map.Entry {
+    // Note: This class cannot easily be made clonable.  While the actual
+    // implementation of a clone would be simple, defining the semantics is
+    // difficult.  If a shallow clone is implemented, then entry.next.prev !=
+    // entry, which is unintuitive and probably breaks all sorts of assumptions
+    // in code that uses this implementation.  If a deep clone is
+    // implementated, then what happens when the linked list is cyclical (as is
+    // the case with SequencedHashMap)?  It's impossible to know in the clone
+    // when to stop cloning, and thus you end up in a recursive loop,
+    // continuously cloning the "next" in the list.
+
+    private final Object key;
+    private Object value;
+    
+    // package private to allow the SequencedHashMap to access and manipulate
+    // them.
+    Entry next = null;
+    Entry prev = null;
+
+    public Entry(Object key, Object value) {
+      this.key = key;
+      this.value = value;
+    }
+
+    // per Map.Entry.getKey()
+    public Object getKey() { 
+      return this.key; 
+    }
+
+    // per Map.Entry.getValue()
+    public Object getValue() { 
+      return this.value; 
+    }
+
+    // per Map.Entry.setValue()
+    public Object setValue(Object value) { 
+      Object oldValue = this.value;
+      this.value = value; 
+      return oldValue;
+    }
+
+    public int hashCode() { 
+      // implemented per api docs for Map.Entry.hashCode()
+      return ((getKey() == null ? 0 : getKey().hashCode()) ^
+              (getValue()==null ? 0 : getValue().hashCode())); 
+    }
+
+    public boolean equals(Object obj) {
+      if(obj == null) return false;
+      if(obj == this) return true;
+      if(!(obj instanceof Map.Entry)) return false;
+
+      Map.Entry other = (Map.Entry)obj;
+
+      // implemented per api docs for Map.Entry.equals(Object) 
+      return((getKey() == null ?
+              other.getKey() == null : 
+              getKey().equals(other.getKey()))  &&
+             (getValue() == null ?
+              other.getValue() == null : 
+              getValue().equals(other.getValue())));
+    }
+    public String toString() {
+      return "[" + getKey() + "=" + getValue() + "]";
+    }
+  }
+
+  /**
+   *  Construct an empty sentinel used to hold the head (sentinel.next) and the
+   *  tail (sentinel.prev) of the list.  The sentinal has a <code>null</code>
+   *  key and value.
+   **/
+  private static final Entry createSentinel() {
+    Entry s = new Entry(null, null);
+    s.prev = s;
+    s.next = s;
+    return s;
+  }
+
+  /**
+   *  Sentinel used to hold the head and tail of the list of entries.
+   **/
+  private Entry sentinel;
+
+  /**
+   *  Map of keys to entries
+   **/
+  private HashMap entries;
+
+  /**
+   *  Construct a new sequenced hash map with default initial size and load
+   *  factor.
+   **/
+  public SequencedHashMap() {
+    sentinel = createSentinel();
+    entries = new HashMap();
+  }
+
+  /**
+   *  Construct a new sequenced hash map with the specified initial size and
+   *  default load factor.
+   *
+   *  @param initialSize the initial size for the hash table 
+   *
+   *  @see HashMap#HashMap(int)
+   **/
+  public SequencedHashMap(int initialSize) {
+    sentinel = createSentinel();
+    entries = new HashMap(initialSize);
+  }
+
+  /**
+   *  Construct a new sequenced hash map with the specified initial size and
+   *  load factor.
+   *
+   *  @param initialSize the initial size for the hash table 
+   *
+   *  @param loadFactor the load factor for the hash table.
+   *
+   *  @see HashMap#HashMap(int,float)
+   **/
+  public SequencedHashMap(int initialSize, float loadFactor) {
+    sentinel = createSentinel();
+    entries = new HashMap(initialSize, loadFactor);
+  }
+
+  /**
+   *  Construct a new sequenced hash map and add all the elements in the
+   *  specified map.  The order in which the mappings in the specified map are
+   *  added is defined by {@link #putAll(Map)}.  
+   **/
+  public SequencedHashMap(Map m) {
+    this();
+    putAll(m);
+  }
+
+  /**
+   *  Removes an internal entry from the linked list.  This does not remove
+   *  it from the underlying map.
+   **/
+  private void removeEntry(Entry entry) {
+    entry.next.prev = entry.prev;
+    entry.prev.next = entry.next;    
+  }
+
+  /**
+   *  Inserts a new internal entry to the tail of the linked list.  This does
+   *  not add the entry to the underlying map.
+   **/
+  private void insertEntry(Entry entry) {
+    entry.next = sentinel;
+    entry.prev = sentinel.prev;
+    sentinel.prev.next = entry;
+    sentinel.prev = entry;
+  }
+
+  // per Map.size()
+  public int size() {
+    // use the underlying Map's size since size is not maintained here.
+    return entries.size();
+  }
+
+  // per Map.isEmpty()
+  public boolean isEmpty() {
+    // for quick check whether the map is entry, we can check the linked list
+    // and see if there's anything in it.
+    return sentinel.next == sentinel;
+  }
+
+  // per Map.containsKey(Object)
+  public boolean containsKey(Object key) {
+    // pass on to underlying map implementation
+    return entries.containsKey(key);
+  }
+
+  // per Map.containsValue(Object)
+  public boolean containsValue(Object value) {
+    // unfortunately, we cannot just pass this call to the underlying map
+    // because we are mapping keys to entries, not keys to values.  The
+    // underlying map doesn't have an efficient implementation anyway, so this
+    // isn't a big deal.
+
+    // do null comparison outside loop so we only need to do it once.  This
+    // provides a tighter, more efficient loop at the expense of slight
+    // code duplication.
+    if(value == null) {
+      for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+        if(pos.getValue() == null) return true;
+      } 
+    } else {
+      for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+        if(value.equals(pos.getValue())) return true;
+      }
+    }
+    return false;      
+  }
+
+  // per Map.get(Object)
+  public Object get(Object o) {
+    // find entry for the specified key object
+    Entry entry = (Entry)entries.get(o);
+    if(entry == null) return null;
+      
+    return entry.getValue();
+  }
+
+  /**
+   *  Return the entry for the "oldest" mapping.  That is, return the Map.Entry
+   *  for the key-value pair that was first put into the map when compared to
+   *  all the other pairings in the map.  This behavior is equivalent to using
+   *  <code>entrySet().iterator().next()</code>, but this method provides an
+   *  optimized implementation.
+   *
+   *  @return The first entry in the sequence, or <code>null</code> if the
+   *  map is empty.
+   **/
+  public Map.Entry getFirst() {
+    // sentinel.next points to the "first" element of the sequence -- the head
+    // of the list, which is exactly the entry we need to return.  We must test
+    // for an empty list though because we don't want to return the sentinel!
+    return (isEmpty()) ? null : sentinel.next;
+  }
+
+  /**
+   *  Return the key for the "oldest" mapping.  That is, return the key for the
+   *  mapping that was first put into the map when compared to all the other
+   *  objects in the map.  This behavior is equivalent to using
+   *  <code>getFirst().getKey()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The first key in the sequence, or <code>null</code> if the
+   *  map is empty.
+   **/
+  public Object getFirstKey() {
+    // sentinel.next points to the "first" element of the sequence -- the head
+    // of the list -- and the requisite key is returned from it.  An empty list
+    // does not need to be tested.  In cases where the list is empty,
+    // sentinel.next will point to the sentinel itself which has a null key,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.next.getKey();
+  }
+
+  /**
+   *  Return the value for the "oldest" mapping.  That is, return the value for
+   *  the mapping that was first put into the map when compared to all the
+   *  other objects in the map.  This behavior is equivalent to using
+   *  <code>getFirst().getValue()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The first value in the sequence, or <code>null</code> if the
+   *  map is empty.
+   **/
+  public Object getFirstValue() {
+    // sentinel.next points to the "first" element of the sequence -- the head
+    // of the list -- and the requisite value is returned from it.  An empty
+    // list does not need to be tested.  In cases where the list is empty,
+    // sentinel.next will point to the sentinel itself which has a null value,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.next.getValue();
+  }
+
+  /**
+   *  Return the entry for the "newest" mapping.  That is, return the Map.Entry
+   *  for the key-value pair that was first put into the map when compared to
+   *  all the other pairings in the map.  The behavior is equivalent to:
+   *
+   *  <pre>
+   *    Object obj = null;
+   *    Iterator iter = entrySet().iterator();
+   *    while(iter.hasNext()) {
+   *      obj = iter.next();
+   *    }
+   *    return (Map.Entry)obj;
+   *  </pre>
+   *
+   *  However, the implementation of this method ensures an O(1) lookup of the
+   *  last key rather than O(n).
+   *
+   *  @return The last entry in the sequence, or <code>null</code> if the map
+   *  is empty.
+   **/
+  public Map.Entry getLast() {
+    // sentinel.prev points to the "last" element of the sequence -- the tail
+    // of the list, which is exactly the entry we need to return.  We must test
+    // for an empty list though because we don't want to return the sentinel!
+    return (isEmpty()) ? null : sentinel.prev;
+  }
+
+  /**
+   *  Return the key for the "newest" mapping.  That is, return the key for the
+   *  mapping that was last put into the map when compared to all the other
+   *  objects in the map.  This behavior is equivalent to using
+   *  <code>getLast().getKey()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The last key in the sequence, or <code>null</code> if the map is
+   *  empty.
+   **/
+  public Object getLastKey() {
+    // sentinel.prev points to the "last" element of the sequence -- the tail
+    // of the list -- and the requisite key is returned from it.  An empty list
+    // does not need to be tested.  In cases where the list is empty,
+    // sentinel.prev will point to the sentinel itself which has a null key,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.prev.getKey();
+  }
+
+  /**
+   *  Return the value for the "newest" mapping.  That is, return the value for
+   *  the mapping that was last put into the map when compared to all the other
+   *  objects in the map.  This behavior is equivalent to using
+   *  <code>getLast().getValue()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The last value in the sequence, or <code>null</code> if the map
+   *  is empty.
+   **/
+  public Object getLastValue() {
+    // sentinel.prev points to the "last" element of the sequence -- the tail
+    // of the list -- and the requisite value is returned from it.  An empty
+    // list does not need to be tested.  In cases where the list is empty,
+    // sentinel.prev will point to the sentinel itself which has a null value,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.prev.getValue();
+  }
+
+  // per Map.put(Object,Object)
+  public Object put(Object key, Object value) {
+
+    Object oldValue = null;
+
+    // lookup the entry for the specified key
+    Entry e = (Entry)entries.get(key);
+
+    // check to see if it already exists
+    if(e != null) {
+      // remove from list so the entry gets "moved" to the end of list
+      removeEntry(e);
+
+      // update value in map
+      oldValue = e.setValue(value);
+
+      // Note: We do not update the key here because its unnecessary.  We only
+      // do comparisons using equals(Object) and we know the specified key and
+      // that in the map are equal in that sense.  This may cause a problem if
+      // someone does not implement their hashCode() and/or equals(Object)
+      // method properly and then use it as a key in this map.  
+    } else {
+      // add new entry
+      e = new Entry(key, value);
+      entries.put(key, e);
+    }
+    // assert(entry in map, but not list)
+
+    // add to list
+    insertEntry(e);
+
+    return oldValue;
+  }
+
+  // per Map.remove(Object)
+  public Object remove(Object key) {
+    Entry e = (Entry)entries.remove(key);
+    if(e == null) return null;
+    removeEntry(e);
+    return e.getValue();
+  }
+
+  /**
+   *  Adds all the mappings in the specified map to this map, replacing any
+   *  mappings that already exist (as per {@link Map#putAll(Map)}).  The order
+   *  in which the entries are added is determined by the iterator returned
+   *  from {@link Map#entrySet()} for the specified map.
+   *
+   *  @param t the mappings that should be added to this map.
+   *
+   *  @exception NullPointerException if <code>t</code> is <code>null</code>
+   **/
+  public void putAll(Map t) {
+    Iterator iter = t.entrySet().iterator();
+    while(iter.hasNext()) {
+      Map.Entry entry = (Map.Entry)iter.next();
+      put(entry.getKey(), entry.getValue());
+    }
+  }
+
+  // per Map.clear()
+  public void clear() {
+    // remove all from the underlying map
+    entries.clear();
+
+    // and the list
+    sentinel.next = sentinel;
+    sentinel.prev = sentinel;
+  }
+
+  // per Map.keySet()
+  public Set keySet() {
+    return new AbstractSet() {
+
+      // required impls
+      public Iterator iterator() { return new OrderedIterator(KEY); }
+      public boolean remove(Object o) {
+        return SequencedHashMap.this.remove(o) != null;
+      }
+
+      // more efficient impls than abstract set
+      public void clear() { 
+        SequencedHashMap.this.clear(); 
+      }
+      public int size() { 
+        return SequencedHashMap.this.size(); 
+      }
+      public boolean isEmpty() { 
+        return SequencedHashMap.this.isEmpty(); 
+      }
+      public boolean contains(Object o) { 
+        return SequencedHashMap.this.containsKey(o);
+      }
+
+    };
+  }
+
+  // per Map.values()
+  public Collection values() {
+    return new AbstractCollection() {
+      // required impl
+      public Iterator iterator() { return new OrderedIterator(VALUE); }
+      public boolean remove(Object value) {
+        // do null comparison outside loop so we only need to do it once.  This
+        // provides a tighter, more efficient loop at the expense of slight
+        // code duplication.
+        if(value == null) {
+          for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+            if(pos.getValue() == null) {
+              SequencedHashMap.this.remove(pos.getKey());
+              return true;
+            }
+          } 
+        } else {
+          for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+            if(value.equals(pos.getValue())) {
+              SequencedHashMap.this.remove(pos.getKey());
+              return true;
+            }
+          }
+        }
+
+        return false;
+      }
+
+      // more efficient impls than abstract collection
+      public void clear() { 
+        SequencedHashMap.this.clear(); 
+      }
+      public int size() { 
+        return SequencedHashMap.this.size(); 
+      }
+      public boolean isEmpty() { 
+        return SequencedHashMap.this.isEmpty(); 
+      }
+      public boolean contains(Object o) {
+        return SequencedHashMap.this.containsValue(o);
+      }
+    };
+  }
+
+  // per Map.entrySet()
+  public Set entrySet() {
+    return new AbstractSet() {
+      // helper
+      private Entry findEntry(Object o) {
+        if(o == null) return null;
+        if(!(o instanceof Map.Entry)) return null;
+        
+        Map.Entry e = (Map.Entry)o;
+        Entry entry = (Entry)entries.get(e.getKey());
+        if(entry.equals(e)) return entry;
+        else return null;
+      }
+
+      // required impl
+      public Iterator iterator() { 
+        return new OrderedIterator(ENTRY); 
+      }
+      public boolean remove(Object o) {
+        Entry e = findEntry(o);
+        if(e == null) return false;
+
+        return SequencedHashMap.this.remove(e.getKey()) != null;
+      }        
+
+      // more efficient impls than abstract collection
+      public void clear() { 
+        SequencedHashMap.this.clear(); 
+      }
+      public int size() { 
+        return SequencedHashMap.this.size(); 
+      }
+      public boolean isEmpty() { 
+        return SequencedHashMap.this.isEmpty(); 
+      }
+      public boolean contains(Object o) {
+        return findEntry(o) != null;
+      }
+    };
+  }
+
+  // constants to define what the iterator should return on "next"
+  private static final int KEY = 0;
+  private static final int VALUE = 1;
+  private static final int ENTRY = 2;
+  private static final int REMOVED_MASK = 0x80000000;
+
+  private class OrderedIterator implements Iterator {
+    /** 
+     *  Holds the type that should be returned from the iterator.  The value
+     *  should be either {@link #KEY}, {@link #VALUE}, or {@link #ENTRY}.  To
+     *  save a tiny bit of memory, this field is also used as a marker for when
+     *  remove has been called on the current object to prevent a second remove
+     *  on the same element.  Essientially, if this value is negative (i.e. the
+     *  bit specified by {@link #REMOVED_MASK} is set), the current position
+     *  has been removed.  If positive, remove can still be called.
+     **/
+    private int returnType;
+
+    /**
+     *  Holds the "current" position in the iterator.  when pos.next is the
+     *  sentinel, we've reached the end of the list.
+     **/
+    private Entry pos = sentinel;
+    
+    /**
+     *  Construct an iterator over the sequenced elements in the order in which
+     *  they were added.  The {@link #next()} method returns the type specified
+     *  by <code>returnType</code> which must be either {@link #KEY}, {@link
+     *  #VALUE}, or {@link #ENTRY}.
+     **/
+    public OrderedIterator(int returnType) {
+      //// Since this is a private inner class, nothing else should have
+      //// access to the constructor.  Since we know the rest of the outer
+      //// class uses the iterator correctly, we can leave of the following
+      //// check:
+      //if(returnType >= 0 && returnType <= 2) {
+      //  throw new IllegalArgumentException("Invalid iterator type");
+      //}
+
+      // Set the "removed" bit so that the iterator starts in a state where
+      // "next" must be called before "remove" will succeed.
+      this.returnType = returnType | REMOVED_MASK;
+    }
+
+    /**
+     *  Returns whether there is any additional elements in the iterator to be
+     *  returned.
+     *
+     *  @return <code>true</code> if there are more elements left to be
+     *  returned from the iterator; <code>false</code> otherwise.
+     **/
+    public boolean hasNext() {
+      return pos.next != sentinel;
+    }
+
+    /**
+     *  Returns the next element from the iterator.
+     *
+     *  @return the next element from the iterator.
+     *
+     *  @exception NoSuchElementException if there are no more elements in the
+     *  iterator.
+     **/
+    public Object next() {
+      if(pos.next == sentinel) {
+        throw new NoSuchElementException();
+      }
+
+      // clear the "removed" flag
+      returnType = returnType & ~REMOVED_MASK;
+
+      pos = pos.next;
+      switch(returnType) {
+      case KEY:
+        return pos.getKey();
+      case VALUE:
+        return pos.getValue();
+      case ENTRY:
+        return pos;
+      default:
+        // should never happen
+        throw new Error("bad iterator type: " + returnType);
+      }
+
+    }
+    
+    /**
+     *  Removes the last element returned from the {@link #next()} method from
+     *  the sequenced map.
+     *
+     *  @exception IllegalStateException if there isn't a "last element" to be
+     *  removed.  That is, if {@link #next()} has never been called, or if
+     *  {@link #remove()} was already called on the element.
+     **/
+    public void remove() {
+      if((returnType & REMOVED_MASK) != 0) {
+        throw new IllegalStateException("remove() must follow next()");
+      }
+
+      // remove the entry
+      SequencedHashMap.this.remove(pos.getKey());
+
+      // set the removed flag
+      returnType = returnType | REMOVED_MASK;
+    }
+  }
+
+  // APIs maintained from previous version of SequencedHashMap for backwards
+  // compatibility
+
+  /**
+   * Creates a shallow copy of this object, preserving the internal structure
+   * by copying only references.  The keys and values themselves are not
+   * <code>clone()</code>'d.  The cloned object maintains the same sequence.
+   *
+   * @return A clone of this instance.  
+   */
+  public Object clone () {
+    // yes, calling super.clone() silly since we're just blowing away all
+    // the stuff that super might be doing anyway, but for motivations on
+    // this, see:
+    // http://www.javaworld.com/javaworld/jw-01-1999/jw-01-object.html
+    SequencedHashMap map = (SequencedHashMap)super.clone();
+
+    // create new, empty sentinel
+    map.sentinel = createSentinel();
+
+    // create a new, empty entry map
+    // note: this does not preserve the initial capacity and load factor.
+    map.entries = new HashMap();
+      
+    // add all the mappings
+    map.putAll(this);
+
+    // Note: We cannot just clone the hashmap and sentinel because we must
+    // duplicate our internal structures.  Cloning those two will not clone all
+    // the other entries they reference, and so the cloned hash map will not be
+    // able to maintain internal consistency because there are two objects with
+    // the same entries.  See discussion in the Entry implementation on why we
+    // cannot implement a clone of the Entry (and thus why we need to recreate
+    // everything).
+
+    return map;
+  }
+
+  /**
+   *  Returns the Map.Entry at the specified index
+   *
+   *  @exception ArrayIndexOutOfBoundsException if the specified index is
+   *  <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   **/
+  private Map.Entry getEntry(int index) {
+    Entry pos = sentinel;
+
+    if(index < 0) {
+      throw new ArrayIndexOutOfBoundsException(index + " < 0");
+    }
+
+    // loop to one before the position
+    int i = -1;
+    while(i < (index-1) && pos.next != sentinel) {
+      i++;
+      pos = pos.next;
+    }
+    // pos.next is the requested position
+    
+    // if sentinel is next, past end of list
+    if(pos.next == sentinel) {
+      throw new ArrayIndexOutOfBoundsException(index + " >= " + (i + 1));
+    }
+
+    return pos.next;
+  }
+
+  /**
+   * Returns the key at the specified index.
+   *
+   *  @exception ArrayIndexOutOfBoundsException if the <code>index</code> is
+   *  <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   */
+  public Object get (int index)
+  {
+    return getEntry(index).getKey();
+  }
+
+  /**
+   * Returns the value at the specified index.
+   *
+   *  @exception ArrayIndexOutOfBoundsException if the <code>index</code> is
+   *  <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   */
+  public Object getValue (int index)
+  {
+    return getEntry(index).getValue();
+  }
+
+  /**
+   * Returns the index of the specified key.
+   */
+  public int indexOf (Object key)
+  {
+    Entry e = (Entry)entries.get(key);
+    int pos = 0;
+    while(e.prev != sentinel) {
+      pos++;
+      e = e.prev;
+    }
+    return pos;
+  }
+
+  /**
+   * Returns a key iterator.
+   */
+  public Iterator iterator ()
+  {
+    return keySet().iterator();
+  }
+
+  /**
+   * Returns the last index of the specified key.
+   */
+  public int lastIndexOf (Object key)
+  {
+    // keys in a map are guarunteed to be unique
+    return indexOf(key);
+  }
+
+  /**
+   * Returns a List view of the keys rather than a set view.  The returned
+   * list is unmodifiable.  This is required because changes to the values of
+   * the list (using {@link java.util.ListIterator#set(Object)}) will
+   * effectively remove the value from the list and reinsert that value at
+   * the end of the list, which is an unexpected side effect of changing the
+   * value of a list.  This occurs because changing the key, changes when the
+   * mapping is added to the map and thus where it appears in the list.
+   *
+   * <P>An alternative to this method is to use {@link #keySet()}
+   *
+   * @see #keySet()
+   * @return The ordered list of keys.  
+   */
+  public List sequence()
+  {
+    List l = new ArrayList(size());
+    Iterator iter = keySet().iterator();
+    while(iter.hasNext()) {
+      l.add(iter.next());
+    }
+      
+    return Collections.unmodifiableList(l);
+  }
+
+  /**
+   * Removes the element at the specified index.
+   *
+   * @param index The index of the object to remove.
+   * @return      The previous value coressponding the <code>key</code>, or
+   *              <code>null</code> if none existed.
+   *
+   * @exception ArrayIndexOutOfBoundsException if the <code>index</code> is
+   * <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   */
+  public Object remove (int index)
+  {
+    return remove(get(index));
+  }
+
+}

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@@ -0,0 +1,249 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/iterators/ArrayListIterator.java,v 1.4 2003/08/31 17:25:49 scolebourne Exp $
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 1999-2003 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowledgement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowledgement may appear in the software itself,
+ *    if and wherever such third-party acknowledgements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Software Foundation.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+package org.apache.commons.collections.iterators;
+
+import java.lang.reflect.Array;
+import java.util.NoSuchElementException;
+
+/**
+ * Implements a {@link java.util.ListIterator ListIterator} over an array. 
+ * <p>
+ * The array can be either an array of object or of primitives. If you know 
+ * that you have an object array, the 
+ * {@link org.apache.commons.collections.iterators.ObjectArrayListIterator ObjectArrayListIterator}
+ * class is a better choice, as it will perform better.
+ * 
+ * <p>
+ * This iterator does not support {@link #add(Object)} or {@link #remove()}, as the array 
+ * cannot be changed in size. The {@link #set(Object)} method is supported however.
+ *
+ * @see org.apache.commons.collections.iterators.ArrayIterator
+ * @see java.util.Iterator
+ * @see java.util.ListIterator
+ *
+ * @since Commons Collections 2.2
+ * @version $Revision: 1.4 $ $Date: 2003/08/31 17:25:49 $
+ *
+ * @author <a href="mailto:neilotoole@users.sourceforge.net">Neil O'Toole</a>
+ * @author Stephen Colebourne
+ */
+public class ArrayListIterator extends ArrayIterator implements ResetableListIterator {
+
+    /**
+     * Holds the index of the last item returned by a call to <code>next()</code> or <code>previous()</code>. This
+     *  is set to <code>-1</code> if neither method has yet been invoked. <code>lastItemIndex</code> is used to to
+     * implement the {@link #set} method.
+     *
+     */
+    protected int lastItemIndex = -1;
+
+    /**
+     * Constructor for use with <code>setArray</code>.
+     * <p>
+     * Using this constructor, the iterator is equivalent to an empty iterator
+     * until {@link #setArray(Object)} is  called to establish the array to iterate over.
+     */
+    public ArrayListIterator() {
+        super();
+    }
+
+    /**
+     * Constructs an ArrayListIterator that will iterate over the values in the
+     * specified array.
+     *
+     * @param array the array to iterate over
+     * @throws IllegalArgumentException if <code>array</code> is not an array.
+     * @throws NullPointerException if <code>array</code> is <code>null</code>
+     */
+    public ArrayListIterator(Object array) {
+        super(array);
+    }
+
+    /**
+     * Constructs an ArrayListIterator that will iterate over the values in the
+     * specified array from a specific start index.
+     *
+     * @param array  the array to iterate over
+     * @param start  the index to start iterating at
+     * @throws IllegalArgumentException if <code>array</code> is not an array.
+     * @throws NullPointerException if <code>array</code> is <code>null</code>
+     * @throws IndexOutOfBoundsException if the start index is out of bounds
+     */
+    public ArrayListIterator(Object array, int start) {
+        super(array, start);
+        this.startIndex = start;
+    }
+
+    /**
+     * Construct an ArrayListIterator that will iterate over a range of values 
+     * in the specified array.
+     *
+     * @param array  the array to iterate over
+     * @param start  the index to start iterating at
+     * @param end  the index (exclusive) to finish iterating at
+     * @throws IllegalArgumentException if <code>array</code> is not an array.
+     * @throws IndexOutOfBoundsException if the start or end index is out of bounds
+     * @throws IllegalArgumentException if end index is before the start
+     * @throws NullPointerException if <code>array</code> is <code>null</code>
+     */
+    public ArrayListIterator(Object array, int start, int end) {
+        super(array, start, end);
+        this.startIndex = start;
+    }
+
+    // ListIterator interface
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns true if there are previous elements to return from the array.
+     *
+     * @return true if there is a previous element to return
+     */
+    public boolean hasPrevious() {
+        return (this.index > this.startIndex);
+    }
+
+    /**
+     * Gets the previous element from the array.
+     * 
+     * @return the previous element
+     * @throws NoSuchElementException if there is no previous element
+     */
+    public Object previous() {
+        if (hasPrevious() == false) {
+            throw new NoSuchElementException();
+        }
+        this.lastItemIndex = --this.index;
+        return Array.get(this.array, this.index);
+    }
+
+    /**
+     * Gets the next element from the array.
+     * 
+     * @return the next element
+     * @throws NoSuchElementException if there is no next element
+     */
+    public Object next() {
+        if (hasNext() == false) {
+            throw new NoSuchElementException();
+        }
+        this.lastItemIndex = this.index;
+        return Array.get(this.array, this.index++);
+    }
+
+    /**
+     * Gets the next index to be retrieved.
+     * 
+     * @return the index of the item to be retrieved next
+     */
+    public int nextIndex() {
+        return this.index;
+    }
+
+    /**
+     * Gets the index of the item to be retrieved if {@link #previous()} is called.
+     * 
+     * @return the index of the item to be retrieved next
+     */
+    public int previousIndex() {
+        return this.index - 1;
+    }
+
+    /**
+     * This iterator does not support modification of its backing collection, and so will
+     * always throw an {@link UnsupportedOperationException} when this method is invoked.
+     *
+     * @throws UnsupportedOperationException always thrown.
+     * @see java.util.ListIterator#set
+     */
+    public void add(Object o) {
+        throw new UnsupportedOperationException("add() method is not supported");
+    }
+
+    /**
+     * Sets the element under the cursor.
+     * <p>
+     * This method sets the element that was returned by the last call 
+     * to {@link #next()} of {@link #previous()}. 
+     * <p>
+     * <b>Note:</b> {@link ListIterator} implementations that support
+     * <code>add()</code> and <code>remove()</code> only allow <code>set()</code> to be called
+     * once per call to <code>next()</code> or <code>previous</code> (see the {@link ListIterator}
+     * javadoc for more details). Since this implementation does
+     * not support <code>add()</code> or <code>remove()</code>, <code>set()</code> may be
+     * called as often as desired.
+     *
+     * @see java.util.ListIterator#set
+     */
+    public void set(Object o) {
+        if (this.lastItemIndex == -1) {
+            throw new IllegalStateException("must call next() or previous() before a call to set()");
+        }
+
+        Array.set(this.array, this.lastItemIndex, o);
+    }
+
+    /**
+     * Resets the iterator back to the start index.
+     */
+    public void reset() {
+        super.reset();
+        this.lastItemIndex = -1;
+    }
+
+}

richedit/src/main/resource/testFiles/commons-collections/revFiles/05b6c7_eedfe8_src#java#org#apache#commons#collections#BeanMap.java

@@ -0,0 +1,841 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/BeanMap.java,v 1.26 2004/01/05 21:37:13 scolebourne Exp $
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 2001-2004 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowledgement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowledgement may appear in the software itself,
+ *    if and wherever such third-party acknowledgements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Software Foundation.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+package org.apache.commons.collections;
+
+import java.beans.BeanInfo;
+import java.beans.IntrospectionException;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.AbstractMap;
+import java.util.AbstractSet;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Set;
+
+import org.apache.commons.collections.list.UnmodifiableList;
+import org.apache.commons.collections.keyvalue.AbstractMapEntry;
+import org.apache.commons.collections.set.UnmodifiableSet;
+
+/** 
+ * An implementation of Map for JavaBeans which uses introspection to
+ * get and put properties in the bean.
+ * <p>
+ * If an exception occurs during attempts to get or set a property then the
+ * property is considered non existent in the Map
+ *
+ * @since Commons Collections 1.0
+ * @version $Revision: 1.26 $ $Date: 2004/01/05 21:37:13 $
+ * 
+ * @author James Strachan
+ * @author Stephen Colebourne
+ */
+public class BeanMap extends AbstractMap implements Cloneable {
+
+    private transient Object bean;
+
+    private transient HashMap readMethods = new HashMap();
+    private transient HashMap writeMethods = new HashMap();
+    private transient HashMap types = new HashMap();
+
+    /**
+     * An empty array.  Used to invoke accessors via reflection.
+     */
+    public static final Object[] NULL_ARGUMENTS = {};
+
+    /**
+     * Maps primitive Class types to transformers.  The transformer
+     * transform strings into the appropriate primitive wrapper.
+     */
+    public static HashMap defaultTransformers = new HashMap();
+    
+    static {
+        defaultTransformers.put( 
+            Boolean.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Boolean.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Character.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return new Character( input.toString().charAt( 0 ) );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Byte.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Byte.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Short.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Short.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Integer.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Integer.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Long.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Long.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Float.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Float.valueOf( input.toString() );
+                }
+            }
+        );
+        defaultTransformers.put( 
+            Double.TYPE, 
+            new Transformer() {
+                public Object transform( Object input ) {
+                    return Double.valueOf( input.toString() );
+                }
+            }
+        );
+    }
+    
+    
+    // Constructors
+    //-------------------------------------------------------------------------
+
+    /**
+     * Constructs a new empty <code>BeanMap</code>.
+     */
+    public BeanMap() {
+    }
+
+    /**
+     * Constructs a new <code>BeanMap</code> that operates on the 
+     * specified bean.  If the given bean is <code>null</code>, then
+     * this map will be empty.
+     *
+     * @param bean  the bean for this map to operate on
+     */
+    public BeanMap(Object bean) {
+        this.bean = bean;
+        initialise();
+    }
+
+    // Map interface
+    //-------------------------------------------------------------------------
+
+    public String toString() {
+        return "BeanMap<" + String.valueOf(bean) + ">";
+    }
+    
+    /**
+     * Clone this bean map using the following process: 
+     *
+     * <ul>
+     * <li>If there is no underlying bean, return a cloned BeanMap without a
+     * bean.
+     *
+     * <li>Since there is an underlying bean, try to instantiate a new bean of
+     * the same type using Class.newInstance().
+     * 
+     * <li>If the instantiation fails, throw a CloneNotSupportedException
+     *
+     * <li>Clone the bean map and set the newly instantiated bean as the
+     * underlying bean for the bean map.
+     *
+     * <li>Copy each property that is both readable and writable from the
+     * existing object to a cloned bean map.  
+     *
+     * <li>If anything fails along the way, throw a
+     * CloneNotSupportedException.
+     *
+     * <ul>
+     */
+    public Object clone() throws CloneNotSupportedException {
+        BeanMap newMap = (BeanMap)super.clone();
+
+        if(bean == null) {
+            // no bean, just an empty bean map at the moment.  return a newly
+            // cloned and empty bean map.
+            return newMap;
+        }
+
+        Object newBean = null;            
+        Class beanClass = null;
+        try {
+            beanClass = bean.getClass();
+            newBean = beanClass.newInstance();
+        } catch (Exception e) {
+            // unable to instantiate
+            throw new CloneNotSupportedException
+                ("Unable to instantiate the underlying bean \"" +
+                 beanClass.getName() + "\": " + e);
+        }
+            
+        try {
+            newMap.setBean(newBean);
+        } catch (Exception exception) {
+            throw new CloneNotSupportedException
+                ("Unable to set bean in the cloned bean map: " + 
+                 exception);
+        }
+            
+        try {
+            // copy only properties that are readable and writable.  If its
+            // not readable, we can't get the value from the old map.  If
+            // its not writable, we can't write a value into the new map.
+            Iterator readableKeys = readMethods.keySet().iterator();
+            while(readableKeys.hasNext()) {
+                Object key = readableKeys.next();
+                if(getWriteMethod(key) != null) {
+                    newMap.put(key, get(key));
+                }
+            }
+        } catch (Exception exception) {
+            throw new CloneNotSupportedException
+                ("Unable to copy bean values to cloned bean map: " +
+                 exception);
+        }
+
+        return newMap;
+    }
+
+    /**
+     * Puts all of the writeable properties from the given BeanMap into this
+     * BeanMap. Read-only and Write-only properties will be ignored.
+     *
+     * @param map  the BeanMap whose properties to put
+     */
+    public void putAllWriteable(BeanMap map) {
+        Iterator readableKeys = map.readMethods.keySet().iterator();
+        while (readableKeys.hasNext()) {
+            Object key = readableKeys.next();
+            if (getWriteMethod(key) != null) {
+                this.put(key, map.get(key));
+            }
+        }
+    }
+
+
+    /**
+     * This method reinitializes the bean map to have default values for the
+     * bean's properties.  This is accomplished by constructing a new instance
+     * of the bean which the map uses as its underlying data source.  This
+     * behavior for <code>clear()</code> differs from the Map contract in that
+     * the mappings are not actually removed from the map (the mappings for a
+     * BeanMap are fixed).
+     */
+    public void clear() {
+        if(bean == null) return;
+
+        Class beanClass = null;
+        try {
+            beanClass = bean.getClass();
+            bean = beanClass.newInstance();
+        }
+        catch (Exception e) {
+            throw new UnsupportedOperationException( "Could not create new instance of class: " + beanClass );
+        }
+    }
+
+    /**
+     * Returns true if the bean defines a property with the given name.
+     * <p>
+     * The given name must be a <code>String</code>; if not, this method
+     * returns false. This method will also return false if the bean
+     * does not define a property with that name.
+     * <p>
+     * Write-only properties will not be matched as the test operates against
+     * property read methods.
+     *
+     * @param name  the name of the property to check
+     * @return false if the given name is null or is not a <code>String</code>;
+     *   false if the bean does not define a property with that name; or
+     *   true if the bean does define a property with that name
+     */
+    public boolean containsKey(Object name) {
+        Method method = getReadMethod(name);
+        return method != null;
+    }
+
+    /**
+     * Returns true if the bean defines a property whose current value is
+     * the given object.
+     *
+     * @param value  the value to check
+     * @return false  true if the bean has at least one property whose 
+     *   current value is that object, false otherwise
+     */
+    public boolean containsValue(Object value) {
+        // use default implementation
+        return super.containsValue(value);
+    }
+
+    /**
+     * Returns the value of the bean's property with the given name.
+     * <p>
+     * The given name must be a {@link String} and must not be 
+     * null; otherwise, this method returns <code>null</code>.
+     * If the bean defines a property with the given name, the value of
+     * that property is returned.  Otherwise, <code>null</code> is 
+     * returned.
+     * <p>
+     * Write-only properties will not be matched as the test operates against
+     * property read methods.
+     *
+     * @param name  the name of the property whose value to return
+     * @return  the value of the property with that name
+     */
+    public Object get(Object name) {
+        if ( bean != null ) {
+            Method method = getReadMethod( name );
+            if ( method != null ) {
+                try {
+                    return method.invoke( bean, NULL_ARGUMENTS );
+                }
+                catch (  IllegalAccessException e ) {
+                    logWarn( e );
+                }
+                catch ( IllegalArgumentException e ) {
+                    logWarn(  e );
+                }
+                catch ( InvocationTargetException e ) {
+                    logWarn(  e );
+                }
+                catch ( NullPointerException e ) {
+                    logWarn(  e );
+                }
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Sets the bean property with the given name to the given value.
+     *
+     * @param name  the name of the property to set
+     * @param value  the value to set that property to
+     * @return  the previous value of that property
+     * @throws IllegalArgumentException  if the given name is null;
+     *   if the given name is not a {@link String}; if the bean doesn't
+     *   define a property with that name; or if the bean property with
+     *   that name is read-only
+     */
+    public Object put(Object name, Object value) throws IllegalArgumentException, ClassCastException {
+        if ( bean != null ) {
+            Object oldValue = get( name );
+            Method method = getWriteMethod( name );
+            if ( method == null ) {
+                throw new IllegalArgumentException( "The bean of type: "+ bean.getClass().getName() + " has no property called: " + name );
+            }
+            try {
+                Object[] arguments = createWriteMethodArguments( method, value );
+                method.invoke( bean, arguments );
+
+                Object newValue = get( name );
+                firePropertyChange( name, oldValue, newValue );
+            }
+            catch ( InvocationTargetException e ) {
+                logInfo( e );
+                throw new IllegalArgumentException( e.getMessage() );
+            }
+            catch ( IllegalAccessException e ) {
+                logInfo( e );
+                throw new IllegalArgumentException( e.getMessage() );
+            }
+            return oldValue;
+        }
+        return null;
+    }
+                    
+    /**
+     * Returns the number of properties defined by the bean.
+     *
+     * @return  the number of properties defined by the bean
+     */
+    public int size() {
+        return readMethods.size();
+    }
+
+    
+    /**
+     * Get the keys for this BeanMap.
+     * <p>
+     * Write-only properties are <b>not</b> included in the returned set of
+     * property names, although it is possible to set their value and to get 
+     * their type.
+     * 
+     * @return BeanMap keys.  The Set returned by this method is not
+     *        modifiable.
+     */
+    public Set keySet() {
+        return UnmodifiableSet.decorate(readMethods.keySet());
+    }
+
+    /**
+     * Gets a Set of MapEntry objects that are the mappings for this BeanMap.
+     * <p>
+     * Each MapEntry can be set but not removed.
+     * 
+     * @return the unmodifiable set of mappings
+     */
+    public Set entrySet() {
+        return UnmodifiableSet.decorate(new AbstractSet() {
+            public Iterator iterator() {
+                return entryIterator();
+            }
+            public int size() {
+              return BeanMap.this.readMethods.size();
+            }
+        });
+    }
+
+    /**
+     * Returns the values for the BeanMap.
+     * 
+     * @return values for the BeanMap.  The returned collection is not
+     *        modifiable.
+     */
+    public Collection values() {
+        ArrayList answer = new ArrayList( readMethods.size() );
+        for ( Iterator iter = valueIterator(); iter.hasNext(); ) {
+            answer.add( iter.next() );
+        }
+        return UnmodifiableList.decorate(answer);
+    }
+
+
+    // Helper methods
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns the type of the property with the given name.
+     *
+     * @param name  the name of the property
+     * @return  the type of the property, or <code>null</code> if no such
+     *  property exists
+     */
+    public Class getType(String name) {
+        return (Class) types.get( name );
+    }
+
+    /**
+     * Convenience method for getting an iterator over the keys.
+     * <p>
+     * Write-only properties will not be returned in the iterator.
+     *
+     * @return an iterator over the keys
+     */
+    public Iterator keyIterator() {
+        return readMethods.keySet().iterator();
+    }
+
+    /**
+     * Convenience method for getting an iterator over the values.
+     *
+     * @return an iterator over the values
+     */
+    public Iterator valueIterator() {
+        final Iterator iter = keyIterator();
+        return new Iterator() {            
+            public boolean hasNext() {
+                return iter.hasNext();
+            }
+            public Object next() {
+                Object key = iter.next();
+                return get(key);
+            }
+            public void remove() {
+                throw new UnsupportedOperationException( "remove() not supported for BeanMap" );
+            }
+        };
+    }
+
+    /**
+     * Convenience method for getting an iterator over the entries.
+     *
+     * @return an iterator over the entries
+     */
+    public Iterator entryIterator() {
+        final Iterator iter = keyIterator();
+        return new Iterator() {            
+            public boolean hasNext() {
+                return iter.hasNext();
+            }            
+            public Object next() {
+                Object key = iter.next();
+                Object value = get(key);
+                return new MyMapEntry( BeanMap.this, key, value );
+            }            
+            public void remove() {
+                throw new UnsupportedOperationException( "remove() not supported for BeanMap" );
+            }
+        };
+    }
+
+
+    // Properties
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns the bean currently being operated on.  The return value may
+     * be null if this map is empty.
+     *
+     * @return the bean being operated on by this map
+     */
+    public Object getBean() {
+        return bean;
+    }
+
+    /**
+     * Sets the bean to be operated on by this map.  The given value may
+     * be null, in which case this map will be empty.
+     *
+     * @param newBean  the new bean to operate on
+     */
+    public void setBean( Object newBean ) {
+        bean = newBean;
+        reinitialise();
+    }
+
+    /**
+     * Returns the accessor for the property with the given name.
+     *
+     * @param name  the name of the property 
+     * @return the accessor method for the property, or null
+     */
+    public Method getReadMethod(String name) {
+        return (Method) readMethods.get(name);
+    }
+
+    /**
+     * Returns the mutator for the property with the given name.
+     *
+     * @param name  the name of the property
+     * @return the mutator method for the property, or null
+     */
+    public Method getWriteMethod(String name) {
+        return (Method) writeMethods.get(name);
+    }
+
+
+    // Implementation methods
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns the accessor for the property with the given name.
+     *
+     * @param name  the name of the property 
+     * @return null if the name is null; null if the name is not a 
+     * {@link String}; null if no such property exists; or the accessor
+     *  method for that property
+     */
+    protected Method getReadMethod( Object name ) {
+        return (Method) readMethods.get( name );
+    }
+
+    /**
+     * Returns the mutator for the property with the given name.
+     *
+     * @param name  the name of the 
+     * @return null if the name is null; null if the name is not a 
+     * {@link String}; null if no such property exists; null if the 
+     * property is read-only; or the mutator method for that property
+     */
+    protected Method getWriteMethod( Object name ) {
+        return (Method) writeMethods.get( name );
+    }
+
+    /**
+     * Reinitializes this bean.  Called during {@link #setBean(Object)}.
+     * Does introspection to find properties.
+     */
+    protected void reinitialise() {
+        readMethods.clear();
+        writeMethods.clear();
+        types.clear();
+        initialise();
+    }
+
+    private void initialise() {
+        if(getBean() == null) return;
+
+        Class  beanClass = getBean().getClass();
+        try {
+            //BeanInfo beanInfo = Introspector.getBeanInfo( bean, null );
+            BeanInfo beanInfo = Introspector.getBeanInfo( beanClass );
+            PropertyDescriptor[] propertyDescriptors = beanInfo.getPropertyDescriptors();
+            if ( propertyDescriptors != null ) {
+                for ( int i = 0; i < propertyDescriptors.length; i++ ) {
+                    PropertyDescriptor propertyDescriptor = propertyDescriptors[i];
+                    if ( propertyDescriptor != null ) {
+                        String name = propertyDescriptor.getName();
+                        Method readMethod = propertyDescriptor.getReadMethod();
+                        Method writeMethod = propertyDescriptor.getWriteMethod();
+                        Class aType = propertyDescriptor.getPropertyType();
+
+                        if ( readMethod != null ) {
+                            readMethods.put( name, readMethod );
+                        }
+                        if ( writeMethods != null ) {
+                            writeMethods.put( name, writeMethod );
+                        }
+                        types.put( name, aType );
+                    }
+                }
+            }
+        }
+        catch ( IntrospectionException e ) {
+            logWarn(  e );
+        }
+    }
+
+    /**
+     * Called during a successful {@link #put(Object,Object)} operation.
+     * Default implementation does nothing.  Override to be notified of
+     * property changes in the bean caused by this map.
+     *
+     * @param key  the name of the property that changed
+     * @param oldValue  the old value for that property
+     * @param newValue  the new value for that property
+     */
+    protected void firePropertyChange( Object key, Object oldValue, Object newValue ) {
+    }
+
+    // Implementation classes
+    //-------------------------------------------------------------------------
+
+    /**
+     * Map entry used by {@link BeanMap}.
+     */
+    protected static class MyMapEntry extends AbstractMapEntry {        
+        private BeanMap owner;
+        
+        /**
+         * Constructs a new <code>MyMapEntry</code>.
+         *
+         * @param owner  the BeanMap this entry belongs to
+         * @param key  the key for this entry
+         * @param value  the value for this entry
+         */
+        protected MyMapEntry( BeanMap owner, Object key, Object value ) {
+            super( key, value );
+            this.owner = owner;
+        }
+
+        /**
+         * Sets the value.
+         *
+         * @param value  the new value for the entry
+         * @return the old value for the entry
+         */
+        public Object setValue(Object value) {
+            Object key = getKey();
+            Object oldValue = owner.get( key );
+
+            owner.put( key, value );
+            Object newValue = owner.get( key );
+            super.setValue( newValue );
+            return oldValue;
+        }
+    }
+
+    /**
+     * Creates an array of parameters to pass to the given mutator method.
+     * If the given object is not the right type to pass to the method 
+     * directly, it will be converted using {@link #convertType(Class,Object)}.
+     *
+     * @param method  the mutator method
+     * @param value  the value to pass to the mutator method
+     * @return an array containing one object that is either the given value
+     *   or a transformed value
+     * @throws IllegalAccessException if {@link #convertType(Class,Object)}
+     *   raises it
+     * @throws IllegalArgumentException if any other exception is raised
+     *   by {@link #convertType(Class,Object)}
+     */
+    protected Object[] createWriteMethodArguments( Method method, Object value ) throws IllegalAccessException, ClassCastException {            
+        try {
+            if ( value != null ) {
+                Class[] types = method.getParameterTypes();
+                if ( types != null && types.length > 0 ) {
+                    Class paramType = types[0];
+                    if ( ! paramType.isAssignableFrom( value.getClass() ) ) {
+                        value = convertType( paramType, value );
+                    }
+                }
+            }
+            Object[] answer = { value };
+            return answer;
+        }
+        catch ( InvocationTargetException e ) {
+            logInfo( e );
+            throw new IllegalArgumentException( e.getMessage() );
+        }
+        catch ( InstantiationException e ) {
+            logInfo( e );
+            throw new IllegalArgumentException( e.getMessage() );
+        }
+    }
+
+    /**
+     * Converts the given value to the given type.  First, reflection is
+     * is used to find a public constructor declared by the given class 
+     * that takes one argument, which must be the precise type of the 
+     * given value.  If such a constructor is found, a new object is
+     * created by passing the given value to that constructor, and the
+     * newly constructed object is returned.<P>
+     *
+     * If no such constructor exists, and the given type is a primitive
+     * type, then the given value is converted to a string using its 
+     * {@link Object#toString() toString()} method, and that string is
+     * parsed into the correct primitve type using, for instance, 
+     * {@link Integer#valueOf(String)} to convert the string into an
+     * <code>int</code>.<P>
+     *
+     * If no special constructor exists and the given type is not a 
+     * primitive type, this method returns the original value.
+     *
+     * @param newType  the type to convert the value to
+     * @param value  the value to convert
+     * @return the converted value
+     * @throws NumberFormatException if newType is a primitive type, and 
+     *  the string representation of the given value cannot be converted
+     *  to that type
+     * @throws InstantiationException  if the constructor found with 
+     *  reflection raises it
+     * @throws InvocationTargetException  if the constructor found with
+     *  reflection raises it
+     * @throws IllegalAccessException  never
+     * @throws IllegalArgumentException  never
+     */
+    protected Object convertType( Class newType, Object value ) 
+        throws InstantiationException, IllegalAccessException, IllegalArgumentException, InvocationTargetException {
+        
+        // try call constructor
+        Class[] types = { value.getClass() };
+        try {
+            Constructor constructor = newType.getConstructor( types );        
+            Object[] arguments = { value };
+            return constructor.newInstance( arguments );
+        }
+        catch ( NoSuchMethodException e ) {
+            // try using the transformers
+            Transformer transformer = getTypeTransformer( newType );
+            if ( transformer != null ) {
+                return transformer.transform( value );
+            }
+            return value;
+        }
+    }
+
+    /**
+     * Returns a transformer for the given primitive type.
+     *
+     * @param aType  the primitive type whose transformer to return
+     * @return a transformer that will convert strings into that type,
+     *  or null if the given type is not a primitive type
+     */
+    protected Transformer getTypeTransformer( Class aType ) {
+        return (Transformer) defaultTransformers.get( aType );
+    }
+
+    /**
+     * Logs the given exception to <code>System.out</code>.  Used to display
+     * warnings while accessing/mutating the bean.
+     *
+     * @param ex  the exception to log
+     */
+    protected void logInfo(Exception ex) {
+        // Deliberately do not use LOG4J or Commons Logging to avoid dependencies
+        System.out.println( "INFO: Exception: " + ex );
+    }
+
+    /**
+     * Logs the given exception to <code>System.err</code>.  Used to display
+     * errors while accessing/mutating the bean.
+     *
+     * @param ex  the exception to log
+     */
+    protected void logWarn(Exception ex) {
+        // Deliberately do not use LOG4J or Commons Logging to avoid dependencies
+        System.out.println( "WARN: Exception: " + ex );
+        ex.printStackTrace();
+    }
+}

richedit/src/main/resource/testFiles/commons-collections/revFiles/2d2aef_fb3daa_src#java#org#apache#commons#collections#map#TransformedMap.java

@@ -0,0 +1,242 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.collections.map;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+import java.util.Map;
+
+import org.apache.commons.collections.IterableMap;
+import org.apache.commons.collections.Transformer;
+
+/**
+ * Decorates another <code>Map</code> to transform objects that are added.
+ * <p>
+ * The Map put methods and Map.Entry setValue method are affected by this class.
+ * Thus objects must be removed or searched for using their transformed form.
+ * For example, if the transformation converts Strings to Integers, you must
+ * use the Integer form to remove objects.
+ * <p>
+ * <strong>Note that TransformedMap is not synchronized and is not thread-safe.</strong>
+ * If you wish to use this map from multiple threads concurrently, you must use
+ * appropriate synchronization. The simplest approach is to wrap this map
+ * using {@link java.util.Collections#synchronizedMap(Map)}. This class may throw
+ * exceptions when accessed by concurrent threads without synchronization.
+ * <p>
+ * This class is Serializable from Commons Collections 3.1.
+ * <p>
+ * @see org.apache.commons.collections.splitmap.TransformedMap
+ *
+ * @since Commons Collections 3.0
+ * @version $Revision$ $Date$
+ *
+ * @author Stephen Colebourne
+ */
+public class TransformedMap<K, V>
+        extends AbstractInputCheckedMapDecorator<K, V>
+        implements Serializable {
+
+    /** Serialization version */
+    private static final long serialVersionUID = 7023152376788900464L;
+
+    /** The transformer to use for the key */
+    protected final Transformer<? super K, ? extends K> keyTransformer;
+    /** The transformer to use for the value */
+    protected final Transformer<? super V, ? extends V> valueTransformer;
+
+    /**
+     * Factory method to create a transforming map.
+     * <p>
+     * If there are any elements already in the map being decorated, they
+     * are NOT transformed.
+     * Contrast this with {@link #decorateTransform}.
+     *
+     * @param map  the map to decorate, must not be null
+     * @param keyTransformer  the transformer to use for key conversion, null means no transformation
+     * @param valueTransformer  the transformer to use for value conversion, null means no transformation
+     * @throws IllegalArgumentException if map is null
+     */
+    public static <K, V> IterableMap<K, V> decorate(Map<K, V> map,
+            Transformer<? super K, ? extends K> keyTransformer,
+            Transformer<? super V, ? extends V> valueTransformer) {
+        return new TransformedMap<K, V>(map, keyTransformer, valueTransformer);
+    }
+
+    /**
+     * Factory method to create a transforming map that will transform
+     * existing contents of the specified map.
+     * <p>
+     * If there are any elements already in the map being decorated, they
+     * will be transformed by this method.
+     * Contrast this with {@link #decorate}.
+     *
+     * @param map  the map to decorate, must not be null
+     * @param keyTransformer  the transformer to use for key conversion, null means no transformation
+     * @param valueTransformer  the transformer to use for value conversion, null means no transformation
+     * @throws IllegalArgumentException if map is null
+     * @since Commons Collections 3.2
+     */
+    public static <K, V> Map<K, V> decorateTransform(Map<K, V> map,
+            Transformer<? super K, ? extends K> keyTransformer,
+            Transformer<? super V, ? extends V> valueTransformer) {
+        TransformedMap<K, V> decorated = new TransformedMap<K, V>(map, keyTransformer, valueTransformer);
+        if (map.size() > 0) {
+            Map<K, V> transformed = decorated.transformMap(map);
+            decorated.clear();
+            decorated.decorated().putAll(transformed);  // avoids double transformation
+        }
+        return decorated;
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Constructor that wraps (not copies).
+     * <p>
+     * If there are any elements already in the collection being decorated, they
+     * are NOT transformed.
+     *
+     * @param map  the map to decorate, must not be null
+     * @param keyTransformer  the transformer to use for key conversion, null means no conversion
+     * @param valueTransformer  the transformer to use for value conversion, null means no conversion
+     * @throws IllegalArgumentException if map is null
+     */
+    protected TransformedMap(Map<K, V> map, Transformer<? super K, ? extends K> keyTransformer,
+            Transformer<? super V, ? extends V> valueTransformer) {
+        super(map);
+        this.keyTransformer = keyTransformer;
+        this.valueTransformer = valueTransformer;
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Write the map out using a custom routine.
+     *
+     * @param out  the output stream
+     * @throws IOException
+     * @since Commons Collections 3.1
+     */
+    private void writeObject(ObjectOutputStream out) throws IOException {
+        out.defaultWriteObject();
+        out.writeObject(map);
+    }
+
+    /**
+     * Read the map in using a custom routine.
+     *
+     * @param in  the input stream
+     * @throws IOException
+     * @throws ClassNotFoundException
+     * @since Commons Collections 3.1
+     */
+    @SuppressWarnings("unchecked")
+    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
+        in.defaultReadObject();
+        map = (Map) in.readObject();
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Transforms a key.
+     * <p>
+     * The transformer itself may throw an exception if necessary.
+     *
+     * @param object  the object to transform
+     * @throws the transformed object
+     */
+    protected K transformKey(K object) {
+        if (keyTransformer == null) {
+            return object;
+        }
+        return keyTransformer.transform(object);
+    }
+
+    /**
+     * Transforms a value.
+     * <p>
+     * The transformer itself may throw an exception if necessary.
+     *
+     * @param object  the object to transform
+     * @throws the transformed object
+     */
+    protected V transformValue(V object) {
+        if (valueTransformer == null) {
+            return object;
+        }
+        return valueTransformer.transform(object);
+    }
+
+    /**
+     * Transforms a map.
+     * <p>
+     * The transformer itself may throw an exception if necessary.
+     *
+     * @param map  the map to transform
+     * @throws the transformed object
+     */
+    @SuppressWarnings("unchecked")
+    protected Map<K, V> transformMap(Map<? extends K, ? extends V> map) {
+        if (map.isEmpty()) {
+            return (Map<K, V>) map;
+        }
+        Map<K, V> result = new LinkedMap<K, V>(map.size());
+
+        for (Map.Entry<? extends K, ? extends V> entry : map.entrySet()) {
+            result.put(transformKey(entry.getKey()), transformValue(entry.getValue()));
+        }
+        return result;
+    }
+
+    /**
+     * Override to transform the value when using <code>setValue</code>.
+     *
+     * @param value  the value to transform
+     * @return the transformed value
+     * @since Commons Collections 3.1
+     */
+    @Override
+    protected V checkSetValue(V value) {
+        return valueTransformer.transform(value);
+    }
+
+    /**
+     * Override to only return true when there is a value transformer.
+     *
+     * @return true if a value transformer is in use
+     * @since Commons Collections 3.1
+     */
+    @Override
+    protected boolean isSetValueChecking() {
+        return (valueTransformer != null);
+    }
+
+    //-----------------------------------------------------------------------
+    @Override
+    public V put(K key, V value) {
+        key = transformKey(key);
+        value = transformValue(value);
+        return decorated().put(key, value);
+    }
+
+    @Override
+    public void putAll(Map<? extends K, ? extends V> mapToCopy) {
+        mapToCopy = transformMap(mapToCopy);
+        decorated().putAll(mapToCopy);
+    }
+
+}

richedit/src/main/resource/testFiles/commons-collections/revFiles/3761b5_3639ab_src#java#org#apache#commons#collections#FastHashMap.java

@@ -0,0 +1,525 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/FastHashMap.java,v 1.3 2001/05/18 00:12:45 rwaldhoff Exp $
+ * $Revision: 1.3 $
+ * $Date: 2001/05/18 00:12:45 $
+ *
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 1999-2001 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowlegement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowlegement may appear in the software itself,
+ *    if and wherever such third-party acknowlegements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Group.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+
+
+package org.apache.commons.collections;
+
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+
+/**
+ * <p>A customized implementation of <code>java.util.HashMap</code> designed
+ * to operate in a multithreaded environment where the large majority of
+ * method calls are read-only, instead of structural changes.  When operating
+ * in "fast" mode, read calls are non-synchronized and write calls perform the
+ * following steps:</p>
+ * <ul>
+ * <li>Clone the existing collection
+ * <li>Perform the modification on the clone
+ * <li>Replace the existing collection with the (modified) clone
+ * </ul>
+ * <p>When first created, objects of this class default to "slow" mode, where
+ * all accesses of any type are synchronized but no cloning takes place.  This
+ * is appropriate for initially populating the collection, followed by a switch
+ * to "fast" mode (by calling <code>setFast(true)</code>) after initialization
+ * is complete.</p>
+ *
+ * <p><strong>NOTE</strong>: If you are creating and accessing a
+ * <code>HashMap</code> only within a single thread, you should use
+ * <code>java.util.HashMap</code> directly (with no synchronization), for
+ * maximum performance.</p>
+ *
+ * @author Craig R. McClanahan
+ * @version $Revision: 1.3 $ $Date: 2001/05/18 00:12:45 $
+ */
+
+public class FastHashMap extends HashMap {
+
+
+    // ----------------------------------------------------------- Constructors
+
+
+    /**
+     * Construct a an empty map.
+     */
+    public FastHashMap() {
+
+        super();
+        this.map = new HashMap();
+
+    }
+
+
+    /**
+     * Construct an empty map with the specified capacity.
+     *
+     * @param capacity The initial capacity of the empty map
+     */
+    public FastHashMap(int capacity) {
+
+        super();
+        this.map = new HashMap(capacity);
+
+    }
+
+
+    /**
+     * Construct an empty map with the specified capacity and load factor.
+     *
+     * @param capacity The initial capacity of the empty map
+     * @param factor The load factor of the new map
+     */
+    public FastHashMap(int capacity, float factor) {
+
+        super();
+        this.map = new HashMap(capacity, factor);
+
+    }
+
+
+    /**
+     * Construct a new map with the same mappings as the specified map.
+     *
+     * @param map The map whose mappings are to be copied
+     */
+    public FastHashMap(Map map) {
+
+        super();
+        this.map = new HashMap(map);
+
+    }
+
+
+    // ----------------------------------------------------- Instance Variables
+
+
+    /**
+     * The underlying map we are managing.
+     */
+    protected HashMap map = null;
+
+
+    // ------------------------------------------------------------- Properties
+
+
+    /**
+     * Are we operating in "fast" mode?
+     */
+    protected boolean fast = false;
+
+    public boolean getFast() {
+        return (this.fast);
+    }
+
+    public void setFast(boolean fast) {
+        this.fast = fast;
+    }
+
+
+    // --------------------------------------------------------- Public Methods
+
+
+    /**
+     * Remove all mappings from this map.
+     */
+    public void clear() {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                temp.clear();
+                map = temp;
+            }
+        } else {
+            synchronized (map) {
+                map.clear();
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a shallow copy of this <code>FastHashMap</code> instance.
+     * The keys and values themselves are not copied.
+     */
+    public Object clone() {
+
+        FastHashMap results = null;
+        if (fast) {
+            results = new FastHashMap(map);
+        } else {
+            synchronized (map) {
+                results = new FastHashMap(map);
+            }
+        }
+        results.setFast(getFast());
+        return (results);
+
+    }
+
+
+    /**
+     * Return <code>true</code> if this map contains a mapping for the
+     * specified key.
+     *
+     * @param key Key to be searched for
+     */
+    public boolean containsKey(Object key) {
+
+        if (fast) {
+            return (map.containsKey(key));
+        } else {
+            synchronized (map) {
+                return (map.containsKey(key));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return <code>true</code> if this map contains one or more keys mapping
+     * to the specified value.
+     *
+     * @param value Value to be searched for
+     */
+    public boolean containsValue(Object value) {
+
+        if (fast) {
+            return (map.containsValue(value));
+        } else {
+            synchronized (map) {
+                return (map.containsValue(value));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a collection view of the mappings contained in this map.  Each
+     * element in the returned collection is a <code>Map.Entry</code>.
+     */
+    public Set entrySet() {
+
+        if (fast) {
+            return (map.entrySet());
+        } else {
+            synchronized (map) {
+                return (map.entrySet());
+            }
+        }
+
+    }
+
+
+    /**
+     * Compare the specified object with this list for equality.  This
+     * implementation uses exactly the code that is used to define the
+     * list equals function in the documentation for the
+     * <code>Map.equals</code> method.
+     *
+     * @param o Object to be compared to this list
+     */
+    public boolean equals(Object o) {
+
+        // Simple tests that require no synchronization
+        if (o == this)
+            return (true);
+        else if (!(o instanceof Map))
+            return (false);
+        Map mo = (Map) o;
+
+        // Compare the two maps for equality
+        if (fast) {
+            if (mo.size() != map.size())
+                return (false);
+            Iterator i = map.entrySet().iterator();
+            while (i.hasNext()) {
+                Map.Entry e = (Map.Entry) i.next();
+                Object key = e.getKey();
+                Object value = e.getValue();
+                if (value == null) {
+                    if (!(mo.get(key) == null && mo.containsKey(key)))
+                        return (false);
+                } else {
+                    if (!value.equals(mo.get(key)))
+                        return (false);
+                }
+            }
+            return (true);
+        } else {
+            synchronized (map) {
+                if (mo.size() != map.size())
+                    return (false);
+                Iterator i = map.entrySet().iterator();
+                while (i.hasNext()) {
+                    Map.Entry e = (Map.Entry) i.next();
+                    Object key = e.getKey();
+                    Object value = e.getValue();
+                    if (value == null) {
+                        if (!(mo.get(key) == null && mo.containsKey(key)))
+                            return (false);
+                    } else {
+                        if (!value.equals(mo.get(key)))
+                            return (false);
+                    }
+                }
+                return (true);
+            }
+        }
+
+    }
+
+
+    /**
+     * Return the value to which this map maps the specified key.  Returns
+     * <code>null</code> if the map contains no mapping for this key, or if
+     * there is a mapping with a value of <code>null</code>.  Use the
+     * <code>containsKey()</code> method to disambiguate these cases.
+     *
+     * @param key Key whose value is to be returned
+     */
+    public Object get(Object key) {
+
+        if (fast) {
+            return (map.get(key));
+        } else {
+            synchronized (map) {
+                return (map.get(key));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return the hash code value for this map.  This implementation uses
+     * exactly the code that is used to define the list hash function in the
+     * documentation for the <code>Map.hashCode</code> method.
+     */
+    public int hashCode() {
+
+        if (fast) {
+            int h = 0;
+            Iterator i = map.entrySet().iterator();
+            while (i.hasNext())
+                h += i.next().hashCode();
+            return (h);
+        } else {
+            synchronized (map) {
+                int h = 0;
+                Iterator i = map.entrySet().iterator();
+                while (i.hasNext())
+                    h += i.next().hashCode();
+                return (h);
+            }
+        }
+
+    }
+
+
+    /**
+     * Return <code>true</code> if this map contains no mappings.
+     */
+    public boolean isEmpty() {
+
+        if (fast) {
+            return (map.isEmpty());
+        } else {
+            synchronized (map) {
+                return (map.isEmpty());
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a set view of the keys contained in this map.
+     */
+    public Set keySet() {
+
+        if (fast) {
+            return (map.keySet());
+        } else {
+            synchronized (map) {
+                return (map.keySet());
+            }
+        }
+
+    }
+
+
+    /**
+     * Associate the specified value with the specified key in this map.
+     * If the map previously contained a mapping for this key, the old
+     * value is replaced and returned.
+     *
+     * @param key The key with which the value is to be associated
+     * @param value The value to be associated with this key
+     */
+    public Object put(Object key, Object value) {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                Object result = temp.put(key, value);
+                map = temp;
+                return (result);
+            }
+        } else {
+            synchronized (map) {
+                return (map.put(key, value));
+            }
+        }
+
+    }
+
+
+    /**
+     * Copy all of the mappings from the specified map to this one, replacing
+     * any mappings with the same keys.
+     *
+     * @param in Map whose mappings are to be copied
+     */
+    public void putAll(Map in) {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                temp.putAll(in);
+                map = temp;
+            }
+        } else {
+            synchronized (map) {
+                map.putAll(in);
+            }
+        }
+
+    }
+
+
+    /**
+     * Remove any mapping for this key, and return any previously
+     * mapped value.
+     *
+     * @param key Key whose mapping is to be removed
+     */
+    public Object remove(Object key) {
+
+        if (fast) {
+            synchronized (this) {
+                HashMap temp = (HashMap) map.clone();
+                Object result = temp.remove(key);
+                map = temp;
+                return (result);
+            }
+        } else {
+            synchronized (map) {
+                return (map.remove(key));
+            }
+        }
+
+    }
+
+
+    /**
+     * Return the number of key-value mappings in this map.
+     */
+    public int size() {
+
+        if (fast) {
+            return (map.size());
+        } else {
+            synchronized (map) {
+                return (map.size());
+            }
+        }
+
+    }
+
+
+    /**
+     * Return a collection view of the values contained in this map.
+     */
+    public Collection values() {
+
+        if (fast) {
+            return (map.values());
+        } else {
+            synchronized (map) {
+                return (map.values());
+            }
+        }
+
+    }
+
+
+}

richedit/src/main/resource/testFiles/commons-collections/revFiles/51c9ef_d65e29_src#java#org#apache#commons#collections#iterators#IteratorChain.java

@@ -0,0 +1,289 @@
+/*
+ *  Copyright 1999-2004 The Apache Software Foundation
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+package org.apache.commons.collections.iterators;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.collections.list.UnmodifiableList;
+
+/**
+ * An IteratorChain is an Iterator that wraps a number of Iterators.
+ * <p>
+ * This class makes multiple iterators look like one to the caller
+ * When any method from the Iterator interface is called, the IteratorChain
+ * will delegate to a single underlying Iterator. The IteratorChain will
+ * invoke the Iterators in sequence until all Iterators are exhausted.
+ * <p>
+ * Under many circumstances, linking Iterators together in this manner is
+ * more efficient (and convenient) than reading out the contents of each
+ * Iterator into a List and creating a new Iterator.
+ * <p>
+ * Calling a method that adds new Iterator<i>after a method in the Iterator
+ * interface has been called</i> will result in an UnsupportedOperationException.
+ * Subclasses should <i>take care</i> to not alter the underlying List of Iterators.
+ * <p>
+ * NOTE: As from version 3.0, the IteratorChain may contain no
+ * iterators. In this case the class will function as an empty iterator.
+ *
+ * @since Commons Collections 2.1
+ * @version $Revision$ $Date$
+ *
+ * @author Morgan Delagrange
+ * @author Stephen Colebourne
+ */
+public class IteratorChain implements Iterator {
+
+	/** The chain of iterators */
+    protected final List iteratorChain = new ArrayList();
+    /** The index of the current iterator */
+    protected int currentIteratorIndex = 0;
+    /** The current iterator */
+    protected Iterator currentIterator = null;
+    /**
+     * The "last used" Iterator is the Iterator upon which
+     * next() or hasNext() was most recently called
+     * used for the remove() operation only
+     */
+    protected Iterator lastUsedIterator = null;
+    /**
+     * ComparatorChain is "locked" after the first time
+     * compare(Object,Object) is called
+     */
+    protected boolean isLocked = false;
+
+    //-----------------------------------------------------------------------
+    /**
+     * Construct an IteratorChain with no Iterators.
+     * <p>
+     * You will normally use {@link #addIterator(Iterator)} to add
+     * some iterators after using this constructor.
+     */
+    public IteratorChain() {
+        super();
+    }
+
+    /**
+     * Construct an IteratorChain with a single Iterator.
+     *
+     * @param iterator first Iterator in the IteratorChain
+     * @throws NullPointerException if the iterator is null
+     */
+    public IteratorChain(Iterator iterator) {
+        super();
+        addIterator(iterator);
+    }
+
+    /**
+     * Constructs a new <code>IteratorChain</code> over the two
+     * given iterators.
+     *
+     * @param a  the first child iterator
+     * @param b  the second child iterator
+     * @throws NullPointerException if either iterator is null
+     */
+    public IteratorChain(Iterator a, Iterator b) {
+        super();
+        addIterator(a);
+        addIterator(b);
+    }
+
+    /**
+     * Constructs a new <code>IteratorChain</code> over the array
+     * of iterators.
+     *
+     * @param iterators  the array of iterators
+     * @throws NullPointerException if iterators array is or contains null
+     */
+    public IteratorChain(Iterator[] iterators) {
+        super();
+        for (int i = 0; i < iterators.length; i++) {
+            addIterator(iterators[i]);
+        }
+    }
+
+    /**
+     * Constructs a new <code>IteratorChain</code> over the collection
+     * of iterators.
+     *
+     * @param iterators  the collection of iterators
+     * @throws NullPointerException if iterators collection is or contains null
+     * @throws ClassCastException if iterators collection doesn't contain an iterator
+     */
+    public IteratorChain(Collection iterators) {
+        super();
+        for (Iterator it = iterators.iterator(); it.hasNext();) {
+            Iterator item = (Iterator) it.next();
+            addIterator(item);
+        }
+    }
+    
+    //-----------------------------------------------------------------------
+    /**
+     * Add an Iterator to the end of the chain
+     *
+     * @param iterator Iterator to add
+     * @throws IllegalStateException if I've already started iterating
+     * @throws NullPointerException if the iterator is null
+     */
+    public void addIterator(Iterator iterator) {
+        checkLocked();
+        if (iterator == null) {
+            throw new NullPointerException("Iterator must not be null");
+        }
+        iteratorChain.add(iterator);
+    }
+
+    /**
+     * Set the Iterator at the given index
+     *
+     * @param index      index of the Iterator to replace
+     * @param iterator   Iterator to place at the given index
+     * @throws IndexOutOfBoundsException if index &lt; 0 or index &gt; size()
+     * @throws IllegalStateException if I've already started iterating
+     * @throws NullPointerException if the iterator is null
+     */
+    public void setIterator(int index, Iterator iterator) throws IndexOutOfBoundsException {
+        checkLocked();
+        if (iterator == null) {
+            throw new NullPointerException("Iterator must not be null");
+        }
+        iteratorChain.set(index, iterator);
+    }
+
+    /**
+     * Get the list of Iterators (unmodifiable)
+     *
+     * @return the unmodifiable list of iterators added
+     */
+    public List getIterators() {
+        return UnmodifiableList.decorate(iteratorChain);
+    }
+
+    /**
+     * Number of Iterators in the current IteratorChain.
+     *
+     * @return Iterator count
+     */
+    public int size() {
+        return iteratorChain.size();
+    }
+
+    /**
+     * Determine if modifications can still be made to the IteratorChain.
+     * IteratorChains cannot be modified once they have executed a method
+     * from the Iterator interface.
+     *
+     * @return true if IteratorChain cannot be modified, false if it can
+     */
+    public boolean isLocked() {
+        return isLocked;
+    }
+
+    /**
+     * Checks whether the iterator chain is now locked and in use.
+     */
+    private void checkLocked() {
+        if (isLocked == true) {
+            throw new UnsupportedOperationException("IteratorChain cannot be changed after the first use of a method from the Iterator interface");
+        }
+    }
+
+    /**
+     * Lock the chain so no more iterators can be added.
+     * This must be called from all Iterator interface methods.
+     */
+    private void lockChain() {
+        if (isLocked == false) {
+            isLocked = true;
+        }
+    }
+
+    /**
+     * Updates the current iterator field to ensure that the current Iterator
+     * is not exhausted
+     */
+    protected void updateCurrentIterator() {
+        if (currentIterator == null) {
+            if (iteratorChain.isEmpty()) {
+                currentIterator = EmptyIterator.INSTANCE;
+            } else {
+                currentIterator = (Iterator) iteratorChain.get(0);
+            }
+            // set last used iterator here, in case the user calls remove
+            // before calling hasNext() or next() (although they shouldn't)
+            lastUsedIterator = currentIterator;
+        }
+
+        while (currentIterator.hasNext() == false && currentIteratorIndex < iteratorChain.size() - 1) {
+            currentIteratorIndex++;
+            currentIterator = (Iterator) iteratorChain.get(currentIteratorIndex);
+        }
+    }
+
+    //-----------------------------------------------------------------------
+    /**
+     * Return true if any Iterator in the IteratorChain has a remaining element.
+     *
+     * @return true if elements remain
+     */
+    public boolean hasNext() {
+        lockChain();
+        updateCurrentIterator();
+        lastUsedIterator = currentIterator;
+
+        return currentIterator.hasNext();
+    }
+
+    /**
+     * Returns the next Object of the current Iterator
+     *
+     * @return Object from the current Iterator
+     * @throws java.util.NoSuchElementException if all the Iterators are exhausted
+     */
+    public Object next() {
+        lockChain();
+        updateCurrentIterator();
+        lastUsedIterator = currentIterator;
+
+        return currentIterator.next();
+    }
+
+    /**
+     * Removes from the underlying collection the last element
+     * returned by the Iterator.  As with next() and hasNext(),
+     * this method calls remove() on the underlying Iterator.
+     * Therefore, this method may throw an
+     * UnsupportedOperationException if the underlying
+     * Iterator does not support this method.
+     *
+     * @throws UnsupportedOperationException
+     *   if the remove operator is not supported by the underlying Iterator
+     * @throws IllegalStateException
+     *   if the next method has not yet been called, or the remove method has
+     *   already been called after the last call to the next method.
+     */
+    public void remove() {
+        lockChain();
+        if( currentIterator == null ) {
+            updateCurrentIterator();
+        }
+        lastUsedIterator.remove();
+    }
+
+}

richedit/src/main/resource/testFiles/commons-collections/revFiles/906468_31bc59_src#java#org#apache#commons#collections#SequencedHashMap.java

@@ -0,0 +1,888 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/SequencedHashMap.java,v 1.4 2002/02/21 13:46:25 mas Exp $
+ * $Revision: 1.4 $
+ * $Date: 2002/02/21 13:46:25 $
+ *
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 1999-2002 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowlegement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowlegement may appear in the software itself,
+ *    if and wherever such third-party acknowlegements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Group.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+package org.apache.commons.collections;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.AbstractCollection;
+import java.util.AbstractMap;
+import java.util.AbstractSet;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.NoSuchElementException;
+
+/**
+ *  A map of objects whose mapping entries are sequenced based on the order in
+ *  which they were added.  This data structure has fast <I>O(1)</I> search
+ *  time, deletion time, and insertion time.
+ *
+ *  This class inherits from {@link java.util.HashMap} purely for backwards
+ *  compatibility.  It should really be inheriting from {@link
+ *  java.util.AbstractMap}, or with a tiny extra bit of work, implement the
+ *  full map interface on its own. APIs should not rely on this class being an
+ *  actual {@link java.util.HashMap}, and instead should recognize it only as a
+ *  generic {@link java.util.Map} (unless, of course, you need the sequencing
+ *  functionality, but even in that case, this class should not be referred to
+ *  as a java.util.HashMap).
+ *
+ *  <P>Although this map is sequenced, it cannot implement {@link
+ *  java.util.List} because of incompatible interface definitions.  The remove
+ *  methods in List and Map have different return values (see: {@link
+ *  java.util.List#remove(Object)} and {@link java.util.Map#remove(Object)}).
+ *
+ *  <P>This class is not thread safe.  When a thread safe implementation is
+ *  required, use {@link Collections#synchronizedMap(Map)} as it is documented,
+ *  or use explicit synchronization controls.
+ *
+ *  @author <a href="mailto:michael@iammichael.org">Michael A. Smith</A>
+ * @author <a href="mailto:dlr@collab.net">Daniel Rall</a>
+ * @author <a href="mailto:hps@intermeta.de">Henning P. Schmiedehausen</a>
+ */
+public class SequencedHashMap extends HashMap {
+
+  /**
+   *  {@link java.util.Map.Entry} that doubles as a node in the linked list
+   *  of sequenced mappings.  
+   **/
+  private static class Entry implements Map.Entry {
+    // Note: This class cannot easily be made clonable.  While the actual
+    // implementation of a clone would be simple, defining the semantics is
+    // difficult.  If a shallow clone is implemented, then entry.next.prev !=
+    // entry, which is unintuitive and probably breaks all sorts of assumptions
+    // in code that uses this implementation.  If a deep clone is
+    // implementated, then what happens when the linked list is cyclical (as is
+    // the case with SequencedHashMap)?  It's impossible to know in the clone
+    // when to stop cloning, and thus you end up in a recursive loop,
+    // continuously cloning the "next" in the list.
+
+    private final Object key;
+    private Object value;
+    
+    // package private to allow the SequencedHashMap to access and manipulate
+    // them.
+    Entry next = null;
+    Entry prev = null;
+
+    public Entry(Object key, Object value) {
+      this.key = key;
+      this.value = value;
+    }
+
+    // per Map.Entry.getKey()
+    public Object getKey() { 
+      return this.key; 
+    }
+
+    // per Map.Entry.getValue()
+    public Object getValue() { 
+      return this.value; 
+    }
+
+    // per Map.Entry.setValue()
+    public Object setValue(Object value) { 
+      Object oldValue = this.value;
+      this.value = value; 
+      return oldValue;
+    }
+
+    public int hashCode() { 
+      // implemented per api docs for Map.Entry.hashCode()
+      return ((getKey() == null ? 0 : getKey().hashCode()) ^
+              (getValue()==null ? 0 : getValue().hashCode())); 
+    }
+
+    public boolean equals(Object obj) {
+      if(obj == null) return false;
+      if(obj == this) return true;
+      if(!(obj instanceof Map.Entry)) return false;
+
+      Map.Entry other = (Map.Entry)obj;
+
+      // implemented per api docs for Map.Entry.equals(Object) 
+      return((getKey() == null ?
+              other.getKey() == null : 
+              getKey().equals(other.getKey()))  &&
+             (getValue() == null ?
+              other.getValue() == null : 
+              getValue().equals(other.getValue())));
+    }
+    public String toString() {
+      return "[" + getKey() + "=" + getValue() + "]";
+    }
+  }
+
+  /**
+   *  Construct an empty sentinel used to hold the head (sentinel.next) and the
+   *  tail (sentinel.prev) of the list.  The sentinal has a <code>null</code>
+   *  key and value.
+   **/
+  private static final Entry createSentinel() {
+    Entry s = new Entry(null, null);
+    s.prev = s;
+    s.next = s;
+    return s;
+  }
+
+  /**
+   *  Sentinel used to hold the head and tail of the list of entries.
+   **/
+  private Entry sentinel;
+
+  /**
+   *  Map of keys to entries
+   **/
+  private HashMap entries;
+
+  /**
+   *  Construct a new sequenced hash map with default initial size and load
+   *  factor.
+   **/
+  public SequencedHashMap() {
+    sentinel = createSentinel();
+    entries = new HashMap();
+  }
+
+  /**
+   *  Construct a new sequenced hash map with the specified initial size and
+   *  default load factor.
+   *
+   *  @param initialSize the initial size for the hash table 
+   *
+   *  @see HashMap#HashMap(int)
+   **/
+  public SequencedHashMap(int initialSize) {
+    sentinel = createSentinel();
+    entries = new HashMap(initialSize);
+  }
+
+  /**
+   *  Construct a new sequenced hash map with the specified initial size and
+   *  load factor.
+   *
+   *  @param initialSize the initial size for the hash table 
+   *
+   *  @param loadFactor the load factor for the hash table.
+   *
+   *  @see HashMap#HashMap(int,float)
+   **/
+  public SequencedHashMap(int initialSize, float loadFactor) {
+    sentinel = createSentinel();
+    entries = new HashMap(initialSize, loadFactor);
+  }
+
+  /**
+   *  Construct a new sequenced hash map and add all the elements in the
+   *  specified map.  The order in which the mappings in the specified map are
+   *  added is defined by {@link #putAll(Map)}.  
+   **/
+  public SequencedHashMap(Map m) {
+    this();
+    putAll(m);
+  }
+
+  /**
+   *  Removes an internal entry from the linked list.  This does not remove
+   *  it from the underlying map.
+   **/
+  private void removeEntry(Entry entry) {
+    entry.next.prev = entry.prev;
+    entry.prev.next = entry.next;    
+  }
+
+  /**
+   *  Inserts a new internal entry to the tail of the linked list.  This does
+   *  not add the entry to the underlying map.
+   **/
+  private void insertEntry(Entry entry) {
+    entry.next = sentinel;
+    entry.prev = sentinel.prev;
+    sentinel.prev.next = entry;
+    sentinel.prev = entry;
+  }
+
+  // per Map.size()
+  public int size() {
+    // use the underlying Map's size since size is not maintained here.
+    return entries.size();
+  }
+
+  // per Map.isEmpty()
+  public boolean isEmpty() {
+    // for quick check whether the map is entry, we can check the linked list
+    // and see if there's anything in it.
+    return sentinel.next == sentinel;
+  }
+
+  // per Map.containsKey(Object)
+  public boolean containsKey(Object key) {
+    // pass on to underlying map implementation
+    return entries.containsKey(key);
+  }
+
+  // per Map.containsValue(Object)
+  public boolean containsValue(Object value) {
+    // unfortunately, we cannot just pass this call to the underlying map
+    // because we are mapping keys to entries, not keys to values.  The
+    // underlying map doesn't have an efficient implementation anyway, so this
+    // isn't a big deal.
+
+    // do null comparison outside loop so we only need to do it once.  This
+    // provides a tighter, more efficient loop at the expense of slight
+    // code duplication.
+    if(value == null) {
+      for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+        if(pos.getValue() == null) return true;
+      } 
+    } else {
+      for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+        if(value.equals(pos.getValue())) return true;
+      }
+    }
+    return false;      
+  }
+
+  // per Map.get(Object)
+  public Object get(Object o) {
+    // find entry for the specified key object
+    Entry entry = (Entry)entries.get(o);
+    if(entry == null) return null;
+      
+    return entry.getValue();
+  }
+
+  /**
+   *  Return the entry for the "oldest" mapping.  That is, return the Map.Entry
+   *  for the key-value pair that was first put into the map when compared to
+   *  all the other pairings in the map.  This behavior is equivalent to using
+   *  <code>entrySet().iterator().next()</code>, but this method provides an
+   *  optimized implementation.
+   *
+   *  @return The first entry in the sequence, or <code>null</code> if the
+   *  map is empty.
+   **/
+  public Map.Entry getFirst() {
+    // sentinel.next points to the "first" element of the sequence -- the head
+    // of the list, which is exactly the entry we need to return.  We must test
+    // for an empty list though because we don't want to return the sentinel!
+    return (isEmpty()) ? null : sentinel.next;
+  }
+
+  /**
+   *  Return the key for the "oldest" mapping.  That is, return the key for the
+   *  mapping that was first put into the map when compared to all the other
+   *  objects in the map.  This behavior is equivalent to using
+   *  <code>getFirst().getKey()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The first key in the sequence, or <code>null</code> if the
+   *  map is empty.
+   **/
+  public Object getFirstKey() {
+    // sentinel.next points to the "first" element of the sequence -- the head
+    // of the list -- and the requisite key is returned from it.  An empty list
+    // does not need to be tested.  In cases where the list is empty,
+    // sentinel.next will point to the sentinel itself which has a null key,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.next.getKey();
+  }
+
+  /**
+   *  Return the value for the "oldest" mapping.  That is, return the value for
+   *  the mapping that was first put into the map when compared to all the
+   *  other objects in the map.  This behavior is equivalent to using
+   *  <code>getFirst().getValue()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The first value in the sequence, or <code>null</code> if the
+   *  map is empty.
+   **/
+  public Object getFirstValue() {
+    // sentinel.next points to the "first" element of the sequence -- the head
+    // of the list -- and the requisite value is returned from it.  An empty
+    // list does not need to be tested.  In cases where the list is empty,
+    // sentinel.next will point to the sentinel itself which has a null value,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.next.getValue();
+  }
+
+  /**
+   *  Return the entry for the "newest" mapping.  That is, return the Map.Entry
+   *  for the key-value pair that was first put into the map when compared to
+   *  all the other pairings in the map.  The behavior is equivalent to:
+   *
+   *  <pre>
+   *    Object obj = null;
+   *    Iterator iter = entrySet().iterator();
+   *    while(iter.hasNext()) {
+   *      obj = iter.next();
+   *    }
+   *    return (Map.Entry)obj;
+   *  </pre>
+   *
+   *  However, the implementation of this method ensures an O(1) lookup of the
+   *  last key rather than O(n).
+   *
+   *  @return The last entry in the sequence, or <code>null</code> if the map
+   *  is empty.
+   **/
+  public Map.Entry getLast() {
+    // sentinel.prev points to the "last" element of the sequence -- the tail
+    // of the list, which is exactly the entry we need to return.  We must test
+    // for an empty list though because we don't want to return the sentinel!
+    return (isEmpty()) ? null : sentinel.prev;
+  }
+
+  /**
+   *  Return the key for the "newest" mapping.  That is, return the key for the
+   *  mapping that was last put into the map when compared to all the other
+   *  objects in the map.  This behavior is equivalent to using
+   *  <code>getLast().getKey()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The last key in the sequence, or <code>null</code> if the map is
+   *  empty.
+   **/
+  public Object getLastKey() {
+    // sentinel.prev points to the "last" element of the sequence -- the tail
+    // of the list -- and the requisite key is returned from it.  An empty list
+    // does not need to be tested.  In cases where the list is empty,
+    // sentinel.prev will point to the sentinel itself which has a null key,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.prev.getKey();
+  }
+
+  /**
+   *  Return the value for the "newest" mapping.  That is, return the value for
+   *  the mapping that was last put into the map when compared to all the other
+   *  objects in the map.  This behavior is equivalent to using
+   *  <code>getLast().getValue()</code>, but this method provides a slightly
+   *  optimized implementation.
+   *
+   *  @return The last value in the sequence, or <code>null</code> if the map
+   *  is empty.
+   **/
+  public Object getLastValue() {
+    // sentinel.prev points to the "last" element of the sequence -- the tail
+    // of the list -- and the requisite value is returned from it.  An empty
+    // list does not need to be tested.  In cases where the list is empty,
+    // sentinel.prev will point to the sentinel itself which has a null value,
+    // which is exactly what we would want to return if the list is empty (a
+    // nice convient way to avoid test for an empty list)
+    return sentinel.prev.getValue();
+  }
+
+  // per Map.put(Object,Object)
+  public Object put(Object key, Object value) {
+
+    Object oldValue = null;
+
+    // lookup the entry for the specified key
+    Entry e = (Entry)entries.get(key);
+
+    // check to see if it already exists
+    if(e != null) {
+      // remove from list so the entry gets "moved" to the end of list
+      removeEntry(e);
+
+      // update value in map
+      oldValue = e.setValue(value);
+
+      // Note: We do not update the key here because its unnecessary.  We only
+      // do comparisons using equals(Object) and we know the specified key and
+      // that in the map are equal in that sense.  This may cause a problem if
+      // someone does not implement their hashCode() and/or equals(Object)
+      // method properly and then use it as a key in this map.  
+    } else {
+      // add new entry
+      e = new Entry(key, value);
+      entries.put(key, e);
+    }
+    // assert(entry in map, but not list)
+
+    // add to list
+    insertEntry(e);
+
+    return oldValue;
+  }
+
+  // per Map.remove(Object)
+  public Object remove(Object key) {
+    Entry e = (Entry)entries.remove(key);
+    if(e == null) return null;
+    removeEntry(e);
+    return e.getValue();
+  }
+
+  /**
+   *  Adds all the mappings in the specified map to this map, replacing any
+   *  mappings that already exist (as per {@link Map#putAll(Map)}).  The order
+   *  in which the entries are added is determined by the iterator returned
+   *  from {@link Map#entrySet()} for the specified map.
+   *
+   *  @param t the mappings that should be added to this map.
+   *
+   *  @exception NullPointerException if <code>t</code> is <code>null</code>
+   **/
+  public void putAll(Map t) {
+    Iterator iter = t.entrySet().iterator();
+    while(iter.hasNext()) {
+      Map.Entry entry = (Map.Entry)iter.next();
+      put(entry.getKey(), entry.getValue());
+    }
+  }
+
+  // per Map.clear()
+  public void clear() {
+    // remove all from the underlying map
+    entries.clear();
+
+    // and the list
+    sentinel.next = sentinel;
+    sentinel.prev = sentinel;
+  }
+
+  // per Map.keySet()
+  public Set keySet() {
+    return new AbstractSet() {
+
+      // required impls
+      public Iterator iterator() { return new OrderedIterator(KEY); }
+      public boolean remove(Object o) {
+        return SequencedHashMap.this.remove(o) != null;
+      }
+
+      // more efficient impls than abstract set
+      public void clear() { 
+        SequencedHashMap.this.clear(); 
+      }
+      public int size() { 
+        return SequencedHashMap.this.size(); 
+      }
+      public boolean isEmpty() { 
+        return SequencedHashMap.this.isEmpty(); 
+      }
+      public boolean contains(Object o) { 
+        return SequencedHashMap.this.containsKey(o);
+      }
+
+    };
+  }
+
+  // per Map.values()
+  public Collection values() {
+    return new AbstractCollection() {
+      // required impl
+      public Iterator iterator() { return new OrderedIterator(VALUE); }
+      public boolean remove(Object value) {
+        // do null comparison outside loop so we only need to do it once.  This
+        // provides a tighter, more efficient loop at the expense of slight
+        // code duplication.
+        if(value == null) {
+          for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+            if(pos.getValue() == null) {
+              SequencedHashMap.this.remove(pos.getKey());
+              return true;
+            }
+          } 
+        } else {
+          for(Entry pos = sentinel.next; pos != sentinel; pos = pos.next) {
+            if(value.equals(pos.getValue())) {
+              SequencedHashMap.this.remove(pos.getKey());
+              return true;
+            }
+          }
+        }
+
+        return false;
+      }
+
+      // more efficient impls than abstract collection
+      public void clear() { 
+        SequencedHashMap.this.clear(); 
+      }
+      public int size() { 
+        return SequencedHashMap.this.size(); 
+      }
+      public boolean isEmpty() { 
+        return SequencedHashMap.this.isEmpty(); 
+      }
+      public boolean contains(Object o) {
+        return SequencedHashMap.this.containsValue(o);
+      }
+    };
+  }
+
+  // per Map.entrySet()
+  public Set entrySet() {
+    return new AbstractSet() {
+      // helper
+      private Entry findEntry(Object o) {
+        if(o == null) return null;
+        if(!(o instanceof Map.Entry)) return null;
+        
+        Map.Entry e = (Map.Entry)o;
+        Entry entry = (Entry)entries.get(e.getKey());
+        if(entry != null && entry.equals(e)) return entry;
+        else return null;
+      }
+
+      // required impl
+      public Iterator iterator() { 
+        return new OrderedIterator(ENTRY); 
+      }
+      public boolean remove(Object o) {
+        Entry e = findEntry(o);
+        if(e == null) return false;
+
+        return SequencedHashMap.this.remove(e.getKey()) != null;
+      }        
+
+      // more efficient impls than abstract collection
+      public void clear() { 
+        SequencedHashMap.this.clear(); 
+      }
+      public int size() { 
+        return SequencedHashMap.this.size(); 
+      }
+      public boolean isEmpty() { 
+        return SequencedHashMap.this.isEmpty(); 
+      }
+      public boolean contains(Object o) {
+        return findEntry(o) != null;
+      }
+    };
+  }
+
+  // constants to define what the iterator should return on "next"
+  private static final int KEY = 0;
+  private static final int VALUE = 1;
+  private static final int ENTRY = 2;
+  private static final int REMOVED_MASK = 0x80000000;
+
+  private class OrderedIterator implements Iterator {
+    /** 
+     *  Holds the type that should be returned from the iterator.  The value
+     *  should be either {@link #KEY}, {@link #VALUE}, or {@link #ENTRY}.  To
+     *  save a tiny bit of memory, this field is also used as a marker for when
+     *  remove has been called on the current object to prevent a second remove
+     *  on the same element.  Essientially, if this value is negative (i.e. the
+     *  bit specified by {@link #REMOVED_MASK} is set), the current position
+     *  has been removed.  If positive, remove can still be called.
+     **/
+    private int returnType;
+
+    /**
+     *  Holds the "current" position in the iterator.  when pos.next is the
+     *  sentinel, we've reached the end of the list.
+     **/
+    private Entry pos = sentinel;
+    
+    /**
+     *  Construct an iterator over the sequenced elements in the order in which
+     *  they were added.  The {@link #next()} method returns the type specified
+     *  by <code>returnType</code> which must be either {@link #KEY}, {@link
+     *  #VALUE}, or {@link #ENTRY}.
+     **/
+    public OrderedIterator(int returnType) {
+      //// Since this is a private inner class, nothing else should have
+      //// access to the constructor.  Since we know the rest of the outer
+      //// class uses the iterator correctly, we can leave of the following
+      //// check:
+      //if(returnType >= 0 && returnType <= 2) {
+      //  throw new IllegalArgumentException("Invalid iterator type");
+      //}
+
+      // Set the "removed" bit so that the iterator starts in a state where
+      // "next" must be called before "remove" will succeed.
+      this.returnType = returnType | REMOVED_MASK;
+    }
+
+    /**
+     *  Returns whether there is any additional elements in the iterator to be
+     *  returned.
+     *
+     *  @return <code>true</code> if there are more elements left to be
+     *  returned from the iterator; <code>false</code> otherwise.
+     **/
+    public boolean hasNext() {
+      return pos.next != sentinel;
+    }
+
+    /**
+     *  Returns the next element from the iterator.
+     *
+     *  @return the next element from the iterator.
+     *
+     *  @exception NoSuchElementException if there are no more elements in the
+     *  iterator.
+     **/
+    public Object next() {
+      if(pos.next == sentinel) {
+        throw new NoSuchElementException();
+      }
+
+      // clear the "removed" flag
+      returnType = returnType & ~REMOVED_MASK;
+
+      pos = pos.next;
+      switch(returnType) {
+      case KEY:
+        return pos.getKey();
+      case VALUE:
+        return pos.getValue();
+      case ENTRY:
+        return pos;
+      default:
+        // should never happen
+        throw new Error("bad iterator type: " + returnType);
+      }
+
+    }
+    
+    /**
+     *  Removes the last element returned from the {@link #next()} method from
+     *  the sequenced map.
+     *
+     *  @exception IllegalStateException if there isn't a "last element" to be
+     *  removed.  That is, if {@link #next()} has never been called, or if
+     *  {@link #remove()} was already called on the element.
+     **/
+    public void remove() {
+      if((returnType & REMOVED_MASK) != 0) {
+        throw new IllegalStateException("remove() must follow next()");
+      }
+
+      // remove the entry
+      SequencedHashMap.this.remove(pos.getKey());
+
+      // set the removed flag
+      returnType = returnType | REMOVED_MASK;
+    }
+  }
+
+  // APIs maintained from previous version of SequencedHashMap for backwards
+  // compatibility
+
+  /**
+   * Creates a shallow copy of this object, preserving the internal structure
+   * by copying only references.  The keys and values themselves are not
+   * <code>clone()</code>'d.  The cloned object maintains the same sequence.
+   *
+   * @return A clone of this instance.  
+   */
+  public Object clone () {
+    // yes, calling super.clone() silly since we're just blowing away all
+    // the stuff that super might be doing anyway, but for motivations on
+    // this, see:
+    // http://www.javaworld.com/javaworld/jw-01-1999/jw-01-object.html
+    SequencedHashMap map = (SequencedHashMap)super.clone();
+
+    // create new, empty sentinel
+    map.sentinel = createSentinel();
+
+    // create a new, empty entry map
+    // note: this does not preserve the initial capacity and load factor.
+    map.entries = new HashMap();
+      
+    // add all the mappings
+    map.putAll(this);
+
+    // Note: We cannot just clone the hashmap and sentinel because we must
+    // duplicate our internal structures.  Cloning those two will not clone all
+    // the other entries they reference, and so the cloned hash map will not be
+    // able to maintain internal consistency because there are two objects with
+    // the same entries.  See discussion in the Entry implementation on why we
+    // cannot implement a clone of the Entry (and thus why we need to recreate
+    // everything).
+
+    return map;
+  }
+
+  /**
+   *  Returns the Map.Entry at the specified index
+   *
+   *  @exception ArrayIndexOutOfBoundsException if the specified index is
+   *  <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   **/
+  private Map.Entry getEntry(int index) {
+    Entry pos = sentinel;
+
+    if(index < 0) {
+      throw new ArrayIndexOutOfBoundsException(index + " < 0");
+    }
+
+    // loop to one before the position
+    int i = -1;
+    while(i < (index-1) && pos.next != sentinel) {
+      i++;
+      pos = pos.next;
+    }
+    // pos.next is the requested position
+    
+    // if sentinel is next, past end of list
+    if(pos.next == sentinel) {
+      throw new ArrayIndexOutOfBoundsException(index + " >= " + (i + 1));
+    }
+
+    return pos.next;
+  }
+
+  /**
+   * Returns the key at the specified index.
+   *
+   *  @exception ArrayIndexOutOfBoundsException if the <code>index</code> is
+   *  <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   */
+  public Object get (int index)
+  {
+    return getEntry(index).getKey();
+  }
+
+  /**
+   * Returns the value at the specified index.
+   *
+   *  @exception ArrayIndexOutOfBoundsException if the <code>index</code> is
+   *  <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   */
+  public Object getValue (int index)
+  {
+    return getEntry(index).getValue();
+  }
+
+  /**
+   * Returns the index of the specified key.
+   */
+  public int indexOf (Object key)
+  {
+    Entry e = (Entry)entries.get(key);
+    int pos = 0;
+    while(e.prev != sentinel) {
+      pos++;
+      e = e.prev;
+    }
+    return pos;
+  }
+
+  /**
+   * Returns a key iterator.
+   */
+  public Iterator iterator ()
+  {
+    return keySet().iterator();
+  }
+
+  /**
+   * Returns the last index of the specified key.
+   */
+  public int lastIndexOf (Object key)
+  {
+    // keys in a map are guarunteed to be unique
+    return indexOf(key);
+  }
+
+  /**
+   * Returns a List view of the keys rather than a set view.  The returned
+   * list is unmodifiable.  This is required because changes to the values of
+   * the list (using {@link java.util.ListIterator#set(Object)}) will
+   * effectively remove the value from the list and reinsert that value at
+   * the end of the list, which is an unexpected side effect of changing the
+   * value of a list.  This occurs because changing the key, changes when the
+   * mapping is added to the map and thus where it appears in the list.
+   *
+   * <P>An alternative to this method is to use {@link #keySet()}
+   *
+   * @see #keySet()
+   * @return The ordered list of keys.  
+   */
+  public List sequence()
+  {
+    List l = new ArrayList(size());
+    Iterator iter = keySet().iterator();
+    while(iter.hasNext()) {
+      l.add(iter.next());
+    }
+      
+    return Collections.unmodifiableList(l);
+  }
+
+  /**
+   * Removes the element at the specified index.
+   *
+   * @param index The index of the object to remove.
+   * @return      The previous value coressponding the <code>key</code>, or
+   *              <code>null</code> if none existed.
+   *
+   * @exception ArrayIndexOutOfBoundsException if the <code>index</code> is
+   * <code>&lt; 0</code> or <code>&gt;</code> the size of the map.
+   */
+  public Object remove (int index)
+  {
+    return remove(get(index));
+  }
+
+}

richedit/src/main/resource/testFiles/commons-collections/revFiles/b6d038_4bdb89_src#java#org#apache#commons#collections#iterators#ArrayListIterator.java

@@ -0,0 +1,250 @@
+/*
+ * $Header: /home/jerenkrantz/tmp/commons/commons-convert/cvs/home/cvs/jakarta-commons//collections/src/java/org/apache/commons/collections/iterators/ArrayListIterator.java,v 1.5 2003/09/29 03:56:12 psteitz Exp $
+ * ====================================================================
+ *
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 1999-2003 The Apache Software Foundation.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * 3. The end-user documentation included with the redistribution, if
+ *    any, must include the following acknowledgement:
+ *       "This product includes software developed by the
+ *        Apache Software Foundation (http://www.apache.org/)."
+ *    Alternately, this acknowledgement may appear in the software itself,
+ *    if and wherever such third-party acknowledgements normally appear.
+ *
+ * 4. The names "The Jakarta Project", "Commons", and "Apache Software
+ *    Foundation" must not be used to endorse or promote products derived
+ *    from this software without prior written permission. For written
+ *    permission, please contact apache@apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache"
+ *    nor may "Apache" appear in their names without prior written
+ *    permission of the Apache Software Foundation.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation.  For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ */
+package org.apache.commons.collections.iterators;
+
+import java.lang.reflect.Array;
+import java.util.NoSuchElementException;
+
+/**
+ * Implements a {@link java.util.ListIterator ListIterator} over an array. 
+ * <p>
+ * The array can be either an array of object or of primitives. If you know 
+ * that you have an object array, the 
+ * {@link org.apache.commons.collections.iterators.ObjectArrayListIterator ObjectArrayListIterator}
+ * class is a better choice, as it will perform better.
+ * 
+ * <p>
+ * This iterator does not support {@link #add(Object)} or {@link #remove()}, as the array 
+ * cannot be changed in size. The {@link #set(Object)} method is supported however.
+ *
+ * @see org.apache.commons.collections.iterators.ArrayIterator
+ * @see java.util.Iterator
+ * @see java.util.ListIterator
+ *
+ * @since Commons Collections 2.2
+ * @version $Revision: 1.5 $ $Date: 2003/09/29 03:56:12 $
+ *
+ * @author <a href="mailto:neilotoole@users.sourceforge.net">Neil O'Toole</a>
+ * @author Stephen Colebourne
+ * @author Phil Steitz
+ */
+public class ArrayListIterator extends ArrayIterator implements ResetableListIterator {
+
+    /**
+     * Holds the index of the last item returned by a call to <code>next()</code> or <code>previous()</code>. This
+     *  is set to <code>-1</code> if neither method has yet been invoked. <code>lastItemIndex</code> is used to to
+     * implement the {@link #set} method.
+     *
+     */
+    protected int lastItemIndex = -1;
+
+    /**
+     * Constructor for use with <code>setArray</code>.
+     * <p>
+     * Using this constructor, the iterator is equivalent to an empty iterator
+     * until {@link #setArray(Object)} is  called to establish the array to iterate over.
+     */
+    public ArrayListIterator() {
+        super();
+    }
+
+    /**
+     * Constructs an ArrayListIterator that will iterate over the values in the
+     * specified array.
+     *
+     * @param array the array to iterate over
+     * @throws IllegalArgumentException if <code>array</code> is not an array.
+     * @throws NullPointerException if <code>array</code> is <code>null</code>
+     */
+    public ArrayListIterator(Object array) {
+        super(array);
+    }
+
+    /**
+     * Constructs an ArrayListIterator that will iterate over the values in the
+     * specified array from a specific start index.
+     *
+     * @param array  the array to iterate over
+     * @param start  the index to start iterating at
+     * @throws IllegalArgumentException if <code>array</code> is not an array.
+     * @throws NullPointerException if <code>array</code> is <code>null</code>
+     * @throws IndexOutOfBoundsException if the start index is out of bounds
+     */
+    public ArrayListIterator(Object array, int start) {
+        super(array, start);
+        this.startIndex = start;
+    }
+
+    /**
+     * Construct an ArrayListIterator that will iterate over a range of values 
+     * in the specified array.
+     *
+     * @param array  the array to iterate over
+     * @param start  the index to start iterating at
+     * @param end  the index (exclusive) to finish iterating at
+     * @throws IllegalArgumentException if <code>array</code> is not an array.
+     * @throws IndexOutOfBoundsException if the start or end index is out of bounds
+     * @throws IllegalArgumentException if end index is before the start
+     * @throws NullPointerException if <code>array</code> is <code>null</code>
+     */
+    public ArrayListIterator(Object array, int start, int end) {
+        super(array, start, end);
+        this.startIndex = start;
+    }
+
+    // ListIterator interface
+    //-------------------------------------------------------------------------
+
+    /**
+     * Returns true if there are previous elements to return from the array.
+     *
+     * @return true if there is a previous element to return
+     */
+    public boolean hasPrevious() {
+        return (this.index > this.startIndex);
+    }
+
+    /**
+     * Gets the previous element from the array.
+     * 
+     * @return the previous element
+     * @throws NoSuchElementException if there is no previous element
+     */
+    public Object previous() {
+        if (hasPrevious() == false) {
+            throw new NoSuchElementException();
+        }
+        this.lastItemIndex = --this.index;
+        return Array.get(this.array, this.index);
+    }
+
+    /**
+     * Gets the next element from the array.
+     * 
+     * @return the next element
+     * @throws NoSuchElementException if there is no next element
+     */
+    public Object next() {
+        if (hasNext() == false) {
+            throw new NoSuchElementException();
+        }
+        this.lastItemIndex = this.index;
+        return Array.get(this.array, this.index++);
+    }
+
+    /**
+     * Gets the next index to be retrieved.
+     * 
+     * @return the index of the item to be retrieved next
+     */
+    public int nextIndex() {
+        return this.index - this.startIndex;
+    }
+
+    /**
+     * Gets the index of the item to be retrieved if {@link #previous()} is called.
+     * 
+     * @return the index of the item to be retrieved next
+     */
+    public int previousIndex() {
+        return this.index - this.startIndex - 1;
+    }
+
+    /**
+     * This iterator does not support modification of its backing collection, and so will
+     * always throw an {@link UnsupportedOperationException} when this method is invoked.
+     *
+     * @throws UnsupportedOperationException always thrown.
+     * @see java.util.ListIterator#set
+     */
+    public void add(Object o) {
+        throw new UnsupportedOperationException("add() method is not supported");
+    }
+
+    /**
+     * Sets the element under the cursor.
+     * <p>
+     * This method sets the element that was returned by the last call 
+     * to {@link #next()} of {@link #previous()}. 
+     * <p>
+     * <b>Note:</b> {@link ListIterator} implementations that support
+     * <code>add()</code> and <code>remove()</code> only allow <code>set()</code> to be called
+     * once per call to <code>next()</code> or <code>previous</code> (see the {@link ListIterator}
+     * javadoc for more details). Since this implementation does
+     * not support <code>add()</code> or <code>remove()</code>, <code>set()</code> may be
+     * called as often as desired.
+     *
+     * @see java.util.ListIterator#set
+     */
+    public void set(Object o) {
+        if (this.lastItemIndex == -1) {
+            throw new IllegalStateException("must call next() or previous() before a call to set()");
+        }
+
+        Array.set(this.array, this.lastItemIndex, o);
+    }
+
+    /**
+     * Resets the iterator back to the start index.
+     */
+    public void reset() {
+        super.reset();
+        this.lastItemIndex = -1;
+    }
+
+}

richedit/src/main/resource/testFiles/commons-compress/prevFiles/prev_4ac67b_0eccda_src#main#java#org#apache#commons#compress#compressors#snappy#SnappyCompressorInputStream.java

@@ -0,0 +1,286 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.commons.compress.compressors.snappy;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.commons.compress.compressors.lz77support.AbstractLZ77CompressorInputStream;
+import org.apache.commons.compress.utils.ByteUtils;
+
+/**
+ * CompressorInputStream for the raw Snappy format.
+ *
+ * <p>This implementation uses an internal buffer in order to handle
+ * the back-references that are at the heart of the LZ77 algorithm.
+ * The size of the buffer must be at least as big as the biggest
+ * offset used in the compressed stream.  The current version of the
+ * Snappy algorithm as defined by Google works on 32k blocks and
+ * doesn't contain offsets bigger than 32k which is the default block
+ * size used by this class.</p>
+ *
+ * @see <a href="https://github.com/google/snappy/blob/master/format_description.txt">Snappy compressed format description</a>
+ * @since 1.7
+ */
+public class SnappyCompressorInputStream extends AbstractLZ77CompressorInputStream {
+
+    /** Mask used to determine the type of "tag" is being processed */
+    private static final int TAG_MASK = 0x03;
+
+    /** Default block size */
+    public static final int DEFAULT_BLOCK_SIZE = 32768;
+
+    /** The size of the uncompressed data */
+    private final int size;
+
+    /** Number of uncompressed bytes still to be read. */
+    private int uncompressedBytesRemaining;
+
+    /** Current state of the stream */
+    private State state = State.NO_BLOCK;
+
+    private boolean endReached = false;
+
+    /**
+     * Constructor using the default buffer size of 32k.
+     * 
+     * @param is
+     *            An InputStream to read compressed data from
+     * 
+     * @throws IOException if reading fails
+     */
+    public SnappyCompressorInputStream(final InputStream is) throws IOException {
+        this(is, DEFAULT_BLOCK_SIZE);
+    }
+
+    /**
+     * Constructor using a configurable buffer size.
+     * 
+     * @param is
+     *            An InputStream to read compressed data from
+     * @param blockSize
+     *            The block size used in compression
+     * 
+     * @throws IOException if reading fails
+     */
+    public SnappyCompressorInputStream(final InputStream is, final int blockSize)
+            throws IOException {
+        super(is, blockSize);
+        uncompressedBytesRemaining = size = (int) readSize();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public int read(final byte[] b, final int off, final int len) throws IOException {
+        if (endReached) {
+            return -1;
+        }
+        switch (state) {
+        case NO_BLOCK:
+            fill();
+            return read(b, off, len);
+        case IN_LITERAL:
+            int litLen = readLiteral(b, off, len);
+            if (!hasMoreDataInBlock()) {
+                state = State.NO_BLOCK;
+            }
+            return litLen;
+        case IN_BACK_REFERENCE:
+            int backReferenceLen = readBackReference(b, off, len);
+            if (!hasMoreDataInBlock()) {
+                state = State.NO_BLOCK;
+            }
+            return backReferenceLen;
+        default:
+            throw new IOException("Unknown stream state " + state);
+        }
+    }
+
+    /**
+     * Try to fill the buffer with the next block of data.
+     */
+    private void fill() throws IOException {
+        if (uncompressedBytesRemaining == 0) {
+            endReached = true;
+            return;
+        }
+
+        int b = readOneByte();
+        if (b == -1) {
+            throw new IOException("Premature end of stream reading block start");
+        }
+        int length = 0;
+        int offset = 0;
+
+        switch (b & TAG_MASK) {
+
+        case 0x00:
+
+            length = readLiteralLength(b);
+            uncompressedBytesRemaining -= length;
+            startLiteral(length);
+            state = State.IN_LITERAL;
+            break;
+
+        case 0x01:
+
+            /*
+             * These elements can encode lengths between [4..11] bytes and
+             * offsets between [0..2047] bytes. (len-4) occupies three bits
+             * and is stored in bits [2..4] of the tag byte. The offset
+             * occupies 11 bits, of which the upper three are stored in the
+             * upper three bits ([5..7]) of the tag byte, and the lower
+             * eight are stored in a byte following the tag byte.
+             */
+
+            length = 4 + ((b >> 2) & 0x07);
+            uncompressedBytesRemaining -= length;
+            offset = (b & 0xE0) << 3;
+            b = readOneByte();
+            if (b == -1) {
+                throw new IOException("Premature end of stream reading back-reference length");
+            }
+            offset |= b;
+
+            startBackReference(offset, length);
+            state = State.IN_BACK_REFERENCE;
+            break;
+
+        case 0x02:
+
+            /*
+             * These elements can encode lengths between [1..64] and offsets
+             * from [0..65535]. (len-1) occupies six bits and is stored in
+             * the upper six bits ([2..7]) of the tag byte. The offset is
+             * stored as a little-endian 16-bit integer in the two bytes
+             * following the tag byte.
+             */
+
+            length = (b >> 2) + 1;
+            uncompressedBytesRemaining -= length;
+
+            offset = (int) ByteUtils.fromLittleEndian(supplier, 2);
+
+            startBackReference(offset, length);
+            state = State.IN_BACK_REFERENCE;
+            break;
+
+        case 0x03:
+
+            /*
+             * These are like the copies with 2-byte offsets (see previous
+             * subsection), except that the offset is stored as a 32-bit
+             * integer instead of a 16-bit integer (and thus will occupy
+             * four bytes).
+             */
+
+            length = (b >> 2) + 1;
+            uncompressedBytesRemaining -= length;
+
+            offset = (int) ByteUtils.fromLittleEndian(supplier, 4) & 0x7fffffff;
+
+            startBackReference(offset, length);
+            state = State.IN_BACK_REFERENCE;
+            break;
+        default:
+            // impossible as TAG_MASK is two bits and all four possible cases have been covered
+            break;
+        }
+    }
+
+    /*
+     * For literals up to and including 60 bytes in length, the
+     * upper six bits of the tag byte contain (len-1). The literal
+     * follows immediately thereafter in the bytestream. - For
+     * longer literals, the (len-1) value is stored after the tag
+     * byte, little-endian. The upper six bits of the tag byte
+     * describe how many bytes are used for the length; 60, 61, 62
+     * or 63 for 1-4 bytes, respectively. The literal itself follows
+     * after the length.
+     */
+    private int readLiteralLength(final int b) throws IOException {
+        int length;
+        switch (b >> 2) {
+        case 60:
+            length = readOneByte();
+            if (length == -1) {
+                throw new IOException("Premature end of stream reading literal length");
+            }
+            break;
+        case 61:
+            length = (int) ByteUtils.fromLittleEndian(supplier, 2);
+            break;
+        case 62:
+            length = (int) ByteUtils.fromLittleEndian(supplier, 3);
+            break;
+        case 63:
+            length = (int) ByteUtils.fromLittleEndian(supplier, 4);
+            break;
+        default:
+            length = b >> 2;
+            break;
+        }
+
+        return length + 1;
+    }
+
+    /**
+     * The stream starts with the uncompressed length (up to a maximum of 2^32 -
+     * 1), stored as a little-endian varint. Varints consist of a series of
+     * bytes, where the lower 7 bits are data and the upper bit is set iff there
+     * are more bytes to be read. In other words, an uncompressed length of 64
+     * would be stored as 0x40, and an uncompressed length of 2097150 (0x1FFFFE)
+     * would be stored as 0xFE 0xFF 0x7F.
+     * 
+     * @return The size of the uncompressed data
+     * 
+     * @throws IOException
+     *             Could not read a byte
+     */
+    private long readSize() throws IOException {
+        int index = 0;
+        long sz = 0;
+        int b = 0;
+
+        do {
+            b = readOneByte();
+            if (b == -1) {
+                throw new IOException("Premature end of stream reading size");
+            }
+            sz |= (b & 0x7f) << (index++ * 7);
+        } while (0 != (b & 0x80));
+        return sz;
+    }
+
+    /**
+     * Get the uncompressed size of the stream
+     * 
+     * @return the uncompressed size
+     */
+    @Override
+    public int getSize() {
+        return size;
+    }
+
+    private enum State {
+        NO_BLOCK, IN_LITERAL, IN_BACK_REFERENCE
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/prevFiles/prev_5273bd_c25c8d_src#main#java#org#apache#commons#compress#archivers#sevenz#Coders.java

@@ -0,0 +1,217 @@
+/*
+ *  Licensed to the Apache Software Foundation (ASF) under one or more
+ *  contributor license agreements.  See the NOTICE file distributed with
+ *  this work for additional information regarding copyright ownership.
+ *  The ASF licenses this file to You under the Apache License, Version 2.0
+ *  (the "License"); you may not use this file except in compliance with
+ *  the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ */
+package org.apache.commons.compress.archivers.sevenz;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.security.GeneralSecurityException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.Arrays;
+
+import javax.crypto.Cipher;
+import javax.crypto.CipherInputStream;
+import javax.crypto.SecretKey;
+import javax.crypto.spec.IvParameterSpec;
+import javax.crypto.spec.SecretKeySpec;
+
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
+import org.tukaani.xz.LZMA2InputStream;
+
+class Coders {
+    static InputStream addDecoder(final InputStream is,
+            final Coder coder, final String password) throws IOException {
+        for (final CoderId coderId : coderTable) {
+            if (Arrays.equals(coderId.id, coder.decompressionMethodId)) {
+                return coderId.coder.decode(is, coder, password);
+            }
+        }
+        throw new IOException("Unsupported compression method " +
+                Arrays.toString(coder.decompressionMethodId));
+    }
+    
+    static CoderId[] coderTable = new CoderId[] {
+        new CoderId(new byte[] { (byte)0x00 }, new CopyDecoder()),
+        new CoderId(new byte[] { (byte)0x21 }, new LZMA2Decoder()),
+        // FIXME: gives corrupt output
+        //new CoderId(new byte[] { (byte)0x04, (byte)0x01, (byte)0x08 }, new DeflateDecoder()),
+        new CoderId(new byte[] { (byte)0x04, (byte)0x02, (byte)0x02 }, new BZIP2Decoder()),
+        new CoderId(new byte[] { (byte)0x06, (byte)0xf1, (byte)0x07, (byte)0x01 }, new AES256SHA256Decoder())
+    };
+    
+    static class CoderId {
+        CoderId(final byte[] id, final CoderBase coder) {
+            this.id = id;
+            this.coder = coder;
+        }
+
+        final byte[] id;
+        final CoderBase coder;
+    }
+    
+    static abstract class CoderBase {
+        abstract InputStream decode(final InputStream in, final Coder coder,
+                String password) throws IOException;
+    }
+    
+    static class CopyDecoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder,
+                String password) throws IOException {
+            return in; 
+        }
+    }
+    
+    static class LZMA2Decoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder,
+                String password) throws IOException {
+            final int dictionarySizeBits = 0xff & coder.properties[0];
+            if ((dictionarySizeBits & (~0x3f)) != 0) {
+                throw new IOException("Unsupported LZMA2 property bits");
+            }
+            if (dictionarySizeBits > 40) {
+                throw new IOException("Dictionary larger than 4GiB maximum size");
+            }
+            final int dictionarySize;
+            if (dictionarySizeBits == 40) {
+                dictionarySize = 0xFFFFffff;
+            } else {
+                dictionarySize = (2 | (dictionarySizeBits & 0x1)) << (dictionarySizeBits / 2 + 11);
+            }
+            return new LZMA2InputStream(in, dictionarySize);
+        }
+    }
+    
+//    static class DeflateDecoder extends CoderBase {
+//        @Override
+//        InputStream decode(final InputStream in, final Coder coder, final String password)
+//                throws IOException {
+//            System.out.println("deflate prop count = " + (coder.properties == null ? -1 : coder.properties.length));
+//            return new DeflaterInputStream(in, new Deflater(Deflater.DEFAULT_COMPRESSION, true));
+//            //return new GZIPInputStream(in);
+//        }
+//    }
+
+    static class BZIP2Decoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder, final String password)
+                throws IOException {
+            return new BZip2CompressorInputStream(in);
+        }
+    }
+
+    static class AES256SHA256Decoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder,
+                final String password) throws IOException {
+            return new InputStream() {
+                private boolean isInitialized = false;
+                private CipherInputStream cipherInputStream = null;
+                
+                private CipherInputStream init() throws IOException {
+                    if (isInitialized) {
+                        return cipherInputStream;
+                    }
+                    final int byte0 = 0xff & coder.properties[0];
+                    final int numCyclesPower = byte0 & 0x3f;
+                    final int byte1 = 0xff & coder.properties[1];
+                    final int ivSize = ((byte0 >> 6) & 1) + (byte1 & 0x0f);
+                    final int saltSize = ((byte0 >> 7) & 1) + (byte1 >> 4);
+                    //debug("numCyclesPower=" + numCyclesPower + ", saltSize=" + saltSize + ", ivSize=" + ivSize);
+                    if (2 + saltSize + ivSize > coder.properties.length) {
+                        throw new IOException("Salt size + IV size too long");
+                    }
+                    final byte[] salt = new byte[saltSize];
+                    System.arraycopy(coder.properties, 2, salt, 0, saltSize);
+                    final byte[] iv = new byte[16];
+                    System.arraycopy(coder.properties, 2 + saltSize, iv, 0, ivSize);
+                    
+                    if (password == null) {
+                        throw new IOException("Cannot read encrypted files without a password");
+                    }
+                    final byte[] passwordBytes = password.getBytes("UTF-16LE");
+                    final byte[] aesKeyBytes;
+                    if (numCyclesPower == 0x3f) {
+                        aesKeyBytes = new byte[32];
+                        System.arraycopy(salt, 0, aesKeyBytes, 0, saltSize);
+                        System.arraycopy(passwordBytes, 0, aesKeyBytes, saltSize,
+                                Math.min(passwordBytes.length, aesKeyBytes.length - saltSize));
+                    } else {
+                        final MessageDigest digest;
+                        try {
+                            digest = MessageDigest.getInstance("SHA-256");
+                        } catch (NoSuchAlgorithmException noSuchAlgorithmException) {
+                            IOException ioe = new IOException("SHA-256 is unsupported by your Java implementation");
+                            ioe.initCause(noSuchAlgorithmException);
+                            throw ioe;
+        // TODO: simplify when Compress requires Java 1.6                
+//                            throw new IOException("SHA-256 is unsupported by your Java implementation",
+//                                    noSuchAlgorithmException);
+                        }
+                        final byte[] extra = new byte[8];
+                        for (long j = 0; j < (1L << numCyclesPower); j++) {
+                            digest.update(salt);
+                            digest.update(passwordBytes);
+                            digest.update(extra);
+                            for (int k = 0; k < extra.length; k++) {
+                                ++extra[k];
+                                if (extra[k] != 0) {
+                                    break;
+                                }
+                            }
+                        }
+                        aesKeyBytes = digest.digest();
+                    }
+                    
+                    final SecretKey aesKey = new SecretKeySpec(aesKeyBytes, "AES");
+                    try {
+                        final Cipher cipher = Cipher.getInstance("AES/CBC/NoPadding");
+                        cipher.init(Cipher.DECRYPT_MODE, aesKey, new IvParameterSpec(iv));
+                        cipherInputStream = new CipherInputStream(in, cipher);
+                        isInitialized = true;
+                        return cipherInputStream;
+                    } catch (GeneralSecurityException generalSecurityException) {
+                        IOException ioe = new IOException("Decryption error " +
+                                "(do you have the JCE Unlimited Strength Jurisdiction Policy Files installed?)");
+                        ioe.initCause(generalSecurityException);
+                        throw ioe;
+        // TODO: simplify when Compress requires Java 1.6                
+//                        throw new IOException("Decryption error " +
+//                                "(do you have the JCE Unlimited Strength Jurisdiction Policy Files installed?)",
+//                                generalSecurityException);
+                    }
+                }
+                
+                @Override
+                public int read() throws IOException {
+                    return init().read();
+                }
+                
+                @Override
+                public int read(byte[] b, int off, int len) throws IOException {
+                    return init().read();
+                }
+                
+                @Override
+                public void close() {
+                }
+            };
+        }
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/prevFiles/prev_b7de91_5273bd_src#main#java#org#apache#commons#compress#archivers#sevenz#SevenZFile.java

@@ -0,0 +1,968 @@
+/*
+ *  Licensed to the Apache Software Foundation (ASF) under one or more
+ *  contributor license agreements.  See the NOTICE file distributed with
+ *  this work for additional information regarding copyright ownership.
+ *  The ASF licenses this file to You under the Apache License, Version 2.0
+ *  (the "License"); you may not use this file except in compliance with
+ *  the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ */
+package org.apache.commons.compress.archivers.sevenz;
+
+import java.io.ByteArrayInputStream;
+import java.io.DataInput;
+import java.io.DataInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.RandomAccessFile;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.zip.CRC32;
+
+import org.apache.commons.compress.utils.CRC32VerifyingInputStream;
+
+/**
+ * Reads a 7z file, using RandomAccessFile under
+ * the covers.
+ * <p>
+ * The 7z file format is a flexible container
+ * that can contain many compression and
+ * encryption types, but at the moment only
+ * only Copy, LZMA2, BZIP2, and AES-256 + SHA-256
+ * are supported, and archive header compression
+ * (when it uses the unsupported LZMA
+ * compression) isn't. So the only archives
+ * that can be read are the following:
+ * <pre>
+ * 7z a -mhc=off [-mhe=on] -mx=0 [-ppassword] archive.7z files
+ * 7z a -mhc=off [-mhe=on] -m0=LZMA2 [-ppassword] archive.7z files
+ * 7z a -mhc=off [-mhe=on] -m0=BZIP2 [-ppassword] archive.7z files
+ * </pre>
+ * <p>
+ * The format is very Windows/Intel specific,
+ * so it uses little-endian byte order,
+ * doesn't store user/group or permission bits,
+ * and represents times using NTFS timestamps
+ * (100 nanosecond units since 1 January 1601).
+ * Hence the official tools recommend against
+ * using it for backup purposes on *nix, and
+ * recommend .tar.7z or .tar.lzma or .tar.xz
+ * instead.  
+ * <p>
+ * Both the header and file contents may be
+ * compressed and/or encrypted. With both
+ * encrypted, neither file names nor file
+ * contents can be read, but the use of
+ * encryption isn't plausibly deniable.
+ * 
+ * @NotThreadSafe
+ */
+public class SevenZFile {
+    private static final boolean DEBUG = false;
+    private static final int SIGNATURE_HEADER_SIZE = 32;
+    private RandomAccessFile file;
+    private final Archive archive;
+    private int currentEntryIndex = -1;
+    private int currentFolderIndex = -1;
+    private InputStream currentFolderInputStream = null;
+    private InputStream currentEntryInputStream = null;
+    private String password;
+        
+    private static final byte[] sevenZSignature = {
+        (byte)'7', (byte)'z', (byte)0xBC, (byte)0xAF, (byte)0x27, (byte)0x1C
+    };
+    
+    public SevenZFile(final File filename, final String password) throws IOException {
+        boolean succeeded = false;
+        this.password = password;
+        this.file = new RandomAccessFile(filename, "r");
+        try {
+            archive = readHeaders();
+            succeeded = true;
+        } finally {
+            if (!succeeded) {
+                this.file.close();
+            }
+        }
+    }
+    
+    public SevenZFile(final File filename) throws IOException {
+        this(filename, null);
+    }
+
+    public void close() {
+        if (file != null) {
+            try {
+                file.close();
+            } catch (IOException ignored) { // NOPMD
+            }
+            file = null;
+        }
+    }
+    
+    private static void debug(String str) {
+        if (DEBUG) {
+            System.out.println(str);
+        }
+    }
+    
+    private static void debug(String fmt, Object... args) {
+        if (DEBUG) {
+            System.out.format(fmt, args);
+        }
+    }
+    
+    public SevenZArchiveEntry getNextEntry() throws IOException {
+        if (currentEntryIndex >= (archive.files.length - 1)) {
+            return null;
+        }
+        ++currentEntryIndex;
+        final SevenZArchiveEntry entry = archive.files[currentEntryIndex];
+        buildDecodingStream();
+        return entry;
+    }
+    
+    private Archive readHeaders() throws IOException {
+        debug("SignatureHeader");
+        
+        final byte[] signature = new byte[6];
+        file.readFully(signature);
+        if (!Arrays.equals(signature, sevenZSignature)) {
+            throw new IOException("Bad 7z signature");
+        }
+        // 7zFormat.txt has it wrong - it's first major then minor
+        final byte archiveVersionMajor = file.readByte();
+        final byte archiveVersionMinor = file.readByte();
+        debug("  archiveVersion major=%d, minor=%d\n",
+                archiveVersionMajor, archiveVersionMinor);
+        if (archiveVersionMajor != 0) {
+            throw new IOException(String.format("Unsupported 7z version (%d,%d)",
+                    archiveVersionMajor, archiveVersionMinor));
+        }
+
+        final int startHeaderCrc = Integer.reverseBytes(file.readInt());
+        final StartHeader startHeader = readStartHeader(startHeaderCrc);
+        
+        final int nextHeaderSizeInt = (int) startHeader.nextHeaderSize;
+        if (nextHeaderSizeInt != startHeader.nextHeaderSize) {
+            throw new IOException("cannot handle nextHeaderSize " + startHeader.nextHeaderSize);
+        }
+        file.seek(SIGNATURE_HEADER_SIZE + startHeader.nextHeaderOffset);
+        final byte[] nextHeader = new byte[nextHeaderSizeInt];
+        file.readFully(nextHeader);
+        final CRC32 crc = new CRC32();
+        crc.update(nextHeader);
+        if (startHeader.nextHeaderCrc != (int) crc.getValue()) {
+            throw new IOException("NextHeader CRC mismatch");
+        }
+        
+        final ByteArrayInputStream byteStream = new ByteArrayInputStream(nextHeader);
+        DataInputStream nextHeaderInputStream = new DataInputStream(
+                byteStream);
+        Archive archive = new Archive();
+        int nid = nextHeaderInputStream.readUnsignedByte();
+        if (nid == NID.kEncodedHeader) {
+            nextHeaderInputStream = readEncodedHeader(nextHeaderInputStream, archive);
+            // Archive gets rebuilt with the new header
+            archive = new Archive();
+            nid = nextHeaderInputStream.readUnsignedByte();
+        }
+        if (nid == NID.kHeader) {
+            readHeader(nextHeaderInputStream, archive);
+        } else {
+            throw new IOException("Broken or unsupported archive: no Header");
+        }
+        return archive;
+    }
+    
+    private StartHeader readStartHeader(final int startHeaderCrc) throws IOException {
+        final StartHeader startHeader = new StartHeader();
+        DataInputStream dataInputStream = null;
+        try {
+             dataInputStream = new DataInputStream(new CRC32VerifyingInputStream(
+                    new BoundedRandomAccessFileInputStream(file, 20), 20, startHeaderCrc));
+             startHeader.nextHeaderOffset = Long.reverseBytes(dataInputStream.readLong());
+             startHeader.nextHeaderSize = Long.reverseBytes(dataInputStream.readLong());
+             startHeader.nextHeaderCrc = Integer.reverseBytes(dataInputStream.readInt());
+             return startHeader;
+        } finally {
+            if (dataInputStream != null) {
+                dataInputStream.close();
+            }
+        }
+    }
+    
+    private void readHeader(final DataInput header, final Archive archive) throws IOException {
+        debug("Header");
+
+        int nid = header.readUnsignedByte();
+        
+        if (nid == NID.kArchiveProperties) {
+            readArchiveProperties(header);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kAdditionalStreamsInfo) {
+            throw new IOException("Additional streams unsupported");
+            //nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kMainStreamsInfo) {
+            readStreamsInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kFilesInfo) {
+            readFilesInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated header");
+        }
+    }
+    
+    private void readArchiveProperties(final DataInput input) throws IOException {
+        // FIXME: the reference implementation just throws them away?
+        debug("ArchiveProperties");
+
+        int nid =  input.readUnsignedByte();
+        while (nid != NID.kEnd) {
+            final long propertySize = readUint64(input);
+            final byte[] property = new byte[(int)propertySize];
+            input.readFully(property);
+            nid = input.readUnsignedByte();
+        }
+    }
+    
+    private DataInputStream readEncodedHeader(final DataInputStream header, final Archive archive) throws IOException {
+        debug("EncodedHeader");
+
+        readStreamsInfo(header, archive);
+        
+        // FIXME: merge with buildDecodingStream()/buildDecoderStack() at some stage?
+        final Folder folder = archive.folders[0];
+        final int firstPackStreamIndex = 0;
+        final long folderOffset = SIGNATURE_HEADER_SIZE + archive.packPos +
+                0;
+        
+        file.seek(folderOffset);
+        InputStream inputStreamStack = new BoundedRandomAccessFileInputStream(file,
+                archive.packSizes[firstPackStreamIndex]);
+        for (final Coder coder : folder.coders) {
+            if (coder.numInStreams != 1 || coder.numOutStreams != 1) {
+                throw new IOException("Multi input/output stream coders are not yet supported");
+            }
+            inputStreamStack = Coders.addDecoder(inputStreamStack, coder, password);
+        }
+        if (folder.hasCrc) {
+            inputStreamStack = new CRC32VerifyingInputStream(inputStreamStack,
+                    folder.getUnpackSize(), folder.crc);
+        }
+        final byte[] nextHeader = new byte[(int)folder.getUnpackSize()];
+        final DataInputStream nextHeaderInputStream = new DataInputStream(inputStreamStack);
+        try {
+            nextHeaderInputStream.readFully(nextHeader);
+        } finally {
+            nextHeaderInputStream.close();
+        }
+        return new DataInputStream(new ByteArrayInputStream(nextHeader));
+
+        
+        //throw new IOException("LZMA compression unsupported, so files with compressed header cannot be read");
+        // FIXME: this extracts the header to an LZMA file which can then be
+        // manually decompressed.
+//        long offset = SIGNATURE_HEADER_SIZE + archive.packPos;
+//        file.seek(offset);
+//        long unpackSize = archive.folders[0].getUnpackSize();
+//        byte[] packed = new byte[(int)archive.packSizes[0]];
+//        file.readFully(packed);
+//        
+//        FileOutputStream fos = new FileOutputStream(new File("/tmp/encodedHeader.7z"));
+//        fos.write(archive.folders[0].coders[0].properties);
+//        // size - assuming < 256
+//        fos.write((int)(unpackSize & 0xff));
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(packed);
+//        fos.close();
+    }
+    
+    private void readStreamsInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("StreamsInfo");
+        
+        int nid = header.readUnsignedByte();
+        
+        if (nid == NID.kPackInfo) {
+            readPackInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kUnpackInfo) {
+            readUnpackInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kSubStreamsInfo) {
+            readSubStreamsInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated StreamsInfo");
+        }
+    }
+    
+    private void readPackInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("PackInfo");
+        
+        archive.packPos = readUint64(header);
+        final long numPackStreams = readUint64(header);
+        debug("  " + numPackStreams + " pack streams");
+        
+        int nid = header.readUnsignedByte();
+        if (nid == NID.kSize) {
+            archive.packSizes = new long[(int)numPackStreams];
+            for (int i = 0; i < archive.packSizes.length; i++) {
+                archive.packSizes[i] = readUint64(header);
+                debug("  pack size %d is %d\n", i, archive.packSizes[i]);
+            }
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kCRC) {
+            archive.packCrcsDefined = readAllOrBits(header, (int)numPackStreams);
+            archive.packCrcs = new int[(int)numPackStreams];
+            for (int i = 0; i < (int)numPackStreams; i++) {
+                if (archive.packCrcsDefined.get(i)) {
+                    archive.packCrcs[i] = Integer.reverseBytes(header.readInt());
+                }
+            }
+            
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated PackInfo (" + nid + ")");
+        }
+    }
+    
+    private void readUnpackInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("UnpackInfo");
+
+        int nid = header.readUnsignedByte();
+        if (nid != NID.kFolder) {
+            throw new IOException("Expected kFolder, got " + nid);
+        }
+        final long numFolders = readUint64(header);
+        debug("  " + numFolders + " folders");
+        final Folder[] folders = new Folder[(int)numFolders];
+        archive.folders = folders;
+        final int external = header.readUnsignedByte();
+        if (external != 0) {
+            throw new IOException("External unsupported");
+        } else {
+            for (int i = 0; i < (int)numFolders; i++) {
+                folders[i] = readFolder(header);
+            }
+        }
+        
+        nid = header.readUnsignedByte();
+        if (nid != NID.kCodersUnpackSize) {
+            throw new IOException("Expected kCodersUnpackSize, got " + nid);
+        }
+        for (final Folder folder : folders) {
+            folder.unpackSizes = new long[(int)folder.totalOutputStreams];
+            for (int i = 0; i < folder.totalOutputStreams; i++) {
+                folder.unpackSizes[i] = readUint64(header);
+            }
+        }
+        
+        nid = header.readUnsignedByte();
+        if (nid == NID.kCRC) {
+            final BitSet crcsDefined = readAllOrBits(header, (int)numFolders);
+            for (int i = 0; i < (int)numFolders; i++) {
+                if (crcsDefined.get(i)) {
+                    folders[i].hasCrc = true;
+                    folders[i].crc = Integer.reverseBytes(header.readInt());
+                } else {
+                    folders[i].hasCrc = false;
+                }
+            }
+            
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated UnpackInfo");
+        }
+    }
+    
+    private void readSubStreamsInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("SubStreamsInfo");
+        
+        for (final Folder folder : archive.folders) {
+            folder.numUnpackSubStreams = 1;
+        }
+        int totalUnpackStreams = archive.folders.length;
+        
+        int nid = header.readUnsignedByte();
+        if (nid == NID.kNumUnpackStream) {
+            totalUnpackStreams = 0;
+            for (final Folder folder : archive.folders) {
+                final long numStreams = readUint64(header);
+                folder.numUnpackSubStreams = (int)numStreams;
+                totalUnpackStreams += numStreams;
+            }
+            nid = header.readUnsignedByte();
+        }
+        
+        final SubStreamsInfo subStreamsInfo = new SubStreamsInfo();
+        subStreamsInfo.unpackSizes = new long[totalUnpackStreams];
+        subStreamsInfo.hasCrc = new BitSet(totalUnpackStreams);
+        subStreamsInfo.crcs = new int[totalUnpackStreams];
+        
+        int nextUnpackStream = 0;
+        for (final Folder folder : archive.folders) {
+            if (folder.numUnpackSubStreams == 0) {
+                continue;
+            }
+            long sum = 0;
+            if (nid == NID.kSize) {
+                for (int i = 0; i < (folder.numUnpackSubStreams - 1); i++) {
+                    final long size = readUint64(header);
+                    subStreamsInfo.unpackSizes[nextUnpackStream++] = size;
+                    sum += size;
+                }
+            }
+            subStreamsInfo.unpackSizes[nextUnpackStream++] = folder.getUnpackSize() - sum;
+        }
+        if (nid == NID.kSize) {
+            nid = header.readUnsignedByte();
+        }
+        
+        int numDigests = 0;
+        for (final Folder folder : archive.folders) {
+            if (folder.numUnpackSubStreams != 1 || !folder.hasCrc) {
+                numDigests += folder.numUnpackSubStreams;
+            }
+        }
+        
+        if (nid == NID.kCRC) {
+            final BitSet hasMissingCrc = readAllOrBits(header, numDigests);
+            final int[] missingCrcs = new int[numDigests];
+            for (int i = 0; i < numDigests; i++) {
+                if (hasMissingCrc.get(i)) {
+                    missingCrcs[i] = Integer.reverseBytes(header.readInt());
+                }
+            }
+            int nextCrc = 0;
+            int nextMissingCrc = 0;
+            for (final Folder folder: archive.folders) {
+                if (folder.numUnpackSubStreams == 1 && folder.hasCrc) {
+                    subStreamsInfo.hasCrc.set(nextCrc, true);
+                    subStreamsInfo.crcs[nextCrc] = folder.crc;
+                    ++nextCrc;
+                } else {
+                    for (int i = 0; i < folder.numUnpackSubStreams; i++) {
+                        subStreamsInfo.hasCrc.set(nextCrc, hasMissingCrc.get(nextMissingCrc));
+                        subStreamsInfo.crcs[nextCrc] = missingCrcs[nextMissingCrc];
+                        ++nextCrc;
+                        ++nextMissingCrc;
+                    }
+                }
+            }
+            
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated SubStreamsInfo");
+        }
+        
+        archive.subStreamsInfo = subStreamsInfo;
+    }
+    
+    private Folder readFolder(final DataInput header) throws IOException {
+        final Folder folder = new Folder();
+        
+        final long numCoders = readUint64(header);
+        final Coder[] coders = new Coder[(int)numCoders];
+        long totalInStreams = 0;
+        long totalOutStreams = 0;
+        for (int i = 0; i < coders.length; i++) {
+            coders[i] = new Coder();
+            int bits = header.readUnsignedByte();
+            final int idSize = bits & 0xf;
+            final boolean isSimple = ((bits & 0x10) == 0);
+            final boolean hasAttributes = ((bits & 0x20) != 0);
+            final boolean moreAlternativeMethods = ((bits & 0x80) != 0);
+            
+            coders[i].decompressionMethodId = new byte[idSize];
+            header.readFully(coders[i].decompressionMethodId);
+            if (isSimple) {
+                coders[i].numInStreams = 1;
+                coders[i].numOutStreams = 1;
+            } else {
+                coders[i].numInStreams = readUint64(header);
+                coders[i].numOutStreams = readUint64(header);
+            }
+            totalInStreams += coders[i].numInStreams;
+            totalOutStreams += coders[i].numOutStreams;
+            if (hasAttributes) {
+                final long propertiesSize = readUint64(header);
+                coders[i].properties = new byte[(int)propertiesSize];
+                header.readFully(coders[i].properties);
+            }
+            if (DEBUG) {
+                final StringBuilder methodStr = new StringBuilder();
+                for (final byte b : coders[i].decompressionMethodId) {
+                    methodStr.append(String.format("%02X", 0xff & b));
+                }
+                debug("  coder entry %d numInStreams=%d, numOutStreams=%d, method=%s, properties=%s\n", i,
+                        coders[i].numInStreams, coders[i].numOutStreams, methodStr.toString(),
+                        Arrays.toString(coders[i].properties));
+            }
+            // would need to keep looping as above:
+            while (moreAlternativeMethods) {
+                throw new IOException("Alternative methods are unsupported, please report. " +
+                        "The reference implementation doesn't support them either.");
+            }
+        }
+        folder.coders = coders;
+        folder.totalInputStreams = totalInStreams;
+        folder.totalOutputStreams = totalOutStreams;
+        
+        if (totalOutStreams == 0) {
+            throw new IOException("Total output streams can't be 0");
+        }
+        final long numBindPairs = totalOutStreams - 1;
+        final BindPair[] bindPairs = new BindPair[(int)numBindPairs];
+        for (int i = 0; i < bindPairs.length; i++) {
+            bindPairs[i] = new BindPair();
+            bindPairs[i].inIndex = readUint64(header);
+            bindPairs[i].outIndex = readUint64(header);
+            debug("  bind pair in=%d out=%d\n", bindPairs[i].inIndex, bindPairs[i].outIndex);
+        }
+        folder.bindPairs = bindPairs;
+        
+        if (totalInStreams < numBindPairs) {
+            throw new IOException("Total input streams can't be less than the number of bind pairs");
+        }
+        final long numPackedStreams = totalInStreams - numBindPairs;
+        final long packedStreams[] = new long[(int)numPackedStreams];
+        if (numPackedStreams == 1) {
+            int i;
+            for (i = 0; i < (int)totalInStreams; i++) {
+                if (folder.findBindPairForInStream(i) < 0) {
+                    break;
+                }
+            }
+            if (i == (int)totalInStreams) {
+                throw new IOException("Couldn't find stream's bind pair index");
+            }
+            packedStreams[0] = i;
+        } else {
+            for (int i = 0; i < (int)numPackedStreams; i++) {
+                packedStreams[i] = readUint64(header);
+            }
+        }
+        folder.packedStreams = packedStreams;
+        
+        return folder;
+    }
+    
+    private BitSet readAllOrBits(final DataInput header, final int size) throws IOException {
+        final int areAllDefined = header.readUnsignedByte();
+        final BitSet bits;
+        if (areAllDefined != 0) {
+            bits = new BitSet(size);
+            for (int i = 0; i < size; i++) {
+                bits.set(i, true);
+            }
+        } else {
+            bits = readBits(header, size);
+        }
+        return bits;
+    }
+    
+    private BitSet readBits(final DataInput header, final int size) throws IOException {
+        final BitSet bits = new BitSet(size);
+        int mask = 0;
+        int cache = 0;
+        for (int i = 0; i < size; i++) {
+            if (mask == 0) {
+                mask = 0x80;
+                cache = header.readUnsignedByte();
+            }
+            bits.set(i, (cache & mask) != 0);
+            mask >>>= 1;
+        }
+        return bits;
+    }
+    
+    private void readFilesInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("FilesInfo");
+
+        final long numFiles = readUint64(header);
+        final SevenZArchiveEntry[] files = new SevenZArchiveEntry[(int)numFiles];
+        for (int i = 0; i < files.length; i++) {
+            files[i] = new SevenZArchiveEntry();
+        }
+        BitSet isEmptyStream = null;
+        BitSet isEmptyFile = null; 
+        BitSet isAnti = null;
+        while (true) {
+            final int propertyType = header.readUnsignedByte();
+            if (propertyType == 0) {
+                break;
+            }
+            long size = readUint64(header);
+            switch (propertyType) {
+                case NID.kEmptyStream: {
+                    debug("  kEmptyStream");
+                    isEmptyStream = readBits(header, files.length);
+                    break;
+                }
+                case NID.kEmptyFile: {
+                    debug("  kEmptyFile");
+                    if (isEmptyStream == null) { // protect against NPE
+                        throw new IOException("Header format error: kEmptyStream must appear before kEmptyFile");
+                    }
+                    isEmptyFile = readBits(header, isEmptyStream.cardinality());
+                    break;
+                }
+                case NID.kAnti: {
+                    debug("  kAnti");
+                    if (isEmptyStream == null) { // protect against NPE
+                        throw new IOException("Header format error: kEmptyStream must appear before kAnti");
+                    }
+                    isAnti = readBits(header, isEmptyStream.cardinality());
+                    break;
+                }
+                case NID.kName: {
+                    debug("  kNames");
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Not implemented");
+                    } else {
+                        if (((size - 1) & 1) != 0) {
+                            throw new IOException("File names length invalid");
+                        }
+                        final byte[] names = new byte[(int)(size - 1)];
+                        header.readFully(names);
+                        int nextFile = 0;
+                        int nextName = 0;
+                        for (int i = 0; i < names.length; i += 2) {
+                            if (names[i] == 0 && names[i+1] == 0) {
+                                files[nextFile++].setName(new String(names, nextName, i-nextName, "UTF-16LE"));
+                                nextName = i + 2;
+                            }
+                        }
+                        if (nextName != names.length || nextFile != files.length) {
+                            throw new IOException("Error parsing file names");
+                        }
+                    }
+                    break;
+                }
+                case NID.kCTime: {
+                    debug("  kCreationTime");
+                    final BitSet timesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasCreationDate(timesDefined.get(i));
+                            if (files[i].getHasCreationDate()) {
+                                files[i].setCreationDate(Long.reverseBytes(header.readLong()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kATime: {
+                    debug("  kLastAccessTime");
+                    final BitSet timesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasAcessDate(timesDefined.get(i));
+                            if (files[i].getHasAcessDate()) {
+                                files[i].setAccessDate(Long.reverseBytes(header.readLong()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kMTime: {
+                    debug("  kLastWriteTime");
+                    final BitSet timesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasLastModifiedDate(timesDefined.get(i));
+                            if (files[i].getHasLastModifiedDate()) {
+                                files[i].setLastModifiedDate(Long.reverseBytes(header.readLong()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kWinAttributes: {
+                    debug("  kWinAttributes");
+                    final BitSet attributesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasWindowsAttributes(attributesDefined.get(i));
+                            if (files[i].getHasWindowsAttributes()) {
+                                files[i].setWindowsAttributes(Integer.reverseBytes(header.readInt()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kStartPos: {
+                    debug("  kStartPos");
+                    throw new IOException("kStartPos is unsupported, please report");
+                }
+                case NID.kDummy: {
+                    debug("  kDummy");
+                    throw new IOException("kDummy is unsupported, please report");
+                }
+                
+                default: {
+                    throw new IOException("Unknown property " + propertyType);
+                    // FIXME: Should actually:
+                    //header.skipBytes((int)size);
+                }
+            }
+        }
+        int nonEmptyFileCounter = 0;
+        int emptyFileCounter = 0;
+        for (int i = 0; i < files.length; i++) {
+            files[i].setHasStream((isEmptyStream == null) ? true : !isEmptyStream.get(i));
+            if (files[i].hasStream()) {
+                files[i].setDirectory(false);
+                files[i].setAntiItem(false);
+                files[i].setHasCrc(archive.subStreamsInfo.hasCrc.get(nonEmptyFileCounter));
+                files[i].setCrc(archive.subStreamsInfo.crcs[nonEmptyFileCounter]);
+                files[i].setSize(archive.subStreamsInfo.unpackSizes[nonEmptyFileCounter]);
+                ++nonEmptyFileCounter;
+            } else {
+                files[i].setDirectory((isEmptyFile == null) ? true : !isEmptyFile.get(emptyFileCounter));
+                files[i].setAntiItem((isAnti == null) ? false : isAnti.get(emptyFileCounter));
+                files[i].setHasCrc(false);
+                files[i].setSize(0);
+                ++emptyFileCounter;
+            }
+        }
+        archive.files = files;
+        calculateStreamMap(archive);
+    }
+    
+    private void calculateStreamMap(final Archive archive) throws IOException {
+        final StreamMap streamMap = new StreamMap();
+        
+        int nextFolderPackStreamIndex = 0;
+        final int numFolders = (archive.folders != null) ? archive.folders.length : 0;
+        streamMap.folderFirstPackStreamIndex = new int[numFolders];
+        for (int i = 0; i < numFolders; i++) {
+            streamMap.folderFirstPackStreamIndex[i] = nextFolderPackStreamIndex;
+            nextFolderPackStreamIndex += archive.folders[i].packedStreams.length;
+        }
+        
+        long nextPackStreamOffset = 0;
+        final int numPackSizes = (archive.packSizes != null) ? archive.packSizes.length : 0;
+        streamMap.packStreamOffsets = new long[numPackSizes];
+        for (int i = 0; i < numPackSizes; i++) {
+            streamMap.packStreamOffsets[i] = nextPackStreamOffset;
+            nextPackStreamOffset += archive.packSizes[i]; 
+        }
+        
+        streamMap.folderFirstFileIndex = new int[numFolders];
+        streamMap.fileFolderIndex = new int[archive.files.length];
+        int nextFolderIndex = 0;
+        int nextFolderUnpackStreamIndex = 0;
+        for (int i = 0; i < archive.files.length; i++) {
+            if (!archive.files[i].hasStream() && nextFolderUnpackStreamIndex == 0) {
+                streamMap.fileFolderIndex[i] = -1;
+                continue;
+            }
+            if (nextFolderUnpackStreamIndex == 0) {
+                for (; nextFolderIndex < archive.folders.length; ++nextFolderIndex) {
+                    streamMap.folderFirstFileIndex[nextFolderIndex] = i;
+                    if (archive.folders[nextFolderIndex].numUnpackSubStreams > 0) {
+                        break;
+                    }
+                }
+                if (nextFolderIndex >= archive.folders.length) {
+                    throw new IOException("Too few folders in archive");
+                }
+            }
+            streamMap.fileFolderIndex[i] = nextFolderIndex;
+            if (!archive.files[i].hasStream()) {
+                continue;
+            }
+            ++nextFolderUnpackStreamIndex;
+            if (nextFolderUnpackStreamIndex >= archive.folders[nextFolderIndex].numUnpackSubStreams) {
+                ++nextFolderIndex;
+                nextFolderUnpackStreamIndex = 0;
+            }
+        }
+        
+        archive.streamMap = streamMap;
+    }
+    
+    private void buildDecodingStream() throws IOException {
+        final int folderIndex = archive.streamMap.fileFolderIndex[currentEntryIndex];
+        if (folderIndex < 0) {
+            currentEntryInputStream = new BoundedInputStream(
+                    new ByteArrayInputStream(new byte[0]), 0);
+            return;
+        }
+        if (currentFolderIndex == folderIndex) {
+            // need to advance the folder input stream past the current file
+            drainPreviousEntry();
+        } else {
+            currentFolderIndex = folderIndex;
+            if (currentFolderInputStream != null) {
+                currentFolderInputStream.close();
+                currentFolderInputStream = null;
+            }
+            
+            final Folder folder = archive.folders[folderIndex];
+            final int firstPackStreamIndex = archive.streamMap.folderFirstPackStreamIndex[folderIndex];
+            final long folderOffset = SIGNATURE_HEADER_SIZE + archive.packPos +
+                    archive.streamMap.packStreamOffsets[firstPackStreamIndex];
+            currentFolderInputStream = buildDecoderStack(folder, folderOffset, firstPackStreamIndex);
+        }
+        final SevenZArchiveEntry file = archive.files[currentEntryIndex];
+        final InputStream fileStream = new BoundedInputStream(
+                currentFolderInputStream, file.getSize());
+        if (file.getHasCrc()) {
+            currentEntryInputStream = new CRC32VerifyingInputStream(
+                    fileStream, file.getSize(), file.getCrc());
+        } else {
+            currentEntryInputStream = fileStream;
+        }
+        
+    }
+    
+    private void drainPreviousEntry() throws IOException {
+        if (currentEntryInputStream != null) {
+            final byte[] buffer = new byte[64*1024];
+            while (currentEntryInputStream.read(buffer) >= 0) { // NOPMD
+            }
+            currentEntryInputStream.close();
+            currentEntryInputStream = null;
+        }
+    }
+    
+    private InputStream buildDecoderStack(final Folder folder, final long folderOffset,
+            final int firstPackStreamIndex) throws IOException {
+        file.seek(folderOffset);
+        InputStream inputStreamStack = new BoundedRandomAccessFileInputStream(file,
+                archive.packSizes[firstPackStreamIndex]);
+        for (final Coder coder : folder.coders) {
+            if (coder.numInStreams != 1 || coder.numOutStreams != 1) {
+                throw new IOException("Multi input/output stream coders are not yet supported");
+            }
+            inputStreamStack = Coders.addDecoder(inputStreamStack, coder, password);
+        }
+        if (folder.hasCrc) {
+            return new CRC32VerifyingInputStream(inputStreamStack,
+                    folder.getUnpackSize(), folder.crc);
+        } else {
+            return inputStreamStack;
+        }
+    }
+    
+    public int read() throws IOException {
+        return currentEntryInputStream.read();
+    }
+    
+    public int read(byte[] b) throws IOException {
+        return read(b, 0, b.length);
+    }
+    
+    public int read(byte[] b, int off, int len) throws IOException {
+        return currentEntryInputStream.read(b, off, len);
+    }
+    
+    private static long readUint64(final DataInput in) throws IOException {
+        int firstByte = in.readUnsignedByte();
+        int mask = 0x80;
+        int value = 0;
+        for (int i = 0; i < 8; i++) {
+            if ((firstByte & mask) == 0) {
+                return value | ((firstByte & (mask - 1)) << (8 * i));
+            }
+            int nextByte = in.readUnsignedByte();
+            value |= (nextByte << (8 * i));
+            mask >>>= 1;
+        }
+        return value;
+    }
+    
+    private static class BoundedInputStream extends InputStream {
+        private final InputStream in;
+        private long bytesRemaining;
+        
+        public BoundedInputStream(final InputStream in, final long size) {
+            this.in = in;
+            bytesRemaining = size;
+        }
+        
+        @Override
+        public int read() throws IOException {
+            if (bytesRemaining > 0) {
+                --bytesRemaining;
+                return in.read();
+            } else {
+                return -1;
+            }
+        }
+
+        @Override
+        public int read(byte[] b, int off, int len) throws IOException {
+            if (bytesRemaining == 0) {
+                return -1;
+            }
+            int bytesToRead = len;
+            if (bytesToRead > bytesRemaining) {
+                bytesToRead = (int) bytesRemaining;
+            }
+            final int bytesRead = in.read(b, off, bytesToRead);
+            if (bytesRead >= 0) {
+                bytesRemaining -= bytesRead;
+            }
+            return bytesRead;
+        }
+
+        @Override
+        public void close() {
+        }
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/prevFiles/prev_d8ca98_2ed556_src#main#java#org#apache#commons#compress#archivers#sevenz#AES256SHA256Decoder.java

@@ -0,0 +1,118 @@
+/*
+ *  Licensed to the Apache Software Foundation (ASF) under one or more
+ *  contributor license agreements.  See the NOTICE file distributed with
+ *  this work for additional information regarding copyright ownership.
+ *  The ASF licenses this file to You under the Apache License, Version 2.0
+ *  (the "License"); you may not use this file except in compliance with
+ *  the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ */
+package org.apache.commons.compress.archivers.sevenz;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.security.GeneralSecurityException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import javax.crypto.Cipher;
+import javax.crypto.CipherInputStream;
+import javax.crypto.SecretKey;
+import javax.crypto.spec.IvParameterSpec;
+import javax.crypto.spec.SecretKeySpec;
+import org.apache.commons.compress.PasswordRequiredException;
+
+class AES256SHA256Decoder extends CoderBase {
+    @Override
+    InputStream decode(final String archiveName, final InputStream in, final long uncompressedLength,
+            final Coder coder, final byte[] passwordBytes, int maxMemoryLimitInKb) throws IOException {
+        return new InputStream() {
+            private boolean isInitialized = false;
+            private CipherInputStream cipherInputStream = null;
+
+            private CipherInputStream init() throws IOException {
+                if (isInitialized) {
+                    return cipherInputStream;
+                }
+                final int byte0 = 0xff & coder.properties[0];
+                final int numCyclesPower = byte0 & 0x3f;
+                final int byte1 = 0xff & coder.properties[1];
+                final int ivSize = ((byte0 >> 6) & 1) + (byte1 & 0x0f);
+                final int saltSize = ((byte0 >> 7) & 1) + (byte1 >> 4);
+                if (2 + saltSize + ivSize > coder.properties.length) {
+                    throw new IOException("Salt size + IV size too long in " + archiveName);
+                }
+                final byte[] salt = new byte[saltSize];
+                System.arraycopy(coder.properties, 2, salt, 0, saltSize);
+                final byte[] iv = new byte[16];
+                System.arraycopy(coder.properties, 2 + saltSize, iv, 0, ivSize);
+
+                if (passwordBytes == null) {
+                    throw new PasswordRequiredException(archiveName);
+                }
+                final byte[] aesKeyBytes;
+                if (numCyclesPower == 0x3f) {
+                    aesKeyBytes = new byte[32];
+                    System.arraycopy(salt, 0, aesKeyBytes, 0, saltSize);
+                    System.arraycopy(passwordBytes, 0, aesKeyBytes, saltSize,
+                                     Math.min(passwordBytes.length, aesKeyBytes.length - saltSize));
+                } else {
+                    final MessageDigest digest;
+                    try {
+                        digest = MessageDigest.getInstance("SHA-256");
+                    } catch (final NoSuchAlgorithmException noSuchAlgorithmException) {
+                        throw new IOException("SHA-256 is unsupported by your Java implementation",
+                            noSuchAlgorithmException);
+                    }
+                    final byte[] extra = new byte[8];
+                    for (long j = 0; j < (1L << numCyclesPower); j++) {
+                        digest.update(salt);
+                        digest.update(passwordBytes);
+                        digest.update(extra);
+                        for (int k = 0; k < extra.length; k++) {
+                            ++extra[k];
+                            if (extra[k] != 0) {
+                                break;
+                            }
+                        }
+                    }
+                    aesKeyBytes = digest.digest();
+                }
+
+                final SecretKey aesKey = new SecretKeySpec(aesKeyBytes, "AES");
+                try {
+                    final Cipher cipher = Cipher.getInstance("AES/CBC/NoPadding");
+                    cipher.init(Cipher.DECRYPT_MODE, aesKey, new IvParameterSpec(iv));
+                    cipherInputStream = new CipherInputStream(in, cipher);
+                    isInitialized = true;
+                    return cipherInputStream;
+                } catch (final GeneralSecurityException generalSecurityException) {
+                    throw new IOException("Decryption error " +
+                        "(do you have the JCE Unlimited Strength Jurisdiction Policy Files installed?)",
+                        generalSecurityException);
+                    }
+            }
+
+            @Override
+            public int read() throws IOException {
+                return init().read();
+            }
+
+            @Override
+            public int read(final byte[] b, final int off, final int len) throws IOException {
+                return init().read(b, off, len);
+            }
+
+            @Override
+            public void close() {
+            }
+        };
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/revFiles/4ac67b_0eccda_src#main#java#org#apache#commons#compress#compressors#snappy#SnappyCompressorInputStream.java

@@ -0,0 +1,286 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.commons.compress.compressors.snappy;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.commons.compress.compressors.lz77support.AbstractLZ77CompressorInputStream;
+import org.apache.commons.compress.utils.ByteUtils;
+
+/**
+ * CompressorInputStream for the raw Snappy format.
+ *
+ * <p>This implementation uses an internal buffer in order to handle
+ * the back-references that are at the heart of the LZ77 algorithm.
+ * The size of the buffer must be at least as big as the biggest
+ * offset used in the compressed stream.  The current version of the
+ * Snappy algorithm as defined by Google works on 32k blocks and
+ * doesn't contain offsets bigger than 32k which is the default block
+ * size used by this class.</p>
+ *
+ * @see <a href="https://github.com/google/snappy/blob/master/format_description.txt">Snappy compressed format description</a>
+ * @since 1.7
+ */
+public class SnappyCompressorInputStream extends AbstractLZ77CompressorInputStream {
+
+    /** Mask used to determine the type of "tag" is being processed */
+    private static final int TAG_MASK = 0x03;
+
+    /** Default block size */
+    public static final int DEFAULT_BLOCK_SIZE = 32768;
+
+    /** The size of the uncompressed data */
+    private final int size;
+
+    /** Number of uncompressed bytes still to be read. */
+    private int uncompressedBytesRemaining;
+
+    /** Current state of the stream */
+    private State state = State.NO_BLOCK;
+
+    private boolean endReached = false;
+
+    /**
+     * Constructor using the default buffer size of 32k.
+     * 
+     * @param is
+     *            An InputStream to read compressed data from
+     * 
+     * @throws IOException if reading fails
+     */
+    public SnappyCompressorInputStream(final InputStream is) throws IOException {
+        this(is, DEFAULT_BLOCK_SIZE);
+    }
+
+    /**
+     * Constructor using a configurable buffer size.
+     * 
+     * @param is
+     *            An InputStream to read compressed data from
+     * @param blockSize
+     *            The block size used in compression
+     * 
+     * @throws IOException if reading fails
+     */
+    public SnappyCompressorInputStream(final InputStream is, final int blockSize)
+            throws IOException {
+        super(is, blockSize);
+        uncompressedBytesRemaining = size = (int) readSize();
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public int read(final byte[] b, final int off, final int len) throws IOException {
+        if (endReached) {
+            return -1;
+        }
+        switch (state) {
+        case NO_BLOCK:
+            fill();
+            return read(b, off, len);
+        case IN_LITERAL:
+            int litLen = readLiteral(b, off, len);
+            if (!hasMoreDataInBlock()) {
+                state = State.NO_BLOCK;
+            }
+            return litLen > 0 ? litLen : read(b, off, len);
+        case IN_BACK_REFERENCE:
+            int backReferenceLen = readBackReference(b, off, len);
+            if (!hasMoreDataInBlock()) {
+                state = State.NO_BLOCK;
+            }
+            return backReferenceLen > 0 ? backReferenceLen : read(b, off, len);
+        default:
+            throw new IOException("Unknown stream state " + state);
+        }
+    }
+
+    /**
+     * Try to fill the buffer with the next block of data.
+     */
+    private void fill() throws IOException {
+        if (uncompressedBytesRemaining == 0) {
+            endReached = true;
+            return;
+        }
+
+        int b = readOneByte();
+        if (b == -1) {
+            throw new IOException("Premature end of stream reading block start");
+        }
+        int length = 0;
+        int offset = 0;
+
+        switch (b & TAG_MASK) {
+
+        case 0x00:
+
+            length = readLiteralLength(b);
+            uncompressedBytesRemaining -= length;
+            startLiteral(length);
+            state = State.IN_LITERAL;
+            break;
+
+        case 0x01:
+
+            /*
+             * These elements can encode lengths between [4..11] bytes and
+             * offsets between [0..2047] bytes. (len-4) occupies three bits
+             * and is stored in bits [2..4] of the tag byte. The offset
+             * occupies 11 bits, of which the upper three are stored in the
+             * upper three bits ([5..7]) of the tag byte, and the lower
+             * eight are stored in a byte following the tag byte.
+             */
+
+            length = 4 + ((b >> 2) & 0x07);
+            uncompressedBytesRemaining -= length;
+            offset = (b & 0xE0) << 3;
+            b = readOneByte();
+            if (b == -1) {
+                throw new IOException("Premature end of stream reading back-reference length");
+            }
+            offset |= b;
+
+            startBackReference(offset, length);
+            state = State.IN_BACK_REFERENCE;
+            break;
+
+        case 0x02:
+
+            /*
+             * These elements can encode lengths between [1..64] and offsets
+             * from [0..65535]. (len-1) occupies six bits and is stored in
+             * the upper six bits ([2..7]) of the tag byte. The offset is
+             * stored as a little-endian 16-bit integer in the two bytes
+             * following the tag byte.
+             */
+
+            length = (b >> 2) + 1;
+            uncompressedBytesRemaining -= length;
+
+            offset = (int) ByteUtils.fromLittleEndian(supplier, 2);
+
+            startBackReference(offset, length);
+            state = State.IN_BACK_REFERENCE;
+            break;
+
+        case 0x03:
+
+            /*
+             * These are like the copies with 2-byte offsets (see previous
+             * subsection), except that the offset is stored as a 32-bit
+             * integer instead of a 16-bit integer (and thus will occupy
+             * four bytes).
+             */
+
+            length = (b >> 2) + 1;
+            uncompressedBytesRemaining -= length;
+
+            offset = (int) ByteUtils.fromLittleEndian(supplier, 4) & 0x7fffffff;
+
+            startBackReference(offset, length);
+            state = State.IN_BACK_REFERENCE;
+            break;
+        default:
+            // impossible as TAG_MASK is two bits and all four possible cases have been covered
+            break;
+        }
+    }
+
+    /*
+     * For literals up to and including 60 bytes in length, the
+     * upper six bits of the tag byte contain (len-1). The literal
+     * follows immediately thereafter in the bytestream. - For
+     * longer literals, the (len-1) value is stored after the tag
+     * byte, little-endian. The upper six bits of the tag byte
+     * describe how many bytes are used for the length; 60, 61, 62
+     * or 63 for 1-4 bytes, respectively. The literal itself follows
+     * after the length.
+     */
+    private int readLiteralLength(final int b) throws IOException {
+        int length;
+        switch (b >> 2) {
+        case 60:
+            length = readOneByte();
+            if (length == -1) {
+                throw new IOException("Premature end of stream reading literal length");
+            }
+            break;
+        case 61:
+            length = (int) ByteUtils.fromLittleEndian(supplier, 2);
+            break;
+        case 62:
+            length = (int) ByteUtils.fromLittleEndian(supplier, 3);
+            break;
+        case 63:
+            length = (int) ByteUtils.fromLittleEndian(supplier, 4);
+            break;
+        default:
+            length = b >> 2;
+            break;
+        }
+
+        return length + 1;
+    }
+
+    /**
+     * The stream starts with the uncompressed length (up to a maximum of 2^32 -
+     * 1), stored as a little-endian varint. Varints consist of a series of
+     * bytes, where the lower 7 bits are data and the upper bit is set iff there
+     * are more bytes to be read. In other words, an uncompressed length of 64
+     * would be stored as 0x40, and an uncompressed length of 2097150 (0x1FFFFE)
+     * would be stored as 0xFE 0xFF 0x7F.
+     * 
+     * @return The size of the uncompressed data
+     * 
+     * @throws IOException
+     *             Could not read a byte
+     */
+    private long readSize() throws IOException {
+        int index = 0;
+        long sz = 0;
+        int b = 0;
+
+        do {
+            b = readOneByte();
+            if (b == -1) {
+                throw new IOException("Premature end of stream reading size");
+            }
+            sz |= (b & 0x7f) << (index++ * 7);
+        } while (0 != (b & 0x80));
+        return sz;
+    }
+
+    /**
+     * Get the uncompressed size of the stream
+     * 
+     * @return the uncompressed size
+     */
+    @Override
+    public int getSize() {
+        return size;
+    }
+
+    private enum State {
+        NO_BLOCK, IN_LITERAL, IN_BACK_REFERENCE
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/revFiles/5273bd_c25c8d_src#main#java#org#apache#commons#compress#archivers#sevenz#Coders.java

@@ -0,0 +1,217 @@
+/*
+ *  Licensed to the Apache Software Foundation (ASF) under one or more
+ *  contributor license agreements.  See the NOTICE file distributed with
+ *  this work for additional information regarding copyright ownership.
+ *  The ASF licenses this file to You under the Apache License, Version 2.0
+ *  (the "License"); you may not use this file except in compliance with
+ *  the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ */
+package org.apache.commons.compress.archivers.sevenz;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.security.GeneralSecurityException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.Arrays;
+
+import javax.crypto.Cipher;
+import javax.crypto.CipherInputStream;
+import javax.crypto.SecretKey;
+import javax.crypto.spec.IvParameterSpec;
+import javax.crypto.spec.SecretKeySpec;
+
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
+import org.tukaani.xz.LZMA2InputStream;
+
+class Coders {
+    static InputStream addDecoder(final InputStream is,
+            final Coder coder, final String password) throws IOException {
+        for (final CoderId coderId : coderTable) {
+            if (Arrays.equals(coderId.id, coder.decompressionMethodId)) {
+                return coderId.coder.decode(is, coder, password);
+            }
+        }
+        throw new IOException("Unsupported compression method " +
+                Arrays.toString(coder.decompressionMethodId));
+    }
+    
+    static CoderId[] coderTable = new CoderId[] {
+        new CoderId(new byte[] { (byte)0x00 }, new CopyDecoder()),
+        new CoderId(new byte[] { (byte)0x21 }, new LZMA2Decoder()),
+        // FIXME: gives corrupt output
+        //new CoderId(new byte[] { (byte)0x04, (byte)0x01, (byte)0x08 }, new DeflateDecoder()),
+        new CoderId(new byte[] { (byte)0x04, (byte)0x02, (byte)0x02 }, new BZIP2Decoder()),
+        new CoderId(new byte[] { (byte)0x06, (byte)0xf1, (byte)0x07, (byte)0x01 }, new AES256SHA256Decoder())
+    };
+    
+    static class CoderId {
+        CoderId(final byte[] id, final CoderBase coder) {
+            this.id = id;
+            this.coder = coder;
+        }
+
+        final byte[] id;
+        final CoderBase coder;
+    }
+    
+    static abstract class CoderBase {
+        abstract InputStream decode(final InputStream in, final Coder coder,
+                String password) throws IOException;
+    }
+    
+    static class CopyDecoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder,
+                String password) throws IOException {
+            return in; 
+        }
+    }
+    
+    static class LZMA2Decoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder,
+                String password) throws IOException {
+            final int dictionarySizeBits = 0xff & coder.properties[0];
+            if ((dictionarySizeBits & (~0x3f)) != 0) {
+                throw new IOException("Unsupported LZMA2 property bits");
+            }
+            if (dictionarySizeBits > 40) {
+                throw new IOException("Dictionary larger than 4GiB maximum size");
+            }
+            final int dictionarySize;
+            if (dictionarySizeBits == 40) {
+                dictionarySize = 0xFFFFffff;
+            } else {
+                dictionarySize = (2 | (dictionarySizeBits & 0x1)) << (dictionarySizeBits / 2 + 11);
+            }
+            return new LZMA2InputStream(in, dictionarySize);
+        }
+    }
+    
+//    static class DeflateDecoder extends CoderBase {
+//        @Override
+//        InputStream decode(final InputStream in, final Coder coder, final String password)
+//                throws IOException {
+//            System.out.println("deflate prop count = " + (coder.properties == null ? -1 : coder.properties.length));
+//            return new DeflaterInputStream(in, new Deflater(Deflater.DEFAULT_COMPRESSION, true));
+//            //return new GZIPInputStream(in);
+//        }
+//    }
+
+    static class BZIP2Decoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder, final String password)
+                throws IOException {
+            return new BZip2CompressorInputStream(in);
+        }
+    }
+
+    static class AES256SHA256Decoder extends CoderBase {
+        @Override
+        InputStream decode(final InputStream in, final Coder coder,
+                final String password) throws IOException {
+            return new InputStream() {
+                private boolean isInitialized = false;
+                private CipherInputStream cipherInputStream = null;
+                
+                private CipherInputStream init() throws IOException {
+                    if (isInitialized) {
+                        return cipherInputStream;
+                    }
+                    final int byte0 = 0xff & coder.properties[0];
+                    final int numCyclesPower = byte0 & 0x3f;
+                    final int byte1 = 0xff & coder.properties[1];
+                    final int ivSize = ((byte0 >> 6) & 1) + (byte1 & 0x0f);
+                    final int saltSize = ((byte0 >> 7) & 1) + (byte1 >> 4);
+                    //debug("numCyclesPower=" + numCyclesPower + ", saltSize=" + saltSize + ", ivSize=" + ivSize);
+                    if (2 + saltSize + ivSize > coder.properties.length) {
+                        throw new IOException("Salt size + IV size too long");
+                    }
+                    final byte[] salt = new byte[saltSize];
+                    System.arraycopy(coder.properties, 2, salt, 0, saltSize);
+                    final byte[] iv = new byte[16];
+                    System.arraycopy(coder.properties, 2 + saltSize, iv, 0, ivSize);
+                    
+                    if (password == null) {
+                        throw new IOException("Cannot read encrypted files without a password");
+                    }
+                    final byte[] passwordBytes = password.getBytes("UTF-16LE");
+                    final byte[] aesKeyBytes;
+                    if (numCyclesPower == 0x3f) {
+                        aesKeyBytes = new byte[32];
+                        System.arraycopy(salt, 0, aesKeyBytes, 0, saltSize);
+                        System.arraycopy(passwordBytes, 0, aesKeyBytes, saltSize,
+                                Math.min(passwordBytes.length, aesKeyBytes.length - saltSize));
+                    } else {
+                        final MessageDigest digest;
+                        try {
+                            digest = MessageDigest.getInstance("SHA-256");
+                        } catch (NoSuchAlgorithmException noSuchAlgorithmException) {
+                            IOException ioe = new IOException("SHA-256 is unsupported by your Java implementation");
+                            ioe.initCause(noSuchAlgorithmException);
+                            throw ioe;
+        // TODO: simplify when Compress requires Java 1.6                
+//                            throw new IOException("SHA-256 is unsupported by your Java implementation",
+//                                    noSuchAlgorithmException);
+                        }
+                        final byte[] extra = new byte[8];
+                        for (long j = 0; j < (1L << numCyclesPower); j++) {
+                            digest.update(salt);
+                            digest.update(passwordBytes);
+                            digest.update(extra);
+                            for (int k = 0; k < extra.length; k++) {
+                                ++extra[k];
+                                if (extra[k] != 0) {
+                                    break;
+                                }
+                            }
+                        }
+                        aesKeyBytes = digest.digest();
+                    }
+                    
+                    final SecretKey aesKey = new SecretKeySpec(aesKeyBytes, "AES");
+                    try {
+                        final Cipher cipher = Cipher.getInstance("AES/CBC/NoPadding");
+                        cipher.init(Cipher.DECRYPT_MODE, aesKey, new IvParameterSpec(iv));
+                        cipherInputStream = new CipherInputStream(in, cipher);
+                        isInitialized = true;
+                        return cipherInputStream;
+                    } catch (GeneralSecurityException generalSecurityException) {
+                        IOException ioe = new IOException("Decryption error " +
+                                "(do you have the JCE Unlimited Strength Jurisdiction Policy Files installed?)");
+                        ioe.initCause(generalSecurityException);
+                        throw ioe;
+        // TODO: simplify when Compress requires Java 1.6                
+//                        throw new IOException("Decryption error " +
+//                                "(do you have the JCE Unlimited Strength Jurisdiction Policy Files installed?)",
+//                                generalSecurityException);
+                    }
+                }
+                
+                @Override
+                public int read() throws IOException {
+                    return init().read();
+                }
+                
+                @Override
+                public int read(byte[] b, int off, int len) throws IOException {
+                    return init().read(b, off, len);
+                }
+                
+                @Override
+                public void close() {
+                }
+            };
+        }
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/revFiles/b7de91_5273bd_src#main#java#org#apache#commons#compress#archivers#sevenz#SevenZFile.java

@@ -0,0 +1,968 @@
+/*
+ *  Licensed to the Apache Software Foundation (ASF) under one or more
+ *  contributor license agreements.  See the NOTICE file distributed with
+ *  this work for additional information regarding copyright ownership.
+ *  The ASF licenses this file to You under the Apache License, Version 2.0
+ *  (the "License"); you may not use this file except in compliance with
+ *  the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ */
+package org.apache.commons.compress.archivers.sevenz;
+
+import java.io.ByteArrayInputStream;
+import java.io.DataInput;
+import java.io.DataInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.RandomAccessFile;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.zip.CRC32;
+
+import org.apache.commons.compress.utils.CRC32VerifyingInputStream;
+
+/**
+ * Reads a 7z file, using RandomAccessFile under
+ * the covers.
+ * <p>
+ * The 7z file format is a flexible container
+ * that can contain many compression and
+ * encryption types, but at the moment only
+ * only Copy, LZMA2, BZIP2, and AES-256 + SHA-256
+ * are supported, and archive header compression
+ * (when it uses the unsupported LZMA
+ * compression) isn't. So the only archives
+ * that can be read are the following:
+ * <pre>
+ * 7z a -mhc=off [-mhe=on] -mx=0 [-ppassword] archive.7z files
+ * 7z a -mhc=off [-mhe=on] -m0=LZMA2 [-ppassword] archive.7z files
+ * 7z a -mhc=off [-mhe=on] -m0=BZIP2 [-ppassword] archive.7z files
+ * </pre>
+ * <p>
+ * The format is very Windows/Intel specific,
+ * so it uses little-endian byte order,
+ * doesn't store user/group or permission bits,
+ * and represents times using NTFS timestamps
+ * (100 nanosecond units since 1 January 1601).
+ * Hence the official tools recommend against
+ * using it for backup purposes on *nix, and
+ * recommend .tar.7z or .tar.lzma or .tar.xz
+ * instead.  
+ * <p>
+ * Both the header and file contents may be
+ * compressed and/or encrypted. With both
+ * encrypted, neither file names nor file
+ * contents can be read, but the use of
+ * encryption isn't plausibly deniable.
+ * 
+ * @NotThreadSafe
+ */
+public class SevenZFile {
+    private static final boolean DEBUG = false;
+    private static final int SIGNATURE_HEADER_SIZE = 32;
+    private RandomAccessFile file;
+    private final Archive archive;
+    private int currentEntryIndex = -1;
+    private int currentFolderIndex = -1;
+    private InputStream currentFolderInputStream = null;
+    private InputStream currentEntryInputStream = null;
+    private String password;
+        
+    private static final byte[] sevenZSignature = {
+        (byte)'7', (byte)'z', (byte)0xBC, (byte)0xAF, (byte)0x27, (byte)0x1C
+    };
+    
+    public SevenZFile(final File filename, final String password) throws IOException {
+        boolean succeeded = false;
+        this.password = password;
+        this.file = new RandomAccessFile(filename, "r");
+        try {
+            archive = readHeaders();
+            succeeded = true;
+        } finally {
+            if (!succeeded) {
+                this.file.close();
+            }
+        }
+    }
+    
+    public SevenZFile(final File filename) throws IOException {
+        this(filename, null);
+    }
+
+    public void close() {
+        if (file != null) {
+            try {
+                file.close();
+            } catch (IOException ignored) { // NOPMD
+            }
+            file = null;
+        }
+    }
+    
+    private static void debug(String str) {
+        if (DEBUG) {
+            System.out.println(str);
+        }
+    }
+    
+    private static void debug(String fmt, Object... args) {
+        if (DEBUG) {
+            System.out.format(fmt, args);
+        }
+    }
+    
+    public SevenZArchiveEntry getNextEntry() throws IOException {
+        if (currentEntryIndex >= (archive.files.length - 1)) {
+            return null;
+        }
+        ++currentEntryIndex;
+        final SevenZArchiveEntry entry = archive.files[currentEntryIndex];
+        buildDecodingStream();
+        return entry;
+    }
+    
+    private Archive readHeaders() throws IOException {
+        debug("SignatureHeader");
+        
+        final byte[] signature = new byte[6];
+        file.readFully(signature);
+        if (!Arrays.equals(signature, sevenZSignature)) {
+            throw new IOException("Bad 7z signature");
+        }
+        // 7zFormat.txt has it wrong - it's first major then minor
+        final byte archiveVersionMajor = file.readByte();
+        final byte archiveVersionMinor = file.readByte();
+        debug("  archiveVersion major=%d, minor=%d\n",
+                archiveVersionMajor, archiveVersionMinor);
+        if (archiveVersionMajor != 0) {
+            throw new IOException(String.format("Unsupported 7z version (%d,%d)",
+                    archiveVersionMajor, archiveVersionMinor));
+        }
+
+        final int startHeaderCrc = Integer.reverseBytes(file.readInt());
+        final StartHeader startHeader = readStartHeader(startHeaderCrc);
+        
+        final int nextHeaderSizeInt = (int) startHeader.nextHeaderSize;
+        if (nextHeaderSizeInt != startHeader.nextHeaderSize) {
+            throw new IOException("cannot handle nextHeaderSize " + startHeader.nextHeaderSize);
+        }
+        file.seek(SIGNATURE_HEADER_SIZE + startHeader.nextHeaderOffset);
+        final byte[] nextHeader = new byte[nextHeaderSizeInt];
+        file.readFully(nextHeader);
+        final CRC32 crc = new CRC32();
+        crc.update(nextHeader);
+        if (startHeader.nextHeaderCrc != (int) crc.getValue()) {
+            throw new IOException("NextHeader CRC mismatch");
+        }
+        
+        final ByteArrayInputStream byteStream = new ByteArrayInputStream(nextHeader);
+        DataInputStream nextHeaderInputStream = new DataInputStream(
+                byteStream);
+        Archive archive = new Archive();
+        int nid = nextHeaderInputStream.readUnsignedByte();
+        if (nid == NID.kEncodedHeader) {
+            nextHeaderInputStream = readEncodedHeader(nextHeaderInputStream, archive);
+            // Archive gets rebuilt with the new header
+            archive = new Archive();
+            nid = nextHeaderInputStream.readUnsignedByte();
+        }
+        if (nid == NID.kHeader) {
+            readHeader(nextHeaderInputStream, archive);
+        } else {
+            throw new IOException("Broken or unsupported archive: no Header");
+        }
+        return archive;
+    }
+    
+    private StartHeader readStartHeader(final int startHeaderCrc) throws IOException {
+        final StartHeader startHeader = new StartHeader();
+        DataInputStream dataInputStream = null;
+        try {
+             dataInputStream = new DataInputStream(new CRC32VerifyingInputStream(
+                    new BoundedRandomAccessFileInputStream(file, 20), 20, startHeaderCrc));
+             startHeader.nextHeaderOffset = Long.reverseBytes(dataInputStream.readLong());
+             startHeader.nextHeaderSize = Long.reverseBytes(dataInputStream.readLong());
+             startHeader.nextHeaderCrc = Integer.reverseBytes(dataInputStream.readInt());
+             return startHeader;
+        } finally {
+            if (dataInputStream != null) {
+                dataInputStream.close();
+            }
+        }
+    }
+    
+    private void readHeader(final DataInput header, final Archive archive) throws IOException {
+        debug("Header");
+
+        int nid = header.readUnsignedByte();
+        
+        if (nid == NID.kArchiveProperties) {
+            readArchiveProperties(header);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kAdditionalStreamsInfo) {
+            throw new IOException("Additional streams unsupported");
+            //nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kMainStreamsInfo) {
+            readStreamsInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kFilesInfo) {
+            readFilesInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated header");
+        }
+    }
+    
+    private void readArchiveProperties(final DataInput input) throws IOException {
+        // FIXME: the reference implementation just throws them away?
+        debug("ArchiveProperties");
+
+        int nid =  input.readUnsignedByte();
+        while (nid != NID.kEnd) {
+            final long propertySize = readUint64(input);
+            final byte[] property = new byte[(int)propertySize];
+            input.readFully(property);
+            nid = input.readUnsignedByte();
+        }
+    }
+    
+    private DataInputStream readEncodedHeader(final DataInputStream header, final Archive archive) throws IOException {
+        debug("EncodedHeader");
+
+        readStreamsInfo(header, archive);
+        
+        // FIXME: merge with buildDecodingStream()/buildDecoderStack() at some stage?
+        final Folder folder = archive.folders[0];
+        final int firstPackStreamIndex = 0;
+        final long folderOffset = SIGNATURE_HEADER_SIZE + archive.packPos +
+                0;
+        
+        file.seek(folderOffset);
+        InputStream inputStreamStack = new BoundedRandomAccessFileInputStream(file,
+                archive.packSizes[firstPackStreamIndex]);
+        for (final Coder coder : folder.coders) {
+            if (coder.numInStreams != 1 || coder.numOutStreams != 1) {
+                throw new IOException("Multi input/output stream coders are not yet supported");
+            }
+            inputStreamStack = Coders.addDecoder(inputStreamStack, coder, password);
+        }
+        if (folder.hasCrc) {
+            inputStreamStack = new CRC32VerifyingInputStream(inputStreamStack,
+                    folder.getUnpackSize(), folder.crc);
+        }
+        final byte[] nextHeader = new byte[(int)folder.getUnpackSize()];
+        final DataInputStream nextHeaderInputStream = new DataInputStream(inputStreamStack);
+        try {
+            nextHeaderInputStream.readFully(nextHeader);
+        } finally {
+            nextHeaderInputStream.close();
+        }
+        return new DataInputStream(new ByteArrayInputStream(nextHeader));
+
+        
+        //throw new IOException("LZMA compression unsupported, so files with compressed header cannot be read");
+        // FIXME: this extracts the header to an LZMA file which can then be
+        // manually decompressed.
+//        long offset = SIGNATURE_HEADER_SIZE + archive.packPos;
+//        file.seek(offset);
+//        long unpackSize = archive.folders[0].getUnpackSize();
+//        byte[] packed = new byte[(int)archive.packSizes[0]];
+//        file.readFully(packed);
+//        
+//        FileOutputStream fos = new FileOutputStream(new File("/tmp/encodedHeader.7z"));
+//        fos.write(archive.folders[0].coders[0].properties);
+//        // size - assuming < 256
+//        fos.write((int)(unpackSize & 0xff));
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(0);
+//        fos.write(packed);
+//        fos.close();
+    }
+    
+    private void readStreamsInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("StreamsInfo");
+        
+        int nid = header.readUnsignedByte();
+        
+        if (nid == NID.kPackInfo) {
+            readPackInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kUnpackInfo) {
+            readUnpackInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kSubStreamsInfo) {
+            readSubStreamsInfo(header, archive);
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated StreamsInfo");
+        }
+    }
+    
+    private void readPackInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("PackInfo");
+        
+        archive.packPos = readUint64(header);
+        final long numPackStreams = readUint64(header);
+        debug("  " + numPackStreams + " pack streams");
+        
+        int nid = header.readUnsignedByte();
+        if (nid == NID.kSize) {
+            archive.packSizes = new long[(int)numPackStreams];
+            for (int i = 0; i < archive.packSizes.length; i++) {
+                archive.packSizes[i] = readUint64(header);
+                debug("  pack size %d is %d\n", i, archive.packSizes[i]);
+            }
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid == NID.kCRC) {
+            archive.packCrcsDefined = readAllOrBits(header, (int)numPackStreams);
+            archive.packCrcs = new int[(int)numPackStreams];
+            for (int i = 0; i < (int)numPackStreams; i++) {
+                if (archive.packCrcsDefined.get(i)) {
+                    archive.packCrcs[i] = Integer.reverseBytes(header.readInt());
+                }
+            }
+            
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated PackInfo (" + nid + ")");
+        }
+    }
+    
+    private void readUnpackInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("UnpackInfo");
+
+        int nid = header.readUnsignedByte();
+        if (nid != NID.kFolder) {
+            throw new IOException("Expected kFolder, got " + nid);
+        }
+        final long numFolders = readUint64(header);
+        debug("  " + numFolders + " folders");
+        final Folder[] folders = new Folder[(int)numFolders];
+        archive.folders = folders;
+        final int external = header.readUnsignedByte();
+        if (external != 0) {
+            throw new IOException("External unsupported");
+        } else {
+            for (int i = 0; i < (int)numFolders; i++) {
+                folders[i] = readFolder(header);
+            }
+        }
+        
+        nid = header.readUnsignedByte();
+        if (nid != NID.kCodersUnpackSize) {
+            throw new IOException("Expected kCodersUnpackSize, got " + nid);
+        }
+        for (final Folder folder : folders) {
+            folder.unpackSizes = new long[(int)folder.totalOutputStreams];
+            for (int i = 0; i < folder.totalOutputStreams; i++) {
+                folder.unpackSizes[i] = readUint64(header);
+            }
+        }
+        
+        nid = header.readUnsignedByte();
+        if (nid == NID.kCRC) {
+            final BitSet crcsDefined = readAllOrBits(header, (int)numFolders);
+            for (int i = 0; i < (int)numFolders; i++) {
+                if (crcsDefined.get(i)) {
+                    folders[i].hasCrc = true;
+                    folders[i].crc = Integer.reverseBytes(header.readInt());
+                } else {
+                    folders[i].hasCrc = false;
+                }
+            }
+            
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated UnpackInfo");
+        }
+    }
+    
+    private void readSubStreamsInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("SubStreamsInfo");
+        
+        for (final Folder folder : archive.folders) {
+            folder.numUnpackSubStreams = 1;
+        }
+        int totalUnpackStreams = archive.folders.length;
+        
+        int nid = header.readUnsignedByte();
+        if (nid == NID.kNumUnpackStream) {
+            totalUnpackStreams = 0;
+            for (final Folder folder : archive.folders) {
+                final long numStreams = readUint64(header);
+                folder.numUnpackSubStreams = (int)numStreams;
+                totalUnpackStreams += numStreams;
+            }
+            nid = header.readUnsignedByte();
+        }
+        
+        final SubStreamsInfo subStreamsInfo = new SubStreamsInfo();
+        subStreamsInfo.unpackSizes = new long[totalUnpackStreams];
+        subStreamsInfo.hasCrc = new BitSet(totalUnpackStreams);
+        subStreamsInfo.crcs = new int[totalUnpackStreams];
+        
+        int nextUnpackStream = 0;
+        for (final Folder folder : archive.folders) {
+            if (folder.numUnpackSubStreams == 0) {
+                continue;
+            }
+            long sum = 0;
+            if (nid == NID.kSize) {
+                for (int i = 0; i < (folder.numUnpackSubStreams - 1); i++) {
+                    final long size = readUint64(header);
+                    subStreamsInfo.unpackSizes[nextUnpackStream++] = size;
+                    sum += size;
+                }
+            }
+            subStreamsInfo.unpackSizes[nextUnpackStream++] = folder.getUnpackSize() - sum;
+        }
+        if (nid == NID.kSize) {
+            nid = header.readUnsignedByte();
+        }
+        
+        int numDigests = 0;
+        for (final Folder folder : archive.folders) {
+            if (folder.numUnpackSubStreams != 1 || !folder.hasCrc) {
+                numDigests += folder.numUnpackSubStreams;
+            }
+        }
+        
+        if (nid == NID.kCRC) {
+            final BitSet hasMissingCrc = readAllOrBits(header, numDigests);
+            final int[] missingCrcs = new int[numDigests];
+            for (int i = 0; i < numDigests; i++) {
+                if (hasMissingCrc.get(i)) {
+                    missingCrcs[i] = Integer.reverseBytes(header.readInt());
+                }
+            }
+            int nextCrc = 0;
+            int nextMissingCrc = 0;
+            for (final Folder folder: archive.folders) {
+                if (folder.numUnpackSubStreams == 1 && folder.hasCrc) {
+                    subStreamsInfo.hasCrc.set(nextCrc, true);
+                    subStreamsInfo.crcs[nextCrc] = folder.crc;
+                    ++nextCrc;
+                } else {
+                    for (int i = 0; i < folder.numUnpackSubStreams; i++) {
+                        subStreamsInfo.hasCrc.set(nextCrc, hasMissingCrc.get(nextMissingCrc));
+                        subStreamsInfo.crcs[nextCrc] = missingCrcs[nextMissingCrc];
+                        ++nextCrc;
+                        ++nextMissingCrc;
+                    }
+                }
+            }
+            
+            nid = header.readUnsignedByte();
+        }
+        
+        if (nid != NID.kEnd) {
+            throw new IOException("Badly terminated SubStreamsInfo");
+        }
+        
+        archive.subStreamsInfo = subStreamsInfo;
+    }
+    
+    private Folder readFolder(final DataInput header) throws IOException {
+        final Folder folder = new Folder();
+        
+        final long numCoders = readUint64(header);
+        final Coder[] coders = new Coder[(int)numCoders];
+        long totalInStreams = 0;
+        long totalOutStreams = 0;
+        for (int i = 0; i < coders.length; i++) {
+            coders[i] = new Coder();
+            int bits = header.readUnsignedByte();
+            final int idSize = bits & 0xf;
+            final boolean isSimple = ((bits & 0x10) == 0);
+            final boolean hasAttributes = ((bits & 0x20) != 0);
+            final boolean moreAlternativeMethods = ((bits & 0x80) != 0);
+            
+            coders[i].decompressionMethodId = new byte[idSize];
+            header.readFully(coders[i].decompressionMethodId);
+            if (isSimple) {
+                coders[i].numInStreams = 1;
+                coders[i].numOutStreams = 1;
+            } else {
+                coders[i].numInStreams = readUint64(header);
+                coders[i].numOutStreams = readUint64(header);
+            }
+            totalInStreams += coders[i].numInStreams;
+            totalOutStreams += coders[i].numOutStreams;
+            if (hasAttributes) {
+                final long propertiesSize = readUint64(header);
+                coders[i].properties = new byte[(int)propertiesSize];
+                header.readFully(coders[i].properties);
+            }
+            if (DEBUG) {
+                final StringBuilder methodStr = new StringBuilder();
+                for (final byte b : coders[i].decompressionMethodId) {
+                    methodStr.append(String.format("%02X", 0xff & b));
+                }
+                debug("  coder entry %d numInStreams=%d, numOutStreams=%d, method=%s, properties=%s\n", i,
+                        coders[i].numInStreams, coders[i].numOutStreams, methodStr.toString(),
+                        Arrays.toString(coders[i].properties));
+            }
+            // would need to keep looping as above:
+            while (moreAlternativeMethods) {
+                throw new IOException("Alternative methods are unsupported, please report. " +
+                        "The reference implementation doesn't support them either.");
+            }
+        }
+        folder.coders = coders;
+        folder.totalInputStreams = totalInStreams;
+        folder.totalOutputStreams = totalOutStreams;
+        
+        if (totalOutStreams == 0) {
+            throw new IOException("Total output streams can't be 0");
+        }
+        final long numBindPairs = totalOutStreams - 1;
+        final BindPair[] bindPairs = new BindPair[(int)numBindPairs];
+        for (int i = 0; i < bindPairs.length; i++) {
+            bindPairs[i] = new BindPair();
+            bindPairs[i].inIndex = readUint64(header);
+            bindPairs[i].outIndex = readUint64(header);
+            debug("  bind pair in=%d out=%d\n", bindPairs[i].inIndex, bindPairs[i].outIndex);
+        }
+        folder.bindPairs = bindPairs;
+        
+        if (totalInStreams < numBindPairs) {
+            throw new IOException("Total input streams can't be less than the number of bind pairs");
+        }
+        final long numPackedStreams = totalInStreams - numBindPairs;
+        final long packedStreams[] = new long[(int)numPackedStreams];
+        if (numPackedStreams == 1) {
+            int i;
+            for (i = 0; i < (int)totalInStreams; i++) {
+                if (folder.findBindPairForInStream(i) < 0) {
+                    break;
+                }
+            }
+            if (i == (int)totalInStreams) {
+                throw new IOException("Couldn't find stream's bind pair index");
+            }
+            packedStreams[0] = i;
+        } else {
+            for (int i = 0; i < (int)numPackedStreams; i++) {
+                packedStreams[i] = readUint64(header);
+            }
+        }
+        folder.packedStreams = packedStreams;
+        
+        return folder;
+    }
+    
+    private BitSet readAllOrBits(final DataInput header, final int size) throws IOException {
+        final int areAllDefined = header.readUnsignedByte();
+        final BitSet bits;
+        if (areAllDefined != 0) {
+            bits = new BitSet(size);
+            for (int i = 0; i < size; i++) {
+                bits.set(i, true);
+            }
+        } else {
+            bits = readBits(header, size);
+        }
+        return bits;
+    }
+    
+    private BitSet readBits(final DataInput header, final int size) throws IOException {
+        final BitSet bits = new BitSet(size);
+        int mask = 0;
+        int cache = 0;
+        for (int i = 0; i < size; i++) {
+            if (mask == 0) {
+                mask = 0x80;
+                cache = header.readUnsignedByte();
+            }
+            bits.set(i, (cache & mask) != 0);
+            mask >>>= 1;
+        }
+        return bits;
+    }
+    
+    private void readFilesInfo(final DataInput header, final Archive archive) throws IOException {
+        debug("FilesInfo");
+
+        final long numFiles = readUint64(header);
+        final SevenZArchiveEntry[] files = new SevenZArchiveEntry[(int)numFiles];
+        for (int i = 0; i < files.length; i++) {
+            files[i] = new SevenZArchiveEntry();
+        }
+        BitSet isEmptyStream = null;
+        BitSet isEmptyFile = null; 
+        BitSet isAnti = null;
+        while (true) {
+            final int propertyType = header.readUnsignedByte();
+            if (propertyType == 0) {
+                break;
+            }
+            long size = readUint64(header);
+            switch (propertyType) {
+                case NID.kEmptyStream: {
+                    debug("  kEmptyStream");
+                    isEmptyStream = readBits(header, files.length);
+                    break;
+                }
+                case NID.kEmptyFile: {
+                    debug("  kEmptyFile");
+                    if (isEmptyStream == null) { // protect against NPE
+                        throw new IOException("Header format error: kEmptyStream must appear before kEmptyFile");
+                    }
+                    isEmptyFile = readBits(header, isEmptyStream.cardinality());
+                    break;
+                }
+                case NID.kAnti: {
+                    debug("  kAnti");
+                    if (isEmptyStream == null) { // protect against NPE
+                        throw new IOException("Header format error: kEmptyStream must appear before kAnti");
+                    }
+                    isAnti = readBits(header, isEmptyStream.cardinality());
+                    break;
+                }
+                case NID.kName: {
+                    debug("  kNames");
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Not implemented");
+                    } else {
+                        if (((size - 1) & 1) != 0) {
+                            throw new IOException("File names length invalid");
+                        }
+                        final byte[] names = new byte[(int)(size - 1)];
+                        header.readFully(names);
+                        int nextFile = 0;
+                        int nextName = 0;
+                        for (int i = 0; i < names.length; i += 2) {
+                            if (names[i] == 0 && names[i+1] == 0) {
+                                files[nextFile++].setName(new String(names, nextName, i-nextName, "UTF-16LE"));
+                                nextName = i + 2;
+                            }
+                        }
+                        if (nextName != names.length || nextFile != files.length) {
+                            throw new IOException("Error parsing file names");
+                        }
+                    }
+                    break;
+                }
+                case NID.kCTime: {
+                    debug("  kCreationTime");
+                    final BitSet timesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasCreationDate(timesDefined.get(i));
+                            if (files[i].getHasCreationDate()) {
+                                files[i].setCreationDate(Long.reverseBytes(header.readLong()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kATime: {
+                    debug("  kLastAccessTime");
+                    final BitSet timesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasAccessDate(timesDefined.get(i));
+                            if (files[i].getHasAccessDate()) {
+                                files[i].setAccessDate(Long.reverseBytes(header.readLong()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kMTime: {
+                    debug("  kLastWriteTime");
+                    final BitSet timesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasLastModifiedDate(timesDefined.get(i));
+                            if (files[i].getHasLastModifiedDate()) {
+                                files[i].setLastModifiedDate(Long.reverseBytes(header.readLong()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kWinAttributes: {
+                    debug("  kWinAttributes");
+                    final BitSet attributesDefined = readAllOrBits(header, files.length);
+                    final int external = header.readUnsignedByte();
+                    if (external != 0) {
+                        throw new IOException("Unimplemented");
+                    } else {
+                        for (int i = 0; i < files.length; i++) {
+                            files[i].setHasWindowsAttributes(attributesDefined.get(i));
+                            if (files[i].getHasWindowsAttributes()) {
+                                files[i].setWindowsAttributes(Integer.reverseBytes(header.readInt()));
+                            }
+                        }
+                    }
+                    break;
+                }
+                case NID.kStartPos: {
+                    debug("  kStartPos");
+                    throw new IOException("kStartPos is unsupported, please report");
+                }
+                case NID.kDummy: {
+                    debug("  kDummy");
+                    throw new IOException("kDummy is unsupported, please report");
+                }
+                
+                default: {
+                    throw new IOException("Unknown property " + propertyType);
+                    // FIXME: Should actually:
+                    //header.skipBytes((int)size);
+                }
+            }
+        }
+        int nonEmptyFileCounter = 0;
+        int emptyFileCounter = 0;
+        for (int i = 0; i < files.length; i++) {
+            files[i].setHasStream((isEmptyStream == null) ? true : !isEmptyStream.get(i));
+            if (files[i].hasStream()) {
+                files[i].setDirectory(false);
+                files[i].setAntiItem(false);
+                files[i].setHasCrc(archive.subStreamsInfo.hasCrc.get(nonEmptyFileCounter));
+                files[i].setCrc(archive.subStreamsInfo.crcs[nonEmptyFileCounter]);
+                files[i].setSize(archive.subStreamsInfo.unpackSizes[nonEmptyFileCounter]);
+                ++nonEmptyFileCounter;
+            } else {
+                files[i].setDirectory((isEmptyFile == null) ? true : !isEmptyFile.get(emptyFileCounter));
+                files[i].setAntiItem((isAnti == null) ? false : isAnti.get(emptyFileCounter));
+                files[i].setHasCrc(false);
+                files[i].setSize(0);
+                ++emptyFileCounter;
+            }
+        }
+        archive.files = files;
+        calculateStreamMap(archive);
+    }
+    
+    private void calculateStreamMap(final Archive archive) throws IOException {
+        final StreamMap streamMap = new StreamMap();
+        
+        int nextFolderPackStreamIndex = 0;
+        final int numFolders = (archive.folders != null) ? archive.folders.length : 0;
+        streamMap.folderFirstPackStreamIndex = new int[numFolders];
+        for (int i = 0; i < numFolders; i++) {
+            streamMap.folderFirstPackStreamIndex[i] = nextFolderPackStreamIndex;
+            nextFolderPackStreamIndex += archive.folders[i].packedStreams.length;
+        }
+        
+        long nextPackStreamOffset = 0;
+        final int numPackSizes = (archive.packSizes != null) ? archive.packSizes.length : 0;
+        streamMap.packStreamOffsets = new long[numPackSizes];
+        for (int i = 0; i < numPackSizes; i++) {
+            streamMap.packStreamOffsets[i] = nextPackStreamOffset;
+            nextPackStreamOffset += archive.packSizes[i]; 
+        }
+        
+        streamMap.folderFirstFileIndex = new int[numFolders];
+        streamMap.fileFolderIndex = new int[archive.files.length];
+        int nextFolderIndex = 0;
+        int nextFolderUnpackStreamIndex = 0;
+        for (int i = 0; i < archive.files.length; i++) {
+            if (!archive.files[i].hasStream() && nextFolderUnpackStreamIndex == 0) {
+                streamMap.fileFolderIndex[i] = -1;
+                continue;
+            }
+            if (nextFolderUnpackStreamIndex == 0) {
+                for (; nextFolderIndex < archive.folders.length; ++nextFolderIndex) {
+                    streamMap.folderFirstFileIndex[nextFolderIndex] = i;
+                    if (archive.folders[nextFolderIndex].numUnpackSubStreams > 0) {
+                        break;
+                    }
+                }
+                if (nextFolderIndex >= archive.folders.length) {
+                    throw new IOException("Too few folders in archive");
+                }
+            }
+            streamMap.fileFolderIndex[i] = nextFolderIndex;
+            if (!archive.files[i].hasStream()) {
+                continue;
+            }
+            ++nextFolderUnpackStreamIndex;
+            if (nextFolderUnpackStreamIndex >= archive.folders[nextFolderIndex].numUnpackSubStreams) {
+                ++nextFolderIndex;
+                nextFolderUnpackStreamIndex = 0;
+            }
+        }
+        
+        archive.streamMap = streamMap;
+    }
+    
+    private void buildDecodingStream() throws IOException {
+        final int folderIndex = archive.streamMap.fileFolderIndex[currentEntryIndex];
+        if (folderIndex < 0) {
+            currentEntryInputStream = new BoundedInputStream(
+                    new ByteArrayInputStream(new byte[0]), 0);
+            return;
+        }
+        if (currentFolderIndex == folderIndex) {
+            // need to advance the folder input stream past the current file
+            drainPreviousEntry();
+        } else {
+            currentFolderIndex = folderIndex;
+            if (currentFolderInputStream != null) {
+                currentFolderInputStream.close();
+                currentFolderInputStream = null;
+            }
+            
+            final Folder folder = archive.folders[folderIndex];
+            final int firstPackStreamIndex = archive.streamMap.folderFirstPackStreamIndex[folderIndex];
+            final long folderOffset = SIGNATURE_HEADER_SIZE + archive.packPos +
+                    archive.streamMap.packStreamOffsets[firstPackStreamIndex];
+            currentFolderInputStream = buildDecoderStack(folder, folderOffset, firstPackStreamIndex);
+        }
+        final SevenZArchiveEntry file = archive.files[currentEntryIndex];
+        final InputStream fileStream = new BoundedInputStream(
+                currentFolderInputStream, file.getSize());
+        if (file.getHasCrc()) {
+            currentEntryInputStream = new CRC32VerifyingInputStream(
+                    fileStream, file.getSize(), file.getCrc());
+        } else {
+            currentEntryInputStream = fileStream;
+        }
+        
+    }
+    
+    private void drainPreviousEntry() throws IOException {
+        if (currentEntryInputStream != null) {
+            final byte[] buffer = new byte[64*1024];
+            while (currentEntryInputStream.read(buffer) >= 0) { // NOPMD
+            }
+            currentEntryInputStream.close();
+            currentEntryInputStream = null;
+        }
+    }
+    
+    private InputStream buildDecoderStack(final Folder folder, final long folderOffset,
+            final int firstPackStreamIndex) throws IOException {
+        file.seek(folderOffset);
+        InputStream inputStreamStack = new BoundedRandomAccessFileInputStream(file,
+                archive.packSizes[firstPackStreamIndex]);
+        for (final Coder coder : folder.coders) {
+            if (coder.numInStreams != 1 || coder.numOutStreams != 1) {
+                throw new IOException("Multi input/output stream coders are not yet supported");
+            }
+            inputStreamStack = Coders.addDecoder(inputStreamStack, coder, password);
+        }
+        if (folder.hasCrc) {
+            return new CRC32VerifyingInputStream(inputStreamStack,
+                    folder.getUnpackSize(), folder.crc);
+        } else {
+            return inputStreamStack;
+        }
+    }
+    
+    public int read() throws IOException {
+        return currentEntryInputStream.read();
+    }
+    
+    public int read(byte[] b) throws IOException {
+        return read(b, 0, b.length);
+    }
+    
+    public int read(byte[] b, int off, int len) throws IOException {
+        return currentEntryInputStream.read(b, off, len);
+    }
+    
+    private static long readUint64(final DataInput in) throws IOException {
+        int firstByte = in.readUnsignedByte();
+        int mask = 0x80;
+        int value = 0;
+        for (int i = 0; i < 8; i++) {
+            if ((firstByte & mask) == 0) {
+                return value | ((firstByte & (mask - 1)) << (8 * i));
+            }
+            int nextByte = in.readUnsignedByte();
+            value |= (nextByte << (8 * i));
+            mask >>>= 1;
+        }
+        return value;
+    }
+    
+    private static class BoundedInputStream extends InputStream {
+        private final InputStream in;
+        private long bytesRemaining;
+        
+        public BoundedInputStream(final InputStream in, final long size) {
+            this.in = in;
+            bytesRemaining = size;
+        }
+        
+        @Override
+        public int read() throws IOException {
+            if (bytesRemaining > 0) {
+                --bytesRemaining;
+                return in.read();
+            } else {
+                return -1;
+            }
+        }
+
+        @Override
+        public int read(byte[] b, int off, int len) throws IOException {
+            if (bytesRemaining == 0) {
+                return -1;
+            }
+            int bytesToRead = len;
+            if (bytesToRead > bytesRemaining) {
+                bytesToRead = (int) bytesRemaining;
+            }
+            final int bytesRead = in.read(b, off, bytesToRead);
+            if (bytesRead >= 0) {
+                bytesRemaining -= bytesRead;
+            }
+            return bytesRead;
+        }
+
+        @Override
+        public void close() {
+        }
+    }
+}

richedit/src/main/resource/testFiles/commons-compress/revFiles/d8ca98_2ed556_src#main#java#org#apache#commons#compress#archivers#sevenz#AES256SHA256Decoder.java

@@ -0,0 +1,121 @@
+/*
+ *  Licensed to the Apache Software Foundation (ASF) under one or more
+ *  contributor license agreements.  See the NOTICE file distributed with
+ *  this work for additional information regarding copyright ownership.
+ *  The ASF licenses this file to You under the Apache License, Version 2.0
+ *  (the "License"); you may not use this file except in compliance with
+ *  the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ */
+package org.apache.commons.compress.archivers.sevenz;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.security.GeneralSecurityException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import javax.crypto.Cipher;
+import javax.crypto.CipherInputStream;
+import javax.crypto.SecretKey;
+import javax.crypto.spec.IvParameterSpec;
+import javax.crypto.spec.SecretKeySpec;
+import org.apache.commons.compress.PasswordRequiredException;
+
+class AES256SHA256Decoder extends CoderBase {
+    @Override
+    InputStream decode(final String archiveName, final InputStream in, final long uncompressedLength,
+            final Coder coder, final byte[] passwordBytes, int maxMemoryLimitInKb) throws IOException {
+        return new InputStream() {
+            private boolean isInitialized = false;
+            private CipherInputStream cipherInputStream = null;
+
+            private CipherInputStream init() throws IOException {
+                if (isInitialized) {
+                    return cipherInputStream;
+                }
+                final int byte0 = 0xff & coder.properties[0];
+                final int numCyclesPower = byte0 & 0x3f;
+                final int byte1 = 0xff & coder.properties[1];
+                final int ivSize = ((byte0 >> 6) & 1) + (byte1 & 0x0f);
+                final int saltSize = ((byte0 >> 7) & 1) + (byte1 >> 4);
+                if (2 + saltSize + ivSize > coder.properties.length) {
+                    throw new IOException("Salt size + IV size too long in " + archiveName);
+                }
+                final byte[] salt = new byte[saltSize];
+                System.arraycopy(coder.properties, 2, salt, 0, saltSize);
+                final byte[] iv = new byte[16];
+                System.arraycopy(coder.properties, 2 + saltSize, iv, 0, ivSize);
+
+                if (passwordBytes == null) {
+                    throw new PasswordRequiredException(archiveName);
+                }
+                final byte[] aesKeyBytes;
+                if (numCyclesPower == 0x3f) {
+                    aesKeyBytes = new byte[32];
+                    System.arraycopy(salt, 0, aesKeyBytes, 0, saltSize);
+                    System.arraycopy(passwordBytes, 0, aesKeyBytes, saltSize,
+                                     Math.min(passwordBytes.length, aesKeyBytes.length - saltSize));
+                } else {
+                    final MessageDigest digest;
+                    try {
+                        digest = MessageDigest.getInstance("SHA-256");
+                    } catch (final NoSuchAlgorithmException noSuchAlgorithmException) {
+                        throw new IOException("SHA-256 is unsupported by your Java implementation",
+                            noSuchAlgorithmException);
+                    }
+                    final byte[] extra = new byte[8];
+                    for (long j = 0; j < (1L << numCyclesPower); j++) {
+                        digest.update(salt);
+                        digest.update(passwordBytes);
+                        digest.update(extra);
+                        for (int k = 0; k < extra.length; k++) {
+                            ++extra[k];
+                            if (extra[k] != 0) {
+                                break;
+                            }
+                        }
+                    }
+                    aesKeyBytes = digest.digest();
+                }
+
+                final SecretKey aesKey = new SecretKeySpec(aesKeyBytes, "AES");
+                try {
+                    final Cipher cipher = Cipher.getInstance("AES/CBC/NoPadding");
+                    cipher.init(Cipher.DECRYPT_MODE, aesKey, new IvParameterSpec(iv));
+                    cipherInputStream = new CipherInputStream(in, cipher);
+                    isInitialized = true;
+                    return cipherInputStream;
+                } catch (final GeneralSecurityException generalSecurityException) {
+                    throw new IOException("Decryption error " +
+                        "(do you have the JCE Unlimited Strength Jurisdiction Policy Files installed?)",
+                        generalSecurityException);
+                    }
+            }
+
+            @Override
+            public int read() throws IOException {
+                return init().read();
+            }
+
+            @Override
+            public int read(final byte[] b, final int off, final int len) throws IOException {
+                return init().read(b, off, len);
+            }
+
+            @Override
+            public void close() throws IOException {
+                if (cipherInputStream != null) {
+                    cipherInputStream.close();
+                }
+            }
+        };
+    }
+}

richedit/src/main/resource/testFiles/commons-configuration/prevFiles/prev_b24b7b_3ac9d8_src#test#org#apache#commons#configuration#TestHierarchicalConfigurationXMLReader.java

@@ -0,0 +1,72 @@
+/*
+ * Copyright 2001-2006 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License")
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.configuration;
+
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMResult;
+import javax.xml.transform.sax.SAXSource;
+
+import org.apache.commons.jxpath.JXPathContext;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.xml.sax.InputSource;
+
+import junit.framework.TestCase;
+
+/**
+ * Test class for HierarchicalConfigurationXMLReader.
+ *
+ * @version $Id$
+ */
+public class TestHierarchicalConfigurationXMLReader extends TestCase
+{
+    private static final String TEST_FILE = "conf/testHierarchicalXMLConfiguration.xml";
+
+    private HierarchicalConfigurationXMLReader parser;
+
+    protected void setUp() throws Exception
+    {
+        XMLConfiguration config =
+        new XMLConfiguration();
+        config.setFileName(TEST_FILE);
+        config.load();
+        parser = new HierarchicalConfigurationXMLReader(config);
+    }
+
+    public void testParse() throws Exception
+    {
+        SAXSource source = new SAXSource(parser, new InputSource());
+        DOMResult result = new DOMResult();
+        Transformer trans = TransformerFactory.newInstance().newTransformer();
+        trans.transform(source, result);
+        Node root = ((Document) result.getNode()).getDocumentElement();
+        JXPathContext ctx = JXPathContext.newContext(root);
+
+        assertEquals("Wrong name of root element", "config", root.getNodeName());
+        assertEquals("Wrong number of children of root", 1, ctx.selectNodes(
+                "/*").size());
+        assertEquals("Wrong number of tables", 2, ctx.selectNodes(
+                "/tables/table").size());
+        assertEquals("Wrong name of first table", "users", ctx
+                .getValue("/tables/table[1]/name"));
+        assertEquals("Wrong number of fields in first table", 5, ctx
+                .selectNodes("/tables/table[1]/fields/field").size());
+        assertEquals("Wrong attribute value", "system", ctx
+                .getValue("/tables/table[1]/@tableType"));
+    }
+}

richedit/src/main/resource/testFiles/commons-configuration/revFiles/b24b7b_3ac9d8_src#test#org#apache#commons#configuration#TestHierarchicalConfigurationXMLReader.java

@@ -0,0 +1,81 @@
+/*
+ * Copyright 2001-2006 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License")
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.configuration;
+
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMResult;
+import javax.xml.transform.sax.SAXSource;
+
+import org.apache.commons.jxpath.JXPathContext;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.xml.sax.InputSource;
+
+import junit.framework.TestCase;
+
+/**
+ * Test class for HierarchicalConfigurationXMLReader.
+ *
+ * @version $Id$
+ */
+public class TestHierarchicalConfigurationXMLReader extends TestCase
+{
+    private static final String TEST_FILE = "conf/testHierarchicalXMLConfiguration.xml";
+
+    private HierarchicalConfigurationXMLReader parser;
+
+    protected void setUp() throws Exception
+    {
+        XMLConfiguration config =
+        new XMLConfiguration();
+        config.setFileName(TEST_FILE);
+        config.load();
+        parser = new HierarchicalConfigurationXMLReader(config);
+    }
+
+    public void testParse() throws Exception
+    {
+        SAXSource source = new SAXSource(parser, new InputSource());
+        DOMResult result = new DOMResult();
+        Transformer trans = TransformerFactory.newInstance().newTransformer();
+        try
+        {
+            //When executed on a JDK 1.3 this line throws a NoSuchMethodError
+            //somewhere deep in Xalan. We simply ignore this.
+            trans.transform(source, result);
+        }
+        catch(NoSuchMethodError ex)
+        {
+            return;
+        }
+        Node root = ((Document) result.getNode()).getDocumentElement();
+        JXPathContext ctx = JXPathContext.newContext(root);
+
+        assertEquals("Wrong name of root element", "config", root.getNodeName());
+        assertEquals("Wrong number of children of root", 1, ctx.selectNodes(
+                "/*").size());
+        assertEquals("Wrong number of tables", 2, ctx.selectNodes(
+                "/tables/table").size());
+        assertEquals("Wrong name of first table", "users", ctx
+                .getValue("/tables/table[1]/name"));
+        assertEquals("Wrong number of fields in first table", 5, ctx
+                .selectNodes("/tables/table[1]/fields/field").size());
+        assertEquals("Wrong attribute value", "system", ctx
+                .getValue("/tables/table[1]/@tableType"));
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_2006f48_4dad2f_insight#insight-camel#src#main#java#org#fusesource#insight#camel#audit#ScriptUtils.java

@@ -0,0 +1,56 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.insight.camel.audit;
+
+import org.codehaus.jackson.map.ObjectMapper;
+
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.Map;
+
+public final class ScriptUtils {
+
+    private static final SimpleDateFormat format;
+    private static final ObjectMapper mapper;
+
+    static {
+        format = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSX");
+        mapper = new ObjectMapper();
+        mapper.setSerializationConfig(mapper.getSerializationConfig().withDateFormat(format));
+    }
+
+    public static String toIso(Date d) {
+        return format.format(d);
+    }
+
+    public static String toJson(Object o) {
+        try {
+            return mapper.writeValueAsString(o);
+        } catch (Exception e) {
+            throw new IllegalArgumentException("Could not serialize " + o, e);
+        }
+    }
+
+    public static Map parseJson(String str) {
+        try {
+            return mapper.readValue(str, Map.class);
+        } catch (Exception e) {
+            throw new IllegalArgumentException("Could not deserialize " + str, e);
+        }
+    }
+
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_6baf6f_ad4e95_fabric#fabric-core-agent-jclouds#src#main#java#org#fusesource#fabric#service#jclouds#JcloudsContainerProvider.java

@@ -0,0 +1,190 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.fusesource.fabric.service.jclouds;
+
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URLDecoder;
+import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import com.google.common.base.Strings;
+import com.google.common.collect.ImmutableSet;
+import com.google.inject.Module;
+import org.fusesource.fabric.api.*;
+import org.fusesource.fabric.api.CreateJCloudsContainerOptions;
+import org.jclouds.compute.ComputeService;
+import org.jclouds.compute.ComputeServiceContext;
+import org.jclouds.compute.ComputeServiceContextFactory;
+import org.jclouds.compute.RunNodesException;
+import org.jclouds.compute.domain.NodeMetadata;
+import org.jclouds.compute.domain.TemplateBuilder;
+import org.jclouds.compute.options.RunScriptOptions;
+import org.jclouds.domain.Credentials;
+import org.jclouds.rest.RestContextFactory;
+
+
+import static org.fusesource.fabric.internal.ContainerProviderUtils.buildStartupScript;
+
+/**
+ * A concrete {@link org.fusesource.fabric.api.ContainerProvider} that creates {@link org.fusesource.fabric.api.Container}s via jclouds {@link ComputeService}.
+ */
+public class JcloudsContainerProvider implements ContainerProvider<CreateJCloudsContainerOptions, CreateJCloudsContainerMetadata> {
+
+    private final ConcurrentMap<String, ComputeService> computeServiceMap = new ConcurrentHashMap<String, ComputeService>();
+
+    public void bind(ComputeService computeService) {
+        if(computeService != null) {
+            String providerName = computeService.getContext().getProviderSpecificContext().getId();
+            if(providerName != null) {
+              computeServiceMap.put(providerName,computeService);
+            }
+        }
+    }
+
+    public void unbind(ComputeService computeService) {
+        if(computeService != null) {
+            String providerName = computeService.getContext().getProviderSpecificContext().getId();
+            if(providerName != null) {
+               computeServiceMap.remove(providerName);
+            }
+        }
+    }
+
+    public ConcurrentMap<String, ComputeService> getComputeServiceMap() {
+        return computeServiceMap;
+    }
+
+    public Set<CreateJCloudsContainerMetadata> create(CreateJCloudsContainerOptions options) throws MalformedURLException, RunNodesException, URISyntaxException {
+        Set<CreateJCloudsContainerMetadata> result = new LinkedHashSet<CreateJCloudsContainerMetadata>();
+
+        ComputeService computeService = computeServiceMap.get(options.getProviderName());
+        if (computeService == null) {
+
+            Iterable<? extends Module> modules = ImmutableSet.of();
+
+            Properties props = new Properties();
+            props.put("provider", options.getProviderName());
+            props.put("identity", options.getIdentity());
+            props.put("credential", options.getCredential());
+            if (!Strings.isNullOrEmpty(options.getOwner()) && options.getProviderName().equals("aws-ec2")) {
+                props.put("jclouds.ec2.ami-owners", options.getOwner());
+            }
+
+            RestContextFactory restFactory = new RestContextFactory();
+            ComputeServiceContext context = new ComputeServiceContextFactory(restFactory).createContext(options.getProviderName(), options.getIdentity(), options.getCredential(), modules, props);
+            computeService = context.getComputeService();
+        }
+
+        TemplateBuilder builder = computeService.templateBuilder();
+        builder.any();
+        switch (options.getInstanceType()) {
+            case Smallest:
+                builder.smallest();
+                break;
+            case Biggest:
+                builder.biggest();
+                break;
+            case Fastest:
+                builder.fastest();
+        }
+
+        if (options.getLocationId() != null) {
+            builder.locationId(options.getLocationId());
+        }
+        if (options.getImageId() != null) {
+            builder.imageId(options.getImageId());
+        }
+        if (options.getHardwareId() != null) {
+            builder.hardwareId(options.getHardwareId());
+        }
+
+        Set<? extends NodeMetadata> metadatas = null;
+
+        metadatas = computeService.createNodesInGroup(options.getGroup(), options.getNumber(), builder.build());
+
+        int suffix = 1;
+        StringBuilder buffer = new StringBuilder();
+        boolean first = true;
+        if (metadatas != null) {
+            for (NodeMetadata nodeMetadata : metadatas) {
+                Credentials credentials = null;
+                //For some cloud providers return do not allow shell access to root, so the user needs to be overrided.
+                if (options.getUser() != null) {
+                    credentials = new Credentials(options.getUser(), nodeMetadata.getCredentials().credential);
+                } else {
+                    credentials = nodeMetadata.getCredentials();
+                }
+                String id = nodeMetadata.getId();
+                Set<String> publicAddresses = nodeMetadata.getPublicAddresses();
+                for (String pa: publicAddresses) {
+                    if (first) {
+                        first = false;
+                    } else {
+                        buffer.append(",");
+                    }
+                    buffer.append(pa + ":" + options.getServicePort());
+                }
+                String containerName = options.getName();
+                if(options.getNumber() > 1) {
+                    containerName+=suffix++;
+                }
+                String script = buildStartupScript(options.name(containerName));
+                if (credentials != null) {
+                    computeService.runScriptOnNode(id, script, RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));
+                } else {
+                    computeService.runScriptOnNode(id, script);
+                }
+
+                CreateJCloudsContainerMetadata jCloudsContainerMetadata = new CreateJCloudsContainerMetadata();
+                jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());
+                jCloudsContainerMetadata.setContainerName(containerName);
+                jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());
+                jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());
+                result.add(jCloudsContainerMetadata);
+
+            }
+        }
+
+        return result;
+    }
+
+    public Map<String, String> parseQuery(String uri) throws URISyntaxException {
+        //TODO: This is copied form URISupport. We should move URISupport to core so that we don't have to copy stuff arround.
+        try {
+            Map<String, String> rc = new HashMap<String, String>();
+            if (uri != null) {
+                String[] parameters = uri.split("&");
+                for (int i = 0; i < parameters.length; i++) {
+                    int p = parameters[i].indexOf("=");
+                    if (p >= 0) {
+                        String name = URLDecoder.decode(parameters[i].substring(0, p), "UTF-8");
+                        String value = URLDecoder.decode(parameters[i].substring(p + 1), "UTF-8");
+                        rc.put(name, value);
+                    } else {
+                        rc.put(parameters[i], null);
+                    }
+                }
+            }
+            return rc;
+        } catch (UnsupportedEncodingException e) {
+            throw (URISyntaxException) new URISyntaxException(e.toString(), "Invalid encoding").initCause(e);
+        }
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_6d0e56_998321_fabric#fabric-agent#src#main#java#org#fusesource#fabric#agent#download#MavenDownloadTask.java

@@ -0,0 +1,476 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.fabric.agent.download;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.concurrent.ExecutorService;
+import javax.xml.parsers.ParserConfigurationException;
+import org.fusesource.fabric.agent.mvn.DownloadableArtifact;
+import org.fusesource.fabric.agent.mvn.MavenConfiguration;
+import org.fusesource.fabric.agent.mvn.MavenRepositoryURL;
+import org.fusesource.fabric.agent.mvn.Parser;
+import org.fusesource.fabric.agent.mvn.Version;
+import org.fusesource.fabric.agent.mvn.VersionRange;
+import org.fusesource.fabric.agent.utils.URLUtils;
+import org.fusesource.fabric.agent.utils.XmlUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+public class MavenDownloadTask extends AbstractDownloadTask implements Runnable {
+
+    /**
+     * Logger.
+     */
+    private static final Logger LOG = LoggerFactory.getLogger(AbstractDownloadTask.class);
+    /**
+     * 2 spaces indent;
+     */
+    private static final String Ix2 = "  ";
+    /**
+     * 4 spaces indent;
+     */
+    private static final String Ix4 = "    ";
+
+    private final MavenRepositoryURL system;
+    private final MavenConfiguration configuration;
+
+    public MavenDownloadTask(String url, MavenRepositoryURL system, MavenConfiguration configuration, ExecutorService executor) {
+        super(url, executor);
+        this.system = system;
+        this.configuration = configuration;
+    }
+
+    protected File download() throws Exception {
+        Parser parser = new Parser(url.substring("mvn:".length()));
+        Set<DownloadableArtifact> downloadables;
+        if (!parser.getVersion().contains("SNAPSHOT")) {
+            downloadables = doCollectPossibleDownloads(parser, Collections.singletonList(system));
+            if (!downloadables.isEmpty()) {
+                DownloadableArtifact artifact = downloadables.iterator().next();
+                URL url = artifact.getArtifactURL();
+                File file = new File(url.getFile());
+                if (file.exists()) {
+                    return file;
+                }
+            }
+        }
+        downloadables = collectPossibleDownloads(parser);
+        if (LOG.isTraceEnabled()) {
+            LOG.trace("Possible download locations for [" + url + "]");
+            for (DownloadableArtifact artifact : downloadables) {
+                LOG.trace("  " + artifact);
+            }
+        }
+        for (DownloadableArtifact artifact : downloadables) {
+            LOG.trace("Downloading [" + artifact + "]");
+            try {
+                configuration.enableProxy(artifact.getArtifactURL());
+                String repository = system.getFile().getAbsolutePath();
+                if (!repository.endsWith(Parser.FILE_SEPARATOR)) {
+                    repository = repository + Parser.FILE_SEPARATOR;
+                }
+                InputStream is = artifact.getInputStream();
+                File file = new File(repository + parser.getArtifactPath());
+                File tmp = new File(file.getAbsolutePath() + ".tmp");
+                tmp.getParentFile().mkdirs();
+                OutputStream os = new FileOutputStream(tmp);
+                copy(is, os);
+                file.delete();
+                tmp.renameTo(file);
+                return file;
+            } catch (IOException ignore) {
+                // go on with next repository
+                LOG.debug(Ix2 + "Could not download [" + artifact + "]");
+                LOG.trace(Ix2 + "Reason [" + ignore.getClass().getName() + ": " + ignore.getMessage() + "]");
+            }
+        }
+        // no artifact found
+        throw new IOException("URL [" + url + "] could not be resolved.");
+    }
+
+    /**
+     * Searches all available repositories for possible artifacts to download. The returned set of downloadable
+     * artifacts (never null, but maybe empty) will be sorted descending by version of the artifact and by positon of
+     * repository in the list of repositories to be searched.
+     *
+     * @return a non null sorted set of artifacts
+     * @throws java.net.MalformedURLException re-thrown
+     */
+    private Set<DownloadableArtifact> collectPossibleDownloads(final Parser parser)
+            throws MalformedURLException {
+        final List<MavenRepositoryURL> repositories = new ArrayList<MavenRepositoryURL>();
+        repositories.addAll(configuration.getRepositories());
+        repositories.add(system);
+        repositories.add(configuration.getLocalRepository());        
+        // if the url contains a prefered repository add that repository as the first repository to be searched
+        if (parser.getRepositoryURL() != null) {
+            repositories.add(
+                    repositories.size() == 0 ? 0 : 1,
+                    parser.getRepositoryURL()
+            );
+        }
+        return doCollectPossibleDownloads(parser, repositories);
+    }
+
+    /**
+     * Search the default repositories for possible artifacts to download.
+     */
+    private Set<DownloadableArtifact> collectDefaultPossibleDownloads(final Parser parser)
+            throws MalformedURLException {
+        return doCollectPossibleDownloads(parser, configuration.getDefaultRepositories());
+    }
+
+    private Set<DownloadableArtifact> doCollectPossibleDownloads(final Parser parser,
+                                                                 final List<MavenRepositoryURL> repositories)
+            throws MalformedURLException {
+        final Set<DownloadableArtifact> downloadables = new TreeSet<DownloadableArtifact>(new DownloadComparator());
+
+        // find artifact type
+        final boolean isLatest = parser.getVersion().contains("LATEST");
+        final boolean isSnapshot = parser.getVersion().endsWith("SNAPSHOT");
+        VersionRange versionRange = null;
+        if (!isLatest && !isSnapshot) {
+            try {
+                versionRange = new VersionRange(parser.getVersion());
+            } catch (Exception ignore) {
+                // well, we do not have a range of versions
+            }
+        }
+        final boolean isVersionRange = versionRange != null;
+        final boolean isExactVersion = !(isLatest || isSnapshot || isVersionRange);
+
+        int priority = 0;
+        for (MavenRepositoryURL repositoryURL : repositories) {
+            LOG.debug("Collecting versions from repository [" + repositoryURL + "]");
+            priority++;
+            try {
+                if (isExactVersion) {
+                    downloadables.add(resolveExactVersion(parser, repositoryURL, priority));
+                } else if (isSnapshot) {
+                    final DownloadableArtifact snapshot =
+                            resolveSnapshotVersion(parser, repositoryURL, priority, parser.getVersion());
+                    downloadables.add(snapshot);
+                    // if we have a local built snapshot we skip the rest of repositories
+                    if (snapshot.isLocalSnapshotBuild()) {
+                        break;
+                    }
+                } else {
+                    final Document metadata = getMetadata(repositoryURL.getURL(),
+                            new String[]
+                                    {
+                                            parser.getArtifactLocalMetdataPath(),
+                                            parser.getArtifactMetdataPath()
+                                    }
+                    );
+                    if (isLatest) {
+                        downloadables.add(resolveLatestVersion(parser, metadata, repositoryURL, priority));
+                    } else {
+                        downloadables.addAll(resolveRangeVersions(parser, metadata, repositoryURL, priority, versionRange));
+                    }
+                }
+            } catch (IOException ignore) {
+                // if metadata cannot be found we go on with the next repository. Maybe we have better luck.
+                LOG.debug(Ix2 + "Skipping repository [" + repositoryURL + "], reason: " + ignore.getMessage());
+            }
+        }
+        return downloadables;
+    }
+
+    /**
+     * Returns maven metadata by looking first for a local metatdata xml file and then for a remote one.
+     * If no metadata file is found or cannot be used an IOException is thrown.
+     *
+     * @param repositoryURL     url of the repository from where the metadata should be parsed
+     * @param metadataLocations array of location paths to try as metadata
+     * @return parsed xml document for the metadata file
+     * @throws java.io.IOException if:
+     *                             metadata file cannot be located
+     */
+    private Document getMetadata(final URL repositoryURL,
+                                 final String[] metadataLocations)
+            throws IOException {
+        LOG.debug(Ix2 + "Resolving metadata");
+        InputStream inputStream = null;
+        String foundLocation = null;
+        for (String location : metadataLocations) {
+            try {
+                // first try to get the artifact local metadata
+                inputStream = prepareInputStream(repositoryURL, location);
+                // get out at first found location
+                foundLocation = location;
+                LOG.trace(Ix4 + "Metadata found: [" + location + "]");
+                break;
+            } catch (IOException ignore) {
+                LOG.trace(Ix4 + "Metadata not found: [" + location + "]");
+            }
+        }
+        if (inputStream == null) {
+            throw new IOException("Metadata not found in repository [" + repositoryURL + "]");
+        }
+        try {
+            return XmlUtils.parseDoc(inputStream);
+        } catch (ParserConfigurationException e) {
+            throw initIOException("Metadata [" + foundLocation + "] could not be parsed.", e);
+        } catch (SAXException e) {
+            throw initIOException("Metadata [" + foundLocation + "] could not be parsed.", e);
+        }
+    }
+
+    /**
+     * Returns a downloadable artifact where the version is fully specified.
+     *
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @return a downloadable artifact
+     * @throws IOException re-thrown
+     */
+    private DownloadableArtifact resolveExactVersion(final Parser parser,
+                                                     final MavenRepositoryURL repositoryURL,
+                                                     final int priority)
+            throws IOException {
+        if (!repositoryURL.isReleasesEnabled()) {
+            throw new IOException("Releases not enabled");
+        }
+        LOG.debug(Ix2 + "Resolving exact version");
+        return new DownloadableArtifact(
+                parser.getVersion(),
+                priority,
+                repositoryURL.getURL(),
+                parser.getArtifactPath(),
+                false, // no local built snapshot
+                configuration.getCertificateCheck()
+        );
+    }
+
+    /**
+     * Resolves the latest version of the artifact.
+     *
+     * @param metadata      parsed metadata xml
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @return a downloadable artifact or throw an IOException if latest version cannot be determined.
+     * @throws IOException if the artifact could not be resolved
+     */
+    private DownloadableArtifact resolveLatestVersion(final Parser parser,
+                                                      final Document metadata,
+                                                      final MavenRepositoryURL repositoryURL,
+                                                      final int priority)
+            throws IOException {
+        LOG.debug(Ix2 + "Resolving latest version");
+        final String version = XmlUtils.getTextContentOfElement(metadata, "versioning/versions/version[last]");
+        if (version != null) {
+            if (version.endsWith("SNAPSHOT")) {
+                return resolveSnapshotVersion(parser, repositoryURL, priority, version);
+            } else {
+                return new DownloadableArtifact(
+                        version,
+                        priority,
+                        repositoryURL.getURL(),
+                        parser.getArtifactPath(version),
+                        false, // no local built snapshot
+                        configuration.getCertificateCheck()
+                );
+            }
+        }
+        throw new IOException("LATEST version could not be resolved.");
+    }
+
+    /**
+     * Resolves snapshot version of the artifact.
+     * Snapshot versions are resolved by parsing the metadata within the directory that contains the version as:
+     * 1. if the metadata containes entries like "versioning/snapshot/timestamp (most likely on remote repos) it will
+     * use the timestamp and buildnumber to point the real version
+     * 2. if the metatdata does not contain the above (most likely a local repo) it will use as version the
+     * versioning/lastUpdated
+     *
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @param version       snapshot version to resolve
+     * @return an input stream to the artifact
+     * @throws IOException if the artifact could not be resolved
+     */
+    private DownloadableArtifact resolveSnapshotVersion(final Parser parser,
+                                                        final MavenRepositoryURL repositoryURL,
+                                                        final int priority,
+                                                        final String version)
+            throws IOException {
+        if (!repositoryURL.isSnapshotsEnabled()) {
+            throw new IOException("Snapshots not enabled");
+        }
+        LOG.debug(Ix2 + "Resolving snapshot version [" + version + "]");
+        try {
+            final Document snapshotMetadata = getMetadata(repositoryURL.getURL(),
+                    new String[]
+                            {
+                                    parser.getVersionLocalMetadataPath(version),
+                                    parser.getVersionMetadataPath(version)
+                            }
+            );
+            final String timestamp =
+                    XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/snapshot/timestamp");
+            final String buildNumber =
+                    XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/snapshot/buildNumber");
+            final String localSnapshot =
+                    XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/snapshot/localCopy");
+            if (timestamp != null && buildNumber != null) {
+                return new DownloadableArtifact(
+                        parser.getSnapshotVersion(version, timestamp, buildNumber),
+                        priority,
+                        repositoryURL.getURL(),
+                        parser.getSnapshotPath(version, timestamp, buildNumber),
+                        localSnapshot != null,
+                        configuration.getCertificateCheck()
+                );
+            } else {
+                String lastUpdated = XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/lastUpdated");
+                if (lastUpdated != null) {
+                    // last updated should contain in the first 8 chars the date and then the time,
+                    // fact that is not compatible with timeStamp from remote repos which has a "." after date
+                    if (lastUpdated.length() > 8) {
+                        lastUpdated = lastUpdated.substring(0, 8) + "." + lastUpdated.substring(8);
+                        return new DownloadableArtifact(
+                                parser.getSnapshotVersion(version, lastUpdated, "0"),
+                                priority,
+                                repositoryURL.getURL(),
+                                parser.getArtifactPath(version),
+                                localSnapshot != null,
+                                configuration.getCertificateCheck()
+                        );
+                    }
+                }
+            }
+        } catch (IOException ignore) {
+            // in this case we could not find any metadata so try to get the *-SNAPSHOT file directly
+        }
+        return new DownloadableArtifact(
+                parser.getVersion(),
+                priority,
+                repositoryURL.getURL(),
+                parser.getArtifactPath(),
+                false, // no local built snapshot
+                configuration.getCertificateCheck()
+        );
+    }
+
+    /**
+     * Resolves all versions that fits the provided range.
+     *
+     * @param metadata      parsed metadata xml
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @param versionRange  version range to fulfill
+     * @return list of downloadable artifacts that match the range
+     * @throws IOException re-thrown
+     */
+    private List<DownloadableArtifact> resolveRangeVersions(final Parser parser,
+                                                            final Document metadata,
+                                                            final MavenRepositoryURL repositoryURL,
+                                                            final int priority,
+                                                            final VersionRange versionRange)
+            throws IOException {
+        LOG.debug(Ix2 + "Resolving versions in range [" + versionRange + "]");
+        final List<DownloadableArtifact> downladables = new ArrayList<DownloadableArtifact>();
+        final List<Element> elements = XmlUtils.getElements(metadata, "versioning/versions/version");
+        if (elements != null && elements.size() > 0) {
+            for (Element element : elements) {
+                final String versionString = XmlUtils.getTextContent(element);
+                if (versionString != null) {
+                    final Version version = new Version(versionString);
+                    if (versionRange.includes(version)) {
+                        if (versionString.endsWith("SNAPSHOT")) {
+                            downladables.add(
+                                    resolveSnapshotVersion(parser, repositoryURL, priority, versionString)
+                            );
+                        } else {
+                            downladables.add(
+                                    new DownloadableArtifact(
+                                            versionString,
+                                            priority,
+                                            repositoryURL.getURL(),
+                                            parser.getArtifactPath(versionString),
+                                            false, // no local built snapshot
+                                            configuration.getCertificateCheck()
+                                    )
+                            );
+                        }
+                    }
+                }
+            }
+        }
+        return downladables;
+    }
+
+    /**
+     * @param repositoryURL url to reporsitory
+     * @param path          a path to the artifact jar file
+     * @return prepared input stream
+     * @throws IOException re-thrown
+     * @see org.ops4j.net.URLUtils#prepareInputStream(java.net.URL, boolean)
+     */
+    private InputStream prepareInputStream(URL repositoryURL, final String path)
+            throws IOException {
+        String repository = repositoryURL.toExternalForm();
+        if (!repository.endsWith(org.ops4j.pax.url.mvn.internal.Parser.FILE_SEPARATOR)) {
+            repository = repository + org.ops4j.pax.url.mvn.internal.Parser.FILE_SEPARATOR;
+        }
+        configuration.enableProxy(repositoryURL);
+        final URL url = new URL(repository + path);
+        LOG.trace("Reading " + url.toExternalForm());
+        return URLUtils.prepareInputStream(url, !configuration.getCertificateCheck());
+    }
+
+    /**
+     * Sorting comparator for downladable artifacts.
+     * The sorting is done by:
+     * 1. descending version
+     * 2. ascending priority.
+     */
+    private static class DownloadComparator
+            implements Comparator<DownloadableArtifact> {
+
+        public int compare(final DownloadableArtifact first,
+                           final DownloadableArtifact second) {
+            // first descending by version
+            int result = -1 * first.getVersion().compareTo(second.getVersion());
+            if (result == 0) {
+                // then ascending by priority
+                if (first.getPriority() < second.getPriority()) {
+                    result = -1;
+                } else if (first.getPriority() > second.getPriority()) {
+                    result = 1;
+                }
+            }
+            return result;
+        }
+
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_74c02c_a4658a_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#DataStoreManager.java

@@ -0,0 +1,189 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.fabric.service;
+
+import java.util.Dictionary;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.concurrent.CopyOnWriteArrayList;
+
+import org.apache.felix.scr.annotations.Activate;
+import org.apache.felix.scr.annotations.Component;
+import org.apache.felix.scr.annotations.Deactivate;
+import org.apache.felix.scr.annotations.Reference;
+import org.apache.felix.scr.annotations.ReferencePolicy;
+import org.apache.felix.scr.annotations.Service;
+import org.fusesource.fabric.api.DataStore;
+import org.fusesource.fabric.api.DataStorePlugin;
+import org.fusesource.fabric.api.DataStoreRegistrationHandler;
+import org.fusesource.fabric.api.DataStoreTemplate;
+import org.fusesource.fabric.api.FabricException;
+import org.fusesource.fabric.api.PlaceholderResolver;
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.ServiceRegistration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.apache.felix.scr.annotations.ReferenceCardinality.OPTIONAL_MULTIPLE;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getProperties;
+
+/**
+ * Manager of {@link DataStore} using configuration to decide which
+ * implementation to export.
+ */
+@Component(name = "org.fusesource.fabric.datastore.manager",
+        description = "Configured DataStore Factory",
+        immediate = true)
+@Service(DataStoreRegistrationHandler.class)
+public class DataStoreManager implements DataStoreRegistrationHandler {
+    private static final transient Logger LOG = LoggerFactory.getLogger(DataStoreManager.class);
+
+    public static final String DATASTORE_TYPE_PID = "org.fusesource.fabric.datastore";
+    public static final String DATASTORE_TYPE_PROPERTY = "type";
+    public static final String DEFAULT_DATASTORE_TYPE = "git";
+
+
+    @Reference(cardinality = OPTIONAL_MULTIPLE,
+            referenceInterface = DataStorePlugin.class,
+            bind = "bindDataStore", unbind = "unbindDataStore",
+            policy = ReferencePolicy.DYNAMIC)
+    private final Map<String, DataStorePlugin> dataStorePlugins = new HashMap<String, DataStorePlugin>();
+
+    private BundleContext bundleContext;
+    private Map<String,String> configuration;
+
+    private String type;
+    private DataStore dataStore;
+    private Dictionary<String, String> properties = new Hashtable<String, String>();
+    private ServiceRegistration<DataStore> registration;
+
+    private final List<DataStoreTemplate> registrationCallbacks = new CopyOnWriteArrayList<DataStoreTemplate>();
+
+
+    @Activate
+    public synchronized void init(BundleContext bundleContext, Map<String,String> configuration) throws Exception {
+        this.bundleContext = bundleContext;
+        this.configuration = configuration;
+        this.type = readType(configuration);
+        updateServiceRegistration();
+    }
+
+    @Deactivate
+    public synchronized void destroy() {
+        unregister();
+    }
+
+    public void updateServiceRegistration() {
+        unregister();
+        if (dataStorePlugins.containsKey(type)) {
+            dataStore = dataStorePlugins.get(type).getDataStore();
+            Properties dataStoreProperties = new Properties();
+            dataStoreProperties.putAll(configuration);
+            dataStore.setDataStoreProperties(dataStoreProperties);
+            dataStore.start();
+            for(DataStoreTemplate callback : registrationCallbacks) {
+                registrationCallbacks.remove(callback);
+                try {
+                    callback.doWith(dataStore);
+                } catch (Exception e) {
+                    throw new FabricException(e);
+                }
+            }
+            properties.put(DATASTORE_TYPE_PROPERTY, type);
+            registration = bundleContext.registerService(DataStore.class, dataStore, properties);
+            LOG.info("Registered DataStore " + dataStore + " with " + properties);
+        }
+    }
+
+    /**
+     * Unregisters the {@link DataStore}.
+     */
+    private void unregister() {
+        if (registration != null) {
+            registration.unregister();
+            registration = null;
+        }
+        if (dataStore != null) {
+            dataStore.stop();
+        }
+    }
+
+    /**
+     * Extracts the type from the specified map or System configuration.
+     * @param configuration The map to use as a source.
+     * @return
+     */
+    private static String readType(Map<String, String> configuration) {
+        if (configuration.containsKey(DATASTORE_TYPE_PROPERTY)) {
+            return configuration.get(DATASTORE_TYPE_PROPERTY);
+        } else {
+            return System.getProperty(DATASTORE_TYPE_PID + "." + DATASTORE_TYPE_PROPERTY, DEFAULT_DATASTORE_TYPE);
+        }
+    }
+
+
+    // Properties
+    //-------------------------------------------------------------------------
+
+    public BundleContext getBundleContext() {
+        return bundleContext;
+    }
+
+    public void setBundleContext(BundleContext bundleContext) {
+        this.bundleContext = bundleContext;
+    }
+
+
+    public synchronized void bindDataStore(DataStorePlugin dataStorePlugin) {
+        if (dataStorePlugin != null) {
+            dataStorePlugins.put(dataStorePlugin.getName(), dataStorePlugin);
+            if (type.equals(dataStorePlugin.getName())) {
+                updateServiceRegistration();
+            }
+        }
+    }
+
+    public synchronized void unbindDataStore(DataStorePlugin dataStorePlugin) {
+        if (dataStorePlugin != null) {
+            dataStorePlugins.remove(dataStorePlugin.getName());
+            if (type.equals(dataStorePlugin.getName())) {
+                updateServiceRegistration();
+            }
+        }
+    }
+
+    public Map<String, String> getConfiguration() {
+        return configuration;
+    }
+
+    public void setConfiguration(Map<String, String> configuration) {
+        this.configuration = configuration;
+    }
+
+    @Override
+    public void addRegistrationCallback(DataStoreTemplate template) {
+        this.registrationCallbacks.add(template);
+    }
+
+    @Override
+    public void removeRegistrationCallback(DataStoreTemplate template) {
+        this.registrationCallbacks.remove(template);
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_b0e8c7_602ea9_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#AbstractDataStore.java

@@ -0,0 +1,713 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.fabric.service;
+
+import org.apache.curator.framework.CuratorFramework;
+import org.apache.curator.framework.recipes.cache.PathChildrenCacheEvent;
+import org.apache.curator.framework.recipes.cache.PathChildrenCacheListener;
+import org.apache.curator.framework.recipes.cache.TreeCache;
+import org.apache.zookeeper.KeeperException;
+import org.fusesource.fabric.api.CreateContainerMetadata;
+import org.fusesource.fabric.api.CreateContainerOptions;
+import org.fusesource.fabric.api.DataStore;
+import org.fusesource.fabric.api.DynamicReference;
+import org.fusesource.fabric.api.FabricException;
+import org.fusesource.fabric.api.PlaceholderResolver;
+import org.fusesource.fabric.api.jcip.GuardedBy;
+import org.fusesource.fabric.api.jcip.ThreadSafe;
+import org.fusesource.fabric.api.scr.AbstractComponent;
+import org.fusesource.fabric.api.scr.InvalidComponentException;
+import org.fusesource.fabric.api.scr.ValidatingReference;
+import org.fusesource.fabric.internal.DataStoreHelpers;
+import org.fusesource.fabric.utils.Base64Encoder;
+import org.fusesource.fabric.utils.Closeables;
+import org.fusesource.fabric.utils.ObjectUtils;
+import org.fusesource.fabric.zookeeper.ZkDefs;
+import org.fusesource.fabric.zookeeper.ZkPath;
+import org.fusesource.fabric.zookeeper.utils.InterpolationHelper;
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.FrameworkUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InvalidClassException;
+import java.io.ObjectInputStream;
+import java.io.ObjectStreamClass;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import static org.fusesource.fabric.internal.DataStoreHelpers.substituteBundleProperty;
+import static org.fusesource.fabric.internal.PlaceholderResolverHelpers.getSchemesForProfileConfigurations;
+import static org.fusesource.fabric.internal.PlaceholderResolverHelpers.waitForPlaceHolderResolvers;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.deleteSafe;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.exists;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getByteData;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getChildren;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getStringData;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getSubstitutedPath;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.setData;
+
+@ThreadSafe
+public abstract class AbstractDataStore extends AbstractComponent implements DataStore, PathChildrenCacheListener {
+
+    private static final transient Logger LOG = LoggerFactory.getLogger(AbstractDataStore.class);
+
+    public static final String REQUIREMENTS_JSON_PATH = "/fabric/configs/org.fusesource.fabric.requirements.json";
+    public static final String JVM_OPTIONS_PATH = "/fabric/configs/org.fusesource.fabric.containers.jvmOptions";
+
+    private final ValidatingReference<CuratorFramework> curator = new ValidatingReference<CuratorFramework>();
+
+    private final ExecutorService callbacksExecutor = Executors.newSingleThreadExecutor();
+    private final ExecutorService cacheExecutor = Executors.newSingleThreadExecutor();
+    private final ExecutorService placeholderExecutor = Executors.newCachedThreadPool();
+    private final AtomicBoolean active = new AtomicBoolean(false);
+
+    @GuardedBy("ConcurrentHashMap") private final ConcurrentMap<String, DynamicReference<PlaceholderResolver>> placeholderResolvers = new ConcurrentHashMap<String, DynamicReference<PlaceholderResolver>>();
+    @GuardedBy("CopyOnWriteArrayList") private final CopyOnWriteArrayList<Runnable> callbacks = new CopyOnWriteArrayList<Runnable>();
+    @GuardedBy("this") private Map<String, String> dataStoreProperties;
+    @GuardedBy("active") private volatile TreeCache treeCache;
+
+    @Override
+    public abstract void importFromFileSystem(String from);
+
+    @Override
+    public void start() {
+        try {
+            if (active.compareAndSet(false, true)) {
+                LOG.info("Starting up DataStore " + this);
+                treeCache = new TreeCache(getCurator(), ZkPath.CONFIGS.getPath(), true, false, true, cacheExecutor);
+                treeCache.start(TreeCache.StartMode.NORMAL);
+                treeCache.getListenable().addListener(this);
+            }
+        } catch (FabricException ex) {
+            throw ex;
+        } catch (Exception ex) {
+            throw new FabricException("Failed to start data store.", ex);
+        }
+    }
+
+    @Override
+    public void stop() {
+        if (active.compareAndSet(true, false)) {
+            treeCache.getListenable().removeListener(this);
+            Closeables.closeQuitely(treeCache);
+            treeCache = null;
+
+            callbacksExecutor.shutdownNow();
+            cacheExecutor.shutdownNow();
+            placeholderExecutor.shutdownNow();
+        }
+    }
+
+    protected TreeCache getTreeCache() {
+        if (!active.get())
+            throw new InvalidComponentException();
+        return treeCache;
+    }
+
+    @Override
+    public synchronized Map<String, String> getDataStoreProperties() {
+        assertValid();
+        return Collections.unmodifiableMap(dataStoreProperties);
+    }
+
+    @Override
+    public synchronized void setDataStoreProperties(Map<String, String> dataStoreProperties) {
+        assertValid();
+        this.dataStoreProperties = new HashMap<String, String>(dataStoreProperties);
+    }
+
+    @Override
+    public void childEvent(CuratorFramework client, PathChildrenCacheEvent event) throws Exception {
+        if (isValid()) {
+            switch (event.getType()) {
+            case CHILD_ADDED:
+            case CHILD_REMOVED:
+            case CHILD_UPDATED:
+            case INITIALIZED:
+                runCallbacks();
+                break;
+        }
+        }
+    }
+
+    protected void runCallbacks() {
+        callbacksExecutor.submit(new Runnable() {
+            @Override
+            public void run() {
+                doRunCallbacks();
+            }
+        });
+    }
+
+    protected void doRunCallbacks() {
+        assertValid();
+        for (Runnable callback : callbacks) {
+            try {
+                if (LOG.isDebugEnabled()) {
+                    LOG.debug("Running callback " + callback);
+                }
+                callback.run();
+            } catch (Throwable e) {
+                LOG.warn("Caught: " + e, e);
+            }
+        }
+    }
+
+    @Override
+    public void trackConfiguration(Runnable callback) {
+        if (isValid()) {
+            callbacks.addIfAbsent(callback);
+        }
+    }
+
+    @Override
+    public void untrackConfiguration(Runnable callback) {
+        callbacks.remove(callback);
+    }
+
+    // PlaceholderResolver stuff
+    //-------------------------------------------------------------------------
+
+    /**
+     * Performs substitution to configuration based on the registered {@link PlaceholderResolver} instances.
+     */
+    public void substituteConfigurations(final Map<String, Map<String, String>> configs) {
+        assertValid();
+
+        //Check for all required resolver schemes.
+        Set<String> requiredSchemes = getSchemesForProfileConfigurations(configs);
+        for (String scheme : requiredSchemes) {
+            placeholderResolvers.putIfAbsent(scheme, new DynamicReference<PlaceholderResolver>());
+        }
+
+        //Wait for resolvers before starting to resolve.
+        final Map<String, PlaceholderResolver> availableResolvers = waitForPlaceHolderResolvers(placeholderExecutor, requiredSchemes, getPlaceholderResolvers());
+
+        for (Map.Entry<String, Map<String, String>> entry : configs.entrySet()) {
+            final String pid = entry.getKey();
+            Map<String, String> props = entry.getValue();
+
+            for (Map.Entry<String, String> e : props.entrySet()) {
+                final String key = e.getKey();
+                final String value = e.getValue();
+                props.put(key, InterpolationHelper.substVars(value, key, null, props, new InterpolationHelper.SubstitutionCallback() {
+                    public String getValue(String toSubstitute) {
+                        if (toSubstitute != null && toSubstitute.contains(":")) {
+                            String scheme = toSubstitute.substring(0, toSubstitute.indexOf(":"));
+                            if (availableResolvers.containsKey(scheme)) {
+                                return availableResolvers.get(scheme).resolve(pid, key, toSubstitute);
+                            }
+                        }
+                        return substituteBundleProperty(toSubstitute, getBundleContext());
+                    }
+                }));
+            }
+        }
+    }
+
+    private Map<String, DynamicReference<PlaceholderResolver>> getPlaceholderResolvers() {
+        return Collections.unmodifiableMap(placeholderResolvers);
+    }
+
+    private BundleContext getBundleContext() {
+        try {
+            return FrameworkUtil.getBundle(AbstractDataStore.class).getBundleContext();
+        } catch (Throwable t) {
+            return null;
+        }
+    }
+
+    // Container stuff
+    //-------------------------------------------------------------------------
+
+    @Override
+    public List<String> getContainers() {
+        assertValid();
+        try {
+            return getChildren(getCurator(), ZkPath.CONFIGS_CONTAINERS.getPath());
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public boolean hasContainer(String containerId) {
+        assertValid();
+        return getContainers().contains(containerId);
+    }
+
+    @Override
+    public String getContainerParent(String containerId) {
+        assertValid();
+        try {
+            String parentName = getStringData(getCurator(), ZkPath.CONTAINER_PARENT.getPath(containerId));
+            return parentName != null ? parentName.trim() : "";
+        } catch (KeeperException.NoNodeException e) {
+            // Ignore
+            return "";
+        } catch (Throwable e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void deleteContainer(String containerId) {
+        assertValid();
+        try {
+            if (getCurator() == null) {
+                throw new IllegalStateException("Zookeeper service not available");
+            }
+            //Wipe all config entries that are related to the container for all versions.
+            for (String version : getVersions()) {
+                deleteSafe(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(version, containerId));
+            }
+            deleteSafe(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            deleteSafe(getCurator(), ZkPath.CONTAINER.getPath(containerId));
+            deleteSafe(getCurator(), ZkPath.CONTAINER_DOMAINS.getPath(containerId));
+            deleteSafe(getCurator(), ZkPath.CONTAINER_PROVISION.getPath(containerId));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void createContainerConfig(CreateContainerOptions options) {
+        assertValid();
+        try {
+            String parent = options.getParent();
+            String containerId = options.getName();
+            String versionId = options.getVersion();
+            Set<String> profileIds = options.getProfiles();
+            StringBuilder sb = new StringBuilder();
+            for (String profileId : profileIds) {
+                if (sb.length() > 0) {
+                    sb.append(" ");
+                }
+                sb.append(profileId);
+            }
+
+            setData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId), versionId);
+            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), sb.toString());
+            setData(getCurator(), ZkPath.CONTAINER_PARENT.getPath(containerId), parent);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void createContainerConfig(CreateContainerMetadata metadata) {
+        assertValid();
+        try {
+            CreateContainerOptions options = metadata.getCreateOptions();
+            String containerId = metadata.getContainerName();
+//            String parent = options.getParent();
+//            String versionId = options.getVersion() != null ? options.getVersion() : getDefaultVersion();
+//            Set<String> profileIds = options.getProfiles();
+//            if (profileIds == null || profileIds.isEmpty()) {
+//                profileIds = new LinkedHashSet<String>();
+//                profileIds.add("default");
+//            }
+//            StringBuilder sb = new StringBuilder();
+//            for (String profileId : profileIds) {
+//                if (sb.length() > 0) {
+//                    sb.append(" ");
+//                }
+//                sb.append(profileId);
+//            }
+//
+//            setData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId), versionId);
+//            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), sb.toString());
+//            setData(getCurator(), ZkPath.CONTAINER_PARENT.getPath(containerId), parent);
+
+            setContainerMetadata(metadata);
+
+            Map<String, String> configuration = metadata.getContainerConfiguration();
+            for (Map.Entry<String, String> entry : configuration.entrySet()) {
+                String key = entry.getKey();
+                String value = entry.getValue();
+                setData(getCurator(), ZkPath.CONTAINER_ENTRY.getPath(metadata.getContainerName(), key), value);
+            }
+
+            // If no resolver specified but a resolver is already present in the registry, use the registry value
+            String resolver = metadata.getOverridenResolver() != null ? metadata.getOverridenResolver() : options.getResolver();
+
+            if (resolver == null && exists(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId)) != null) {
+                resolver = getStringData(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId));
+            } else if (options.getResolver() != null) {
+                // Use the resolver specified in the options and do nothing.
+            } else if (exists(getCurator(), ZkPath.POLICIES.getPath(ZkDefs.RESOLVER)) != null) {
+                // If there is a globlal resolver specified use it.
+                resolver = getStringData(getCurator(), ZkPath.POLICIES.getPath(ZkDefs.RESOLVER));
+            } else {
+                // Fallback to the default resolver
+                resolver = ZkDefs.DEFAULT_RESOLVER;
+            }
+            // Set the resolver if not already set
+            setData(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId), resolver);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public CreateContainerMetadata getContainerMetadata(String containerId, final ClassLoader classLoader) {
+        assertValid();
+        try {
+            byte[] encoded = getByteData(getTreeCache(), ZkPath.CONTAINER_METADATA.getPath(containerId));
+            if (encoded == null) {
+                return null;
+            }
+            byte[] decoded = Base64Encoder.decode(encoded);
+            ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(decoded)) {
+                @Override
+                protected Class<?> resolveClass(ObjectStreamClass desc) throws IOException, ClassNotFoundException {
+                    return classLoader.loadClass(desc.getName());
+                }
+            };
+            return (CreateContainerMetadata) ois.readObject();
+        } catch (ClassNotFoundException e) {
+            return null;
+        } catch (InvalidClassException e) {
+            return null;
+        } catch (KeeperException.NoNodeException e) {
+            return null;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setContainerMetadata(CreateContainerMetadata metadata) {
+        assertValid();
+        //We encode the metadata so that they are more friendly to import/export.
+        try {
+            setData(getCurator(), ZkPath.CONTAINER_METADATA.getPath(metadata.getContainerName()), Base64Encoder.encode(ObjectUtils.toBytes(metadata)));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public String getContainerVersion(String containerId) {
+        assertValid();
+        try {
+            return getStringData(getTreeCache(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setContainerVersion(String containerId, String versionId) {
+        assertValid();
+        try {
+            String oldVersionId = getStringData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            String oldProfileIds = getStringData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(oldVersionId, containerId));
+
+            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), oldProfileIds);
+            setData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId), versionId);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public List<String> getContainerProfiles(String containerId) {
+        assertValid();
+        try {
+            String versionId = getStringData(getTreeCache(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            String str = getStringData(getTreeCache(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId));
+            return str == null || str.isEmpty() ? Collections.<String> emptyList() : Arrays.asList(str.trim().split(" +"));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setContainerProfiles(String containerId, List<String> profileIds) {
+        assertValid();
+        try {
+            String versionId = getStringData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            StringBuilder sb = new StringBuilder();
+            for (String profileId : profileIds) {
+                if (sb.length() > 0) {
+                    sb.append(" ");
+                }
+                sb.append(profileId);
+            }
+            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), sb.toString());
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public boolean isContainerAlive(String id) {
+        assertValid();
+        try {
+            return exists(getCurator(), ZkPath.CONTAINER_ALIVE.getPath(id)) != null;
+        } catch (KeeperException.NoNodeException e) {
+            return false;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public String getContainerAttribute(String containerId, ContainerAttribute attribute, String def, boolean mandatory, boolean substituted) {
+        assertValid();
+        if (attribute == ContainerAttribute.Domains) {
+            try {
+                List<String> list = getCurator().getChildren().forPath(ZkPath.CONTAINER_DOMAINS.getPath(containerId));
+                Collections.sort(list);
+                StringBuilder sb = new StringBuilder();
+                for (String l : list) {
+                    if (sb.length() > 0) {
+                        sb.append("\n");
+                    }
+                    sb.append(l);
+                }
+                return sb.toString();
+            } catch (Exception e) {
+                return "";
+            }
+        } else {
+            try {
+                if (substituted) {
+                    return getSubstitutedPath(getCurator(), getAttributePath(containerId, attribute));
+                } else {
+                    return getStringData(getCurator(), getAttributePath(containerId, attribute));
+                }
+            } catch (KeeperException.NoNodeException e) {
+                if (mandatory) {
+                    throw FabricException.launderThrowable(e);
+                }
+                return def;
+            } catch (Exception e) {
+                throw FabricException.launderThrowable(e);
+            }
+        }
+    }
+
+    @Override
+    public void setContainerAttribute(String containerId, ContainerAttribute attribute, String value) {
+        assertValid();
+        // Special case for resolver
+        // TODO: we could use a double indirection on the ip so that it does not need to change
+        // TODO: something like ${zk:container/${zk:container/resolver}}
+        if (attribute == ContainerAttribute.Resolver) {
+            try {
+                setData(getCurator(), ZkPath.CONTAINER_IP.getPath(containerId), "${zk:" + containerId + "/" + value + "}");
+                setData(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId), value);
+            } catch (Exception e) {
+                throw FabricException.launderThrowable(e);
+            }
+        } else {
+            try {
+                //                if (value == null) {
+                //                    deleteSafe(zk, getAttributePath(containerId, attribute));
+                //                } else {
+                setData(getCurator(), getAttributePath(containerId, attribute), value);
+                //                }
+            } catch (KeeperException.NoNodeException e) {
+                // Ignore
+            } catch (Exception e) {
+                throw FabricException.launderThrowable(e);
+            }
+        }
+    }
+
+    @Override
+    public String getDefaultVersion() {
+        assertValid();
+        try {
+            String version = null;
+            if (getTreeCache().getCurrentData(ZkPath.CONFIG_DEFAULT_VERSION.getPath()) != null) {
+                version = getStringData(getTreeCache(), ZkPath.CONFIG_DEFAULT_VERSION.getPath());
+            }
+            if (version == null || version.isEmpty()) {
+                version = ZkDefs.DEFAULT_VERSION;
+                setData(getCurator(), ZkPath.CONFIG_DEFAULT_VERSION.getPath(), version);
+                setData(getCurator(), ZkPath.CONFIG_VERSION.getPath(version), (String) null);
+            }
+            return version;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setDefaultVersion(String versionId) {
+        assertValid();
+        try {
+            setData(getCurator(), ZkPath.CONFIG_DEFAULT_VERSION.getPath(), versionId);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    // Profile methods
+    //-------------------------------------------------------------------------
+
+    @Override
+    public boolean hasProfile(String version, String profile) {
+        assertValid();
+        return getProfile(version, profile, false) != null;
+    }
+
+    // Implementation
+    //-------------------------------------------------------------------------
+
+    private String getAttributePath(String containerId, ContainerAttribute attribute) {
+        switch (attribute) {
+        case BlueprintStatus:
+            return ZkPath.CONTAINER_EXTENDER_STATUS.getPath(containerId, "blueprint");
+        case SpringStatus:
+            return ZkPath.CONTAINER_EXTENDER_STATUS.getPath(containerId, "spring");
+        case ProvisionStatus:
+            return ZkPath.CONTAINER_PROVISION_RESULT.getPath(containerId);
+        case ProvisionException:
+            return ZkPath.CONTAINER_PROVISION_EXCEPTION.getPath(containerId);
+        case ProvisionList:
+            return ZkPath.CONTAINER_PROVISION_LIST.getPath(containerId);
+        case Location:
+            return ZkPath.CONTAINER_LOCATION.getPath(containerId);
+        case GeoLocation:
+            return ZkPath.CONTAINER_GEOLOCATION.getPath(containerId);
+        case Resolver:
+            return ZkPath.CONTAINER_RESOLVER.getPath(containerId);
+        case Ip:
+            return ZkPath.CONTAINER_IP.getPath(containerId);
+        case LocalIp:
+            return ZkPath.CONTAINER_LOCAL_IP.getPath(containerId);
+        case LocalHostName:
+            return ZkPath.CONTAINER_LOCAL_HOSTNAME.getPath(containerId);
+        case PublicIp:
+            return ZkPath.CONTAINER_PUBLIC_IP.getPath(containerId);
+        case PublicHostName:
+            return ZkPath.CONTAINER_PUBLIC_HOSTNAME.getPath(containerId);
+        case ManualIp:
+            return ZkPath.CONTAINER_MANUAL_IP.getPath(containerId);
+        case BindAddress:
+            return ZkPath.CONTAINER_BINDADDRESS.getPath(containerId);
+        case JmxUrl:
+            return ZkPath.CONTAINER_JMX.getPath(containerId);
+        case JolokiaUrl:
+            return ZkPath.CONTAINER_JOLOKIA.getPath(containerId);
+        case HttpUrl:
+            return ZkPath.CONTAINER_HTTP.getPath(containerId);
+        case SshUrl:
+            return ZkPath.CONTAINER_SSH.getPath(containerId);
+        case PortMin:
+            return ZkPath.CONTAINER_PORT_MIN.getPath(containerId);
+        case PortMax:
+            return ZkPath.CONTAINER_PORT_MAX.getPath(containerId);
+        case ProcessId:
+            return ZkPath.CONTAINER_PROCESS_ID.getPath(containerId);
+        case OpenShift:
+            return ZkPath.CONTAINER_OPENSHIFT.getPath(containerId);
+        default:
+            throw new IllegalArgumentException("Unsupported container attribute " + attribute);
+        }
+    }
+
+    @Override
+    public Map<String, String> getProfileAttributes(String version, String profile) {
+        assertValid();
+        Map<String, String> attributes = new HashMap<String, String>();
+        Map<String, String> config = getConfiguration(version, profile, AGENT_PID);
+        for (Map.Entry<String, String> entry : config.entrySet()) {
+            String key = entry.getKey();
+            if (key.startsWith(ATTRIBUTE_PREFIX)) {
+                String attribute = key.substring(ATTRIBUTE_PREFIX.length());
+                String value = entry.getValue();
+                attributes.put(attribute, value);
+            }
+        }
+        return attributes;
+    }
+
+    @Override
+    public void setProfileAttribute(final String version, final String profile, final String key, final String value) {
+        assertValid();
+        Map<String, String> config = getConfiguration(version, profile, AGENT_PID);
+        if (value != null) {
+            config.put(ATTRIBUTE_PREFIX + key, value);
+        } else {
+            config.remove(key);
+        }
+        setConfiguration(version, profile, AGENT_PID, config);
+    }
+
+    @Override
+    public Map<String, Map<String, String>> getConfigurations(String version, String profile) {
+        assertValid();
+        try {
+            Map<String, Map<String, String>> configurations = new HashMap<String, Map<String, String>>();
+            Map<String, byte[]> configs = getFileConfigurations(version, profile);
+            for (Map.Entry<String, byte[]> entry : configs.entrySet()) {
+                if (entry.getKey().endsWith(".properties")) {
+                    String pid = DataStoreHelpers.stripSuffix(entry.getKey(), ".properties");
+                    configurations.put(pid, DataStoreHelpers.toMap(DataStoreHelpers.toProperties(entry.getValue())));
+                }
+            }
+            return configurations;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    public CuratorFramework getCurator() {
+        return curator.get();
+    }
+
+    // [FIXME] Test case polutes public API
+    public void bindCuratorForTesting(CuratorFramework curator) {
+        bindCurator(curator);
+    }
+
+    protected void bindCurator(CuratorFramework curator) {
+        this.curator.bind(curator);
+    }
+
+    protected void unbindCurator(CuratorFramework curator) {
+        this.curator.unbind(curator);
+    }
+
+    protected void bindPlaceholderResolver(PlaceholderResolver resolver) {
+        placeholderResolvers.putIfAbsent(resolver.getScheme(), new DynamicReference<PlaceholderResolver>());
+        placeholderResolvers.get(resolver.getScheme()).bind(resolver);
+    }
+
+    protected void unbindPlaceholderResolver(PlaceholderResolver resolver) {
+        placeholderResolvers.get(resolver.getScheme()).unbind();
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_cb3362_cfb295_fabric#fabric-features-service#src#main#java#org#fusesource#fabric#features#FabricFeaturesServiceImpl.java

@@ -0,0 +1,399 @@
+package org.fusesource.fabric.features;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Collection;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+import org.apache.karaf.features.Feature;
+import org.apache.karaf.features.FeaturesService;
+import org.apache.karaf.features.Repository;
+import org.apache.karaf.features.internal.FeatureValidationUtil;
+import org.apache.karaf.features.internal.FeaturesServiceImpl;
+import org.apache.karaf.features.internal.RepositoryImpl;
+import org.apache.zookeeper.KeeperException;
+import org.fusesource.fabric.api.Container;
+import org.fusesource.fabric.api.FabricService;
+import org.fusesource.fabric.api.Profile;
+import org.fusesource.fabric.api.Version;
+import org.fusesource.fabric.zookeeper.IZKClient;
+import org.fusesource.fabric.zookeeper.ZkPath;
+import org.linkedin.zookeeper.client.LifecycleListener;
+import org.linkedin.zookeeper.tracker.NodeEvent;
+import org.linkedin.zookeeper.tracker.NodeEventsListener;
+import org.linkedin.zookeeper.tracker.ZKStringDataReader;
+import org.linkedin.zookeeper.tracker.ZooKeeperTreeTracker;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.fusesource.fabric.utils.features.FeatureUtils.search;
+
+/**
+ * A FeaturesService implementation for Fabric managed containers.
+ */
+public class FabricFeaturesServiceImpl extends FeaturesServiceImpl implements FeaturesService, NodeEventsListener<String>, LifecycleListener {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(FeaturesService.class);
+
+    private FabricService fabricService;
+    private IZKClient zooKeeper;
+
+    private ZooKeeperTreeTracker<String> profilesTracker;
+
+
+    private final Set<Repository> repositories = new HashSet<Repository>();
+    private final Set<Feature> allfeatures = new HashSet<Feature>();
+    private final Set<Feature> installed = new HashSet<Feature>();
+
+    public void init() throws Exception {
+    }
+
+    public void destroy() throws Exception {
+        profilesTracker.destroy();
+    }
+
+    @Override
+    public void onEvents(Collection<NodeEvent<String>> nodeEvents) {
+        try {
+            repositories.clear();
+            listRepositories();
+            allfeatures.clear();
+            listFeatures();
+            installed.clear();
+            listInstalledFeatures();
+        } catch (Exception e) {
+            LOGGER.error("Error while updating FeaturesService information from Fabric Registry.", e);
+        }
+
+    }
+
+    @Override
+    public void onConnected() {
+        profilesTracker = new ZooKeeperTreeTracker<String>(zooKeeper, new ZKStringDataReader(), ZkPath.CONFIG_VERSIONS.getPath());
+        try {
+            profilesTracker.track(this);
+        } catch (InterruptedException e) {
+            LOGGER.error("Error while setting tracker for Fabric Features Service.", e);
+        } catch (KeeperException e) {
+            LOGGER.error("Error while setting tracker for Fabric Features Service.", e);
+        }
+        onEvents(null);
+    }
+
+    @Override
+    public void onDisconnected() {
+    }
+
+    @Override
+    public void validateRepository(URI uri) throws Exception {
+        FeatureValidationUtil.validate(uri);
+    }
+
+    @Override
+    public void addRepository(URI uri) throws Exception {
+        addRepository(uri, true);
+    }
+
+    @Override
+    public void addRepository(URI uri, boolean b) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, please use fabric:profile-edit --repositories %s target-profile instead. See fabric:profile-edit for more information.", uri.toString()));
+    }
+
+    @Override
+    public void removeRepository(URI uri) throws Exception {
+        removeRepository(uri, true);
+    }
+
+    @Override
+    public void removeRepository(URI uri, boolean b) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, please use fabric:profile-edit --delete --repositories %s target-profile instead. See fabric:profile-edit for more information.", uri.toString()));
+    }
+
+    @Override
+    public void restoreRepository(URI uri) throws Exception {
+    }
+
+    /**
+     * Lists all {@link Repository} entries found in any {@link Profile} of the current {@link Container} {@link Version}.
+     *
+     * @return
+     */
+    @Override
+    public Repository[] listRepositories() {
+        if (repositories.isEmpty()) {
+            Set<String> repositoryUris = new LinkedHashSet<String>();
+            Container container = fabricService.getCurrentContainer();
+            Version version = container.getVersion();
+            Profile[] profiles = fabricService.getProfiles(version.getName());
+            if (profiles != null) {
+                for (Profile profile : profiles) {
+                    if (profile.getRepositories() != null) {
+                        for (String uri : profile.getRepositories()) {
+                            repositoryUris.add(uri);
+                            addRepositoryUri(uri, repositoryUris);
+                        }
+                    }
+                }
+            }
+
+            for (String uri : repositoryUris) {
+                try {
+                    repositories.add(new RepositoryImpl(new URI(uri)));
+                } catch (URISyntaxException e) {
+                    LOGGER.debug("Error while adding repository with uri {}.", uri);
+                }
+            }
+        }
+        return repositories.toArray(new Repository[repositories.size()]);
+    }
+
+    @Override
+    public void installFeature(String s) throws Exception {
+        installFeature(s, (EnumSet) null);
+    }
+
+    @Override
+    public void installFeature(String s, EnumSet<Option> options) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", s));
+    }
+
+    @Override
+    public void installFeature(String s, String s2) throws Exception {
+        installFeature(s, s2, null);
+    }
+
+    @Override
+    public void installFeature(String s, String s2, EnumSet<Option> options) throws Exception {
+        String featureName = s;
+        if (s2 != null && s2.equals("0.0.0")) {
+            featureName = s + "/" + s2;
+        }
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", featureName));
+    }
+
+    @Override
+    public void installFeature(Feature feature, EnumSet<Option> options) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", feature.getName()));
+    }
+
+    @Override
+    public void installFeatures(Set<Feature> features, EnumSet<Option> options) throws Exception {
+        StringBuffer sb = new StringBuffer();
+        for (Feature feature : features) {
+            sb.append("--feature ").append(feature.getName());
+        }
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", sb.toString()));
+    }
+
+    @Override
+    public void uninstallFeature(String s) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --delete --features %s target-profile instead. See fabric:profile-edit for more information.", s));
+    }
+
+    @Override
+    public void uninstallFeature(String s, String s2) throws Exception {
+        String featureName = s;
+        if (s2 != null && s2.equals("0.0.0")) {
+            featureName = s + "/" + s2;
+        }
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", featureName));
+    }
+
+    @Override
+    public Feature[] listFeatures() throws Exception {
+        if (allfeatures.isEmpty()) {
+            Repository[] repositories = listRepositories();
+            for (Repository repository : repositories) {
+                for (Feature feature : repository.getFeatures()) {
+                    if (!allfeatures.contains(feature)) {
+                        allfeatures.add(feature);
+                    }
+                }
+            }
+        }
+        return allfeatures.toArray(new Feature[allfeatures.size()]);
+    }
+
+    @Override
+    public Feature[] listInstalledFeatures() {
+        if (installed.isEmpty()) {
+            try {
+                Map<String, Map<String, Feature>> allFeatures = getFeatures(listProfileRepositories());
+                Container container = fabricService.getCurrentContainer();
+                Profile[] profiles = container.getProfiles();
+
+                if (profiles != null) {
+                    for (Profile profile : profiles) {
+                        List<String> featureNames = profile.getFeatures();
+                        for (String featureName : featureNames) {
+                            try {
+                                Feature f;
+                                if (featureName.contains("/")) {
+                                    String[] parts = featureName.split("/");
+                                    String name = parts[0];
+                                    String version = parts[1];
+                                    f = allFeatures.get(name).get(version);
+                                } else {
+                                    TreeMap<String, Feature> versionMap = (TreeMap<String, Feature>) allFeatures.get(featureName);
+                                    f = versionMap.lastEntry().getValue();
+                                }
+                                addFeatures(f, installed);
+                            } catch (Exception ex) {
+                                LOGGER.debug("Error while adding {} to the features list");
+                            }
+                        }
+                    }
+                }
+            } catch (Exception e) {
+                LOGGER.error("Error retrieveing features.", e);
+            }
+        }
+        return installed.toArray(new Feature[installed.size()]);
+    }
+
+
+    @Override
+    public boolean isInstalled(Feature feature) {
+        if (installed.isEmpty()) {
+            listInstalledFeatures();
+        }
+        return installed.contains(feature);
+    }
+
+
+    protected Map<String, Map<String, Feature>> getFeatures(Repository[] repositories) throws Exception {
+        Map<String, Map<String, Feature>> features = new HashMap<String, Map<String, Feature>>();
+        for (Repository repo : repositories) {
+            for (Feature f : repo.getFeatures()) {
+                if (features.get(f.getName()) == null) {
+                    Map<String, Feature> versionMap = new TreeMap<String, Feature>();
+                    versionMap.put(f.getVersion(), f);
+                    features.put(f.getName(), versionMap);
+                } else {
+                    features.get(f.getName()).put(f.getVersion(), f);
+                }
+            }
+        }
+        return features;
+    }
+
+
+    /**
+     * Lists all {@link Repository} enties found in the {@link Profile}s assigned to the current {@link Container}.
+     *
+     * @return
+     */
+    private Repository[] listProfileRepositories() {
+        Set<String> repositoryUris = new LinkedHashSet<String>();
+        Set<Repository> repositories = new LinkedHashSet<Repository>();
+        Container container = fabricService.getCurrentContainer();
+        Set<Profile> profilesWithParents = new HashSet<Profile>();
+
+        Profile[] profiles = container.getProfiles();
+        if (profiles != null) {
+            for (Profile profile : profiles) {
+                addProfiles(profile, profilesWithParents);
+            }
+            for (Profile profile : profilesWithParents) {
+                if (profile.getRepositories() != null) {
+                    for (String uri : profile.getRepositories()) {
+                        repositoryUris.add(uri);
+                        addRepositoryUri(uri, repositoryUris);
+                    }
+                }
+            }
+        }
+
+        for (String uri : repositoryUris) {
+            try {
+                repositories.add(new RepositoryImpl(new URI(uri)));
+            } catch (URISyntaxException e) {
+                LOGGER.debug("Error while adding repository with uri {}.", uri);
+            }
+        }
+        return repositories.toArray(new Repository[repositories.size()]);
+    }
+
+
+    /**
+     * Adds the {@link URI} of {@link Feature} {@link Repository} and its internals to the set of repositories {@link URI}s.
+     *
+     * @param uri
+     * @param repositoryUris
+     */
+    protected void addRepositoryUri(String uri, Set<String> repositoryUris) {
+        if (repositoryUris.contains(uri)) {
+            return;
+        }
+        repositoryUris.add(uri);
+        try {
+            Repository repository = new RepositoryImpl(new URI(uri));
+            URI[] internalUris = repository.getRepositories();
+            if (internalUris != null) {
+                for (URI u : internalUris) {
+                    addRepositoryUri(u.toString(), repositoryUris);
+                }
+            }
+        } catch (Exception e) {
+            LOGGER.debug("Error while adding internal repositories of {}.", uri);
+        }
+    }
+
+    /**
+     * Adds {@link Profile} and its parents to the set of {@link Profile}s.
+     *
+     * @param profile
+     * @param profiles
+     */
+    protected void addProfiles(Profile profile, Set<Profile> profiles) {
+        if (profiles.contains(profile)) {
+            return;
+        }
+
+        profiles.add(profile);
+        for (Profile parent : profile.getParents()) {
+            addProfiles(parent, profiles);
+        }
+    }
+
+    /**
+     * Adds {@link Feature} and its dependencies to the set of {@link Feature}s.
+     *
+     * @param feature
+     * @param features
+     */
+    protected void addFeatures(Feature feature, Set<Feature> features) {
+        if (features.contains(feature)) {
+            return;
+        }
+
+        features.add(feature);
+        for (Feature dependency : feature.getDependencies()) {
+            addFeatures(search(dependency.getName(), dependency.getVersion(), repositories), features);
+        }
+    }
+
+
+
+    public FabricService getFabricService() {
+        return fabricService;
+    }
+
+    public void setFabricService(FabricService fabricService) {
+        this.fabricService = fabricService;
+    }
+
+    public IZKClient getZooKeeper() {
+        return zooKeeper;
+    }
+
+    public void setZooKeeper(IZKClient zooKeeper) {
+        this.zooKeeper = zooKeeper;
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Export.java

@@ -0,0 +1,158 @@
+/**
+ * Copyright (C) 2011, FuseSource Corp.  All rights reserved.
+ * http://fusesource.com
+ *
+ * The software in this package is published under the terms of the
+ * CDDL license a copy of which has been included with this distribution
+ * in the license.txt file.
+ */
+package org.fusesource.fabric.zookeeper.commands;
+
+import org.apache.felix.gogo.commands.Argument;
+import org.apache.felix.gogo.commands.Command;
+import org.apache.felix.gogo.commands.Option;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.*;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.getPatterns;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.matches;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.merge;
+
+@Command(name = "export", scope = "zk", description = "Export data from zookeeper")
+public class Export extends ZooKeeperCommandSupport {
+
+    @Argument(description="path of the directory to export to")
+    String target = "." + File.separator + "export";
+
+    @Option(name="-f", aliases={"--regex"}, description="regex to filter on what paths to export, can specify this option more than once for additional filters", multiValued=true)
+    String regex[];
+
+    @Option(name="-rf", aliases={"--reverse-regex"}, description="regex to filter what paths to exclude from the export, can specify this option more than once for additional filters", multiValued=true)
+    String nregex[];
+
+    @Option(name="-p", aliases={"--path"}, description="Top level context to export")
+    String topLevel = "/";
+
+    @Option(name="-d", aliases={"--delete"}, description="Clear target directory before exporting (CAUTION! Performs recursive delete!)")
+    boolean delete;
+
+    @Option(name="--dry-run", description="Runs the export but instead prints out what's going to happen rather than performing the action")
+    boolean dryRun = false;
+
+    File ignore = new File(".fabricignore");
+    File include = new File(".fabricinclude");
+
+    @Override
+    protected Object doExecute() throws Exception {
+        if (ignore.exists() && ignore.isFile()) {
+            nregex = merge(ignore, nregex);
+        }
+        if (include.exists() && include.isFile()) {
+            regex = merge(include, regex);
+        }
+        export(topLevel);
+        System.out.printf("Export to %s completed successfully\n", target);
+        return null;
+    }
+
+    private void delete(File parent) throws Exception {
+        if (!parent.exists()) {
+            return;
+        }
+        if (parent.isDirectory()) {
+            for (File f : parent.listFiles()) {
+                delete(f);
+            }
+        }
+        parent.delete();
+    }
+
+    protected void export(String path) throws Exception {
+        if (!path.endsWith("/")) {
+            path = path + "/";
+        }
+        if (!path.startsWith("/")) {
+            path = "/" + path;
+        }
+        List<Pattern> include = getPatterns(regex);
+        List<Pattern> exclude = getPatterns(nregex);
+        List<String> paths = getZooKeeper().getAllChildren(path);
+        SortedSet<File> directories = new TreeSet<File>();
+        Map<File, String> settings = new HashMap<File, String>();
+
+        for(String p : paths) {
+            p = path + p;
+            if (!matches(include, p) || matches(exclude, p)) {
+                continue;
+            }
+            byte[] data = getZooKeeper().getData(p);
+            if (data != null) {
+                settings.put(new File(target + File.separator + p + ".cfg"), new String(data));
+            } else {
+                directories.add(new File(target + File.separator + p));
+            }
+        }
+
+        if (delete) {
+            if (!dryRun) {
+                delete(new File(target));
+            } else {
+                System.out.printf("Deleting %s and everything under it\n", new File(target));
+            }
+        }
+
+        for (File d : directories) {
+            if (d.exists() && !d.isDirectory()) {
+                throw new IllegalArgumentException("Directory " + d + " exists but is not a directory");
+            }
+            if (!d.exists()) {
+                if (!dryRun) {
+                    if (!d.mkdirs()) {
+                        throw new RuntimeException("Failed to create directory " + d);
+                    }
+                } else {
+                    System.out.printf("Creating directory path : %s\n", d);
+                }
+            }
+        }
+        for (File f : settings.keySet()) {
+            if (f.exists() && !f.isFile()) {
+                throw new IllegalArgumentException("File " + f + " exists but is not a file");
+            }
+            if (!f.getParentFile().exists()) {
+                if (!dryRun) {
+                    if (!f.getParentFile().mkdirs()) {
+                        throw new RuntimeException("Failed to create directory " + f.getParentFile());
+                    }
+                } else {
+                    System.out.printf("Creating directory path : %s\n", f);
+                }
+            }
+            if (!f.exists()) {
+                try {
+                    if (!dryRun) {
+                        if (!f.createNewFile()) {
+                            throw new RuntimeException("Failed to create file " + f);
+                        }
+                    } else {
+                        System.out.printf("Creating file : %s\n", f);
+                    }
+                } catch (IOException io) {
+                    throw new RuntimeException("Failed to create file " + f + " : " + io);
+                }
+            }
+            if (!dryRun) {
+                FileWriter writer = new FileWriter(f, false);
+                writer.write(settings.get(f));
+                writer.close();
+            } else {
+                System.out.printf("Writing value \"%s\" to file : %s\n", settings.get(f), f);
+            }
+        }
+    }
+}

richedit/src/main/resource/testFiles/fuse/prevFiles/prev_d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Import.java

@@ -0,0 +1,204 @@
+/**
+ * Copyright (C) 2011, FuseSource Corp.  All rights reserved.
+ * http://fusesource.com
+ *
+ * The software in this package is published under the terms of the
+ * CDDL license a copy of which has been included with this distribution
+ * in the license.txt file.
+ */
+package org.fusesource.fabric.zookeeper.commands;
+
+import org.apache.felix.gogo.commands.Argument;
+import org.apache.felix.gogo.commands.Command;
+import org.apache.felix.gogo.commands.Option;
+import org.apache.zookeeper.CreateMode;
+import org.apache.zookeeper.ZooDefs;
+
+import java.io.*;
+import java.net.URL;
+import java.util.*;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.getPatterns;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.matches;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.merge;
+
+@Command(name = "import", scope = "zk", description = "Import data into zookeeper")
+public class Import extends ZooKeeperCommandSupport {
+
+    @Argument(description = "Location of the file or filesystem to load")
+    protected String source = "." + File.separator + "import";
+
+    @Option(name="-d", aliases={"--delete"}, description="Delete any paths not in the tree being imported, ignored when importing a properties file (CAUTION!)")
+    boolean delete = false;
+
+    @Option(name="-t", aliases={"--target"}, description="Target location in ZooKeeper tree to import to")
+    String target = "/";
+
+    @Option(name="-props", aliases={"--properties"}, description="Argument is URL pointing to a properties file")
+    boolean properties = false;
+
+    @Option(name="-fs", aliases={"--filesystem"}, description="Argument is the top level directory of a local filesystem tree")
+    boolean filesystem = true;
+
+    @Option(name="-f", aliases={"--regex"}, description="regex to filter on what paths to import, can specify this option more than once for additional filters", multiValued=true)
+    String regex[];
+
+    @Option(name="-rf", aliases={"--reverse-regex"}, description="regex to filter what paths to exclude, can specify this option more than once for additional filters", multiValued=true)
+    protected String[] nregex;
+
+    @Option(name="--dry-run", description="Runs the import but prints out what's going to happen instead of making any changes")
+    boolean dryRun = false;
+
+    File ignore = new File(".fabricignore");
+    File include = new File(".fabricinclude");
+
+    @Override
+    protected Object doExecute() throws Exception {
+        if (ignore.exists() && ignore.isFile()) {
+            nregex = merge(ignore, nregex);
+        }
+        if (include.exists() && include.isFile()) {
+            regex = merge(include, regex);
+        }
+        if (properties == true) {
+            filesystem = false;
+        }
+        if (filesystem == true) {
+            properties = false;
+        }
+        if (properties) {
+            readPropertiesFile();
+        }
+        if (filesystem) {
+            readFileSystem();
+        }
+        System.out.println("Successfully imported settings from " + source);
+        return null;
+    }
+
+    private String stripPath(String path) {
+        String strs[] = path.split(source);
+        if (strs.length == 0) {
+            return "";
+        }
+        return strs[strs.length - 1].substring(0, strs[1].length() - ".cfg".length());
+    }
+
+    private String buildZKPath(File parent, File current) {
+        String rc = "";
+        if (current != null && !parent.equals(current)) {
+            rc = buildZKPath(parent, current.getParentFile()) + "/" + current.getName();
+        }
+        return rc;
+    }
+
+    private void getCandidates(File parent, File current, Map<String, String> settings) throws Exception {
+        if (current.isDirectory()) {
+            for (File child : current.listFiles(new FileFilter() {
+                @Override
+                public boolean accept(File file) {
+                    if (file.isDirectory() || file.getName().endsWith(".cfg")) {
+                        return true;
+                    }
+                    return false;
+                }
+            })) {
+                getCandidates(parent, child, settings);
+            }
+            String p = buildZKPath(parent, current).replaceFirst("/", "");
+            settings.put(p, null);
+        } else {
+            BufferedInputStream in = new BufferedInputStream(new FileInputStream(current));
+            byte[] contents = new byte[in.available()];
+            in.read(contents);
+            in.close();
+            String p = buildZKPath(parent, current).replaceFirst("/", "");
+            if (p.endsWith(".cfg")) {
+                p = p.substring(0, p.length() - ".cfg".length());
+            }
+            settings.put(p, new String(contents));
+        }
+    }
+
+    private void readFileSystem() throws Exception {
+        Map<String, String> settings = new TreeMap<String, String>();
+        File s = new File(source);
+        getCandidates(s, s, settings);
+        List<Pattern> include = getPatterns(regex);
+        List<Pattern> exclude = getPatterns(nregex);
+
+        if (!target.endsWith("/")) {
+            target = target + "/";
+        }
+        if (!target.startsWith("/")) {
+            target = "/" + target;
+        }
+
+        List<String> paths = new ArrayList<String>();
+
+        for(String key : settings.keySet()) {
+            String data = settings.get(key);
+            key = target + key;
+            paths.add(key);
+            if (!matches(include, key) || matches(exclude, key)) {
+                continue;
+            }
+            if (!dryRun) {
+                getZooKeeper().createOrSetWithParents(key, data, ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);
+            } else {
+                System.out.printf("Creating path \"%s\" with value \"%s\"\n", key, data);
+            }
+        }
+
+        if (delete) {
+            deletePathsNotIn(paths);
+        }
+    }
+
+    private void deletePathsNotIn(List<String> paths) throws Exception {
+        List<String> zkPaths = getZooKeeper().getAllChildren(target);
+
+        for (String path : zkPaths) {
+            path = "/" + path;
+            if (!paths.contains(path)) {
+                if (!dryRun) {
+                    getZooKeeper().deleteWithChildren(path);
+                } else {
+                    System.out.printf("Deleting path %s and everything under it\n", path);
+                }
+            }
+        }
+
+    }
+
+    private void readPropertiesFile() throws Exception {
+        List<Pattern> includes = getPatterns(regex);
+        List<Pattern> excludes = getPatterns(nregex);
+        InputStream in = new BufferedInputStream(new URL(source).openStream());
+        List<String> paths = new ArrayList<String>();
+        Properties props = new Properties();
+        props.load(in);
+        for (Enumeration names = props.propertyNames(); names.hasMoreElements();) {
+            String name = (String) names.nextElement();
+            String value = props.getProperty(name);
+            if (value != null && value.isEmpty()) {
+                value = null;
+            }
+            if (!name.startsWith("/")) {
+                name = "/" + name;
+            }
+            name = target + name;
+            if (!matches(includes, name) || matches(excludes, name)) {
+                continue;
+            }
+            if (!dryRun) {
+                getZooKeeper().createOrSetWithParents(name, value, ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);
+            } else {
+                System.out.printf("Creating path \"%s\" with value \"%s\"\n", name, value);
+            }
+        }
+    }
+
+}

richedit/src/main/resource/testFiles/fuse/revFiles/2006f48_4dad2f_insight#insight-camel#src#main#java#org#fusesource#insight#camel#audit#ScriptUtils.java

@@ -0,0 +1,91 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.insight.camel.audit;
+
+import org.codehaus.jackson.map.ObjectMapper;
+import org.codehaus.jackson.map.SerializationConfig;
+
+import java.text.SimpleDateFormat;
+import java.util.Collection;
+import java.util.Date;
+import java.util.Map;
+
+public final class ScriptUtils {
+
+    private static final SimpleDateFormat format;
+    private static final ObjectMapper mapper;
+
+    static {
+        format = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSX");
+        mapper = new ObjectMapper();
+        mapper.setSerializationConfig(
+                mapper.getSerializationConfig()
+                      .withDateFormat(format)
+        );
+    }
+
+    public static String toIso(Date d) {
+        return format.format(d);
+    }
+
+    public static String toJson(Object o) {
+        try {
+            if (o instanceof Collection) {
+                StringBuilder sb = new StringBuilder();
+                sb.append("[");
+                for (Object c : (Collection) o) {
+                    if (sb.length() > 1) {
+                        sb.append(",");
+                    }
+                    sb.append(toJson(c));
+                }
+                sb.append("]");
+                return sb.toString();
+            } else if (o instanceof Map) {
+                StringBuilder sb = new StringBuilder();
+                sb.append("{");
+                for (Map.Entry<Object, Object> e : ((Map<Object, Object>) o).entrySet()) {
+                    if (sb.length() > 1) {
+                        sb.append(",");
+                    }
+                    sb.append(toJson(e.getKey().toString()));
+                    sb.append(":");
+                    sb.append(toJson(e.getValue()));
+                }
+                sb.append("}");
+                return sb.toString();
+            } else if (o == null) {
+                return "null";
+            } else if (o instanceof Date) {
+                return "\"" + toIso((Date) o) + "\"";
+            } else {
+                return mapper.writeValueAsString(o.toString());
+            }
+        } catch (Exception e) {
+            throw new IllegalArgumentException("Could not serialize " + o, e);
+        }
+    }
+
+    public static Map parseJson(String str) {
+        try {
+            return mapper.readValue(str, Map.class);
+        } catch (Exception e) {
+            throw new IllegalArgumentException("Could not deserialize " + str, e);
+        }
+    }
+
+}

richedit/src/main/resource/testFiles/fuse/revFiles/6baf6f_ad4e95_fabric#fabric-core-agent-jclouds#src#main#java#org#fusesource#fabric#service#jclouds#JcloudsContainerProvider.java

@@ -0,0 +1,184 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.fusesource.fabric.service.jclouds;
+
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URLDecoder;
+import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import com.google.common.base.Strings;
+import com.google.common.collect.ImmutableSet;
+import com.google.inject.Module;
+import org.fusesource.fabric.api.*;
+import org.fusesource.fabric.api.CreateJCloudsContainerOptions;
+import org.jclouds.compute.ComputeService;
+import org.jclouds.compute.ComputeServiceContext;
+import org.jclouds.compute.ComputeServiceContextFactory;
+import org.jclouds.compute.RunNodesException;
+import org.jclouds.compute.domain.NodeMetadata;
+import org.jclouds.compute.domain.TemplateBuilder;
+import org.jclouds.compute.options.RunScriptOptions;
+import org.jclouds.domain.Credentials;
+import org.jclouds.rest.RestContextFactory;
+
+
+import static org.fusesource.fabric.internal.ContainerProviderUtils.buildStartupScript;
+
+/**
+ * A concrete {@link org.fusesource.fabric.api.ContainerProvider} that creates {@link org.fusesource.fabric.api.Container}s via jclouds {@link ComputeService}.
+ */
+public class JcloudsContainerProvider implements ContainerProvider<CreateJCloudsContainerOptions, CreateJCloudsContainerMetadata> {
+
+    private final ConcurrentMap<String, ComputeService> computeServiceMap = new ConcurrentHashMap<String, ComputeService>();
+
+    public void bind(ComputeService computeService) {
+        if(computeService != null) {
+            String providerName = computeService.getContext().getProviderSpecificContext().getId();
+            if(providerName != null) {
+              computeServiceMap.put(providerName,computeService);
+            }
+        }
+    }
+
+    public void unbind(ComputeService computeService) {
+        if(computeService != null) {
+            String providerName = computeService.getContext().getProviderSpecificContext().getId();
+            if(providerName != null) {
+               computeServiceMap.remove(providerName);
+            }
+        }
+    }
+
+    public ConcurrentMap<String, ComputeService> getComputeServiceMap() {
+        return computeServiceMap;
+    }
+
+    public Set<CreateJCloudsContainerMetadata> create(CreateJCloudsContainerOptions options) throws MalformedURLException, RunNodesException, URISyntaxException, InterruptedException {
+       final Set<CreateJCloudsContainerMetadata> result = new LinkedHashSet<CreateJCloudsContainerMetadata>();
+
+        ComputeService computeService = computeServiceMap.get(options.getProviderName());
+        if (computeService == null) {
+
+            Iterable<? extends Module> modules = ImmutableSet.of();
+
+            Properties props = new Properties();
+            props.put("provider", options.getProviderName());
+            props.put("identity", options.getIdentity());
+            props.put("credential", options.getCredential());
+            if (!Strings.isNullOrEmpty(options.getOwner()) && options.getProviderName().equals("aws-ec2")) {
+                props.put("jclouds.ec2.ami-owners", options.getOwner());
+            }
+
+            RestContextFactory restFactory = new RestContextFactory();
+            ComputeServiceContext context = new ComputeServiceContextFactory(restFactory).createContext(options.getProviderName(), options.getIdentity(), options.getCredential(), modules, props);
+            computeService = context.getComputeService();
+        }
+
+        TemplateBuilder builder = computeService.templateBuilder();
+        builder.any();
+        switch (options.getInstanceType()) {
+            case Smallest:
+                builder.smallest();
+                break;
+            case Biggest:
+                builder.biggest();
+                break;
+            case Fastest:
+                builder.fastest();
+        }
+
+        if (options.getLocationId() != null) {
+            builder.locationId(options.getLocationId());
+        }
+        if (options.getImageId() != null) {
+            builder.imageId(options.getImageId());
+        }
+        if (options.getHardwareId() != null) {
+            builder.hardwareId(options.getHardwareId());
+        }
+
+        Set<? extends NodeMetadata> metadatas = null;
+
+        metadatas = computeService.createNodesInGroup(options.getGroup(), options.getNumber(), builder.build());
+
+        Thread.sleep(5000);
+
+        int suffix = 1;
+        StringBuilder buffer = new StringBuilder();
+        boolean first = true;
+        if (metadatas != null) {
+            for (NodeMetadata nodeMetadata : metadatas) {
+                Credentials credentials = null;
+                //For some cloud providers return do not allow shell access to root, so the user needs to be overrided.
+                if (options.getUser() != null) {
+                    credentials = new Credentials(options.getUser(), nodeMetadata.getCredentials().credential);
+                } else {
+                    credentials = nodeMetadata.getCredentials();
+                }
+                String id = nodeMetadata.getId();
+                Set<String> publicAddresses = nodeMetadata.getPublicAddresses();
+
+                String containerName = options.getName();
+                if(options.getNumber() > 1) {
+                    containerName+=suffix++;
+                }
+                String script = buildStartupScript(options.name(containerName));
+                if (credentials != null) {
+                    computeService.runScriptOnNode(id, script, RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));
+                } else {
+                    computeService.runScriptOnNode(id, script);
+                }
+
+                CreateJCloudsContainerMetadata jCloudsContainerMetadata = new CreateJCloudsContainerMetadata();
+                jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());
+                jCloudsContainerMetadata.setContainerName(containerName);
+                jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());
+                jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());
+                result.add(jCloudsContainerMetadata);
+            }
+        }
+
+        return result;
+    }
+
+    public Map<String, String> parseQuery(String uri) throws URISyntaxException {
+        //TODO: This is copied form URISupport. We should move URISupport to core so that we don't have to copy stuff arround.
+        try {
+            Map<String, String> rc = new HashMap<String, String>();
+            if (uri != null) {
+                String[] parameters = uri.split("&");
+                for (int i = 0; i < parameters.length; i++) {
+                    int p = parameters[i].indexOf("=");
+                    if (p >= 0) {
+                        String name = URLDecoder.decode(parameters[i].substring(0, p), "UTF-8");
+                        String value = URLDecoder.decode(parameters[i].substring(p + 1), "UTF-8");
+                        rc.put(name, value);
+                    } else {
+                        rc.put(parameters[i], null);
+                    }
+                }
+            }
+            return rc;
+        } catch (UnsupportedEncodingException e) {
+            throw (URISyntaxException) new URISyntaxException(e.toString(), "Invalid encoding").initCause(e);
+        }
+    }
+}

richedit/src/main/resource/testFiles/fuse/revFiles/6d0e56_998321_fabric#fabric-agent#src#main#java#org#fusesource#fabric#agent#download#MavenDownloadTask.java

@@ -0,0 +1,486 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.fabric.agent.download;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.concurrent.ExecutorService;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.fusesource.fabric.agent.mvn.DownloadableArtifact;
+import org.fusesource.fabric.agent.mvn.MavenConfiguration;
+import org.fusesource.fabric.agent.mvn.MavenRepositoryURL;
+import org.fusesource.fabric.agent.mvn.Parser;
+import org.fusesource.fabric.agent.mvn.Version;
+import org.fusesource.fabric.agent.mvn.VersionRange;
+import org.fusesource.fabric.agent.utils.URLUtils;
+import org.fusesource.fabric.agent.utils.XmlUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+public class MavenDownloadTask extends AbstractDownloadTask implements Runnable {
+
+    /**
+     * Logger.
+     */
+    private static final Logger LOG = LoggerFactory.getLogger(AbstractDownloadTask.class);
+    /**
+     * 2 spaces indent;
+     */
+    private static final String Ix2 = "  ";
+    /**
+     * 4 spaces indent;
+     */
+    private static final String Ix4 = "    ";
+
+    private final MavenRepositoryURL system;
+    private final MavenConfiguration configuration;
+
+    public MavenDownloadTask(String url, MavenRepositoryURL system, MavenConfiguration configuration, ExecutorService executor) {
+        super(url, executor);
+        this.system = system;
+        this.configuration = configuration;
+    }
+
+    protected File download() throws Exception {
+        Parser parser = new Parser(url.substring("mvn:".length()));
+        Set<DownloadableArtifact> downloadables;
+        if (!parser.getVersion().contains("SNAPSHOT")) {
+            downloadables = doCollectPossibleDownloads(parser, Collections.singletonList(system));
+            if (!downloadables.isEmpty()) {
+                DownloadableArtifact artifact = downloadables.iterator().next();
+                URL url = artifact.getArtifactURL();
+                File file = new File(url.getFile());
+                if (file.exists()) {
+                    return file;
+                }
+            }
+        }
+        downloadables = collectPossibleDownloads(parser);
+        if (LOG.isTraceEnabled()) {
+            LOG.trace("Possible download locations for [" + url + "]");
+            for (DownloadableArtifact artifact : downloadables) {
+                LOG.trace("  " + artifact);
+            }
+        }
+        for (DownloadableArtifact artifact : downloadables) {
+            LOG.trace("Downloading [" + artifact + "]");
+            try {
+                configuration.enableProxy(artifact.getArtifactURL());
+                String repository = system.getFile().getAbsolutePath();
+                if (!repository.endsWith(Parser.FILE_SEPARATOR)) {
+                    repository = repository + Parser.FILE_SEPARATOR;
+                }
+                InputStream is = artifact.getInputStream();
+                File file = new File(repository + parser.getArtifactPath());
+                file.getParentFile().mkdirs();
+                if (!file.getParentFile().isDirectory()) {
+                    throw new IOException("Unable to create directory " + file.getParentFile().toString());
+                }
+                File tmp = File.createTempFile("fabric-agent-", null, file.getParentFile());
+                OutputStream os = new FileOutputStream(tmp);
+                copy(is, os);
+                is.close();
+                os.close();
+                if (file.exists() && !file.delete()) {
+                    throw new IOException("Unable to delete file: " + file.toString());
+                }
+                if (!tmp.renameTo(file)) {
+                    throw new IOException("Unable to rename file " + tmp.toString() + " to " + file.toString());
+                }
+                return file;
+            } catch (IOException ignore) {
+                // go on with next repository
+                LOG.debug(Ix2 + "Could not download [" + artifact + "]");
+                LOG.trace(Ix2 + "Reason [" + ignore.getClass().getName() + ": " + ignore.getMessage() + "]");
+            }
+        }
+        // no artifact found
+        throw new IOException("URL [" + url + "] could not be resolved.");
+    }
+
+    /**
+     * Searches all available repositories for possible artifacts to download. The returned set of downloadable
+     * artifacts (never null, but maybe empty) will be sorted descending by version of the artifact and by positon of
+     * repository in the list of repositories to be searched.
+     *
+     * @return a non null sorted set of artifacts
+     * @throws java.net.MalformedURLException re-thrown
+     */
+    private Set<DownloadableArtifact> collectPossibleDownloads(final Parser parser)
+            throws MalformedURLException {
+        final List<MavenRepositoryURL> repositories = new ArrayList<MavenRepositoryURL>();
+        repositories.addAll(configuration.getRepositories());
+        repositories.add(system);
+        repositories.add(configuration.getLocalRepository());        
+        // if the url contains a prefered repository add that repository as the first repository to be searched
+        if (parser.getRepositoryURL() != null) {
+            repositories.add(
+                    repositories.size() == 0 ? 0 : 1,
+                    parser.getRepositoryURL()
+            );
+        }
+        return doCollectPossibleDownloads(parser, repositories);
+    }
+
+    /**
+     * Search the default repositories for possible artifacts to download.
+     */
+    private Set<DownloadableArtifact> collectDefaultPossibleDownloads(final Parser parser)
+            throws MalformedURLException {
+        return doCollectPossibleDownloads(parser, configuration.getDefaultRepositories());
+    }
+
+    private Set<DownloadableArtifact> doCollectPossibleDownloads(final Parser parser,
+                                                                 final List<MavenRepositoryURL> repositories)
+            throws MalformedURLException {
+        final Set<DownloadableArtifact> downloadables = new TreeSet<DownloadableArtifact>(new DownloadComparator());
+
+        // find artifact type
+        final boolean isLatest = parser.getVersion().contains("LATEST");
+        final boolean isSnapshot = parser.getVersion().endsWith("SNAPSHOT");
+        VersionRange versionRange = null;
+        if (!isLatest && !isSnapshot) {
+            try {
+                versionRange = new VersionRange(parser.getVersion());
+            } catch (Exception ignore) {
+                // well, we do not have a range of versions
+            }
+        }
+        final boolean isVersionRange = versionRange != null;
+        final boolean isExactVersion = !(isLatest || isSnapshot || isVersionRange);
+
+        int priority = 0;
+        for (MavenRepositoryURL repositoryURL : repositories) {
+            LOG.debug("Collecting versions from repository [" + repositoryURL + "]");
+            priority++;
+            try {
+                if (isExactVersion) {
+                    downloadables.add(resolveExactVersion(parser, repositoryURL, priority));
+                } else if (isSnapshot) {
+                    final DownloadableArtifact snapshot =
+                            resolveSnapshotVersion(parser, repositoryURL, priority, parser.getVersion());
+                    downloadables.add(snapshot);
+                    // if we have a local built snapshot we skip the rest of repositories
+                    if (snapshot.isLocalSnapshotBuild()) {
+                        break;
+                    }
+                } else {
+                    final Document metadata = getMetadata(repositoryURL.getURL(),
+                            new String[]
+                                    {
+                                            parser.getArtifactLocalMetdataPath(),
+                                            parser.getArtifactMetdataPath()
+                                    }
+                    );
+                    if (isLatest) {
+                        downloadables.add(resolveLatestVersion(parser, metadata, repositoryURL, priority));
+                    } else {
+                        downloadables.addAll(resolveRangeVersions(parser, metadata, repositoryURL, priority, versionRange));
+                    }
+                }
+            } catch (IOException ignore) {
+                // if metadata cannot be found we go on with the next repository. Maybe we have better luck.
+                LOG.debug(Ix2 + "Skipping repository [" + repositoryURL + "], reason: " + ignore.getMessage());
+            }
+        }
+        return downloadables;
+    }
+
+    /**
+     * Returns maven metadata by looking first for a local metatdata xml file and then for a remote one.
+     * If no metadata file is found or cannot be used an IOException is thrown.
+     *
+     * @param repositoryURL     url of the repository from where the metadata should be parsed
+     * @param metadataLocations array of location paths to try as metadata
+     * @return parsed xml document for the metadata file
+     * @throws java.io.IOException if:
+     *                             metadata file cannot be located
+     */
+    private Document getMetadata(final URL repositoryURL,
+                                 final String[] metadataLocations)
+            throws IOException {
+        LOG.debug(Ix2 + "Resolving metadata");
+        InputStream inputStream = null;
+        String foundLocation = null;
+        for (String location : metadataLocations) {
+            try {
+                // first try to get the artifact local metadata
+                inputStream = prepareInputStream(repositoryURL, location);
+                // get out at first found location
+                foundLocation = location;
+                LOG.trace(Ix4 + "Metadata found: [" + location + "]");
+                break;
+            } catch (IOException ignore) {
+                LOG.trace(Ix4 + "Metadata not found: [" + location + "]");
+            }
+        }
+        if (inputStream == null) {
+            throw new IOException("Metadata not found in repository [" + repositoryURL + "]");
+        }
+        try {
+            return XmlUtils.parseDoc(inputStream);
+        } catch (ParserConfigurationException e) {
+            throw initIOException("Metadata [" + foundLocation + "] could not be parsed.", e);
+        } catch (SAXException e) {
+            throw initIOException("Metadata [" + foundLocation + "] could not be parsed.", e);
+        }
+    }
+
+    /**
+     * Returns a downloadable artifact where the version is fully specified.
+     *
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @return a downloadable artifact
+     * @throws IOException re-thrown
+     */
+    private DownloadableArtifact resolveExactVersion(final Parser parser,
+                                                     final MavenRepositoryURL repositoryURL,
+                                                     final int priority)
+            throws IOException {
+        if (!repositoryURL.isReleasesEnabled()) {
+            throw new IOException("Releases not enabled");
+        }
+        LOG.debug(Ix2 + "Resolving exact version");
+        return new DownloadableArtifact(
+                parser.getVersion(),
+                priority,
+                repositoryURL.getURL(),
+                parser.getArtifactPath(),
+                false, // no local built snapshot
+                configuration.getCertificateCheck()
+        );
+    }
+
+    /**
+     * Resolves the latest version of the artifact.
+     *
+     * @param metadata      parsed metadata xml
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @return a downloadable artifact or throw an IOException if latest version cannot be determined.
+     * @throws IOException if the artifact could not be resolved
+     */
+    private DownloadableArtifact resolveLatestVersion(final Parser parser,
+                                                      final Document metadata,
+                                                      final MavenRepositoryURL repositoryURL,
+                                                      final int priority)
+            throws IOException {
+        LOG.debug(Ix2 + "Resolving latest version");
+        final String version = XmlUtils.getTextContentOfElement(metadata, "versioning/versions/version[last]");
+        if (version != null) {
+            if (version.endsWith("SNAPSHOT")) {
+                return resolveSnapshotVersion(parser, repositoryURL, priority, version);
+            } else {
+                return new DownloadableArtifact(
+                        version,
+                        priority,
+                        repositoryURL.getURL(),
+                        parser.getArtifactPath(version),
+                        false, // no local built snapshot
+                        configuration.getCertificateCheck()
+                );
+            }
+        }
+        throw new IOException("LATEST version could not be resolved.");
+    }
+
+    /**
+     * Resolves snapshot version of the artifact.
+     * Snapshot versions are resolved by parsing the metadata within the directory that contains the version as:
+     * 1. if the metadata containes entries like "versioning/snapshot/timestamp (most likely on remote repos) it will
+     * use the timestamp and buildnumber to point the real version
+     * 2. if the metatdata does not contain the above (most likely a local repo) it will use as version the
+     * versioning/lastUpdated
+     *
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @param version       snapshot version to resolve
+     * @return an input stream to the artifact
+     * @throws IOException if the artifact could not be resolved
+     */
+    private DownloadableArtifact resolveSnapshotVersion(final Parser parser,
+                                                        final MavenRepositoryURL repositoryURL,
+                                                        final int priority,
+                                                        final String version)
+            throws IOException {
+        if (!repositoryURL.isSnapshotsEnabled()) {
+            throw new IOException("Snapshots not enabled");
+        }
+        LOG.debug(Ix2 + "Resolving snapshot version [" + version + "]");
+        try {
+            final Document snapshotMetadata = getMetadata(repositoryURL.getURL(),
+                    new String[]
+                            {
+                                    parser.getVersionLocalMetadataPath(version),
+                                    parser.getVersionMetadataPath(version)
+                            }
+            );
+            final String timestamp =
+                    XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/snapshot/timestamp");
+            final String buildNumber =
+                    XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/snapshot/buildNumber");
+            final String localSnapshot =
+                    XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/snapshot/localCopy");
+            if (timestamp != null && buildNumber != null) {
+                return new DownloadableArtifact(
+                        parser.getSnapshotVersion(version, timestamp, buildNumber),
+                        priority,
+                        repositoryURL.getURL(),
+                        parser.getSnapshotPath(version, timestamp, buildNumber),
+                        localSnapshot != null,
+                        configuration.getCertificateCheck()
+                );
+            } else {
+                String lastUpdated = XmlUtils.getTextContentOfElement(snapshotMetadata, "versioning/lastUpdated");
+                if (lastUpdated != null) {
+                    // last updated should contain in the first 8 chars the date and then the time,
+                    // fact that is not compatible with timeStamp from remote repos which has a "." after date
+                    if (lastUpdated.length() > 8) {
+                        lastUpdated = lastUpdated.substring(0, 8) + "." + lastUpdated.substring(8);
+                        return new DownloadableArtifact(
+                                parser.getSnapshotVersion(version, lastUpdated, "0"),
+                                priority,
+                                repositoryURL.getURL(),
+                                parser.getArtifactPath(version),
+                                localSnapshot != null,
+                                configuration.getCertificateCheck()
+                        );
+                    }
+                }
+            }
+        } catch (IOException ignore) {
+            // in this case we could not find any metadata so try to get the *-SNAPSHOT file directly
+        }
+        return new DownloadableArtifact(
+                parser.getVersion(),
+                priority,
+                repositoryURL.getURL(),
+                parser.getArtifactPath(),
+                false, // no local built snapshot
+                configuration.getCertificateCheck()
+        );
+    }
+
+    /**
+     * Resolves all versions that fits the provided range.
+     *
+     * @param metadata      parsed metadata xml
+     * @param repositoryURL the url of the repository to download from
+     * @param priority      repository priority
+     * @param versionRange  version range to fulfill
+     * @return list of downloadable artifacts that match the range
+     * @throws IOException re-thrown
+     */
+    private List<DownloadableArtifact> resolveRangeVersions(final Parser parser,
+                                                            final Document metadata,
+                                                            final MavenRepositoryURL repositoryURL,
+                                                            final int priority,
+                                                            final VersionRange versionRange)
+            throws IOException {
+        LOG.debug(Ix2 + "Resolving versions in range [" + versionRange + "]");
+        final List<DownloadableArtifact> downladables = new ArrayList<DownloadableArtifact>();
+        final List<Element> elements = XmlUtils.getElements(metadata, "versioning/versions/version");
+        if (elements != null && elements.size() > 0) {
+            for (Element element : elements) {
+                final String versionString = XmlUtils.getTextContent(element);
+                if (versionString != null) {
+                    final Version version = new Version(versionString);
+                    if (versionRange.includes(version)) {
+                        if (versionString.endsWith("SNAPSHOT")) {
+                            downladables.add(
+                                    resolveSnapshotVersion(parser, repositoryURL, priority, versionString)
+                            );
+                        } else {
+                            downladables.add(
+                                    new DownloadableArtifact(
+                                            versionString,
+                                            priority,
+                                            repositoryURL.getURL(),
+                                            parser.getArtifactPath(versionString),
+                                            false, // no local built snapshot
+                                            configuration.getCertificateCheck()
+                                    )
+                            );
+                        }
+                    }
+                }
+            }
+        }
+        return downladables;
+    }
+
+    /**
+     * @param repositoryURL url to reporsitory
+     * @param path          a path to the artifact jar file
+     * @return prepared input stream
+     * @throws IOException re-thrown
+     * @see org.ops4j.net.URLUtils#prepareInputStream(java.net.URL, boolean)
+     */
+    private InputStream prepareInputStream(URL repositoryURL, final String path)
+            throws IOException {
+        String repository = repositoryURL.toExternalForm();
+        if (!repository.endsWith(org.ops4j.pax.url.mvn.internal.Parser.FILE_SEPARATOR)) {
+            repository = repository + org.ops4j.pax.url.mvn.internal.Parser.FILE_SEPARATOR;
+        }
+        configuration.enableProxy(repositoryURL);
+        final URL url = new URL(repository + path);
+        LOG.trace("Reading " + url.toExternalForm());
+        return URLUtils.prepareInputStream(url, !configuration.getCertificateCheck());
+    }
+
+    /**
+     * Sorting comparator for downladable artifacts.
+     * The sorting is done by:
+     * 1. descending version
+     * 2. ascending priority.
+     */
+    private static class DownloadComparator
+            implements Comparator<DownloadableArtifact> {
+
+        public int compare(final DownloadableArtifact first,
+                           final DownloadableArtifact second) {
+            // first descending by version
+            int result = -1 * first.getVersion().compareTo(second.getVersion());
+            if (result == 0) {
+                // then ascending by priority
+                if (first.getPriority() < second.getPriority()) {
+                    result = -1;
+                } else if (first.getPriority() > second.getPriority()) {
+                    result = 1;
+                }
+            }
+            return result;
+        }
+
+    }
+}

richedit/src/main/resource/testFiles/fuse/revFiles/74c02c_a4658a_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#DataStoreManager.java

@@ -0,0 +1,189 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.fabric.service;
+
+import java.util.Dictionary;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.concurrent.CopyOnWriteArrayList;
+
+import org.apache.felix.scr.annotations.Activate;
+import org.apache.felix.scr.annotations.Component;
+import org.apache.felix.scr.annotations.Deactivate;
+import org.apache.felix.scr.annotations.Reference;
+import org.apache.felix.scr.annotations.ReferencePolicy;
+import org.apache.felix.scr.annotations.Service;
+import org.fusesource.fabric.api.DataStore;
+import org.fusesource.fabric.api.DataStorePlugin;
+import org.fusesource.fabric.api.DataStoreRegistrationHandler;
+import org.fusesource.fabric.api.DataStoreTemplate;
+import org.fusesource.fabric.api.FabricException;
+import org.fusesource.fabric.api.PlaceholderResolver;
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.ServiceRegistration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.apache.felix.scr.annotations.ReferenceCardinality.OPTIONAL_MULTIPLE;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getProperties;
+
+/**
+ * Manager of {@link DataStore} using configuration to decide which
+ * implementation to export.
+ */
+@Component(name = "org.fusesource.fabric.datastore.manager",
+        description = "Configured DataStore Factory",
+        immediate = true)
+@Service(DataStoreRegistrationHandler.class)
+public class DataStoreManager implements DataStoreRegistrationHandler {
+    private static final transient Logger LOG = LoggerFactory.getLogger(DataStoreManager.class);
+
+    public static final String DATASTORE_TYPE_PID = "org.fusesource.fabric.datastore";
+    public static final String DATASTORE_TYPE_PROPERTY = "type";
+    public static final String DEFAULT_DATASTORE_TYPE = "git";
+
+
+    @Reference(cardinality = OPTIONAL_MULTIPLE,
+            referenceInterface = DataStorePlugin.class,
+            bind = "bindDataStore", unbind = "unbindDataStore",
+            policy = ReferencePolicy.DYNAMIC)
+    private final Map<String, DataStorePlugin> dataStorePlugins = new HashMap<String, DataStorePlugin>();
+
+    private BundleContext bundleContext;
+    private Map<String,String> configuration;
+
+    private String type;
+    private DataStore dataStore;
+    private Dictionary<String, String> properties = new Hashtable<String, String>();
+    private ServiceRegistration<DataStore> registration;
+
+    private final List<DataStoreTemplate> registrationCallbacks = new CopyOnWriteArrayList<DataStoreTemplate>();
+
+
+    @Activate
+    public synchronized void init(BundleContext bundleContext, Map<String,String> configuration) throws Exception {
+        this.bundleContext = bundleContext;
+        this.configuration = configuration;
+        this.type = readType(configuration);
+        updateServiceRegistration();
+    }
+
+    @Deactivate
+    public synchronized void destroy() {
+        unregister();
+    }
+
+    public void updateServiceRegistration() {
+        unregister();
+        if (dataStorePlugins.containsKey(type)) {
+            dataStore = dataStorePlugins.get(type).getDataStore();
+            Properties dataStoreProperties = new Properties();
+            dataStoreProperties.putAll(configuration);
+            dataStore.setDataStoreProperties(dataStoreProperties);
+            dataStore.start();
+            for(DataStoreTemplate callback : registrationCallbacks) {
+                registrationCallbacks.remove(callback);
+                try {
+                    callback.doWith(dataStore);
+                } catch (Exception e) {
+                    throw new FabricException(e);
+                }
+            }
+            properties.put(DATASTORE_TYPE_PROPERTY, type);
+            registration = bundleContext.registerService(DataStore.class, dataStore, properties);
+            LOG.info("Registered DataStore " + dataStore + " with " + properties);
+        }
+    }
+
+    /**
+     * Unregisters the {@link DataStore}.
+     */
+    private void unregister() {
+        if (registration != null) {
+            registration.unregister();
+            registration = null;
+        }
+        if (dataStore != null) {
+            dataStore.stop();
+        }
+    }
+
+    /**
+     * Extracts the type from the specified map or System configuration.
+     * @param configuration The map to use as a source.
+     * @return
+     */
+    private static String readType(Map<String, String> configuration) {
+        if (configuration.containsKey(DATASTORE_TYPE_PROPERTY)) {
+            return configuration.get(DATASTORE_TYPE_PROPERTY);
+        } else {
+            return System.getProperty(DATASTORE_TYPE_PID + "." + DATASTORE_TYPE_PROPERTY, DEFAULT_DATASTORE_TYPE);
+        }
+    }
+
+
+    // Properties
+    //-------------------------------------------------------------------------
+
+    public BundleContext getBundleContext() {
+        return bundleContext;
+    }
+
+    public void setBundleContext(BundleContext bundleContext) {
+        this.bundleContext = bundleContext;
+    }
+
+
+    public synchronized void bindDataStore(DataStorePlugin dataStorePlugin) {
+        if (dataStorePlugin != null) {
+            dataStorePlugins.put(dataStorePlugin.getName(), dataStorePlugin);
+            if (type != null && type.equals(dataStorePlugin.getName())) {
+                updateServiceRegistration();
+            }
+        }
+    }
+
+    public synchronized void unbindDataStore(DataStorePlugin dataStorePlugin) {
+        if (dataStorePlugin != null) {
+            dataStorePlugins.remove(dataStorePlugin.getName());
+            if (type != null && type.equals(dataStorePlugin.getName())) {
+                updateServiceRegistration();
+            }
+        }
+    }
+
+    public Map<String, String> getConfiguration() {
+        return configuration;
+    }
+
+    public void setConfiguration(Map<String, String> configuration) {
+        this.configuration = configuration;
+    }
+
+    @Override
+    public void addRegistrationCallback(DataStoreTemplate template) {
+        this.registrationCallbacks.add(template);
+    }
+
+    @Override
+    public void removeRegistrationCallback(DataStoreTemplate template) {
+        this.registrationCallbacks.remove(template);
+    }
+}

richedit/src/main/resource/testFiles/fuse/revFiles/b0e8c7_602ea9_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#AbstractDataStore.java

@@ -0,0 +1,713 @@
+/**
+ * Copyright (C) FuseSource, Inc.
+ * http://fusesource.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.fusesource.fabric.service;
+
+import org.apache.curator.framework.CuratorFramework;
+import org.apache.curator.framework.recipes.cache.PathChildrenCacheEvent;
+import org.apache.curator.framework.recipes.cache.PathChildrenCacheListener;
+import org.apache.curator.framework.recipes.cache.TreeCache;
+import org.apache.zookeeper.KeeperException;
+import org.fusesource.fabric.api.CreateContainerMetadata;
+import org.fusesource.fabric.api.CreateContainerOptions;
+import org.fusesource.fabric.api.DataStore;
+import org.fusesource.fabric.api.DynamicReference;
+import org.fusesource.fabric.api.FabricException;
+import org.fusesource.fabric.api.PlaceholderResolver;
+import org.fusesource.fabric.api.jcip.GuardedBy;
+import org.fusesource.fabric.api.jcip.ThreadSafe;
+import org.fusesource.fabric.api.scr.AbstractComponent;
+import org.fusesource.fabric.api.scr.InvalidComponentException;
+import org.fusesource.fabric.api.scr.ValidatingReference;
+import org.fusesource.fabric.internal.DataStoreHelpers;
+import org.fusesource.fabric.utils.Base64Encoder;
+import org.fusesource.fabric.utils.Closeables;
+import org.fusesource.fabric.utils.ObjectUtils;
+import org.fusesource.fabric.zookeeper.ZkDefs;
+import org.fusesource.fabric.zookeeper.ZkPath;
+import org.fusesource.fabric.zookeeper.utils.InterpolationHelper;
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.FrameworkUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InvalidClassException;
+import java.io.ObjectInputStream;
+import java.io.ObjectStreamClass;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import static org.fusesource.fabric.internal.DataStoreHelpers.substituteBundleProperty;
+import static org.fusesource.fabric.internal.PlaceholderResolverHelpers.getSchemesForProfileConfigurations;
+import static org.fusesource.fabric.internal.PlaceholderResolverHelpers.waitForPlaceHolderResolvers;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.deleteSafe;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.exists;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getByteData;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getChildren;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getStringData;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.getSubstitutedPath;
+import static org.fusesource.fabric.zookeeper.utils.ZooKeeperUtils.setData;
+
+@ThreadSafe
+public abstract class AbstractDataStore extends AbstractComponent implements DataStore, PathChildrenCacheListener {
+
+    private static final transient Logger LOG = LoggerFactory.getLogger(AbstractDataStore.class);
+
+    public static final String REQUIREMENTS_JSON_PATH = "/fabric/configs/org.fusesource.fabric.requirements.json";
+    public static final String JVM_OPTIONS_PATH = "/fabric/configs/org.fusesource.fabric.containers.jvmOptions";
+
+    private final ValidatingReference<CuratorFramework> curator = new ValidatingReference<CuratorFramework>();
+
+    private final ExecutorService callbacksExecutor = Executors.newSingleThreadExecutor();
+    private final ExecutorService cacheExecutor = Executors.newSingleThreadExecutor();
+    private final ExecutorService placeholderExecutor = Executors.newCachedThreadPool();
+    private final AtomicBoolean active = new AtomicBoolean(false);
+
+    @GuardedBy("ConcurrentHashMap") private final ConcurrentMap<String, DynamicReference<PlaceholderResolver>> placeholderResolvers = new ConcurrentHashMap<String, DynamicReference<PlaceholderResolver>>();
+    @GuardedBy("CopyOnWriteArrayList") private final CopyOnWriteArrayList<Runnable> callbacks = new CopyOnWriteArrayList<Runnable>();
+    @GuardedBy("this") private Map<String, String> dataStoreProperties;
+    @GuardedBy("active") private volatile TreeCache treeCache;
+
+    @Override
+    public abstract void importFromFileSystem(String from);
+
+    @Override
+    public void start() {
+        try {
+            if (active.compareAndSet(false, true)) {
+                LOG.info("Starting up DataStore " + this);
+                treeCache = new TreeCache(getCurator(), ZkPath.CONFIGS.getPath(), true, false, true, cacheExecutor);
+                treeCache.start(TreeCache.StartMode.NORMAL);
+                treeCache.getListenable().addListener(this);
+            }
+        } catch (FabricException ex) {
+            throw ex;
+        } catch (Exception ex) {
+            throw new FabricException("Failed to start data store.", ex);
+        }
+    }
+
+    @Override
+    public void stop() {
+        if (active.compareAndSet(true, false)) {
+            treeCache.getListenable().removeListener(this);
+            Closeables.closeQuitely(treeCache);
+            treeCache = null;
+
+            callbacksExecutor.shutdownNow();
+            cacheExecutor.shutdownNow();
+            placeholderExecutor.shutdownNow();
+        }
+    }
+
+    protected TreeCache getTreeCache() {
+        if (!active.get())
+            throw new InvalidComponentException();
+        return treeCache;
+    }
+
+    @Override
+    public synchronized Map<String, String> getDataStoreProperties() {
+        assertValid();
+        return Collections.unmodifiableMap(dataStoreProperties);
+    }
+
+    @Override
+    public synchronized void setDataStoreProperties(Map<String, String> dataStoreProperties) {
+        assertValid();
+        this.dataStoreProperties = new HashMap<String, String>(dataStoreProperties);
+    }
+
+    @Override
+    public void childEvent(CuratorFramework client, PathChildrenCacheEvent event) throws Exception {
+        if (isValid()) {
+            switch (event.getType()) {
+            case CHILD_ADDED:
+            case CHILD_REMOVED:
+            case CHILD_UPDATED:
+            case INITIALIZED:
+                runCallbacks();
+                break;
+        }
+        }
+    }
+
+    protected void runCallbacks() {
+        callbacksExecutor.submit(new Runnable() {
+            @Override
+            public void run() {
+                doRunCallbacks();
+            }
+        });
+    }
+
+    protected void doRunCallbacks() {
+        assertValid();
+        for (Runnable callback : callbacks) {
+            try {
+                if (LOG.isDebugEnabled()) {
+                    LOG.debug("Running callback " + callback);
+                }
+                callback.run();
+            } catch (Throwable e) {
+                LOG.warn("Caught: " + e, e);
+            }
+        }
+    }
+
+    @Override
+    public void trackConfiguration(Runnable callback) {
+        if (isValid()) {
+            callbacks.addIfAbsent(callback);
+        }
+    }
+
+    @Override
+    public void untrackConfiguration(Runnable callback) {
+        callbacks.remove(callback);
+    }
+
+    // PlaceholderResolver stuff
+    //-------------------------------------------------------------------------
+
+    /**
+     * Performs substitution to configuration based on the registered {@link PlaceholderResolver} instances.
+     */
+    public void substituteConfigurations(final Map<String, Map<String, String>> configs) {
+        assertValid();
+
+        //Check for all required resolver schemes.
+        Set<String> requiredSchemes = getSchemesForProfileConfigurations(configs);
+        for (String scheme : requiredSchemes) {
+            placeholderResolvers.putIfAbsent(scheme, new DynamicReference<PlaceholderResolver>());
+        }
+
+        //Wait for resolvers before starting to resolve.
+        final Map<String, PlaceholderResolver> availableResolvers = waitForPlaceHolderResolvers(placeholderExecutor, requiredSchemes, getPlaceholderResolvers());
+
+        for (Map.Entry<String, Map<String, String>> entry : configs.entrySet()) {
+            final String pid = entry.getKey();
+            Map<String, String> props = entry.getValue();
+
+            for (Map.Entry<String, String> e : props.entrySet()) {
+                final String key = e.getKey();
+                final String value = e.getValue();
+                props.put(key, InterpolationHelper.substVars(value, key, null, props, new InterpolationHelper.SubstitutionCallback() {
+                    public String getValue(String toSubstitute) {
+                        if (toSubstitute != null && toSubstitute.contains(":")) {
+                            String scheme = toSubstitute.substring(0, toSubstitute.indexOf(":"));
+                            if (availableResolvers.containsKey(scheme)) {
+                                return availableResolvers.get(scheme).resolve(configs, pid, key, toSubstitute);
+                            }
+                        }
+                        return substituteBundleProperty(toSubstitute, getBundleContext());
+                    }
+                }));
+            }
+        }
+    }
+
+    private Map<String, DynamicReference<PlaceholderResolver>> getPlaceholderResolvers() {
+        return Collections.unmodifiableMap(placeholderResolvers);
+    }
+
+    private BundleContext getBundleContext() {
+        try {
+            return FrameworkUtil.getBundle(AbstractDataStore.class).getBundleContext();
+        } catch (Throwable t) {
+            return null;
+        }
+    }
+
+    // Container stuff
+    //-------------------------------------------------------------------------
+
+    @Override
+    public List<String> getContainers() {
+        assertValid();
+        try {
+            return getChildren(getCurator(), ZkPath.CONFIGS_CONTAINERS.getPath());
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public boolean hasContainer(String containerId) {
+        assertValid();
+        return getContainers().contains(containerId);
+    }
+
+    @Override
+    public String getContainerParent(String containerId) {
+        assertValid();
+        try {
+            String parentName = getStringData(getCurator(), ZkPath.CONTAINER_PARENT.getPath(containerId));
+            return parentName != null ? parentName.trim() : "";
+        } catch (KeeperException.NoNodeException e) {
+            // Ignore
+            return "";
+        } catch (Throwable e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void deleteContainer(String containerId) {
+        assertValid();
+        try {
+            if (getCurator() == null) {
+                throw new IllegalStateException("Zookeeper service not available");
+            }
+            //Wipe all config entries that are related to the container for all versions.
+            for (String version : getVersions()) {
+                deleteSafe(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(version, containerId));
+            }
+            deleteSafe(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            deleteSafe(getCurator(), ZkPath.CONTAINER.getPath(containerId));
+            deleteSafe(getCurator(), ZkPath.CONTAINER_DOMAINS.getPath(containerId));
+            deleteSafe(getCurator(), ZkPath.CONTAINER_PROVISION.getPath(containerId));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void createContainerConfig(CreateContainerOptions options) {
+        assertValid();
+        try {
+            String parent = options.getParent();
+            String containerId = options.getName();
+            String versionId = options.getVersion();
+            Set<String> profileIds = options.getProfiles();
+            StringBuilder sb = new StringBuilder();
+            for (String profileId : profileIds) {
+                if (sb.length() > 0) {
+                    sb.append(" ");
+                }
+                sb.append(profileId);
+            }
+
+            setData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId), versionId);
+            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), sb.toString());
+            setData(getCurator(), ZkPath.CONTAINER_PARENT.getPath(containerId), parent);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void createContainerConfig(CreateContainerMetadata metadata) {
+        assertValid();
+        try {
+            CreateContainerOptions options = metadata.getCreateOptions();
+            String containerId = metadata.getContainerName();
+//            String parent = options.getParent();
+//            String versionId = options.getVersion() != null ? options.getVersion() : getDefaultVersion();
+//            Set<String> profileIds = options.getProfiles();
+//            if (profileIds == null || profileIds.isEmpty()) {
+//                profileIds = new LinkedHashSet<String>();
+//                profileIds.add("default");
+//            }
+//            StringBuilder sb = new StringBuilder();
+//            for (String profileId : profileIds) {
+//                if (sb.length() > 0) {
+//                    sb.append(" ");
+//                }
+//                sb.append(profileId);
+//            }
+//
+//            setData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId), versionId);
+//            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), sb.toString());
+//            setData(getCurator(), ZkPath.CONTAINER_PARENT.getPath(containerId), parent);
+
+            setContainerMetadata(metadata);
+
+            Map<String, String> configuration = metadata.getContainerConfiguration();
+            for (Map.Entry<String, String> entry : configuration.entrySet()) {
+                String key = entry.getKey();
+                String value = entry.getValue();
+                setData(getCurator(), ZkPath.CONTAINER_ENTRY.getPath(metadata.getContainerName(), key), value);
+            }
+
+            // If no resolver specified but a resolver is already present in the registry, use the registry value
+            String resolver = metadata.getOverridenResolver() != null ? metadata.getOverridenResolver() : options.getResolver();
+
+            if (resolver == null && exists(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId)) != null) {
+                resolver = getStringData(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId));
+            } else if (options.getResolver() != null) {
+                // Use the resolver specified in the options and do nothing.
+            } else if (exists(getCurator(), ZkPath.POLICIES.getPath(ZkDefs.RESOLVER)) != null) {
+                // If there is a globlal resolver specified use it.
+                resolver = getStringData(getCurator(), ZkPath.POLICIES.getPath(ZkDefs.RESOLVER));
+            } else {
+                // Fallback to the default resolver
+                resolver = ZkDefs.DEFAULT_RESOLVER;
+            }
+            // Set the resolver if not already set
+            setData(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId), resolver);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public CreateContainerMetadata getContainerMetadata(String containerId, final ClassLoader classLoader) {
+        assertValid();
+        try {
+            byte[] encoded = getByteData(getTreeCache(), ZkPath.CONTAINER_METADATA.getPath(containerId));
+            if (encoded == null) {
+                return null;
+            }
+            byte[] decoded = Base64Encoder.decode(encoded);
+            ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(decoded)) {
+                @Override
+                protected Class<?> resolveClass(ObjectStreamClass desc) throws IOException, ClassNotFoundException {
+                    return classLoader.loadClass(desc.getName());
+                }
+            };
+            return (CreateContainerMetadata) ois.readObject();
+        } catch (ClassNotFoundException e) {
+            return null;
+        } catch (InvalidClassException e) {
+            return null;
+        } catch (KeeperException.NoNodeException e) {
+            return null;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setContainerMetadata(CreateContainerMetadata metadata) {
+        assertValid();
+        //We encode the metadata so that they are more friendly to import/export.
+        try {
+            setData(getCurator(), ZkPath.CONTAINER_METADATA.getPath(metadata.getContainerName()), Base64Encoder.encode(ObjectUtils.toBytes(metadata)));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public String getContainerVersion(String containerId) {
+        assertValid();
+        try {
+            return getStringData(getTreeCache(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setContainerVersion(String containerId, String versionId) {
+        assertValid();
+        try {
+            String oldVersionId = getStringData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            String oldProfileIds = getStringData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(oldVersionId, containerId));
+
+            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), oldProfileIds);
+            setData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId), versionId);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public List<String> getContainerProfiles(String containerId) {
+        assertValid();
+        try {
+            String versionId = getStringData(getTreeCache(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            String str = getStringData(getTreeCache(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId));
+            return str == null || str.isEmpty() ? Collections.<String> emptyList() : Arrays.asList(str.trim().split(" +"));
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setContainerProfiles(String containerId, List<String> profileIds) {
+        assertValid();
+        try {
+            String versionId = getStringData(getCurator(), ZkPath.CONFIG_CONTAINER.getPath(containerId));
+            StringBuilder sb = new StringBuilder();
+            for (String profileId : profileIds) {
+                if (sb.length() > 0) {
+                    sb.append(" ");
+                }
+                sb.append(profileId);
+            }
+            setData(getCurator(), ZkPath.CONFIG_VERSIONS_CONTAINER.getPath(versionId, containerId), sb.toString());
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public boolean isContainerAlive(String id) {
+        assertValid();
+        try {
+            return exists(getCurator(), ZkPath.CONTAINER_ALIVE.getPath(id)) != null;
+        } catch (KeeperException.NoNodeException e) {
+            return false;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public String getContainerAttribute(String containerId, ContainerAttribute attribute, String def, boolean mandatory, boolean substituted) {
+        assertValid();
+        if (attribute == ContainerAttribute.Domains) {
+            try {
+                List<String> list = getCurator().getChildren().forPath(ZkPath.CONTAINER_DOMAINS.getPath(containerId));
+                Collections.sort(list);
+                StringBuilder sb = new StringBuilder();
+                for (String l : list) {
+                    if (sb.length() > 0) {
+                        sb.append("\n");
+                    }
+                    sb.append(l);
+                }
+                return sb.toString();
+            } catch (Exception e) {
+                return "";
+            }
+        } else {
+            try {
+                if (substituted) {
+                    return getSubstitutedPath(getCurator(), getAttributePath(containerId, attribute));
+                } else {
+                    return getStringData(getCurator(), getAttributePath(containerId, attribute));
+                }
+            } catch (KeeperException.NoNodeException e) {
+                if (mandatory) {
+                    throw FabricException.launderThrowable(e);
+                }
+                return def;
+            } catch (Exception e) {
+                throw FabricException.launderThrowable(e);
+            }
+        }
+    }
+
+    @Override
+    public void setContainerAttribute(String containerId, ContainerAttribute attribute, String value) {
+        assertValid();
+        // Special case for resolver
+        // TODO: we could use a double indirection on the ip so that it does not need to change
+        // TODO: something like ${zk:container/${zk:container/resolver}}
+        if (attribute == ContainerAttribute.Resolver) {
+            try {
+                setData(getCurator(), ZkPath.CONTAINER_IP.getPath(containerId), "${zk:" + containerId + "/" + value + "}");
+                setData(getCurator(), ZkPath.CONTAINER_RESOLVER.getPath(containerId), value);
+            } catch (Exception e) {
+                throw FabricException.launderThrowable(e);
+            }
+        } else {
+            try {
+                //                if (value == null) {
+                //                    deleteSafe(zk, getAttributePath(containerId, attribute));
+                //                } else {
+                setData(getCurator(), getAttributePath(containerId, attribute), value);
+                //                }
+            } catch (KeeperException.NoNodeException e) {
+                // Ignore
+            } catch (Exception e) {
+                throw FabricException.launderThrowable(e);
+            }
+        }
+    }
+
+    @Override
+    public String getDefaultVersion() {
+        assertValid();
+        try {
+            String version = null;
+            if (getTreeCache().getCurrentData(ZkPath.CONFIG_DEFAULT_VERSION.getPath()) != null) {
+                version = getStringData(getTreeCache(), ZkPath.CONFIG_DEFAULT_VERSION.getPath());
+            }
+            if (version == null || version.isEmpty()) {
+                version = ZkDefs.DEFAULT_VERSION;
+                setData(getCurator(), ZkPath.CONFIG_DEFAULT_VERSION.getPath(), version);
+                setData(getCurator(), ZkPath.CONFIG_VERSION.getPath(version), (String) null);
+            }
+            return version;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    @Override
+    public void setDefaultVersion(String versionId) {
+        assertValid();
+        try {
+            setData(getCurator(), ZkPath.CONFIG_DEFAULT_VERSION.getPath(), versionId);
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    // Profile methods
+    //-------------------------------------------------------------------------
+
+    @Override
+    public boolean hasProfile(String version, String profile) {
+        assertValid();
+        return getProfile(version, profile, false) != null;
+    }
+
+    // Implementation
+    //-------------------------------------------------------------------------
+
+    private String getAttributePath(String containerId, ContainerAttribute attribute) {
+        switch (attribute) {
+        case BlueprintStatus:
+            return ZkPath.CONTAINER_EXTENDER_STATUS.getPath(containerId, "blueprint");
+        case SpringStatus:
+            return ZkPath.CONTAINER_EXTENDER_STATUS.getPath(containerId, "spring");
+        case ProvisionStatus:
+            return ZkPath.CONTAINER_PROVISION_RESULT.getPath(containerId);
+        case ProvisionException:
+            return ZkPath.CONTAINER_PROVISION_EXCEPTION.getPath(containerId);
+        case ProvisionList:
+            return ZkPath.CONTAINER_PROVISION_LIST.getPath(containerId);
+        case Location:
+            return ZkPath.CONTAINER_LOCATION.getPath(containerId);
+        case GeoLocation:
+            return ZkPath.CONTAINER_GEOLOCATION.getPath(containerId);
+        case Resolver:
+            return ZkPath.CONTAINER_RESOLVER.getPath(containerId);
+        case Ip:
+            return ZkPath.CONTAINER_IP.getPath(containerId);
+        case LocalIp:
+            return ZkPath.CONTAINER_LOCAL_IP.getPath(containerId);
+        case LocalHostName:
+            return ZkPath.CONTAINER_LOCAL_HOSTNAME.getPath(containerId);
+        case PublicIp:
+            return ZkPath.CONTAINER_PUBLIC_IP.getPath(containerId);
+        case PublicHostName:
+            return ZkPath.CONTAINER_PUBLIC_HOSTNAME.getPath(containerId);
+        case ManualIp:
+            return ZkPath.CONTAINER_MANUAL_IP.getPath(containerId);
+        case BindAddress:
+            return ZkPath.CONTAINER_BINDADDRESS.getPath(containerId);
+        case JmxUrl:
+            return ZkPath.CONTAINER_JMX.getPath(containerId);
+        case JolokiaUrl:
+            return ZkPath.CONTAINER_JOLOKIA.getPath(containerId);
+        case HttpUrl:
+            return ZkPath.CONTAINER_HTTP.getPath(containerId);
+        case SshUrl:
+            return ZkPath.CONTAINER_SSH.getPath(containerId);
+        case PortMin:
+            return ZkPath.CONTAINER_PORT_MIN.getPath(containerId);
+        case PortMax:
+            return ZkPath.CONTAINER_PORT_MAX.getPath(containerId);
+        case ProcessId:
+            return ZkPath.CONTAINER_PROCESS_ID.getPath(containerId);
+        case OpenShift:
+            return ZkPath.CONTAINER_OPENSHIFT.getPath(containerId);
+        default:
+            throw new IllegalArgumentException("Unsupported container attribute " + attribute);
+        }
+    }
+
+    @Override
+    public Map<String, String> getProfileAttributes(String version, String profile) {
+        assertValid();
+        Map<String, String> attributes = new HashMap<String, String>();
+        Map<String, String> config = getConfiguration(version, profile, AGENT_PID);
+        for (Map.Entry<String, String> entry : config.entrySet()) {
+            String key = entry.getKey();
+            if (key.startsWith(ATTRIBUTE_PREFIX)) {
+                String attribute = key.substring(ATTRIBUTE_PREFIX.length());
+                String value = entry.getValue();
+                attributes.put(attribute, value);
+            }
+        }
+        return attributes;
+    }
+
+    @Override
+    public void setProfileAttribute(final String version, final String profile, final String key, final String value) {
+        assertValid();
+        Map<String, String> config = getConfiguration(version, profile, AGENT_PID);
+        if (value != null) {
+            config.put(ATTRIBUTE_PREFIX + key, value);
+        } else {
+            config.remove(key);
+        }
+        setConfiguration(version, profile, AGENT_PID, config);
+    }
+
+    @Override
+    public Map<String, Map<String, String>> getConfigurations(String version, String profile) {
+        assertValid();
+        try {
+            Map<String, Map<String, String>> configurations = new HashMap<String, Map<String, String>>();
+            Map<String, byte[]> configs = getFileConfigurations(version, profile);
+            for (Map.Entry<String, byte[]> entry : configs.entrySet()) {
+                if (entry.getKey().endsWith(".properties")) {
+                    String pid = DataStoreHelpers.stripSuffix(entry.getKey(), ".properties");
+                    configurations.put(pid, DataStoreHelpers.toMap(DataStoreHelpers.toProperties(entry.getValue())));
+                }
+            }
+            return configurations;
+        } catch (Exception e) {
+            throw FabricException.launderThrowable(e);
+        }
+    }
+
+    public CuratorFramework getCurator() {
+        return curator.get();
+    }
+
+    // [FIXME] Test case polutes public API
+    public void bindCuratorForTesting(CuratorFramework curator) {
+        bindCurator(curator);
+    }
+
+    protected void bindCurator(CuratorFramework curator) {
+        this.curator.bind(curator);
+    }
+
+    protected void unbindCurator(CuratorFramework curator) {
+        this.curator.unbind(curator);
+    }
+
+    protected void bindPlaceholderResolver(PlaceholderResolver resolver) {
+        placeholderResolvers.putIfAbsent(resolver.getScheme(), new DynamicReference<PlaceholderResolver>());
+        placeholderResolvers.get(resolver.getScheme()).bind(resolver);
+    }
+
+    protected void unbindPlaceholderResolver(PlaceholderResolver resolver) {
+        placeholderResolvers.get(resolver.getScheme()).unbind();
+    }
+}

richedit/src/main/resource/testFiles/fuse/revFiles/cb3362_cfb295_fabric#fabric-features-service#src#main#java#org#fusesource#fabric#features#FabricFeaturesServiceImpl.java

@@ -0,0 +1,407 @@
+package org.fusesource.fabric.features;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Collection;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+import org.apache.karaf.features.Feature;
+import org.apache.karaf.features.FeaturesService;
+import org.apache.karaf.features.Repository;
+import org.apache.karaf.features.internal.FeatureValidationUtil;
+import org.apache.karaf.features.internal.FeaturesServiceImpl;
+import org.apache.karaf.features.internal.RepositoryImpl;
+import org.apache.zookeeper.KeeperException;
+import org.fusesource.fabric.api.Container;
+import org.fusesource.fabric.api.FabricService;
+import org.fusesource.fabric.api.Profile;
+import org.fusesource.fabric.api.Version;
+import org.fusesource.fabric.zookeeper.IZKClient;
+import org.fusesource.fabric.zookeeper.ZkPath;
+import org.linkedin.zookeeper.client.LifecycleListener;
+import org.linkedin.zookeeper.tracker.NodeEvent;
+import org.linkedin.zookeeper.tracker.NodeEventsListener;
+import org.linkedin.zookeeper.tracker.ZKStringDataReader;
+import org.linkedin.zookeeper.tracker.ZooKeeperTreeTracker;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.fusesource.fabric.utils.features.FeatureUtils.search;
+
+/**
+ * A FeaturesService implementation for Fabric managed containers.
+ */
+public class FabricFeaturesServiceImpl extends FeaturesServiceImpl implements FeaturesService, NodeEventsListener<String>, LifecycleListener {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(FeaturesService.class);
+
+    private FabricService fabricService;
+    private IZKClient zooKeeper;
+
+    private ZooKeeperTreeTracker<String> profilesTracker;
+
+
+    private final Set<Repository> repositories = new HashSet<Repository>();
+    private final Set<Feature> allfeatures = new HashSet<Feature>();
+    private final Set<Feature> installed = new HashSet<Feature>();
+
+    public void init() throws Exception {
+    }
+
+    public void destroy() throws Exception {
+        profilesTracker.destroy();
+    }
+
+    @Override
+    public void onEvents(Collection<NodeEvent<String>> nodeEvents) {
+        try {
+            repositories.clear();
+            listRepositories();
+            allfeatures.clear();
+            listFeatures();
+            installed.clear();
+            listInstalledFeatures();
+        } catch (Exception e) {
+            LOGGER.error("Error while updating FeaturesService information from Fabric Registry.", e);
+        }
+
+    }
+
+    @Override
+    public void onConnected() {
+        profilesTracker = new ZooKeeperTreeTracker<String>(zooKeeper, new ZKStringDataReader(), ZkPath.CONFIG_VERSIONS.getPath());
+        try {
+            profilesTracker.track(this);
+        } catch (InterruptedException e) {
+            LOGGER.error("Error while setting tracker for Fabric Features Service.", e);
+        } catch (KeeperException e) {
+            LOGGER.error("Error while setting tracker for Fabric Features Service.", e);
+        }
+        onEvents(null);
+    }
+
+    @Override
+    public void onDisconnected() {
+    }
+
+    @Override
+    public void validateRepository(URI uri) throws Exception {
+        FeatureValidationUtil.validate(uri);
+    }
+
+    @Override
+    public void addRepository(URI uri) throws Exception {
+        addRepository(uri, true);
+    }
+
+    @Override
+    public void addRepository(URI uri, boolean b) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, please use fabric:profile-edit --repositories %s target-profile instead. See fabric:profile-edit for more information.", uri.toString()));
+    }
+
+    @Override
+    public void removeRepository(URI uri) throws Exception {
+        removeRepository(uri, true);
+    }
+
+    @Override
+    public void removeRepository(URI uri, boolean b) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, please use fabric:profile-edit --delete --repositories %s target-profile instead. See fabric:profile-edit for more information.", uri.toString()));
+    }
+
+    @Override
+    public void restoreRepository(URI uri) throws Exception {
+    }
+
+    /**
+     * Lists all {@link Repository} entries found in any {@link Profile} of the current {@link Container} {@link Version}.
+     *
+     * @return
+     */
+    @Override
+    public Repository[] listRepositories() {
+        if (repositories.isEmpty()) {
+            Set<String> repositoryUris = new LinkedHashSet<String>();
+            Container container = fabricService.getCurrentContainer();
+            Version version = container.getVersion();
+            Profile[] profiles = fabricService.getProfiles(version.getName());
+            if (profiles != null) {
+                for (Profile profile : profiles) {
+                    if (profile.getRepositories() != null) {
+                        for (String uri : profile.getRepositories()) {
+                            repositoryUris.add(uri);
+                            addRepositoryUri(uri, repositoryUris);
+                        }
+                    }
+                }
+            }
+
+            for (String uri : repositoryUris) {
+                try {
+                    repositories.add(new RepositoryImpl(new URI(uri)));
+                } catch (URISyntaxException e) {
+                    LOGGER.debug("Error while adding repository with uri {}.", uri);
+                }
+            }
+        }
+        return repositories.toArray(new Repository[repositories.size()]);
+    }
+
+    @Override
+    public void installFeature(String s) throws Exception {
+        installFeature(s, (EnumSet) null);
+    }
+
+    @Override
+    public void installFeature(String s, EnumSet<Option> options) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", s));
+    }
+
+    @Override
+    public void installFeature(String s, String s2) throws Exception {
+        installFeature(s, s2, null);
+    }
+
+    @Override
+    public void installFeature(String s, String s2, EnumSet<Option> options) throws Exception {
+        String featureName = s;
+        if (s2 != null && s2.equals("0.0.0")) {
+            featureName = s + "/" + s2;
+        }
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", featureName));
+    }
+
+    @Override
+    public void installFeature(Feature feature, EnumSet<Option> options) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", feature.getName()));
+    }
+
+    @Override
+    public void installFeatures(Set<Feature> features, EnumSet<Option> options) throws Exception {
+        StringBuffer sb = new StringBuffer();
+        for (Feature feature : features) {
+            sb.append("--feature ").append(feature.getName());
+        }
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", sb.toString()));
+    }
+
+    @Override
+    public void uninstallFeature(String s) throws Exception {
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --delete --features %s target-profile instead. See fabric:profile-edit for more information.", s));
+    }
+
+    @Override
+    public void uninstallFeature(String s, String s2) throws Exception {
+        String featureName = s;
+        if (s2 != null && s2.equals("0.0.0")) {
+            featureName = s + "/" + s2;
+        }
+        throw new UnsupportedOperationException(String.format("The container is managed by fabric, pleas use fabric:profile-edit --features %s target-profile instead. See fabric:profile-edit for more information.", featureName));
+    }
+
+    @Override
+    public Feature[] listFeatures() throws Exception {
+        if (allfeatures.isEmpty()) {
+            Repository[] repositories = listRepositories();
+            for (Repository repository : repositories) {
+                try {
+                    for (Feature feature : repository.getFeatures()) {
+                        if (!allfeatures.contains(feature)) {
+                            allfeatures.add(feature);
+                        }
+                    }
+                } catch (Exception ex) {
+                    LOGGER.debug("Could not load features from %s.", repository.getURI());
+                }
+            }
+        }
+        return allfeatures.toArray(new Feature[allfeatures.size()]);
+    }
+
+    @Override
+    public Feature[] listInstalledFeatures() {
+        if (installed.isEmpty()) {
+            try {
+                Map<String, Map<String, Feature>> allFeatures = getFeatures(listProfileRepositories());
+                Container container = fabricService.getCurrentContainer();
+                Profile[] profiles = container.getProfiles();
+
+                if (profiles != null) {
+                    for (Profile profile : profiles) {
+                        List<String> featureNames = profile.getFeatures();
+                        for (String featureName : featureNames) {
+                            try {
+                                Feature f;
+                                if (featureName.contains("/")) {
+                                    String[] parts = featureName.split("/");
+                                    String name = parts[0];
+                                    String version = parts[1];
+                                    f = allFeatures.get(name).get(version);
+                                } else {
+                                    TreeMap<String, Feature> versionMap = (TreeMap<String, Feature>) allFeatures.get(featureName);
+                                    f = versionMap.lastEntry().getValue();
+                                }
+                                addFeatures(f, installed);
+                            } catch (Exception ex) {
+                                LOGGER.debug("Error while adding {} to the features list");
+                            }
+                        }
+                    }
+                }
+            } catch (Exception e) {
+                LOGGER.error("Error retrieveing features.", e);
+            }
+        }
+        return installed.toArray(new Feature[installed.size()]);
+    }
+
+
+    @Override
+    public boolean isInstalled(Feature feature) {
+        if (installed.isEmpty()) {
+            listInstalledFeatures();
+        }
+        return installed.contains(feature);
+    }
+
+
+    protected Map<String, Map<String, Feature>> getFeatures(Repository[] repositories) throws Exception {
+        Map<String, Map<String, Feature>> features = new HashMap<String, Map<String, Feature>>();
+        for (Repository repo : repositories) {
+            try {
+                for (Feature f : repo.getFeatures()) {
+                    if (features.get(f.getName()) == null) {
+                        Map<String, Feature> versionMap = new TreeMap<String, Feature>();
+                        versionMap.put(f.getVersion(), f);
+                        features.put(f.getName(), versionMap);
+                    } else {
+                        features.get(f.getName()).put(f.getVersion(), f);
+                    }
+                }
+            } catch (Exception ex) {
+                LOGGER.debug("Could not load features from %s.", repo.getURI());
+            }
+        }
+        return features;
+    }
+
+
+    /**
+     * Lists all {@link Repository} enties found in the {@link Profile}s assigned to the current {@link Container}.
+     *
+     * @return
+     */
+    private Repository[] listProfileRepositories() {
+        Set<String> repositoryUris = new LinkedHashSet<String>();
+        Set<Repository> repositories = new LinkedHashSet<Repository>();
+        Container container = fabricService.getCurrentContainer();
+        Set<Profile> profilesWithParents = new HashSet<Profile>();
+
+        Profile[] profiles = container.getProfiles();
+        if (profiles != null) {
+            for (Profile profile : profiles) {
+                addProfiles(profile, profilesWithParents);
+            }
+            for (Profile profile : profilesWithParents) {
+                if (profile.getRepositories() != null) {
+                    for (String uri : profile.getRepositories()) {
+                        repositoryUris.add(uri);
+                        addRepositoryUri(uri, repositoryUris);
+                    }
+                }
+            }
+        }
+
+        for (String uri : repositoryUris) {
+            try {
+                repositories.add(new RepositoryImpl(new URI(uri)));
+            } catch (URISyntaxException e) {
+                LOGGER.debug("Error while adding repository with uri {}.", uri);
+            }
+        }
+        return repositories.toArray(new Repository[repositories.size()]);
+    }
+
+
+    /**
+     * Adds the {@link URI} of {@link Feature} {@link Repository} and its internals to the set of repositories {@link URI}s.
+     *
+     * @param uri
+     * @param repositoryUris
+     */
+    protected void addRepositoryUri(String uri, Set<String> repositoryUris) {
+        if (repositoryUris.contains(uri)) {
+            return;
+        }
+        repositoryUris.add(uri);
+        try {
+            Repository repository = new RepositoryImpl(new URI(uri));
+            URI[] internalUris = repository.getRepositories();
+            if (internalUris != null) {
+                for (URI u : internalUris) {
+                    addRepositoryUri(u.toString(), repositoryUris);
+                }
+            }
+        } catch (Exception e) {
+            LOGGER.debug("Error while adding internal repositories of {}.", uri);
+        }
+    }
+
+    /**
+     * Adds {@link Profile} and its parents to the set of {@link Profile}s.
+     *
+     * @param profile
+     * @param profiles
+     */
+    protected void addProfiles(Profile profile, Set<Profile> profiles) {
+        if (profiles.contains(profile)) {
+            return;
+        }
+
+        profiles.add(profile);
+        for (Profile parent : profile.getParents()) {
+            addProfiles(parent, profiles);
+        }
+    }
+
+    /**
+     * Adds {@link Feature} and its dependencies to the set of {@link Feature}s.
+     *
+     * @param feature
+     * @param features
+     */
+    protected void addFeatures(Feature feature, Set<Feature> features) {
+        if (features.contains(feature)) {
+            return;
+        }
+
+        features.add(feature);
+        for (Feature dependency : feature.getDependencies()) {
+            addFeatures(search(dependency.getName(), dependency.getVersion(), repositories), features);
+        }
+    }
+
+
+
+    public FabricService getFabricService() {
+        return fabricService;
+    }
+
+    public void setFabricService(FabricService fabricService) {
+        this.fabricService = fabricService;
+    }
+
+    public IZKClient getZooKeeper() {
+        return zooKeeper;
+    }
+
+    public void setZooKeeper(IZKClient zooKeeper) {
+        this.zooKeeper = zooKeeper;
+    }
+}

richedit/src/main/resource/testFiles/fuse/revFiles/d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Export.java

@@ -0,0 +1,158 @@
+/**
+ * Copyright (C) 2011, FuseSource Corp.  All rights reserved.
+ * http://fusesource.com
+ *
+ * The software in this package is published under the terms of the
+ * CDDL license a copy of which has been included with this distribution
+ * in the license.txt file.
+ */
+package org.fusesource.fabric.zookeeper.commands;
+
+import org.apache.felix.gogo.commands.Argument;
+import org.apache.felix.gogo.commands.Command;
+import org.apache.felix.gogo.commands.Option;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.*;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.getPatterns;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.matches;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.merge;
+
+@Command(name = "export", scope = "zk", description = "Export data from zookeeper")
+public class Export extends ZooKeeperCommandSupport {
+
+    @Argument(description="path of the directory to export to")
+    String target = "." + File.separator + "export";
+
+    @Option(name="-f", aliases={"--regex"}, description="regex to filter on what paths to export, can specify this option more than once for additional filters", multiValued=true)
+    String regex[];
+
+    @Option(name="-rf", aliases={"--reverse-regex"}, description="regex to filter what paths to exclude from the export, can specify this option more than once for additional filters", multiValued=true)
+    String nregex[];
+
+    @Option(name="-p", aliases={"--path"}, description="Top level context to export")
+    String topLevel = "/";
+
+    @Option(name="-d", aliases={"--delete"}, description="Clear target directory before exporting (CAUTION! Performs recursive delete!)")
+    boolean delete;
+
+    @Option(name="--dry-run", description="Runs the export but instead prints out what's going to happen rather than performing the action")
+    boolean dryRun = false;
+
+    File ignore = new File(".fabricignore");
+    File include = new File(".fabricinclude");
+
+    @Override
+    protected Object doExecute() throws Exception {
+        if (ignore.exists() && ignore.isFile()) {
+            nregex = merge(ignore, nregex);
+        }
+        if (include.exists() && include.isFile()) {
+            regex = merge(include, regex);
+        }
+        export(topLevel);
+        System.out.printf("Export to %s completed successfully\n", target);
+        return null;
+    }
+
+    private void delete(File parent) throws Exception {
+        if (!parent.exists()) {
+            return;
+        }
+        if (parent.isDirectory()) {
+            for (File f : parent.listFiles()) {
+                delete(f);
+            }
+        }
+        parent.delete();
+    }
+
+    protected void export(String path) throws Exception {
+        if (!path.endsWith("/")) {
+            path = path + "/";
+        }
+        if (!path.startsWith("/")) {
+            path = "/" + path;
+        }
+        List<Pattern> include = getPatterns(regex);
+        List<Pattern> exclude = getPatterns(nregex);
+        List<String> paths = getZooKeeper().getAllChildren(path);
+        SortedSet<File> directories = new TreeSet<File>();
+        Map<File, String> settings = new HashMap<File, String>();
+
+        for(String p : paths) {
+            p = path + p;
+            if (!matches(include, p, true) || matches(exclude, p, false)) {
+                continue;
+            }
+            byte[] data = getZooKeeper().getData(p);
+            if (data != null) {
+                settings.put(new File(target + File.separator + p + ".cfg"), new String(data));
+            } else {
+                directories.add(new File(target + File.separator + p));
+            }
+        }
+
+        if (delete) {
+            if (!dryRun) {
+                delete(new File(target));
+            } else {
+                System.out.printf("Deleting %s and everything under it\n", new File(target));
+            }
+        }
+
+        for (File d : directories) {
+            if (d.exists() && !d.isDirectory()) {
+                throw new IllegalArgumentException("Directory " + d + " exists but is not a directory");
+            }
+            if (!d.exists()) {
+                if (!dryRun) {
+                    if (!d.mkdirs()) {
+                        throw new RuntimeException("Failed to create directory " + d);
+                    }
+                } else {
+                    System.out.printf("Creating directory path : %s\n", d);
+                }
+            }
+        }
+        for (File f : settings.keySet()) {
+            if (f.exists() && !f.isFile()) {
+                throw new IllegalArgumentException("File " + f + " exists but is not a file");
+            }
+            if (!f.getParentFile().exists()) {
+                if (!dryRun) {
+                    if (!f.getParentFile().mkdirs()) {
+                        throw new RuntimeException("Failed to create directory " + f.getParentFile());
+                    }
+                } else {
+                    System.out.printf("Creating directory path : %s\n", f);
+                }
+            }
+            if (!f.exists()) {
+                try {
+                    if (!dryRun) {
+                        if (!f.createNewFile()) {
+                            throw new RuntimeException("Failed to create file " + f);
+                        }
+                    } else {
+                        System.out.printf("Creating file : %s\n", f);
+                    }
+                } catch (IOException io) {
+                    throw new RuntimeException("Failed to create file " + f + " : " + io);
+                }
+            }
+            if (!dryRun) {
+                FileWriter writer = new FileWriter(f, false);
+                writer.write(settings.get(f));
+                writer.close();
+            } else {
+                System.out.printf("Writing value \"%s\" to file : %s\n", settings.get(f), f);
+            }
+        }
+    }
+}

richedit/src/main/resource/testFiles/fuse/revFiles/d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Import.java

@@ -0,0 +1,204 @@
+/**
+ * Copyright (C) 2011, FuseSource Corp.  All rights reserved.
+ * http://fusesource.com
+ *
+ * The software in this package is published under the terms of the
+ * CDDL license a copy of which has been included with this distribution
+ * in the license.txt file.
+ */
+package org.fusesource.fabric.zookeeper.commands;
+
+import org.apache.felix.gogo.commands.Argument;
+import org.apache.felix.gogo.commands.Command;
+import org.apache.felix.gogo.commands.Option;
+import org.apache.zookeeper.CreateMode;
+import org.apache.zookeeper.ZooDefs;
+
+import java.io.*;
+import java.net.URL;
+import java.util.*;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.getPatterns;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.matches;
+import static org.fusesource.fabric.zookeeper.commands.RegexSupport.merge;
+
+@Command(name = "import", scope = "zk", description = "Import data into zookeeper")
+public class Import extends ZooKeeperCommandSupport {
+
+    @Argument(description = "Location of the file or filesystem to load")
+    protected String source = "." + File.separator + "import";
+
+    @Option(name="-d", aliases={"--delete"}, description="Delete any paths not in the tree being imported, ignored when importing a properties file (CAUTION!)")
+    boolean delete = false;
+
+    @Option(name="-t", aliases={"--target"}, description="Target location in ZooKeeper tree to import to")
+    String target = "/";
+
+    @Option(name="-props", aliases={"--properties"}, description="Argument is URL pointing to a properties file")
+    boolean properties = false;
+
+    @Option(name="-fs", aliases={"--filesystem"}, description="Argument is the top level directory of a local filesystem tree")
+    boolean filesystem = true;
+
+    @Option(name="-f", aliases={"--regex"}, description="regex to filter on what paths to import, can specify this option more than once for additional filters", multiValued=true)
+    String regex[];
+
+    @Option(name="-rf", aliases={"--reverse-regex"}, description="regex to filter what paths to exclude, can specify this option more than once for additional filters", multiValued=true)
+    protected String[] nregex;
+
+    @Option(name="--dry-run", description="Runs the import but prints out what's going to happen instead of making any changes")
+    boolean dryRun = false;
+
+    File ignore = new File(".fabricignore");
+    File include = new File(".fabricinclude");
+
+    @Override
+    protected Object doExecute() throws Exception {
+        if (ignore.exists() && ignore.isFile()) {
+            nregex = merge(ignore, nregex);
+        }
+        if (include.exists() && include.isFile()) {
+            regex = merge(include, regex);
+        }
+        if (properties == true) {
+            filesystem = false;
+        }
+        if (filesystem == true) {
+            properties = false;
+        }
+        if (properties) {
+            readPropertiesFile();
+        }
+        if (filesystem) {
+            readFileSystem();
+        }
+        System.out.println("Successfully imported settings from " + source);
+        return null;
+    }
+
+    private String stripPath(String path) {
+        String strs[] = path.split(source);
+        if (strs.length == 0) {
+            return "";
+        }
+        return strs[strs.length - 1].substring(0, strs[1].length() - ".cfg".length());
+    }
+
+    private String buildZKPath(File parent, File current) {
+        String rc = "";
+        if (current != null && !parent.equals(current)) {
+            rc = buildZKPath(parent, current.getParentFile()) + "/" + current.getName();
+        }
+        return rc;
+    }
+
+    private void getCandidates(File parent, File current, Map<String, String> settings) throws Exception {
+        if (current.isDirectory()) {
+            for (File child : current.listFiles(new FileFilter() {
+                @Override
+                public boolean accept(File file) {
+                    if (file.isDirectory() || file.getName().endsWith(".cfg")) {
+                        return true;
+                    }
+                    return false;
+                }
+            })) {
+                getCandidates(parent, child, settings);
+            }
+            String p = buildZKPath(parent, current).replaceFirst("/", "");
+            settings.put(p, null);
+        } else {
+            BufferedInputStream in = new BufferedInputStream(new FileInputStream(current));
+            byte[] contents = new byte[in.available()];
+            in.read(contents);
+            in.close();
+            String p = buildZKPath(parent, current).replaceFirst("/", "");
+            if (p.endsWith(".cfg")) {
+                p = p.substring(0, p.length() - ".cfg".length());
+            }
+            settings.put(p, new String(contents));
+        }
+    }
+
+    private void readFileSystem() throws Exception {
+        Map<String, String> settings = new TreeMap<String, String>();
+        File s = new File(source);
+        getCandidates(s, s, settings);
+        List<Pattern> include = getPatterns(regex);
+        List<Pattern> exclude = getPatterns(nregex);
+
+        if (!target.endsWith("/")) {
+            target = target + "/";
+        }
+        if (!target.startsWith("/")) {
+            target = "/" + target;
+        }
+
+        List<String> paths = new ArrayList<String>();
+
+        for(String key : settings.keySet()) {
+            String data = settings.get(key);
+            key = target + key;
+            paths.add(key);
+            if (!matches(include, key, true) || matches(exclude, key, false)) {
+                continue;
+            }
+            if (!dryRun) {
+                getZooKeeper().createOrSetWithParents(key, data, ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);
+            } else {
+                System.out.printf("Creating path \"%s\" with value \"%s\"\n", key, data);
+            }
+        }
+
+        if (delete) {
+            deletePathsNotIn(paths);
+        }
+    }
+
+    private void deletePathsNotIn(List<String> paths) throws Exception {
+        List<String> zkPaths = getZooKeeper().getAllChildren(target);
+
+        for (String path : zkPaths) {
+            path = "/" + path;
+            if (!paths.contains(path)) {
+                if (!dryRun) {
+                    getZooKeeper().deleteWithChildren(path);
+                } else {
+                    System.out.printf("Deleting path %s and everything under it\n", path);
+                }
+            }
+        }
+
+    }
+
+    private void readPropertiesFile() throws Exception {
+        List<Pattern> includes = getPatterns(regex);
+        List<Pattern> excludes = getPatterns(nregex);
+        InputStream in = new BufferedInputStream(new URL(source).openStream());
+        List<String> paths = new ArrayList<String>();
+        Properties props = new Properties();
+        props.load(in);
+        for (Enumeration names = props.propertyNames(); names.hasMoreElements();) {
+            String name = (String) names.nextElement();
+            String value = props.getProperty(name);
+            if (value != null && value.isEmpty()) {
+                value = null;
+            }
+            if (!name.startsWith("/")) {
+                name = "/" + name;
+            }
+            name = target + name;
+            if (!matches(includes, name, true) || matches(excludes, name, false)) {
+                continue;
+            }
+            if (!dryRun) {
+                getZooKeeper().createOrSetWithParents(name, value, ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);
+            } else {
+                System.out.printf("Creating path \"%s\" with value \"%s\"\n", name, value);
+            }
+        }
+    }
+
+}

richedit/src/main/resource/testFiles/metadata/prevFiles/prev_017a3f_580eac_web#src#main#java#org#jboss#metadata#parser#jbossweb#ContainerListenerMetaDataParser.java

@@ -0,0 +1,73 @@
+/*
+ * JBoss, Home of Professional Open Source.
+ * Copyright 2010, Red Hat, Inc., and individual contributors
+ * as indicated by the @author tags. See the copyright.txt file in the
+ * distribution for a full listing of individual contributors.
+ *
+ * This is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This software is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this software; if not, write to the Free
+ * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
+ */
+
+package org.jboss.metadata.parser.jbossweb;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import org.jboss.metadata.javaee.spec.ParamValueMetaData;
+import org.jboss.metadata.parser.ee.ParamValueMetaDataParser;
+import org.jboss.metadata.parser.util.MetaDataElementParser;
+import org.jboss.metadata.web.jboss.ContainerListenerMetaData;
+import org.jboss.metadata.web.jboss.ContainerListenerType;
+
+/**
+ * @author Remy Maucherat
+ */
+public class ContainerListenerMetaDataParser extends MetaDataElementParser {
+
+    public static ContainerListenerMetaData parse(XMLStreamReader reader) throws XMLStreamException {
+    	ContainerListenerMetaData containerListener = new ContainerListenerMetaData();
+
+        // Handle elements
+        while (reader.hasNext() && reader.nextTag() != END_ELEMENT) {
+            final Element element = Element.forName(reader.getLocalName());
+            switch (element) {
+                case CLASS_NAME:
+                	containerListener.setListenerClass(getElementText(reader));
+                    break;
+                case MODULE:
+                	containerListener.setModule(getElementText(reader));
+                    break;
+                case LISTENER_TYPE:
+                	containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));
+                    break;
+                case PARAM:
+                    List<ParamValueMetaData> params = containerListener.getParams();
+                    if (params == null) {
+                    	params = new ArrayList<ParamValueMetaData>();
+                    	containerListener.setParams(params);
+                    }
+                    params.add(ParamValueMetaDataParser.parse(reader));
+                    break;
+                default: throw unexpectedElement(reader);
+            }
+        }
+
+        return containerListener;
+    }
+
+}

richedit/src/main/resource/testFiles/metadata/prevFiles/prev_674226_73eff3_common#src#main#java#org#jboss#metadata#parser#ee#ServiceReferenceMetaDataParser.java

@@ -0,0 +1,140 @@
+/*
+ * JBoss, Home of Professional Open Source.
+ * Copyright 2010, Red Hat, Inc., and individual contributors
+ * as indicated by the @author tags. See the copyright.txt file in the
+ * distribution for a full listing of individual contributors.
+ *
+ * This is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This software is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this software; if not, write to the Free
+ * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
+ */
+
+package org.jboss.metadata.parser.ee;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.namespace.QName;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import org.jboss.metadata.parser.util.MetaDataElementParser;
+import org.jboss.metadata.javaee.jboss.JBossPortComponentRef;
+import org.jboss.metadata.javaee.jboss.JBossServiceReferenceMetaData;
+import org.jboss.metadata.javaee.spec.DescriptionGroupMetaData;
+import org.jboss.metadata.javaee.spec.DescriptionsImpl;
+import org.jboss.metadata.javaee.spec.EJBReferenceMetaData;
+import org.jboss.metadata.javaee.spec.EJBReferenceType;
+import org.jboss.metadata.javaee.spec.EnvironmentEntryMetaData;
+import org.jboss.metadata.javaee.spec.MessageDestinationMetaData;
+import org.jboss.metadata.javaee.spec.PortComponentRef;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlerChainMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlerChainsMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlerMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlersMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceMetaData;
+
+/**
+ * @author Remy Maucherat
+ */
+public class ServiceReferenceMetaDataParser extends MetaDataElementParser {
+
+    public static ServiceReferenceMetaData parse(XMLStreamReader reader) throws XMLStreamException {
+        JBossServiceReferenceMetaData serviceReference = new JBossServiceReferenceMetaData();
+
+        // Handle attributes
+        final int count = reader.getAttributeCount();
+        for (int i = 0; i < count; i ++) {
+            final String value = reader.getAttributeValue(i);
+            if (attributeHasNamespace(reader, i)) {
+                continue;
+            }
+            final Attribute attribute = Attribute.forName(reader.getAttributeLocalName(i));
+            switch (attribute) {
+                case ID: {
+                    serviceReference.setId(value);
+                    break;
+                }
+                default: throw unexpectedAttribute(reader, i);
+            }
+        }
+
+        DescriptionGroupMetaData descriptionGroup = new DescriptionGroupMetaData();
+        // Handle elements
+        while (reader.hasNext() && reader.nextTag() != END_ELEMENT) {
+            if (DescriptionGroupMetaDataParser.parse(reader, descriptionGroup)) {
+                if (serviceReference.getDescriptionGroup() == null) {
+                    serviceReference.setDescriptionGroup(descriptionGroup);
+                }
+                continue;
+            }
+            if (ResourceInjectionMetaDataParser.parse(reader, serviceReference)) {
+                continue;
+            }
+            final Element element = Element.forName(reader.getLocalName());
+            switch (element) {
+                case SERVICE_REF_NAME:
+                    serviceReference.setServiceRefName(getElementText(reader));
+                    break;
+                case SERVICE_INTERFACE:
+                    serviceReference.setServiceInterface(getElementText(reader));
+                    break;
+                case SERVICE_REF_TYPE:
+                    serviceReference.setServiceRefType(getElementText(reader));
+                    break;
+                case WSDL_FILE:
+                    serviceReference.setWsdlFile(getElementText(reader));
+                    break;
+                case JAXRPC_MAPPING_FILE:
+                    serviceReference.setJaxrpcMappingFile(getElementText(reader));
+                    break;
+                case SERVICE_QNAME:
+                    serviceReference.setServiceQname(QName.valueOf(getElementText(reader)));
+                    break;
+                case PORT_COMPONENT_REF:
+                    List<JBossPortComponentRef> portComponentRefs = (List<JBossPortComponentRef>) serviceReference.getPortComponentRef();
+                    if (portComponentRefs == null) {
+                        portComponentRefs = new ArrayList<JBossPortComponentRef>();
+                        serviceReference.setJBossPortComponentRef(portComponentRefs);
+                    }
+                    portComponentRefs.add(PortComponentRefParser.parse(reader));
+                    break;
+                case HANDLER:
+                    ServiceReferenceHandlersMetaData handlers = serviceReference.getHandlers();
+                    if (handlers == null) {
+                        handlers = new ServiceReferenceHandlersMetaData();
+                        serviceReference.setHandlers(handlers);
+                    }
+                    handlers.add(ServiceReferenceHandlerMetaDataParser.parse(reader));
+                    break;
+                case HANDLER_CHAIN:
+                    ServiceReferenceHandlerChainsMetaData handlerChains = serviceReference.getHandlerChains();
+                    if (handlerChains == null) {
+                        handlerChains = new ServiceReferenceHandlerChainsMetaData();
+                        handlerChains.setHandlers(new ArrayList<ServiceReferenceHandlerChainMetaData>());
+                        serviceReference.setHandlerChains(handlerChains);
+                    }
+                    handlerChains.getHandlers().add(ServiceReferenceHandlerChainMetaDataParser.parse(reader));
+                    break;
+                case WSDL_OVERRIDE:
+                    serviceReference.setWsdlOverride(getElementText(reader));
+                    break;
+                default: throw unexpectedElement(reader);
+            }
+        }
+
+        return serviceReference;
+    }
+
+}

richedit/src/main/resource/testFiles/metadata/prevFiles/prev_a82665_e8bff4_appclient#src#main#java#org#jboss#metadata#appclient#parser#spec#ApplicationClientMetaDataParser.java

@@ -0,0 +1,130 @@
+/*
+ * JBoss, Home of Professional Open Source.
+ * Copyright 2010, Red Hat, Inc., and individual contributors
+ * as indicated by the @author tags. See the copyright.txt file in the
+ * distribution for a full listing of individual contributors.
+ *
+ * This is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This software is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this software; if not, write to the Free
+ * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
+ */
+
+package org.jboss.metadata.appclient.parser.spec;
+
+import org.jboss.metadata.appclient.spec.AppClientEnvironmentRefsGroupMetaData;
+import org.jboss.metadata.appclient.spec.ApplicationClientMetaData;
+import org.jboss.metadata.javaee.spec.DescriptionGroupMetaData;
+import org.jboss.metadata.parser.ee.DescriptionGroupMetaDataParser;
+import org.jboss.metadata.parser.ee.EnvironmentRefsGroupMetaDataParser;
+import org.jboss.metadata.parser.util.MetaDataElementParser;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+/**
+ * Parses an application-client.xml file and creates metadata out of it
+ * <p/>
+ * @author Stuart Douglas
+ */
+public class ApplicationClientMetaDataParser extends MetaDataElementParser
+{
+
+   public static final ApplicationClientMetaDataParser INSTANCE = new ApplicationClientMetaDataParser();
+
+   public ApplicationClientMetaData parse(XMLStreamReader reader) throws XMLStreamException
+   {
+      reader.require(START_DOCUMENT, null, null);
+      // Read until the first start element
+      while (reader.hasNext() && reader.next() != START_ELEMENT)
+      {
+
+      }
+
+      ApplicationClientMetaData appClientMetadata = new ApplicationClientMetaData();
+
+      processAttributes(appClientMetadata, reader);
+
+      // parse and create metadata out of the elements under the root ejb-jar element
+      processElements(appClientMetadata, reader);
+
+      return appClientMetadata;
+   }
+
+   protected void processAttribute(ApplicationClientMetaData metaData, XMLStreamReader reader, int i) throws XMLStreamException
+   {
+      final String value = reader.getAttributeValue(i);
+      if (attributeHasNamespace(reader, i))
+      {
+         return;
+      }
+      final ApplicationClientAttribute ejbJarAttribute = ApplicationClientAttribute.forName(reader.getAttributeLocalName(i));
+      switch (ejbJarAttribute)
+      {
+         case ID:
+         {
+            metaData.setId(value);
+            break;
+         }
+         case VERSION:
+         {
+             metaData.setVersion(value);
+         }
+         case METADATA_COMPLETE:
+         {
+            metaData.setMetadataComplete(true);
+            break;
+         }
+         default:
+            throw unexpectedAttribute(reader, i);
+      }
+   }
+
+   protected void processAttributes(final ApplicationClientMetaData applicationClientMetaData, XMLStreamReader reader) throws XMLStreamException
+   {
+      // Handle attributes and set them in the EjbJarMetaData
+      final int count = reader.getAttributeCount();
+      for (int i = 0; i < count; i++)
+      {
+         processAttribute(applicationClientMetaData, reader, i);
+      }
+   }
+
+   protected void processElements(final ApplicationClientMetaData applicationClientMetaData, XMLStreamReader reader) throws XMLStreamException
+   {
+
+        final DescriptionGroupMetaData descriptionGroup = new DescriptionGroupMetaData();
+        final AppClientEnvironmentRefsGroupMetaData environmentRefsGroupMetaData = new AppClientEnvironmentRefsGroupMetaData();
+        // Handle elements
+        while (reader.hasNext() && reader.nextTag() != END_ELEMENT) {
+            if (DescriptionGroupMetaDataParser.parse(reader, descriptionGroup)) {
+                continue;
+            }
+            if (EnvironmentRefsGroupMetaDataParser.parseRemote(reader, environmentRefsGroupMetaData)) {
+                continue;
+            }
+            final AppClientElement element = AppClientElement.forName(reader.getLocalName());
+            switch (element) {
+                case CALLBACK_HANDLER: {
+                    applicationClientMetaData.setCallbackHandler(getElementText(reader));
+                    break;
+                }
+                default:
+                    throw unexpectedElement(reader);
+            }
+        }
+        applicationClientMetaData.setDescriptionGroup(descriptionGroup);
+        applicationClientMetaData.setEnvironmentRefsGroupMetaData(environmentRefsGroupMetaData);
+
+   }
+}

richedit/src/main/resource/testFiles/metadata/revFiles/017a3f_580eac_web#src#main#java#org#jboss#metadata#parser#jbossweb#ContainerListenerMetaDataParser.java

@@ -0,0 +1,77 @@
+/*
+ * JBoss, Home of Professional Open Source.
+ * Copyright 2010, Red Hat, Inc., and individual contributors
+ * as indicated by the @author tags. See the copyright.txt file in the
+ * distribution for a full listing of individual contributors.
+ *
+ * This is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This software is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this software; if not, write to the Free
+ * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
+ */
+
+package org.jboss.metadata.parser.jbossweb;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import org.jboss.metadata.javaee.spec.ParamValueMetaData;
+import org.jboss.metadata.parser.ee.ParamValueMetaDataParser;
+import org.jboss.metadata.parser.util.MetaDataElementParser;
+import org.jboss.metadata.web.jboss.ContainerListenerMetaData;
+import org.jboss.metadata.web.jboss.ContainerListenerType;
+
+/**
+ * @author Remy Maucherat
+ */
+public class ContainerListenerMetaDataParser extends MetaDataElementParser {
+
+    public static ContainerListenerMetaData parse(XMLStreamReader reader) throws XMLStreamException {
+    	ContainerListenerMetaData containerListener = new ContainerListenerMetaData();
+
+        // Handle elements
+        while (reader.hasNext() && reader.nextTag() != END_ELEMENT) {
+            final Element element = Element.forName(reader.getLocalName());
+            switch (element) {
+                case CLASS_NAME:
+                	containerListener.setListenerClass(getElementText(reader));
+                    break;
+                case MODULE:
+                	containerListener.setModule(getElementText(reader));
+                    break;
+                case LISTENER_TYPE:
+                    try {
+                        containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));
+                    } catch (IllegalArgumentException e) {
+                        throw unexpectedValue(reader, e);
+                    }
+                    break;
+                case PARAM:
+                    List<ParamValueMetaData> params = containerListener.getParams();
+                    if (params == null) {
+                    	params = new ArrayList<ParamValueMetaData>();
+                    	containerListener.setParams(params);
+                    }
+                    params.add(ParamValueMetaDataParser.parse(reader));
+                    break;
+                default: throw unexpectedElement(reader);
+            }
+        }
+
+        return containerListener;
+    }
+
+}

richedit/src/main/resource/testFiles/metadata/revFiles/674226_73eff3_common#src#main#java#org#jboss#metadata#parser#ee#ServiceReferenceMetaDataParser.java

@@ -0,0 +1,140 @@
+/*
+ * JBoss, Home of Professional Open Source.
+ * Copyright 2010, Red Hat, Inc., and individual contributors
+ * as indicated by the @author tags. See the copyright.txt file in the
+ * distribution for a full listing of individual contributors.
+ *
+ * This is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This software is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this software; if not, write to the Free
+ * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
+ */
+
+package org.jboss.metadata.parser.ee;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.namespace.QName;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import org.jboss.metadata.parser.util.MetaDataElementParser;
+import org.jboss.metadata.javaee.jboss.JBossPortComponentRef;
+import org.jboss.metadata.javaee.jboss.JBossServiceReferenceMetaData;
+import org.jboss.metadata.javaee.spec.DescriptionGroupMetaData;
+import org.jboss.metadata.javaee.spec.DescriptionsImpl;
+import org.jboss.metadata.javaee.spec.EJBReferenceMetaData;
+import org.jboss.metadata.javaee.spec.EJBReferenceType;
+import org.jboss.metadata.javaee.spec.EnvironmentEntryMetaData;
+import org.jboss.metadata.javaee.spec.MessageDestinationMetaData;
+import org.jboss.metadata.javaee.spec.PortComponentRef;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlerChainMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlerChainsMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlerMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceHandlersMetaData;
+import org.jboss.metadata.javaee.spec.ServiceReferenceMetaData;
+
+/**
+ * @author Remy Maucherat
+ */
+public class ServiceReferenceMetaDataParser extends MetaDataElementParser {
+
+    public static ServiceReferenceMetaData parse(XMLStreamReader reader) throws XMLStreamException {
+        JBossServiceReferenceMetaData serviceReference = new JBossServiceReferenceMetaData();
+
+        // Handle attributes
+        final int count = reader.getAttributeCount();
+        for (int i = 0; i < count; i ++) {
+            final String value = reader.getAttributeValue(i);
+            if (attributeHasNamespace(reader, i)) {
+                continue;
+            }
+            final Attribute attribute = Attribute.forName(reader.getAttributeLocalName(i));
+            switch (attribute) {
+                case ID: {
+                    serviceReference.setId(value);
+                    break;
+                }
+                default: throw unexpectedAttribute(reader, i);
+            }
+        }
+
+        DescriptionGroupMetaData descriptionGroup = new DescriptionGroupMetaData();
+        // Handle elements
+        while (reader.hasNext() && reader.nextTag() != END_ELEMENT) {
+            if (DescriptionGroupMetaDataParser.parse(reader, descriptionGroup)) {
+                if (serviceReference.getDescriptionGroup() == null) {
+                    serviceReference.setDescriptionGroup(descriptionGroup);
+                }
+                continue;
+            }
+            if (ResourceInjectionMetaDataParser.parse(reader, serviceReference)) {
+                continue;
+            }
+            final Element element = Element.forName(reader.getLocalName());
+            switch (element) {
+                case SERVICE_REF_NAME:
+                    serviceReference.setServiceRefName(getElementText(reader));
+                    break;
+                case SERVICE_INTERFACE:
+                    serviceReference.setServiceInterface(getElementText(reader));
+                    break;
+                case SERVICE_REF_TYPE:
+                    serviceReference.setServiceRefType(getElementText(reader));
+                    break;
+                case WSDL_FILE:
+                    serviceReference.setWsdlFile(getElementText(reader));
+                    break;
+                case JAXRPC_MAPPING_FILE:
+                    serviceReference.setJaxrpcMappingFile(getElementText(reader));
+                    break;
+                case SERVICE_QNAME:
+                    serviceReference.setServiceQname(parseQName(reader, getElementText(reader)));
+                    break;
+                case PORT_COMPONENT_REF:
+                    List<JBossPortComponentRef> portComponentRefs = (List<JBossPortComponentRef>) serviceReference.getPortComponentRef();
+                    if (portComponentRefs == null) {
+                        portComponentRefs = new ArrayList<JBossPortComponentRef>();
+                        serviceReference.setJBossPortComponentRef(portComponentRefs);
+                    }
+                    portComponentRefs.add(PortComponentRefParser.parse(reader));
+                    break;
+                case HANDLER:
+                    ServiceReferenceHandlersMetaData handlers = serviceReference.getHandlers();
+                    if (handlers == null) {
+                        handlers = new ServiceReferenceHandlersMetaData();
+                        serviceReference.setHandlers(handlers);
+                    }
+                    handlers.add(ServiceReferenceHandlerMetaDataParser.parse(reader));
+                    break;
+                case HANDLER_CHAIN:
+                    ServiceReferenceHandlerChainsMetaData handlerChains = serviceReference.getHandlerChains();
+                    if (handlerChains == null) {
+                        handlerChains = new ServiceReferenceHandlerChainsMetaData();
+                        handlerChains.setHandlers(new ArrayList<ServiceReferenceHandlerChainMetaData>());
+                        serviceReference.setHandlerChains(handlerChains);
+                    }
+                    handlerChains.getHandlers().add(ServiceReferenceHandlerChainMetaDataParser.parse(reader));
+                    break;
+                case WSDL_OVERRIDE:
+                    serviceReference.setWsdlOverride(getElementText(reader));
+                    break;
+                default: throw unexpectedElement(reader);
+            }
+        }
+
+        return serviceReference;
+    }
+
+}

richedit/src/main/resource/testFiles/metadata/revFiles/a82665_e8bff4_appclient#src#main#java#org#jboss#metadata#appclient#parser#spec#ApplicationClientMetaDataParser.java

@@ -0,0 +1,131 @@
+/*
+ * JBoss, Home of Professional Open Source.
+ * Copyright 2010, Red Hat, Inc., and individual contributors
+ * as indicated by the @author tags. See the copyright.txt file in the
+ * distribution for a full listing of individual contributors.
+ *
+ * This is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This software is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this software; if not, write to the Free
+ * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
+ */
+
+package org.jboss.metadata.appclient.parser.spec;
+
+import org.jboss.metadata.appclient.spec.AppClientEnvironmentRefsGroupMetaData;
+import org.jboss.metadata.appclient.spec.ApplicationClientMetaData;
+import org.jboss.metadata.javaee.spec.DescriptionGroupMetaData;
+import org.jboss.metadata.parser.ee.DescriptionGroupMetaDataParser;
+import org.jboss.metadata.parser.ee.EnvironmentRefsGroupMetaDataParser;
+import org.jboss.metadata.parser.util.MetaDataElementParser;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+/**
+ * Parses an application-client.xml file and creates metadata out of it
+ * <p/>
+ * @author Stuart Douglas
+ */
+public class ApplicationClientMetaDataParser extends MetaDataElementParser
+{
+
+   public static final ApplicationClientMetaDataParser INSTANCE = new ApplicationClientMetaDataParser();
+
+   public ApplicationClientMetaData parse(XMLStreamReader reader) throws XMLStreamException
+   {
+      reader.require(START_DOCUMENT, null, null);
+      // Read until the first start element
+      while (reader.hasNext() && reader.next() != START_ELEMENT)
+      {
+
+      }
+
+      ApplicationClientMetaData appClientMetadata = new ApplicationClientMetaData();
+
+      processAttributes(appClientMetadata, reader);
+
+      // parse and create metadata out of the elements under the root ejb-jar element
+      processElements(appClientMetadata, reader);
+
+      return appClientMetadata;
+   }
+
+   protected void processAttribute(ApplicationClientMetaData metaData, XMLStreamReader reader, int i) throws XMLStreamException
+   {
+      final String value = reader.getAttributeValue(i);
+      if (attributeHasNamespace(reader, i))
+      {
+         return;
+      }
+      final ApplicationClientAttribute ejbJarAttribute = ApplicationClientAttribute.forName(reader.getAttributeLocalName(i));
+      switch (ejbJarAttribute)
+      {
+         case ID:
+         {
+            metaData.setId(value);
+            break;
+         }
+         case VERSION:
+         {
+             metaData.setVersion(value);
+             break;
+         }
+         case METADATA_COMPLETE:
+         {
+            metaData.setMetadataComplete(Boolean.parseBoolean(value));
+            break;
+         }
+         default:
+            throw unexpectedAttribute(reader, i);
+      }
+   }
+
+   protected void processAttributes(final ApplicationClientMetaData applicationClientMetaData, XMLStreamReader reader) throws XMLStreamException
+   {
+      // Handle attributes and set them in the EjbJarMetaData
+      final int count = reader.getAttributeCount();
+      for (int i = 0; i < count; i++)
+      {
+         processAttribute(applicationClientMetaData, reader, i);
+      }
+   }
+
+   protected void processElements(final ApplicationClientMetaData applicationClientMetaData, XMLStreamReader reader) throws XMLStreamException
+   {
+
+        final DescriptionGroupMetaData descriptionGroup = new DescriptionGroupMetaData();
+        final AppClientEnvironmentRefsGroupMetaData environmentRefsGroupMetaData = new AppClientEnvironmentRefsGroupMetaData();
+        // Handle elements
+        while (reader.hasNext() && reader.nextTag() != END_ELEMENT) {
+            if (DescriptionGroupMetaDataParser.parse(reader, descriptionGroup)) {
+                continue;
+            }
+            if (EnvironmentRefsGroupMetaDataParser.parseRemote(reader, environmentRefsGroupMetaData)) {
+                continue;
+            }
+            final AppClientElement element = AppClientElement.forName(reader.getLocalName());
+            switch (element) {
+                case CALLBACK_HANDLER: {
+                    applicationClientMetaData.setCallbackHandler(getElementText(reader));
+                    break;
+                }
+                default:
+                    throw unexpectedElement(reader);
+            }
+        }
+        applicationClientMetaData.setDescriptionGroup(descriptionGroup);
+        applicationClientMetaData.setEnvironmentRefsGroupMetaData(environmentRefsGroupMetaData);
+
+   }
+}

richedit/src/test/java/edu/lu/uni/serval/BaseTest.java

@@ -4,11 +4,15 @@ package edu.lu.uni.serval;
 
 import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
 import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.utils.CallShell;
+import org.yaml.snakeyaml.Yaml;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.List;
+import java.util.Map;
 import java.util.Properties;
 
 public class BaseTest {
@@ -46,4 +50,53 @@ public class BaseTest {
         }
 
     }
+
+    public List<HierarchicalActionSet> getHierarchicalActionSets4java(String s) throws IOException {
+        Properties appProps = new Properties();
+
+
+        Yaml yaml = new Yaml();
+//        InputStream inputStream = this.getClass()
+//                .getClassLoader()
+//                .getResourceAsStream("customer.yaml");
+        Map<String, Object> obj = yaml.load(new FileInputStream("src/main/resource/config.yml"));
+
+//        appProps.load(new FileInputStream(appConfigPath));
+        Map<String, Object> fixminer = (Map<String, Object>) obj.get("fixminer");
+        Map<String, Object> dataset = (Map<String, Object>) obj.get("dataset");
+        String srcMLPath = (String) fixminer.get("srcMLPath");
+        String inputPath = (String) dataset.get("inputPath");
+//        appProps.load(new FileInputStream("src/main/resource/app.properties"));
+//        String srcMLPath = appProps.getProperty("srcMLPath", "FORKJOIN");
+//        String root = appProps.getProperty("inputPath");
+
+        String root = "src/main/resource/testFiles";
+        String project = s.split("_")[0];
+        root = root + "/"+project+"/";
+        String filename = s.replace(project+"_","");
+        try{
+            File revFile = new File(root + "revFiles/" + filename);
+            File prevFile = new File(root + "prevFiles/prev_" + filename);
+
+            EDiffHunkParser parser = new EDiffHunkParser();
+
+
+            List<HierarchicalActionSet> hierarchicalActionSets = parser.parseChangedSourceCodeWithGumTree2(prevFile, revFile, srcMLPath,true);
+            return hierarchicalActionSets;
+        }catch (NullPointerException n){
+
+            String cmd1 = "mkdir -p " + System.getProperty("user.dir")+"/" + root + n.getMessage().split(root)[1].split("/")[0];
+            String cmd = "cp " +inputPath+"/" +project+"/"+n.getMessage().split(root)[1] + " "+System.getProperty("user.dir")+"/"+n.getMessage();
+            CallShell cs = new CallShell();
+            try {
+                cs.runShell(cmd1);
+                cs.runShell(cmd);
+            } catch (Exception e) {
+                e.printStackTrace();
+            }
+            return null;
+
+        }
+
+    }
 }

richedit/src/test/java/edu/lu/uni/serval/TestJavaMiner.java

@@ -0,0 +1,842 @@
+package edu.lu.uni.serval;
+
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
+import org.junit.Assert;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import java.io.IOException;
+import java.util.List;
+
+
+public class TestJavaMiner extends BaseTest {
+
+    //commons-codec_55a865_ecec1c_src#main#java#org#apache#commons#codec#StringEncoderComparator.java.txt_0
+
+    @Test
+    public void test_gzip_051ed8_8b83dc() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-codec_55a865_ecec1c_src#main#java#org#apache#commons#codec#StringEncoderComparator.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD TypeDeclaration@@[public]StringEncoderComparator, [Comparator] @TO@ [@SuppressWarnings(\"rawtypes\"), public]StringEncoderComparator, [Comparator] @AT@ 1206 @LENGTH@ 1756\n" +
+                "---INS SingleMemberAnnotation@@@SuppressWarnings(\"rawtypes\") @TO@ TypeDeclaration@@[public]StringEncoderComparator, [Comparator] @AT@ 1206 @LENGTH@ 29\n");
+    }
+
+    //
+    @Test
+    public void test_commons_configuration_b24b7b_3ac9d8() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-configuration_b24b7b_3ac9d8_src#test#org#apache#commons#configuration#TestHierarchicalConfigurationXMLReader.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"INS TryStatement@@try {  trans.transform(source,result);} catch (NoSuchMethodError ex) {  return;} @TO@ MethodDeclaration@@public, void, MethodName:testParse, Exception,  @AT@ 1804 @LENGTH@ 284\n" +
+                "---MOV ExpressionStatement@@MethodInvocation:trans.transform(source,result) @TO@ TryStatement@@try {  trans.transform(source,result);} catch (NoSuchMethodError ex) {  return;} @AT@ 1804 @LENGTH@ 32\n" +
+                "---INS CatchClause@@catch (NoSuchMethodError ex) {  return;} @TO@ TryStatement@@try {  trans.transform(source,result);} catch (NoSuchMethodError ex) {  return;} @AT@ 2021 @LENGTH@ 67\n" +
+                "------INS SingleVariableDeclaration@@NoSuchMethodError ex @TO@ CatchClause@@catch (NoSuchMethodError ex) {  return;} @AT@ 2027 @LENGTH@ 20\n" +
+                "---------INS SimpleType@@NoSuchMethodError @TO@ SingleVariableDeclaration@@NoSuchMethodError ex @AT@ 2027 @LENGTH@ 17\n" +
+                "---------INS SimpleName@@ex @TO@ SingleVariableDeclaration@@NoSuchMethodError ex @AT@ 2045 @LENGTH@ 2\n" +
+                "------INS ReturnStatement@@ @TO@ CatchClause@@catch (NoSuchMethodError ex) {  return;} @AT@ 2071 @LENGTH@ 7\n");
+    }
+
+    //commons-collections_05b6c7_eedfe8_src#java#org#apache#commons#collections#BeanMap.java
+    @Test
+    public void test_commons_collections_05b6c7_eedfe8() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_05b6c7_eedfe8_src#java#org#apache#commons#collections#BeanMap.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ReturnStatement@@MethodInvocation:get((String)key) @TO@ MethodInvocation:get(key) @AT@ 18236 @LENGTH@ 27\n" +
+                "---UPD MethodInvocation@@get((String)key) @TO@ get(key) @AT@ 18243 @LENGTH@ 19\n" +
+                "------UPD SimpleName@@MethodName:get:[(String)key] @TO@ MethodName:get:[key] @AT@ 18243 @LENGTH@ 19\n" +
+                "---------INS SimpleName@@key @TO@ SimpleName@@MethodName:get:[(String)key] @AT@ 18247 @LENGTH@ 3\n" +
+                "---------DEL CastExpression@@(String)key @AT@ 18248 @LENGTH@ 12\n" +
+                "------------DEL SimpleType@@String @AT@ 18249 @LENGTH@ 6\n" +
+                "------------DEL SimpleName@@key @AT@ 18257 @LENGTH@ 3\n");
+    }
+
+    //commons-collections_906468_31bc59_src#java#org#apache#commons#collections#SequencedHashMap.java
+    @Test
+    public void test_commons_collections_906468_31bc59() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_906468_31bc59_src#java#org#apache#commons#collections#SequencedHashMap.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD IfStatement@@if (entry.equals(e)) return entry; else return null; @TO@ if (entry != null && entry.equals(e)) return entry; else return null; @AT@ 21117 @LENGTH@ 59\n" +
+                "---INS InfixExpression@@entry != null && entry.equals(e) @TO@ IfStatement@@if (entry.equals(e)) return entry; else return null; @AT@ 21116 @LENGTH@ 32\n" +
+                "------INS InfixExpression@@entry != null @TO@ InfixExpression@@entry != null && entry.equals(e) @AT@ 21116 @LENGTH@ 13\n" +
+                "---------INS SimpleName@@entry @TO@ InfixExpression@@entry != null @AT@ 21116 @LENGTH@ 5\n" +
+                "---------INS Operator@@!= @TO@ InfixExpression@@entry != null @AT@ 21121 @LENGTH@ 2\n" +
+                "---------INS NullLiteral@@null @TO@ InfixExpression@@entry != null @AT@ 21125 @LENGTH@ 4\n" +
+                "------MOV MethodInvocation@@entry.equals(e) @TO@ InfixExpression@@entry != null && entry.equals(e) @AT@ 21120 @LENGTH@ 15\n" +
+                "------INS Operator@@&& @TO@ InfixExpression@@entry != null && entry.equals(e) @AT@ 21129 @LENGTH@ 2\n");
+    }
+
+    //commons-compress_5273bd_c25c8d_src#main#java#org#apache#commons#compress#archivers#sevenz#Coders.java
+    @Test
+    public void test_commons_compress_5273bd_c25c8d() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-compress_5273bd_c25c8d_src#main#java#org#apache#commons#compress#archivers#sevenz#Coders.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ReturnStatement@@MethodInvocation:init().read() @TO@ MethodInvocation:init().read(b,off,len) @AT@ 9806 @LENGTH@ 21\n" +
+                "---UPD MethodInvocation@@init().read() @TO@ init().read(b,off,len) @AT@ 9813 @LENGTH@ 13\n" +
+                "------UPD SimpleName@@MethodName:read:[] @TO@ MethodName:read:[b, off, len] @AT@ 9820 @LENGTH@ 6\n" +
+                "---------INS SimpleName@@b @TO@ SimpleName@@MethodName:read:[] @AT@ 9825 @LENGTH@ 1\n" +
+                "---------INS SimpleName@@off @TO@ SimpleName@@MethodName:read:[] @AT@ 9828 @LENGTH@ 3\n" +
+                "---------INS SimpleName@@len @TO@ SimpleName@@MethodName:read:[] @AT@ 9833 @LENGTH@ 3\n");
+    }
+
+    //commons-compress_d8ca98_2ed556_src#main#java#org#apache#commons#compress#archivers#sevenz#AES256SHA256Decoder.java
+    @Test
+    public void test_commons_compress_d8ca98_2ed556() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-compress_d8ca98_2ed556_src#main#java#org#apache#commons#compress#archivers#sevenz#AES256SHA256Decoder.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD MethodDeclaration@@public, void, MethodName:close,  @TO@ public, void, MethodName:close, IOException,  @AT@ 5337 @LENGTH@ 35\n" +
+                "---INS SimpleType@@IOException @TO@ MethodDeclaration@@public, void, MethodName:close,  @AT@ 5364 @LENGTH@ 11\n" +
+                "---INS IfStatement@@if (cipherInputStream != null) {  cipherInputStream.close();} @TO@ MethodDeclaration@@public, void, MethodName:close,  @AT@ 5394 @LENGTH@ 97\n" +
+                "------INS InfixExpression@@cipherInputStream != null @TO@ IfStatement@@if (cipherInputStream != null) {  cipherInputStream.close();} @AT@ 5398 @LENGTH@ 25\n" +
+                "---------INS SimpleName@@cipherInputStream @TO@ InfixExpression@@cipherInputStream != null @AT@ 5398 @LENGTH@ 17\n" +
+                "---------INS Operator@@!= @TO@ InfixExpression@@cipherInputStream != null @AT@ 5415 @LENGTH@ 2\n" +
+                "---------INS NullLiteral@@null @TO@ InfixExpression@@cipherInputStream != null @AT@ 5419 @LENGTH@ 4\n" +
+                "------INS Block@@ThenBody:{  cipherInputStream.close();} @TO@ IfStatement@@if (cipherInputStream != null) {  cipherInputStream.close();} @AT@ 5425 @LENGTH@ 66\n" +
+                "---------INS ExpressionStatement@@MethodInvocation:cipherInputStream.close() @TO@ Block@@ThenBody:{  cipherInputStream.close();} @AT@ 5447 @LENGTH@ 26\n" +
+                "------------INS MethodInvocation@@cipherInputStream.close() @TO@ ExpressionStatement@@MethodInvocation:cipherInputStream.close() @AT@ 5447 @LENGTH@ 25\n" +
+                "---------------INS SimpleName@@Name:cipherInputStream @TO@ MethodInvocation@@cipherInputStream.close() @AT@ 5447 @LENGTH@ 17\n" +
+                "---------------INS SimpleName@@MethodName:close:[] @TO@ MethodInvocation@@cipherInputStream.close() @AT@ 5465 @LENGTH@ 7\n");
+    }
+
+    //fuse_2006f48_4dad2f_insight#insight-camel#src#main#java#org#fusesource#insight#camel#audit#ScriptUtils.java
+    @Test
+    public void test_fuse_2006f48_4dad2f() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_2006f48_4dad2f_insight#insight-camel#src#main#java#org#fusesource#insight#camel#audit#ScriptUtils.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD TryStatement@@try {  return mapper.writeValueAsString(o);} catch (Exception e) {  throw new IllegalArgumentException(\"Could not serialize \" + o,e);} @TO@ try {  if (o instanceof Collection) {    StringBuilder sb=new StringBuilder();    sb.append(\"[\");    for (    Object c : (Collection)o) {      if (sb.length() > 1) {        sb.append(\",\");      }      sb.append(toJson(c));    }    sb.append(\"]\");    return sb.toString();  } else   if (o instanceof Map) {    StringBuilder sb=new StringBuilder();    sb.append(\"{\");    for (    Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {      if (sb.length() > 1) {        sb.append(\",\");      }      sb.append(toJson(e.getKey().toString()));      sb.append(\":\");      sb.append(toJson(e.getValue()));    }    sb.append(\"}\");    return sb.toString();  } else   if (o == null) {    return \"null\";  } else   if (o instanceof Date) {    return \"\\\"\" + toIso((Date)o) + \"\\\"\";  } else {    return mapper.writeValueAsString(o.toString());  }} catch (Exception e) {  throw new IllegalArgumentException(\"Could not serialize \" + o,e);} @AT@ 1282 @LENGTH@ 175\n" +
+                "---DEL ReturnStatement@@MethodInvocation:mapper.writeValueAsString(o) @AT@ 1300 @LENGTH@ 36\n" +
+                "---INS IfStatement@@if (o instanceof Collection) {  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} else if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ TryStatement@@try {  return mapper.writeValueAsString(o);} catch (Exception e) {  throw new IllegalArgumentException(\"Could not serialize \" + o,e);} @AT@ 1431 @LENGTH@ 1233\n" +
+                "------INS InstanceofExpression@@o instanceof Collection @TO@ IfStatement@@if (o instanceof Collection) {  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} else if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 1435 @LENGTH@ 23\n" +
+                "---------INS SimpleName@@o @TO@ InstanceofExpression@@o instanceof Collection @AT@ 1435 @LENGTH@ 1\n" +
+                "---------INS Instanceof@@instanceof @TO@ InstanceofExpression@@o instanceof Collection @AT@ 1437 @LENGTH@ 10\n" +
+                "---------INS SimpleType@@Collection @TO@ InstanceofExpression@@o instanceof Collection @AT@ 1448 @LENGTH@ 10\n" +
+                "------INS Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} @TO@ IfStatement@@if (o instanceof Collection) {  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} else if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 1460 @LENGTH@ 388\n" +
+                "---------INS VariableDeclarationStatement@@StringBuilder sb=new StringBuilder(); @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} @AT@ 1478 @LENGTH@ 39\n" +
+                "------------INS SimpleType@@StringBuilder @TO@ VariableDeclarationStatement@@StringBuilder sb=new StringBuilder(); @AT@ 1478 @LENGTH@ 13\n" +
+                "------------INS VariableDeclarationFragment@@sb=new StringBuilder() @TO@ VariableDeclarationStatement@@StringBuilder sb=new StringBuilder(); @AT@ 1492 @LENGTH@ 24\n" +
+                "---------------INS SimpleName@@sb @TO@ VariableDeclarationFragment@@sb=new StringBuilder() @AT@ 1492 @LENGTH@ 2\n" +
+                "---------------INS ClassInstanceCreation@@StringBuilder[] @TO@ VariableDeclarationFragment@@sb=new StringBuilder() @AT@ 1497 @LENGTH@ 19\n" +
+                "------------------INS New@@new @TO@ ClassInstanceCreation@@StringBuilder[] @AT@ 1497 @LENGTH@ 3\n" +
+                "------------------INS SimpleType@@StringBuilder @TO@ ClassInstanceCreation@@StringBuilder[] @AT@ 1501 @LENGTH@ 13\n" +
+                "---------INS ExpressionStatement@@MethodInvocation:sb.append(\"[\") @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} @AT@ 1534 @LENGTH@ 15\n" +
+                "------------INS MethodInvocation@@sb.append(\"[\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\"[\") @AT@ 1534 @LENGTH@ 14\n" +
+                "---------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\"[\") @AT@ 1534 @LENGTH@ 2\n" +
+                "---------------INS SimpleName@@MethodName:append:[\"[\"] @TO@ MethodInvocation@@sb.append(\"[\") @AT@ 1537 @LENGTH@ 11\n" +
+                "------------------INS StringLiteral@@\"[\" @TO@ SimpleName@@MethodName:append:[\"[\"] @AT@ 1544 @LENGTH@ 3\n" +
+                "---------INS EnhancedForStatement@@for (Object c : (Collection)o) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(c));} @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} @AT@ 1566 @LENGTH@ 198\n" +
+                "------------INS SingleVariableDeclaration@@Object c @TO@ EnhancedForStatement@@for (Object c : (Collection)o) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(c));} @AT@ 1571 @LENGTH@ 8\n" +
+                "---------------INS SimpleType@@Object @TO@ SingleVariableDeclaration@@Object c @AT@ 1571 @LENGTH@ 6\n" +
+                "---------------INS SimpleName@@c @TO@ SingleVariableDeclaration@@Object c @AT@ 1578 @LENGTH@ 1\n" +
+                "------------INS CastExpression@@(Collection)o @TO@ EnhancedForStatement@@for (Object c : (Collection)o) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(c));} @AT@ 1582 @LENGTH@ 14\n" +
+                "---------------INS SimpleType@@Collection @TO@ CastExpression@@(Collection)o @AT@ 1583 @LENGTH@ 10\n" +
+                "---------------INS SimpleName@@o @TO@ CastExpression@@(Collection)o @AT@ 1595 @LENGTH@ 1\n" +
+                "------------INS IfStatement@@if (sb.length() > 1) {  sb.append(\",\");} @TO@ EnhancedForStatement@@for (Object c : (Collection)o) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(c));} @AT@ 1620 @LENGTH@ 84\n" +
+                "---------------INS InfixExpression@@sb.length() > 1 @TO@ IfStatement@@if (sb.length() > 1) {  sb.append(\",\");} @AT@ 1624 @LENGTH@ 15\n" +
+                "------------------INS MethodInvocation@@sb.length() @TO@ InfixExpression@@sb.length() > 1 @AT@ 1624 @LENGTH@ 11\n" +
+                "---------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.length() @AT@ 1624 @LENGTH@ 2\n" +
+                "---------------------INS SimpleName@@MethodName:length:[] @TO@ MethodInvocation@@sb.length() @AT@ 1627 @LENGTH@ 8\n" +
+                "------------------INS Operator@@> @TO@ InfixExpression@@sb.length() > 1 @AT@ 1635 @LENGTH@ 1\n" +
+                "------------------INS NumberLiteral@@1 @TO@ InfixExpression@@sb.length() > 1 @AT@ 1638 @LENGTH@ 1\n" +
+                "---------------INS Block@@ThenBody:{  sb.append(\",\");} @TO@ IfStatement@@if (sb.length() > 1) {  sb.append(\",\");} @AT@ 1641 @LENGTH@ 63\n" +
+                "------------------INS ExpressionStatement@@MethodInvocation:sb.append(\",\") @TO@ Block@@ThenBody:{  sb.append(\",\");} @AT@ 1667 @LENGTH@ 15\n" +
+                "---------------------INS MethodInvocation@@sb.append(\",\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\",\") @AT@ 1667 @LENGTH@ 14\n" +
+                "------------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\",\") @AT@ 1667 @LENGTH@ 2\n" +
+                "------------------------INS SimpleName@@MethodName:append:[\",\"] @TO@ MethodInvocation@@sb.append(\",\") @AT@ 1670 @LENGTH@ 11\n" +
+                "---------------------------INS StringLiteral@@\",\" @TO@ SimpleName@@MethodName:append:[\",\"] @AT@ 1677 @LENGTH@ 3\n" +
+                "------------INS ExpressionStatement@@MethodInvocation:sb.append(toJson(c)) @TO@ EnhancedForStatement@@for (Object c : (Collection)o) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(c));} @AT@ 1725 @LENGTH@ 21\n" +
+                "---------------INS MethodInvocation@@sb.append(toJson(c)) @TO@ ExpressionStatement@@MethodInvocation:sb.append(toJson(c)) @AT@ 1725 @LENGTH@ 20\n" +
+                "------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(toJson(c)) @AT@ 1725 @LENGTH@ 2\n" +
+                "------------------INS SimpleName@@MethodName:append:[toJson(c)] @TO@ MethodInvocation@@sb.append(toJson(c)) @AT@ 1728 @LENGTH@ 17\n" +
+                "---------------------INS MethodInvocation@@toJson(c) @TO@ SimpleName@@MethodName:append:[toJson(c)] @AT@ 1735 @LENGTH@ 9\n" +
+                "------------------------INS SimpleName@@MethodName:toJson:[c] @TO@ MethodInvocation@@toJson(c) @AT@ 1735 @LENGTH@ 9\n" +
+                "---------------------------INS SimpleName@@c @TO@ SimpleName@@MethodName:toJson:[c] @AT@ 1742 @LENGTH@ 1\n" +
+                "---------INS ExpressionStatement@@MethodInvocation:sb.append(\"]\") @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} @AT@ 1781 @LENGTH@ 15\n" +
+                "------------INS MethodInvocation@@sb.append(\"]\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\"]\") @AT@ 1781 @LENGTH@ 14\n" +
+                "---------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\"]\") @AT@ 1781 @LENGTH@ 2\n" +
+                "---------------INS SimpleName@@MethodName:append:[\"]\"] @TO@ MethodInvocation@@sb.append(\"]\") @AT@ 1784 @LENGTH@ 11\n" +
+                "------------------INS StringLiteral@@\"]\" @TO@ SimpleName@@MethodName:append:[\"]\"] @AT@ 1791 @LENGTH@ 3\n" +
+                "---------INS ReturnStatement@@MethodInvocation:sb.toString() @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} @AT@ 1813 @LENGTH@ 21\n" +
+                "------------INS MethodInvocation@@sb.toString() @TO@ ReturnStatement@@MethodInvocation:sb.toString() @AT@ 1820 @LENGTH@ 13\n" +
+                "---------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.toString() @AT@ 1820 @LENGTH@ 2\n" +
+                "---------------INS SimpleName@@MethodName:toString:[] @TO@ MethodInvocation@@sb.toString() @AT@ 1823 @LENGTH@ 10\n" +
+                "------INS Block@@ElseBody:if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ IfStatement@@if (o instanceof Collection) {  StringBuilder sb=new StringBuilder();  sb.append(\"[\");  for (  Object c : (Collection)o) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(c));  }  sb.append(\"]\");  return sb.toString();} else if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 1854 @LENGTH@ 810\n" +
+                "---------INS IfStatement@@if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ Block@@ElseBody:if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 1854 @LENGTH@ 810\n" +
+                "------------INS InstanceofExpression@@o instanceof Map @TO@ IfStatement@@if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 1858 @LENGTH@ 16\n" +
+                "---------------INS SimpleName@@o @TO@ InstanceofExpression@@o instanceof Map @AT@ 1858 @LENGTH@ 1\n" +
+                "---------------INS Instanceof@@instanceof @TO@ InstanceofExpression@@o instanceof Map @AT@ 1860 @LENGTH@ 10\n" +
+                "---------------INS SimpleType@@Map @TO@ InstanceofExpression@@o instanceof Map @AT@ 1871 @LENGTH@ 3\n" +
+                "------------INS Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} @TO@ IfStatement@@if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 1876 @LENGTH@ 538\n" +
+                "---------------INS VariableDeclarationStatement@@StringBuilder sb=new StringBuilder(); @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} @AT@ 1894 @LENGTH@ 39\n" +
+                "------------------INS SimpleType@@StringBuilder @TO@ VariableDeclarationStatement@@StringBuilder sb=new StringBuilder(); @AT@ 1894 @LENGTH@ 13\n" +
+                "------------------INS VariableDeclarationFragment@@sb=new StringBuilder() @TO@ VariableDeclarationStatement@@StringBuilder sb=new StringBuilder(); @AT@ 1908 @LENGTH@ 24\n" +
+                "---------------------INS SimpleName@@sb @TO@ VariableDeclarationFragment@@sb=new StringBuilder() @AT@ 1908 @LENGTH@ 2\n" +
+                "---------------------INS ClassInstanceCreation@@StringBuilder[] @TO@ VariableDeclarationFragment@@sb=new StringBuilder() @AT@ 1913 @LENGTH@ 19\n" +
+                "------------------------INS New@@new @TO@ ClassInstanceCreation@@StringBuilder[] @AT@ 1913 @LENGTH@ 3\n" +
+                "------------------------INS SimpleType@@StringBuilder @TO@ ClassInstanceCreation@@StringBuilder[] @AT@ 1917 @LENGTH@ 13\n" +
+                "---------------INS ExpressionStatement@@MethodInvocation:sb.append(\"{\") @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} @AT@ 1950 @LENGTH@ 15\n" +
+                "------------------INS MethodInvocation@@sb.append(\"{\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\"{\") @AT@ 1950 @LENGTH@ 14\n" +
+                "---------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\"{\") @AT@ 1950 @LENGTH@ 2\n" +
+                "---------------------INS SimpleName@@MethodName:append:[\"{\"] @TO@ MethodInvocation@@sb.append(\"{\") @AT@ 1953 @LENGTH@ 11\n" +
+                "------------------------INS StringLiteral@@\"{\" @TO@ SimpleName@@MethodName:append:[\"{\"] @AT@ 1960 @LENGTH@ 3\n" +
+                "---------------INS EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} @AT@ 1982 @LENGTH@ 348\n" +
+                "------------------INS SingleVariableDeclaration@@Map.Entry<Object,Object> e @TO@ EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @AT@ 1987 @LENGTH@ 27\n" +
+                "---------------------INS ParameterizedType@@Map.Entry<Object,Object> @TO@ SingleVariableDeclaration@@Map.Entry<Object,Object> e @AT@ 1987 @LENGTH@ 25\n" +
+                "------------------------INS SimpleType@@Map.Entry @TO@ ParameterizedType@@Map.Entry<Object,Object> @AT@ 1987 @LENGTH@ 9\n" +
+                "------------------------INS SimpleType@@Object @TO@ ParameterizedType@@Map.Entry<Object,Object> @AT@ 1997 @LENGTH@ 6\n" +
+                "------------------------INS SimpleType@@Object @TO@ ParameterizedType@@Map.Entry<Object,Object> @AT@ 2005 @LENGTH@ 6\n" +
+                "---------------------INS SimpleName@@e @TO@ SingleVariableDeclaration@@Map.Entry<Object,Object> e @AT@ 2013 @LENGTH@ 1\n" +
+                "------------------INS MethodInvocation@@((Map<Object,Object>)o).entrySet() @TO@ EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @AT@ 2017 @LENGTH@ 36\n" +
+                "---------------------INS ParenthesizedExpression@@((Map<Object,Object>)o) @TO@ MethodInvocation@@((Map<Object,Object>)o).entrySet() @AT@ 2017 @LENGTH@ 25\n" +
+                "------------------------INS CastExpression@@(Map<Object,Object>)o @TO@ ParenthesizedExpression@@((Map<Object,Object>)o) @AT@ 2018 @LENGTH@ 23\n" +
+                "---------------------------INS ParameterizedType@@Map<Object,Object> @TO@ CastExpression@@(Map<Object,Object>)o @AT@ 2019 @LENGTH@ 19\n" +
+                "------------------------------INS SimpleType@@Map @TO@ ParameterizedType@@Map<Object,Object> @AT@ 2019 @LENGTH@ 3\n" +
+                "------------------------------INS SimpleType@@Object @TO@ ParameterizedType@@Map<Object,Object> @AT@ 2023 @LENGTH@ 6\n" +
+                "------------------------------INS SimpleType@@Object @TO@ ParameterizedType@@Map<Object,Object> @AT@ 2031 @LENGTH@ 6\n" +
+                "---------------------------INS SimpleName@@o @TO@ CastExpression@@(Map<Object,Object>)o @AT@ 2040 @LENGTH@ 1\n" +
+                "---------------------INS SimpleName@@MethodName:entrySet:[] @TO@ MethodInvocation@@((Map<Object,Object>)o).entrySet() @AT@ 2043 @LENGTH@ 10\n" +
+                "------------------INS IfStatement@@if (sb.length() > 1) {  sb.append(\",\");} @TO@ EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @AT@ 2077 @LENGTH@ 84\n" +
+                "---------------------INS InfixExpression@@sb.length() > 1 @TO@ IfStatement@@if (sb.length() > 1) {  sb.append(\",\");} @AT@ 2081 @LENGTH@ 15\n" +
+                "------------------------INS MethodInvocation@@sb.length() @TO@ InfixExpression@@sb.length() > 1 @AT@ 2081 @LENGTH@ 11\n" +
+                "---------------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.length() @AT@ 2081 @LENGTH@ 2\n" +
+                "---------------------------INS SimpleName@@MethodName:length:[] @TO@ MethodInvocation@@sb.length() @AT@ 2084 @LENGTH@ 8\n" +
+                "------------------------INS Operator@@> @TO@ InfixExpression@@sb.length() > 1 @AT@ 2092 @LENGTH@ 1\n" +
+                "------------------------INS NumberLiteral@@1 @TO@ InfixExpression@@sb.length() > 1 @AT@ 2095 @LENGTH@ 1\n" +
+                "---------------------INS Block@@ThenBody:{  sb.append(\",\");} @TO@ IfStatement@@if (sb.length() > 1) {  sb.append(\",\");} @AT@ 2098 @LENGTH@ 63\n" +
+                "------------------------INS ExpressionStatement@@MethodInvocation:sb.append(\",\") @TO@ Block@@ThenBody:{  sb.append(\",\");} @AT@ 2124 @LENGTH@ 15\n" +
+                "---------------------------INS MethodInvocation@@sb.append(\",\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\",\") @AT@ 2124 @LENGTH@ 14\n" +
+                "------------------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\",\") @AT@ 2124 @LENGTH@ 2\n" +
+                "------------------------------INS SimpleName@@MethodName:append:[\",\"] @TO@ MethodInvocation@@sb.append(\",\") @AT@ 2127 @LENGTH@ 11\n" +
+                "---------------------------------INS StringLiteral@@\",\" @TO@ SimpleName@@MethodName:append:[\",\"] @AT@ 2134 @LENGTH@ 3\n" +
+                "------------------INS ExpressionStatement@@MethodInvocation:sb.append(toJson(e.getKey().toString())) @TO@ EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @AT@ 2182 @LENGTH@ 41\n" +
+                "---------------------INS MethodInvocation@@sb.append(toJson(e.getKey().toString())) @TO@ ExpressionStatement@@MethodInvocation:sb.append(toJson(e.getKey().toString())) @AT@ 2182 @LENGTH@ 40\n" +
+                "------------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(toJson(e.getKey().toString())) @AT@ 2182 @LENGTH@ 2\n" +
+                "------------------------INS SimpleName@@MethodName:append:[toJson(e.getKey().toString())] @TO@ MethodInvocation@@sb.append(toJson(e.getKey().toString())) @AT@ 2185 @LENGTH@ 37\n" +
+                "---------------------------INS MethodInvocation@@toJson(e.getKey().toString()) @TO@ SimpleName@@MethodName:append:[toJson(e.getKey().toString())] @AT@ 2192 @LENGTH@ 29\n" +
+                "------------------------------INS SimpleName@@MethodName:toJson:[e.getKey().toString()] @TO@ MethodInvocation@@toJson(e.getKey().toString()) @AT@ 2192 @LENGTH@ 29\n" +
+                "---------------------------------INS MethodInvocation@@e.getKey().toString() @TO@ SimpleName@@MethodName:toJson:[e.getKey().toString()] @AT@ 2199 @LENGTH@ 21\n" +
+                "------------------------------------INS MethodInvocation@@MethodName:getKey:[] @TO@ MethodInvocation@@e.getKey().toString() @AT@ 2199 @LENGTH@ 10\n" +
+                "------------------------------------INS SimpleName@@Name:e @TO@ MethodInvocation@@e.getKey().toString() @AT@ 2199 @LENGTH@ 1\n" +
+                "------------------------------------INS SimpleName@@MethodName:toString:[] @TO@ MethodInvocation@@e.getKey().toString() @AT@ 2210 @LENGTH@ 10\n" +
+                "------------------------------INS SimpleName@@MethodName:toJson:[e.getKey().toString()] @TO@ MethodInvocation@@toJson(e.getKey().toString()) @AT@ 2192 @LENGTH@ 29\n" +
+                "---------------------------------INS MethodInvocation@@e.getKey().toString() @TO@ SimpleName@@MethodName:toJson:[e.getKey().toString()] @AT@ 2199 @LENGTH@ 21\n" +
+                "------------------------------------INS MethodInvocation@@MethodName:getKey:[] @TO@ MethodInvocation@@e.getKey().toString() @AT@ 2199 @LENGTH@ 10\n" +
+                "------------------------------------INS SimpleName@@Name:e @TO@ MethodInvocation@@e.getKey().toString() @AT@ 2199 @LENGTH@ 1\n" +
+                "------------------------------------INS SimpleName@@MethodName:toString:[] @TO@ MethodInvocation@@e.getKey().toString() @AT@ 2210 @LENGTH@ 10\n" +
+                "------------------INS ExpressionStatement@@MethodInvocation:sb.append(\":\") @TO@ EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @AT@ 2244 @LENGTH@ 15\n" +
+                "---------------------INS MethodInvocation@@sb.append(\":\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\":\") @AT@ 2244 @LENGTH@ 14\n" +
+                "------------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\":\") @AT@ 2244 @LENGTH@ 2\n" +
+                "------------------------INS SimpleName@@MethodName:append:[\":\"] @TO@ MethodInvocation@@sb.append(\":\") @AT@ 2247 @LENGTH@ 11\n" +
+                "---------------------------INS StringLiteral@@\":\" @TO@ SimpleName@@MethodName:append:[\":\"] @AT@ 2254 @LENGTH@ 3\n" +
+                "------------------INS ExpressionStatement@@MethodInvocation:sb.append(toJson(e.getValue())) @TO@ EnhancedForStatement@@for (Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {  if (sb.length() > 1) {    sb.append(\",\");  }  sb.append(toJson(e.getKey().toString()));  sb.append(\":\");  sb.append(toJson(e.getValue()));} @AT@ 2280 @LENGTH@ 32\n" +
+                "---------------------INS MethodInvocation@@sb.append(toJson(e.getValue())) @TO@ ExpressionStatement@@MethodInvocation:sb.append(toJson(e.getValue())) @AT@ 2280 @LENGTH@ 31\n" +
+                "------------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(toJson(e.getValue())) @AT@ 2280 @LENGTH@ 2\n" +
+                "------------------------INS SimpleName@@MethodName:append:[toJson(e.getValue())] @TO@ MethodInvocation@@sb.append(toJson(e.getValue())) @AT@ 2283 @LENGTH@ 28\n" +
+                "---------------------------INS MethodInvocation@@toJson(e.getValue()) @TO@ SimpleName@@MethodName:append:[toJson(e.getValue())] @AT@ 2290 @LENGTH@ 20\n" +
+                "------------------------------INS SimpleName@@MethodName:toJson:[e.getValue()] @TO@ MethodInvocation@@toJson(e.getValue()) @AT@ 2290 @LENGTH@ 20\n" +
+                "---------------------------------INS MethodInvocation@@e.getValue() @TO@ SimpleName@@MethodName:toJson:[e.getValue()] @AT@ 2297 @LENGTH@ 12\n" +
+                "------------------------------------INS SimpleName@@Name:e @TO@ MethodInvocation@@e.getValue() @AT@ 2297 @LENGTH@ 1\n" +
+                "------------------------------------INS SimpleName@@MethodName:getValue:[] @TO@ MethodInvocation@@e.getValue() @AT@ 2299 @LENGTH@ 10\n" +
+                "------------------------------INS SimpleName@@MethodName:toJson:[e.getValue()] @TO@ MethodInvocation@@toJson(e.getValue()) @AT@ 2290 @LENGTH@ 20\n" +
+                "---------------------------------INS MethodInvocation@@e.getValue() @TO@ SimpleName@@MethodName:toJson:[e.getValue()] @AT@ 2297 @LENGTH@ 12\n" +
+                "------------------------------------INS SimpleName@@Name:e @TO@ MethodInvocation@@e.getValue() @AT@ 2297 @LENGTH@ 1\n" +
+                "------------------------------------INS SimpleName@@MethodName:getValue:[] @TO@ MethodInvocation@@e.getValue() @AT@ 2299 @LENGTH@ 10\n" +
+                "---------------INS ExpressionStatement@@MethodInvocation:sb.append(\"}\") @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} @AT@ 2347 @LENGTH@ 15\n" +
+                "------------------INS MethodInvocation@@sb.append(\"}\") @TO@ ExpressionStatement@@MethodInvocation:sb.append(\"}\") @AT@ 2347 @LENGTH@ 14\n" +
+                "---------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.append(\"}\") @AT@ 2347 @LENGTH@ 2\n" +
+                "---------------------INS SimpleName@@MethodName:append:[\"}\"] @TO@ MethodInvocation@@sb.append(\"}\") @AT@ 2350 @LENGTH@ 11\n" +
+                "------------------------INS StringLiteral@@\"}\" @TO@ SimpleName@@MethodName:append:[\"}\"] @AT@ 2357 @LENGTH@ 3\n" +
+                "---------------INS ReturnStatement@@MethodInvocation:sb.toString() @TO@ Block@@ThenBody:{  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} @AT@ 2379 @LENGTH@ 21\n" +
+                "------------------INS MethodInvocation@@sb.toString() @TO@ ReturnStatement@@MethodInvocation:sb.toString() @AT@ 2386 @LENGTH@ 13\n" +
+                "---------------------INS SimpleName@@Name:sb @TO@ MethodInvocation@@sb.toString() @AT@ 2386 @LENGTH@ 2\n" +
+                "---------------------INS SimpleName@@MethodName:toString:[] @TO@ MethodInvocation@@sb.toString() @AT@ 2389 @LENGTH@ 10\n" +
+                "------------INS Block@@ElseBody:if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ IfStatement@@if (o instanceof Map) {  StringBuilder sb=new StringBuilder();  sb.append(\"{\");  for (  Map.Entry<Object,Object> e : ((Map<Object,Object>)o).entrySet()) {    if (sb.length() > 1) {      sb.append(\",\");    }    sb.append(toJson(e.getKey().toString()));    sb.append(\":\");    sb.append(toJson(e.getValue()));  }  sb.append(\"}\");  return sb.toString();} else if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2420 @LENGTH@ 244\n" +
+                "---------------INS IfStatement@@if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ Block@@ElseBody:if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2420 @LENGTH@ 244\n" +
+                "------------------INS InfixExpression@@o == null @TO@ IfStatement@@if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2424 @LENGTH@ 9\n" +
+                "---------------------INS SimpleName@@o @TO@ InfixExpression@@o == null @AT@ 2424 @LENGTH@ 1\n" +
+                "---------------------INS Operator@@== @TO@ InfixExpression@@o == null @AT@ 2425 @LENGTH@ 2\n" +
+                "---------------------INS NullLiteral@@null @TO@ InfixExpression@@o == null @AT@ 2429 @LENGTH@ 4\n" +
+                "------------------INS Block@@ThenBody:{  return \"null\";} @TO@ IfStatement@@if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2435 @LENGTH@ 46\n" +
+                "---------------------INS ReturnStatement@@StringLiteral:\"null\" @TO@ Block@@ThenBody:{  return \"null\";} @AT@ 2453 @LENGTH@ 14\n" +
+                "------------------------INS StringLiteral@@\"null\" @TO@ ReturnStatement@@StringLiteral:\"null\" @AT@ 2460 @LENGTH@ 6\n" +
+                "------------------INS Block@@ElseBody:if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ IfStatement@@if (o == null) {  return \"null\";} else if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2487 @LENGTH@ 177\n" +
+                "---------------------INS IfStatement@@if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @TO@ Block@@ElseBody:if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2487 @LENGTH@ 177\n" +
+                "------------------------INS InstanceofExpression@@o instanceof Date @TO@ IfStatement@@if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2491 @LENGTH@ 17\n" +
+                "---------------------------INS SimpleName@@o @TO@ InstanceofExpression@@o instanceof Date @AT@ 2491 @LENGTH@ 1\n" +
+                "---------------------------INS Instanceof@@instanceof @TO@ InstanceofExpression@@o instanceof Date @AT@ 2493 @LENGTH@ 10\n" +
+                "---------------------------INS SimpleType@@Date @TO@ InstanceofExpression@@o instanceof Date @AT@ 2504 @LENGTH@ 4\n" +
+                "------------------------INS Block@@ThenBody:{  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} @TO@ IfStatement@@if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2510 @LENGTH@ 69\n" +
+                "---------------------------INS ReturnStatement@@InfixExpression:\"\\\"\" + toIso((Date)o) + \"\\\"\" @TO@ Block@@ThenBody:{  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} @AT@ 2528 @LENGTH@ 37\n" +
+                "------------------------------INS InfixExpression@@\"\\\"\" + toIso((Date)o) + \"\\\"\" @TO@ ReturnStatement@@InfixExpression:\"\\\"\" + toIso((Date)o) + \"\\\"\" @AT@ 2535 @LENGTH@ 29\n" +
+                "---------------------------------INS StringLiteral@@\"\\\"\" @TO@ InfixExpression@@\"\\\"\" + toIso((Date)o) + \"\\\"\" @AT@ 2535 @LENGTH@ 4\n" +
+                "---------------------------------INS Operator@@+ @TO@ InfixExpression@@\"\\\"\" + toIso((Date)o) + \"\\\"\" @AT@ 2539 @LENGTH@ 1\n" +
+                "---------------------------------INS MethodInvocation@@toIso((Date)o) @TO@ InfixExpression@@\"\\\"\" + toIso((Date)o) + \"\\\"\" @AT@ 2542 @LENGTH@ 15\n" +
+                "------------------------------------INS SimpleName@@MethodName:toIso:[(Date)o] @TO@ MethodInvocation@@toIso((Date)o) @AT@ 2542 @LENGTH@ 15\n" +
+                "---------------------------------------INS CastExpression@@(Date)o @TO@ SimpleName@@MethodName:toIso:[(Date)o] @AT@ 2548 @LENGTH@ 8\n" +
+                "------------------------------------------INS SimpleType@@Date @TO@ CastExpression@@(Date)o @AT@ 2549 @LENGTH@ 4\n" +
+                "------------------------------------------INS SimpleName@@o @TO@ CastExpression@@(Date)o @AT@ 2555 @LENGTH@ 1\n" +
+                "------------------------------------INS SimpleName@@MethodName:toIso:[(Date)o] @TO@ MethodInvocation@@toIso((Date)o) @AT@ 2542 @LENGTH@ 15\n" +
+                "---------------------------------------INS CastExpression@@(Date)o @TO@ SimpleName@@MethodName:toIso:[(Date)o] @AT@ 2548 @LENGTH@ 8\n" +
+                "------------------------------------------INS SimpleType@@Date @TO@ CastExpression@@(Date)o @AT@ 2549 @LENGTH@ 4\n" +
+                "------------------------------------------INS SimpleName@@o @TO@ CastExpression@@(Date)o @AT@ 2555 @LENGTH@ 1\n" +
+                "---------------------------------INS StringLiteral@@\"\\\"\" @TO@ InfixExpression@@\"\\\"\" + toIso((Date)o) + \"\\\"\" @AT@ 2560 @LENGTH@ 4\n" +
+                "------------------------INS Block@@ElseBody:{  return mapper.writeValueAsString(o.toString());} @TO@ IfStatement@@if (o instanceof Date) {  return \"\\\"\" + toIso((Date)o) + \"\\\"\";} else {  return mapper.writeValueAsString(o.toString());} @AT@ 2585 @LENGTH@ 79\n" +
+                "---------------------------INS ReturnStatement@@MethodInvocation:mapper.writeValueAsString(o.toString()) @TO@ Block@@ElseBody:{  return mapper.writeValueAsString(o.toString());} @AT@ 2603 @LENGTH@ 47\n" +
+                "------------------------------MOV MethodInvocation@@mapper.writeValueAsString(o) @TO@ ReturnStatement@@MethodInvocation:mapper.writeValueAsString(o.toString()) @AT@ 1307 @LENGTH@ 28\n" +
+                "---------------------------------UPD SimpleName@@MethodName:writeValueAsString:[o] @TO@ MethodName:writeValueAsString:[o.toString()] @AT@ 1314 @LENGTH@ 21\n" +
+                "------------------------------------DEL SimpleName@@o @AT@ 1333 @LENGTH@ 1\n" +
+                "------------------------------------INS MethodInvocation@@o.toString() @TO@ SimpleName@@MethodName:writeValueAsString:[o] @AT@ 2636 @LENGTH@ 12\n" +
+                "---------------------------------------INS SimpleName@@Name:o @TO@ MethodInvocation@@o.toString() @AT@ 2636 @LENGTH@ 1\n" +
+                "---------------------------------------INS SimpleName@@MethodName:toString:[] @TO@ MethodInvocation@@o.toString() @AT@ 2638 @LENGTH@ 10\n");
+    }
+
+    //commons-collections_045fda_add3a9_src#main#java#org#apache#commons#collections#map#AbstractHashedMap.java
+    @Test
+    public void test_collections_045fda_add3a9() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_045fda_add3a9_src#main#java#org#apache#commons#collections#map#AbstractHashedMap.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD CatchClause@@catch (final CloneNotSupportedException ex) {  return null;} @TO@ catch (final CloneNotSupportedException ex) {  throw new InternalError();} @AT@ 44401 @LENGTH@ 104\n" +
+                "---DEL ReturnStatement@@NullLiteral:null @AT@ 44459 @LENGTH@ 12\n" +
+                "------DEL NullLiteral@@null @AT@ 44466 @LENGTH@ 4\n" +
+                "---INS ThrowStatement@@ClassInstanceCreation:new InternalError() @TO@ CatchClause@@catch (final CloneNotSupportedException ex) {  return null;} @AT@ 44530 @LENGTH@ 26\n" +
+                "------INS ClassInstanceCreation@@InternalError[] @TO@ ThrowStatement@@ClassInstanceCreation:new InternalError() @AT@ 44536 @LENGTH@ 19\n" +
+                "---------INS New@@new @TO@ ClassInstanceCreation@@InternalError[] @AT@ 44536 @LENGTH@ 3\n" +
+                "---------INS SimpleType@@InternalError @TO@ ClassInstanceCreation@@InternalError[] @AT@ 44540 @LENGTH@ 13\n");
+    }
+
+
+    //metadata_a82665_e8bff4_appclient#src#main#java#org#jboss#metadata#appclient#parser#spec#ApplicationClientMetaDataParser.java
+    @Test
+    public void test_metadata_a82665_e8bff4() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("metadata_a82665_e8bff4_appclient#src#main#java#org#jboss#metadata#appclient#parser#spec#ApplicationClientMetaDataParser.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD SwitchStatement@@switch (ejbJarAttribute) {case ID:{    metaData.setId(value);    break;  }case VERSION:{  metaData.setVersion(value);}case METADATA_COMPLETE:{metaData.setMetadataComplete(true);break;}default :throw unexpectedAttribute(reader,i);} @TO@ switch (ejbJarAttribute) {case ID:{    metaData.setId(value);    break;  }case VERSION:{  metaData.setVersion(value);  break;}case METADATA_COMPLETE:{metaData.setMetadataComplete(Boolean.parseBoolean(value));break;}default :throw unexpectedAttribute(reader,i);} @AT@ 2859 @LENGTH@ 410\n" +
+                "---INS BreakStatement@@ @TO@ SwitchStatement@@switch (ejbJarAttribute) {case ID:{    metaData.setId(value);    break;  }case VERSION:{  metaData.setVersion(value);}case METADATA_COMPLETE:{metaData.setMetadataComplete(true);break;}default :throw unexpectedAttribute(reader,i);} @AT@ 3074 @LENGTH@ 6\n" +
+                "---UPD ExpressionStatement@@MethodInvocation:metaData.setMetadataComplete(true) @TO@ MethodInvocation:metaData.setMetadataComplete(Boolean.parseBoolean(value)) @AT@ 3128 @LENGTH@ 35\n" +
+                "------UPD MethodInvocation@@metaData.setMetadataComplete(true) @TO@ metaData.setMetadataComplete(Boolean.parseBoolean(value)) @AT@ 3128 @LENGTH@ 34\n" +
+                "---------UPD SimpleName@@MethodName:setMetadataComplete:[true] @TO@ MethodName:setMetadataComplete:[Boolean.parseBoolean(value)] @AT@ 3137 @LENGTH@ 25\n" +
+                "------------DEL BooleanLiteral@@true @AT@ 3157 @LENGTH@ 4\n" +
+                "------------INS MethodInvocation@@Boolean.parseBoolean(value) @TO@ SimpleName@@MethodName:setMetadataComplete:[true] @AT@ 3177 @LENGTH@ 27\n" +
+                "---------------INS SimpleName@@Name:Boolean @TO@ MethodInvocation@@Boolean.parseBoolean(value) @AT@ 3177 @LENGTH@ 7\n" +
+                "---------------INS SimpleName@@MethodName:parseBoolean:[value] @TO@ MethodInvocation@@Boolean.parseBoolean(value) @AT@ 3185 @LENGTH@ 19\n" +
+                "------------------INS SimpleName@@value @TO@ SimpleName@@MethodName:parseBoolean:[value] @AT@ 3198 @LENGTH@ 5\n");
+    }
+
+
+
+    //fuse_6baf6f_ad4e95_fabric#fabric-core-agent-jclouds#src#main#java#org#fusesource#fabric#service#jclouds#JcloudsContainerProvider.java
+    @Test
+    public void test_fuse_6baf6f_ad4e95() throws IOException {
+        //null pointer
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_6baf6f_ad4e95_fabric#fabric-core-agent-jclouds#src#main#java#org#fusesource#fabric#service#jclouds#JcloudsContainerProvider.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD MethodDeclaration@@public, Set<CreateJCloudsContainerMetadata>, MethodName:create, CreateJCloudsContainerOptions options, MalformedURLException, RunNodesException, URISyntaxException,  @TO@ public, Set<CreateJCloudsContainerMetadata>, MethodName:create, CreateJCloudsContainerOptions options, MalformedURLException, RunNodesException, URISyntaxException, InterruptedException,  @AT@ 2863 @LENGTH@ 4271\n" +
+                "---INS SimpleType@@InterruptedException @TO@ MethodDeclaration@@public, Set<CreateJCloudsContainerMetadata>, MethodName:create, CreateJCloudsContainerOptions options, MalformedURLException, RunNodesException, URISyntaxException,  @AT@ 3021 @LENGTH@ 20\n" +
+                "---UPD VariableDeclarationStatement@@Set<CreateJCloudsContainerMetadata> result=new LinkedHashSet<CreateJCloudsContainerMetadata>(); @TO@ final Set<CreateJCloudsContainerMetadata> result=new LinkedHashSet<CreateJCloudsContainerMetadata>(); @AT@ 3030 @LENGTH@ 97\n" +
+                "------INS Modifier@@final @TO@ VariableDeclarationStatement@@Set<CreateJCloudsContainerMetadata> result=new LinkedHashSet<CreateJCloudsContainerMetadata>(); @AT@ 3051 @LENGTH@ 5\n" +
+                "---INS ExpressionStatement@@MethodInvocation:Thread.sleep(5000) @TO@ MethodDeclaration@@public, Set<CreateJCloudsContainerMetadata>, MethodName:create, CreateJCloudsContainerOptions options, MalformedURLException, RunNodesException, URISyntaxException,  @AT@ 5007 @LENGTH@ 19\n" +
+                "------INS MethodInvocation@@Thread.sleep(5000) @TO@ ExpressionStatement@@MethodInvocation:Thread.sleep(5000) @AT@ 5007 @LENGTH@ 18\n" +
+                "---------INS SimpleName@@Name:Thread @TO@ MethodInvocation@@Thread.sleep(5000) @AT@ 5007 @LENGTH@ 6\n" +
+                "---------INS SimpleName@@MethodName:sleep:[5000] @TO@ MethodInvocation@@Thread.sleep(5000) @AT@ 5014 @LENGTH@ 11\n" +
+                "------------INS NumberLiteral@@5000 @TO@ SimpleName@@MethodName:sleep:[5000] @AT@ 5020 @LENGTH@ 4\n" +
+                "---UPD IfStatement@@if (metadatas != null) {  for (  NodeMetadata nodeMetadata : metadatas) {    Credentials credentials=null;    if (options.getUser() != null) {      credentials=new Credentials(options.getUser(),nodeMetadata.getCredentials().credential);    } else {      credentials=nodeMetadata.getCredentials();    }    String id=nodeMetadata.getId();    Set<String> publicAddresses=nodeMetadata.getPublicAddresses();    for (    String pa : publicAddresses) {      if (first) {        first=false;      } else {        buffer.append(\",\");      }      buffer.append(pa + \":\" + options.getServicePort());    }    String containerName=options.getName();    if (options.getNumber() > 1) {      containerName+=suffix++;    }    String script=buildStartupScript(options.name(containerName));    if (credentials != null) {      computeService.runScriptOnNode(id,script,RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));    } else {      computeService.runScriptOnNode(id,script);    }    CreateJCloudsContainerMetadata jCloudsContainerMetadata=new CreateJCloudsContainerMetadata();    jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());    jCloudsContainerMetadata.setContainerName(containerName);    jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());    jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());    result.add(jCloudsContainerMetadata);  }} @TO@ if (metadatas != null) {  for (  NodeMetadata nodeMetadata : metadatas) {    Credentials credentials=null;    if (options.getUser() != null) {      credentials=new Credentials(options.getUser(),nodeMetadata.getCredentials().credential);    } else {      credentials=nodeMetadata.getCredentials();    }    String id=nodeMetadata.getId();    Set<String> publicAddresses=nodeMetadata.getPublicAddresses();    String containerName=options.getName();    if (options.getNumber() > 1) {      containerName+=suffix++;    }    String script=buildStartupScript(options.name(containerName));    if (credentials != null) {      computeService.runScriptOnNode(id,script,RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));    } else {      computeService.runScriptOnNode(id,script);    }    CreateJCloudsContainerMetadata jCloudsContainerMetadata=new CreateJCloudsContainerMetadata();    jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());    jCloudsContainerMetadata.setContainerName(containerName);    jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());    jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());    result.add(jCloudsContainerMetadata);  }} @AT@ 5086 @LENGTH@ 2018\n" +
+                "------UPD Block@@ThenBody:{  for (  NodeMetadata nodeMetadata : metadatas) {    Credentials credentials=null;    if (options.getUser() != null) {      credentials=new Credentials(options.getUser(),nodeMetadata.getCredentials().credential);    } else {      credentials=nodeMetadata.getCredentials();    }    String id=nodeMetadata.getId();    Set<String> publicAddresses=nodeMetadata.getPublicAddresses();    for (    String pa : publicAddresses) {      if (first) {        first=false;      } else {        buffer.append(\",\");      }      buffer.append(pa + \":\" + options.getServicePort());    }    String containerName=options.getName();    if (options.getNumber() > 1) {      containerName+=suffix++;    }    String script=buildStartupScript(options.name(containerName));    if (credentials != null) {      computeService.runScriptOnNode(id,script,RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));    } else {      computeService.runScriptOnNode(id,script);    }    CreateJCloudsContainerMetadata jCloudsContainerMetadata=new CreateJCloudsContainerMetadata();    jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());    jCloudsContainerMetadata.setContainerName(containerName);    jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());    jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());    result.add(jCloudsContainerMetadata);  }} @TO@ ThenBody:{  for (  NodeMetadata nodeMetadata : metadatas) {    Credentials credentials=null;    if (options.getUser() != null) {      credentials=new Credentials(options.getUser(),nodeMetadata.getCredentials().credential);    } else {      credentials=nodeMetadata.getCredentials();    }    String id=nodeMetadata.getId();    Set<String> publicAddresses=nodeMetadata.getPublicAddresses();    String containerName=options.getName();    if (options.getNumber() > 1) {      containerName+=suffix++;    }    String script=buildStartupScript(options.name(containerName));    if (credentials != null) {      computeService.runScriptOnNode(id,script,RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));    } else {      computeService.runScriptOnNode(id,script);    }    CreateJCloudsContainerMetadata jCloudsContainerMetadata=new CreateJCloudsContainerMetadata();    jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());    jCloudsContainerMetadata.setContainerName(containerName);    jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());    jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());    result.add(jCloudsContainerMetadata);  }} @AT@ 5109 @LENGTH@ 1995\n" +
+                "---------UPD EnhancedForStatement@@for (NodeMetadata nodeMetadata : metadatas) {  Credentials credentials=null;  if (options.getUser() != null) {    credentials=new Credentials(options.getUser(),nodeMetadata.getCredentials().credential);  } else {    credentials=nodeMetadata.getCredentials();  }  String id=nodeMetadata.getId();  Set<String> publicAddresses=nodeMetadata.getPublicAddresses();  for (  String pa : publicAddresses) {    if (first) {      first=false;    } else {      buffer.append(\",\");    }    buffer.append(pa + \":\" + options.getServicePort());  }  String containerName=options.getName();  if (options.getNumber() > 1) {    containerName+=suffix++;  }  String script=buildStartupScript(options.name(containerName));  if (credentials != null) {    computeService.runScriptOnNode(id,script,RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));  } else {    computeService.runScriptOnNode(id,script);  }  CreateJCloudsContainerMetadata jCloudsContainerMetadata=new CreateJCloudsContainerMetadata();  jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());  jCloudsContainerMetadata.setContainerName(containerName);  jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());  jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());  result.add(jCloudsContainerMetadata);} @TO@ for (NodeMetadata nodeMetadata : metadatas) {  Credentials credentials=null;  if (options.getUser() != null) {    credentials=new Credentials(options.getUser(),nodeMetadata.getCredentials().credential);  } else {    credentials=nodeMetadata.getCredentials();  }  String id=nodeMetadata.getId();  Set<String> publicAddresses=nodeMetadata.getPublicAddresses();  String containerName=options.getName();  if (options.getNumber() > 1) {    containerName+=suffix++;  }  String script=buildStartupScript(options.name(containerName));  if (credentials != null) {    computeService.runScriptOnNode(id,script,RunScriptOptions.Builder.overrideCredentialsWith(credentials).runAsRoot(false));  } else {    computeService.runScriptOnNode(id,script);  }  CreateJCloudsContainerMetadata jCloudsContainerMetadata=new CreateJCloudsContainerMetadata();  jCloudsContainerMetadata.setNodeId(nodeMetadata.getId());  jCloudsContainerMetadata.setContainerName(containerName);  jCloudsContainerMetadata.setPublicAddresses(nodeMetadata.getPublicAddresses());  jCloudsContainerMetadata.setHostname(nodeMetadata.getHostname());  result.add(jCloudsContainerMetadata);} @AT@ 5123 @LENGTH@ 1971\n" +
+                "------------DEL EnhancedForStatement@@for (String pa : publicAddresses) {  if (first) {    first=false;  } else {    buffer.append(\",\");  }  buffer.append(pa + \":\" + options.getServicePort());} @AT@ 5753 @LENGTH@ 291\n" +
+                "---------------DEL SingleVariableDeclaration@@String pa @AT@ 5758 @LENGTH@ 9\n" +
+                "------------------DEL SimpleType@@String @AT@ 5758 @LENGTH@ 6\n" +
+                "------------------DEL SimpleName@@pa @AT@ 5765 @LENGTH@ 2\n" +
+                "---------------DEL SimpleName@@publicAddresses @AT@ 5769 @LENGTH@ 15\n" +
+                "---------------DEL IfStatement@@if (first) {  first=false;} else {  buffer.append(\",\");} @AT@ 5808 @LENGTH@ 146\n" +
+                "------------------DEL SimpleName@@first @AT@ 5812 @LENGTH@ 5\n" +
+                "------------------DEL Block@@ThenBody:{  first=false;} @AT@ 5819 @LENGTH@ 62\n" +
+                "---------------------DEL ExpressionStatement@@Assignment:first=false @AT@ 5845 @LENGTH@ 14\n" +
+                "------------------------DEL Assignment@@first=false @AT@ 5845 @LENGTH@ 13\n" +
+                "---------------------------DEL SimpleName@@first @AT@ 5845 @LENGTH@ 5\n" +
+                "---------------------------DEL Operator@@= @AT@ 5850 @LENGTH@ 1\n" +
+                "---------------------------DEL BooleanLiteral@@false @AT@ 5853 @LENGTH@ 5\n" +
+                "------------------DEL Block@@ElseBody:{  buffer.append(\",\");} @AT@ 5887 @LENGTH@ 67\n" +
+                "---------------------DEL ExpressionStatement@@MethodInvocation:buffer.append(\",\") @AT@ 5913 @LENGTH@ 19\n" +
+                "------------------------DEL MethodInvocation@@buffer.append(\",\") @AT@ 5913 @LENGTH@ 18\n" +
+                "---------------------------DEL SimpleName@@Name:buffer @AT@ 5913 @LENGTH@ 6\n" +
+                "---------------------------DEL SimpleName@@MethodName:append:[\",\"] @AT@ 5920 @LENGTH@ 11\n" +
+                "------------------------------DEL StringLiteral@@\",\" @AT@ 5927 @LENGTH@ 3\n" +
+                "---------------DEL ExpressionStatement@@MethodInvocation:buffer.append(pa + \":\" + options.getServicePort()) @AT@ 5975 @LENGTH@ 51\n" +
+                "------------------DEL MethodInvocation@@buffer.append(pa + \":\" + options.getServicePort()) @AT@ 5975 @LENGTH@ 50\n" +
+                "---------------------DEL SimpleName@@Name:buffer @AT@ 5975 @LENGTH@ 6\n" +
+                "---------------------DEL SimpleName@@MethodName:append:[pa + \":\" + options.getServicePort()] @AT@ 5982 @LENGTH@ 43\n" +
+                "------------------------DEL InfixExpression@@pa + \":\" + options.getServicePort() @AT@ 5989 @LENGTH@ 35\n" +
+                "---------------------------DEL SimpleName@@pa @AT@ 5989 @LENGTH@ 2\n" +
+                "---------------------------DEL Operator@@+ @AT@ 5991 @LENGTH@ 1\n" +
+                "---------------------------DEL StringLiteral@@\":\" @AT@ 5994 @LENGTH@ 3\n" +
+                "---------------------------DEL MethodInvocation@@options.getServicePort() @AT@ 6000 @LENGTH@ 24\n" +
+                "------------------------------DEL SimpleName@@Name:options @AT@ 6000 @LENGTH@ 7\n" +
+                "------------------------------DEL SimpleName@@MethodName:getServicePort:[] @AT@ 6008 @LENGTH@ 16\n");
+    }
+
+
+
+    //commons-collections_51c9ef_d65e29_src#java#org#apache#commons#collections#iterators#IteratorChain.java
+    @Test
+    public void test_collections_51c9ef_d65e29() throws IOException {
+        //MOVE - DEL 2 action example
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_51c9ef_d65e29_src#java#org#apache#commons#collections#iterators#IteratorChain.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"INS IfStatement@@if (currentIterator == null) {  updateCurrentIterator();} @TO@ MethodDeclaration@@public, void, MethodName:remove,  @AT@ 9501 @LENGTH@ 78\n" +
+                "---INS InfixExpression@@currentIterator == null @TO@ IfStatement@@if (currentIterator == null) {  updateCurrentIterator();} @AT@ 9505 @LENGTH@ 23\n" +
+                "------INS SimpleName@@currentIterator @TO@ InfixExpression@@currentIterator == null @AT@ 9505 @LENGTH@ 15\n" +
+                "------INS Operator@@== @TO@ InfixExpression@@currentIterator == null @AT@ 9520 @LENGTH@ 2\n" +
+                "------INS NullLiteral@@null @TO@ InfixExpression@@currentIterator == null @AT@ 9524 @LENGTH@ 4\n" +
+                "---INS Block@@ThenBody:{  updateCurrentIterator();} @TO@ IfStatement@@if (currentIterator == null) {  updateCurrentIterator();} @AT@ 9531 @LENGTH@ 48\n" +
+                "------INS ExpressionStatement@@MethodInvocation:updateCurrentIterator() @TO@ Block@@ThenBody:{  updateCurrentIterator();} @AT@ 9545 @LENGTH@ 24\n" +
+                "---------MOV MethodInvocation@@MethodName:updateCurrentIterator:[] @TO@ ExpressionStatement@@MethodInvocation:updateCurrentIterator() @AT@ 9522 @LENGTH@ 23\n");
+    }
+
+
+
+    //fuse_d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Export.java
+    @Test
+    public void test_fuse_d6d40b_b37c85() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Export.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD IfStatement@@if (!matches(include,p) || matches(exclude,p)) {  continue;} @TO@ if (!matches(include,p,true) || matches(exclude,p,false)) {  continue;} @AT@ 3334 @LENGTH@ 90\n" +
+                "---UPD InfixExpression@@!matches(include,p) || matches(exclude,p) @TO@ !matches(include,p,true) || matches(exclude,p,false) @AT@ 3338 @LENGTH@ 43\n" +
+                "------UPD PrefixExpression@@!matches(include,p) @TO@ !matches(include,p,true) @AT@ 3338 @LENGTH@ 20\n" +
+                "---------UPD MethodInvocation@@matches(include,p) @TO@ matches(include,p,true) @AT@ 3339 @LENGTH@ 19\n" +
+                "------------UPD SimpleName@@MethodName:matches:[include, p] @TO@ MethodName:matches:[include, p, true] @AT@ 3339 @LENGTH@ 19\n" +
+                "---------------INS BooleanLiteral@@true @TO@ SimpleName@@MethodName:matches:[include, p] @AT@ 3359 @LENGTH@ 4\n" +
+                "------UPD MethodInvocation@@matches(exclude,p) @TO@ matches(exclude,p,false) @AT@ 3362 @LENGTH@ 19\n" +
+                "---------UPD SimpleName@@MethodName:matches:[exclude, p] @TO@ MethodName:matches:[exclude, p, false] @AT@ 3362 @LENGTH@ 19\n" +
+                "------------INS BooleanLiteral@@false @TO@ SimpleName@@MethodName:matches:[exclude, p] @AT@ 3388 @LENGTH@ 5\n");
+    }
+
+    //fuse_d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Import.java
+    @Test
+    public void test_fuse_d6d40b_b37c85_() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_d6d40b_b37c85_fabric-zookeeper-commands#src#main#java#org#fusesource#fabric#zookeeper#commands#Import.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),2);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD IfStatement@@if (!matches(include,key) || matches(exclude,key)) {  continue;} @TO@ if (!matches(include,key,true) || matches(exclude,key,false)) {  continue;} @AT@ 5493 @LENGTH@ 94\n" +
+                "---UPD InfixExpression@@!matches(include,key) || matches(exclude,key) @TO@ !matches(include,key,true) || matches(exclude,key,false) @AT@ 5497 @LENGTH@ 47\n" +
+                "------UPD PrefixExpression@@!matches(include,key) @TO@ !matches(include,key,true) @AT@ 5497 @LENGTH@ 22\n" +
+                "---------UPD MethodInvocation@@matches(include,key) @TO@ matches(include,key,true) @AT@ 5498 @LENGTH@ 21\n" +
+                "------------UPD SimpleName@@MethodName:matches:[include, key] @TO@ MethodName:matches:[include, key, true] @AT@ 5498 @LENGTH@ 21\n" +
+                "---------------INS BooleanLiteral@@true @TO@ SimpleName@@MethodName:matches:[include, key] @AT@ 5520 @LENGTH@ 4\n" +
+                "------UPD MethodInvocation@@matches(exclude,key) @TO@ matches(exclude,key,false) @AT@ 5523 @LENGTH@ 21\n" +
+                "---------UPD SimpleName@@MethodName:matches:[exclude, key] @TO@ MethodName:matches:[exclude, key, false] @AT@ 5523 @LENGTH@ 21\n" +
+                "------------INS BooleanLiteral@@false @TO@ SimpleName@@MethodName:matches:[exclude, key] @AT@ 5551 @LENGTH@ 5\n");
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD IfStatement@@if (!matches(include,key) || matches(exclude,key)) {  continue;} @TO@ if (!matches(include,key,true) || matches(exclude,key,false)) {  continue;} @AT@ 5493 @LENGTH@ 94\n" +
+                "---UPD InfixExpression@@!matches(include,key) || matches(exclude,key) @TO@ !matches(include,key,true) || matches(exclude,key,false) @AT@ 5497 @LENGTH@ 47\n" +
+                "------UPD PrefixExpression@@!matches(include,key) @TO@ !matches(include,key,true) @AT@ 5497 @LENGTH@ 22\n" +
+                "---------UPD MethodInvocation@@matches(include,key) @TO@ matches(include,key,true) @AT@ 5498 @LENGTH@ 21\n" +
+                "------------UPD SimpleName@@MethodName:matches:[include, key] @TO@ MethodName:matches:[include, key, true] @AT@ 5498 @LENGTH@ 21\n" +
+                "---------------INS BooleanLiteral@@true @TO@ SimpleName@@MethodName:matches:[include, key] @AT@ 5520 @LENGTH@ 4\n" +
+                "------UPD MethodInvocation@@matches(exclude,key) @TO@ matches(exclude,key,false) @AT@ 5523 @LENGTH@ 21\n" +
+                "---------UPD SimpleName@@MethodName:matches:[exclude, key] @TO@ MethodName:matches:[exclude, key, false] @AT@ 5523 @LENGTH@ 21\n" +
+                "------------INS BooleanLiteral@@false @TO@ SimpleName@@MethodName:matches:[exclude, key] @AT@ 5551 @LENGTH@ 5\n");
+    }
+
+    //fuse_6d0e56_998321_fabric#fabric-agent#src#main#java#org#fusesource#fabric#agent#DeploymentAgent.java
+    @Test
+    public void test_fuse_6d0e56_998321() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_6d0e56_998321_fabric#fabric-agent#src#main#java#org#fusesource#fabric#agent#DeploymentAgent.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD CatchClause@@catch (IOException e) {  errors.add(e);} @TO@ catch (Throwable e) {  errors.add(e);} @AT@ 42072 @LENGTH@ 84\n" +
+                "---UPD SingleVariableDeclaration@@IOException e @TO@ Throwable e @AT@ 42079 @LENGTH@ 13\n" +
+                "------UPD SimpleType@@IOException @TO@ Throwable @AT@ 42079 @LENGTH@ 11\n");
+    }
+
+    //fuse_b0e8c7_602ea9_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#AbstractDataStore.java
+    @Test
+    public void test_fuse_b0e8c7_602ea9() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_b0e8c7_602ea9_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#AbstractDataStore.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ReturnStatement@@MethodInvocation:availableResolvers.get(scheme).resolve(pid,key,toSubstitute) @TO@ MethodInvocation:availableResolvers.get(scheme).resolve(configs,pid,key,toSubstitute) @AT@ 9506 @LENGTH@ 70\n" +
+                "---UPD MethodInvocation@@availableResolvers.get(scheme).resolve(pid,key,toSubstitute) @TO@ availableResolvers.get(scheme).resolve(configs,pid,key,toSubstitute) @AT@ 9513 @LENGTH@ 62\n" +
+                "------UPD SimpleName@@MethodName:resolve:[pid, key, toSubstitute] @TO@ MethodName:resolve:[configs, pid, key, toSubstitute] @AT@ 9544 @LENGTH@ 31\n" +
+                "---------INS SimpleName@@configs @TO@ SimpleName@@MethodName:resolve:[pid, key, toSubstitute] @AT@ 9552 @LENGTH@ 7\n");
+    }
+
+
+    //commons-collections_2d2aef_fb3daa_src#java#org#apache#commons#collections#map#TransformedMap.java
+    @Test
+    public void test_collections_2d2aef_fb3daa() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_2d2aef_fb3daa_src#java#org#apache#commons#collections#map#TransformedMap.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ExpressionStatement@@MethodInvocation:result.put((K)transformKey(entry.getKey()),transformValue(entry.getValue())) @TO@ MethodInvocation:result.put(transformKey(entry.getKey()),transformValue(entry.getValue())) @AT@ 7727 @LENGTH@ 79\n" +
+                "---UPD MethodInvocation@@result.put((K)transformKey(entry.getKey()),transformValue(entry.getValue())) @TO@ result.put(transformKey(entry.getKey()),transformValue(entry.getValue())) @AT@ 7727 @LENGTH@ 78\n" +
+                "------UPD SimpleName@@MethodName:put:[(K)transformKey(entry.getKey()), transformValue(entry.getValue())] @TO@ MethodName:put:[transformKey(entry.getKey()), transformValue(entry.getValue())] @AT@ 7734 @LENGTH@ 71\n" +
+                "---------DEL CastExpression@@(K)transformKey(entry.getKey()) @AT@ 7738 @LENGTH@ 32\n" +
+                "------------DEL SimpleType@@K @AT@ 7739 @LENGTH@ 1\n" +
+                "---------MOV MethodInvocation@@transformKey(entry.getKey()) @TO@ SimpleName@@MethodName:put:[(K)transformKey(entry.getKey()), transformValue(entry.getValue())] @AT@ 7742 @LENGTH@ 28\n");
+    }
+
+
+    //fuse_6d0e56_998321_fabric#fabric-agent#src#main#java#org#fusesource#fabric#agent#download#MavenDownloadTask.java
+    @Test
+    public void test_fuse_6d0e56_998321_() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_6d0e56_998321_fabric#fabric-agent#src#main#java#org#fusesource#fabric#agent#download#MavenDownloadTask.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @TO@ try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  file.getParentFile().mkdirs();  if (!file.getParentFile().isDirectory()) {    throw new IOException(\"Unable to create directory \" + file.getParentFile().toString());  }  File tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile());  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  is.close();  os.close();  if (file.exists() && !file.delete()) {    throw new IOException(\"Unable to delete file: \" + file.toString());  }  if (!tmp.renameTo(file)) {    throw new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString());  }  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 3516 @LENGTH@ 1028\n" +
+                "---DEL VariableDeclarationStatement@@File tmp=new File(file.getAbsolutePath() + \".tmp\"); @AT@ 3971 @LENGTH@ 53\n" +
+                "------DEL VariableDeclarationFragment@@tmp=new File(file.getAbsolutePath() + \".tmp\") @AT@ 3976 @LENGTH@ 47\n" +
+                "---------DEL ClassInstanceCreation@@File[file.getAbsolutePath() + \".tmp\"] @AT@ 3982 @LENGTH@ 41\n" +
+                "---INS ExpressionStatement@@MethodInvocation:file.getParentFile().mkdirs() @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 3972 @LENGTH@ 30\n" +
+                "------INS MethodInvocation@@file.getParentFile().mkdirs() @TO@ ExpressionStatement@@MethodInvocation:file.getParentFile().mkdirs() @AT@ 3972 @LENGTH@ 29\n" +
+                "---------INS MethodInvocation@@MethodName:getParentFile:[] @TO@ MethodInvocation@@file.getParentFile().mkdirs() @AT@ 3972 @LENGTH@ 20\n" +
+                "---------INS SimpleName@@Name:file @TO@ MethodInvocation@@file.getParentFile().mkdirs() @AT@ 3972 @LENGTH@ 4\n" +
+                "---------INS SimpleName@@MethodName:mkdirs:[] @TO@ MethodInvocation@@file.getParentFile().mkdirs() @AT@ 3993 @LENGTH@ 8\n" +
+                "---INS IfStatement@@if (!file.getParentFile().isDirectory()) {  throw new IOException(\"Unable to create directory \" + file.getParentFile().toString());} @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 4019 @LENGTH@ 168\n" +
+                "------INS PrefixExpression@@!file.getParentFile().isDirectory() @TO@ IfStatement@@if (!file.getParentFile().isDirectory()) {  throw new IOException(\"Unable to create directory \" + file.getParentFile().toString());} @AT@ 4023 @LENGTH@ 35\n" +
+                "---------INS Operator@@! @TO@ PrefixExpression@@!file.getParentFile().isDirectory() @AT@ 4023 @LENGTH@ 1\n" +
+                "---------INS MethodInvocation@@file.getParentFile().isDirectory() @TO@ PrefixExpression@@!file.getParentFile().isDirectory() @AT@ 4024 @LENGTH@ 34\n" +
+                "------------INS MethodInvocation@@MethodName:getParentFile:[] @TO@ MethodInvocation@@file.getParentFile().isDirectory() @AT@ 4024 @LENGTH@ 20\n" +
+                "------------INS SimpleName@@Name:file @TO@ MethodInvocation@@file.getParentFile().isDirectory() @AT@ 4024 @LENGTH@ 4\n" +
+                "------------INS SimpleName@@MethodName:isDirectory:[] @TO@ MethodInvocation@@file.getParentFile().isDirectory() @AT@ 4045 @LENGTH@ 13\n" +
+                "------INS Block@@ThenBody:{  throw new IOException(\"Unable to create directory \" + file.getParentFile().toString());} @TO@ IfStatement@@if (!file.getParentFile().isDirectory()) {  throw new IOException(\"Unable to create directory \" + file.getParentFile().toString());} @AT@ 4060 @LENGTH@ 127\n" +
+                "---------INS ThrowStatement@@ClassInstanceCreation:new IOException(\"Unable to create directory \" + file.getParentFile().toString()) @TO@ Block@@ThenBody:{  throw new IOException(\"Unable to create directory \" + file.getParentFile().toString());} @AT@ 4082 @LENGTH@ 87\n" +
+                "------------INS ClassInstanceCreation@@IOException[\"Unable to create directory \" + file.getParentFile().toString()] @TO@ ThrowStatement@@ClassInstanceCreation:new IOException(\"Unable to create directory \" + file.getParentFile().toString()) @AT@ 4088 @LENGTH@ 80\n" +
+                "---------------INS New@@new @TO@ ClassInstanceCreation@@IOException[\"Unable to create directory \" + file.getParentFile().toString()] @AT@ 4088 @LENGTH@ 3\n" +
+                "---------------INS SimpleType@@IOException @TO@ ClassInstanceCreation@@IOException[\"Unable to create directory \" + file.getParentFile().toString()] @AT@ 4092 @LENGTH@ 11\n" +
+                "---------------INS InfixExpression@@\"Unable to create directory \" + file.getParentFile().toString() @TO@ ClassInstanceCreation@@IOException[\"Unable to create directory \" + file.getParentFile().toString()] @AT@ 4104 @LENGTH@ 63\n" +
+                "------------------INS StringLiteral@@\"Unable to create directory \" @TO@ InfixExpression@@\"Unable to create directory \" + file.getParentFile().toString() @AT@ 4104 @LENGTH@ 29\n" +
+                "------------------INS Operator@@+ @TO@ InfixExpression@@\"Unable to create directory \" + file.getParentFile().toString() @AT@ 4133 @LENGTH@ 1\n" +
+                "------------------INS MethodInvocation@@file.getParentFile().toString() @TO@ InfixExpression@@\"Unable to create directory \" + file.getParentFile().toString() @AT@ 4136 @LENGTH@ 31\n" +
+                "---------------------INS MethodInvocation@@MethodName:getParentFile:[] @TO@ MethodInvocation@@file.getParentFile().toString() @AT@ 4136 @LENGTH@ 20\n" +
+                "---------------------INS SimpleName@@Name:file @TO@ MethodInvocation@@file.getParentFile().toString() @AT@ 4136 @LENGTH@ 4\n" +
+                "---------------------INS SimpleName@@MethodName:toString:[] @TO@ MethodInvocation@@file.getParentFile().toString() @AT@ 4157 @LENGTH@ 10\n" +
+                "---DEL ExpressionStatement@@MethodInvocation:tmp.getParentFile().mkdirs() @AT@ 4041 @LENGTH@ 29\n" +
+                "------DEL MethodInvocation@@tmp.getParentFile().mkdirs() @AT@ 4041 @LENGTH@ 28\n" +
+                "---------DEL MethodInvocation@@MethodName:getParentFile:[] @AT@ 4041 @LENGTH@ 19\n" +
+                "---DEL ExpressionStatement@@MethodInvocation:file.delete() @AT@ 4178 @LENGTH@ 14\n" +
+                "------DEL MethodInvocation@@file.delete() @AT@ 4178 @LENGTH@ 13\n" +
+                "---INS VariableDeclarationStatement@@File tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile()); @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 4204 @LENGTH@ 76\n" +
+                "------MOV SimpleType@@File @TO@ VariableDeclarationStatement@@File tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile()); @AT@ 3971 @LENGTH@ 4\n" +
+                "------INS VariableDeclarationFragment@@tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile()) @TO@ VariableDeclarationStatement@@File tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile()); @AT@ 4209 @LENGTH@ 70\n" +
+                "---------MOV SimpleName@@tmp @TO@ VariableDeclarationFragment@@tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile()) @AT@ 3976 @LENGTH@ 3\n" +
+                "---------INS MethodInvocation@@File.createTempFile(\"fabric-agent-\",null,file.getParentFile()) @TO@ VariableDeclarationFragment@@tmp=File.createTempFile(\"fabric-agent-\",null,file.getParentFile()) @AT@ 4215 @LENGTH@ 64\n" +
+                "------------INS SimpleName@@Name:File @TO@ MethodInvocation@@File.createTempFile(\"fabric-agent-\",null,file.getParentFile()) @AT@ 4215 @LENGTH@ 4\n" +
+                "------------INS SimpleName@@MethodName:createTempFile:[\"fabric-agent-\", null, file.getParentFile()] @TO@ MethodInvocation@@File.createTempFile(\"fabric-agent-\",null,file.getParentFile()) @AT@ 4220 @LENGTH@ 59\n" +
+                "---------------INS StringLiteral@@\"fabric-agent-\" @TO@ SimpleName@@MethodName:createTempFile:[\"fabric-agent-\", null, file.getParentFile()] @AT@ 4235 @LENGTH@ 15\n" +
+                "---------------INS NullLiteral@@null @TO@ SimpleName@@MethodName:createTempFile:[\"fabric-agent-\", null, file.getParentFile()] @AT@ 4252 @LENGTH@ 4\n" +
+                "---------------INS MethodInvocation@@file.getParentFile() @TO@ SimpleName@@MethodName:createTempFile:[\"fabric-agent-\", null, file.getParentFile()] @AT@ 4258 @LENGTH@ 20\n" +
+                "------------------INS SimpleName@@Name:file @TO@ MethodInvocation@@file.getParentFile() @AT@ 4258 @LENGTH@ 4\n" +
+                "------------------INS SimpleName@@MethodName:getParentFile:[] @TO@ MethodInvocation@@file.getParentFile() @AT@ 4263 @LENGTH@ 15\n" +
+                "---DEL ExpressionStatement@@MethodInvocation:tmp.renameTo(file) @AT@ 4209 @LENGTH@ 19\n" +
+                "---INS ExpressionStatement@@MethodInvocation:is.close() @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 4388 @LENGTH@ 11\n" +
+                "------INS MethodInvocation@@is.close() @TO@ ExpressionStatement@@MethodInvocation:is.close() @AT@ 4388 @LENGTH@ 10\n" +
+                "---------INS SimpleName@@Name:is @TO@ MethodInvocation@@is.close() @AT@ 4388 @LENGTH@ 2\n" +
+                "---------INS SimpleName@@MethodName:close:[] @TO@ MethodInvocation@@is.close() @AT@ 4391 @LENGTH@ 7\n" +
+                "---INS ExpressionStatement@@MethodInvocation:os.close() @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 4416 @LENGTH@ 11\n" +
+                "------INS MethodInvocation@@os.close() @TO@ ExpressionStatement@@MethodInvocation:os.close() @AT@ 4416 @LENGTH@ 10\n" +
+                "---------INS SimpleName@@Name:os @TO@ MethodInvocation@@os.close() @AT@ 4416 @LENGTH@ 2\n" +
+                "---------INS SimpleName@@MethodName:close:[] @TO@ MethodInvocation@@os.close() @AT@ 4419 @LENGTH@ 7\n" +
+                "---INS IfStatement@@if (file.exists() && !file.delete()) {  throw new IOException(\"Unable to delete file: \" + file.toString());} @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 4444 @LENGTH@ 144\n" +
+                "------INS InfixExpression@@file.exists() && !file.delete() @TO@ IfStatement@@if (file.exists() && !file.delete()) {  throw new IOException(\"Unable to delete file: \" + file.toString());} @AT@ 4448 @LENGTH@ 31\n" +
+                "---------INS MethodInvocation@@file.exists() @TO@ InfixExpression@@file.exists() && !file.delete() @AT@ 4448 @LENGTH@ 13\n" +
+                "------------INS SimpleName@@Name:file @TO@ MethodInvocation@@file.exists() @AT@ 4448 @LENGTH@ 4\n" +
+                "------------INS SimpleName@@MethodName:exists:[] @TO@ MethodInvocation@@file.exists() @AT@ 4453 @LENGTH@ 8\n" +
+                "---------INS Operator@@&& @TO@ InfixExpression@@file.exists() && !file.delete() @AT@ 4461 @LENGTH@ 2\n" +
+                "---------INS PrefixExpression@@!file.delete() @TO@ InfixExpression@@file.exists() && !file.delete() @AT@ 4465 @LENGTH@ 14\n" +
+                "------------INS Operator@@! @TO@ PrefixExpression@@!file.delete() @AT@ 4465 @LENGTH@ 1\n" +
+                "------------INS MethodInvocation@@file.delete() @TO@ PrefixExpression@@!file.delete() @AT@ 4466 @LENGTH@ 13\n" +
+                "---------------INS SimpleName@@Name:file @TO@ MethodInvocation@@file.delete() @AT@ 4466 @LENGTH@ 4\n" +
+                "---------------INS SimpleName@@MethodName:delete:[] @TO@ MethodInvocation@@file.delete() @AT@ 4471 @LENGTH@ 8\n" +
+                "------INS Block@@ThenBody:{  throw new IOException(\"Unable to delete file: \" + file.toString());} @TO@ IfStatement@@if (file.exists() && !file.delete()) {  throw new IOException(\"Unable to delete file: \" + file.toString());} @AT@ 4481 @LENGTH@ 107\n" +
+                "---------INS ThrowStatement@@ClassInstanceCreation:new IOException(\"Unable to delete file: \" + file.toString()) @TO@ Block@@ThenBody:{  throw new IOException(\"Unable to delete file: \" + file.toString());} @AT@ 4503 @LENGTH@ 67\n" +
+                "------------INS ClassInstanceCreation@@IOException[\"Unable to delete file: \" + file.toString()] @TO@ ThrowStatement@@ClassInstanceCreation:new IOException(\"Unable to delete file: \" + file.toString()) @AT@ 4509 @LENGTH@ 60\n" +
+                "---------------MOV New@@new @TO@ ClassInstanceCreation@@IOException[\"Unable to delete file: \" + file.toString()] @AT@ 3982 @LENGTH@ 3\n" +
+                "---------------MOV SimpleType@@File @TO@ ClassInstanceCreation@@IOException[\"Unable to delete file: \" + file.toString()] @AT@ 3986 @LENGTH@ 4\n" +
+                "---------------MOV InfixExpression@@file.getAbsolutePath() + \".tmp\" @TO@ ClassInstanceCreation@@IOException[\"Unable to delete file: \" + file.toString()] @AT@ 3991 @LENGTH@ 31\n" +
+                "------------------UPD MethodInvocation@@file.getAbsolutePath() @TO@ file.toString() @AT@ 3991 @LENGTH@ 22\n" +
+                "---------------------UPD SimpleName@@MethodName:getAbsolutePath:[] @TO@ MethodName:toString:[] @AT@ 3996 @LENGTH@ 17\n" +
+                "------------------DEL Operator@@+ @AT@ 4013 @LENGTH@ 1\n" +
+                "------------------DEL StringLiteral@@\".tmp\" @AT@ 4016 @LENGTH@ 6\n" +
+                "------------------INS StringLiteral@@\"Unable to delete file: \" @TO@ InfixExpression@@file.getAbsolutePath() + \".tmp\" @AT@ 4525 @LENGTH@ 25\n" +
+                "------------------INS Operator@@+ @TO@ InfixExpression@@file.getAbsolutePath() + \".tmp\" @AT@ 4550 @LENGTH@ 1\n" +
+                "---INS IfStatement@@if (!tmp.renameTo(file)) {  throw new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString());} @TO@ TryStatement@@try {  configuration.enableProxy(artifact.getArtifactURL());  String repository=system.getFile().getAbsolutePath();  if (!repository.endsWith(Parser.FILE_SEPARATOR)) {    repository=repository + Parser.FILE_SEPARATOR;  }  InputStream is=artifact.getInputStream();  File file=new File(repository + parser.getArtifactPath());  File tmp=new File(file.getAbsolutePath() + \".tmp\");  tmp.getParentFile().mkdirs();  OutputStream os=new FileOutputStream(tmp);  copy(is,os);  file.delete();  tmp.renameTo(file);  return file;} catch (IOException ignore) {  LOG.debug(Ix2 + \"Could not download [\" + artifact+ \"]\");  LOG.trace(Ix2 + \"Reason [\" + ignore.getClass().getName()+ \": \"+ ignore.getMessage()+ \"]\");} @AT@ 4605 @LENGTH@ 157\n" +
+                "------INS PrefixExpression@@!tmp.renameTo(file) @TO@ IfStatement@@if (!tmp.renameTo(file)) {  throw new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString());} @AT@ 4609 @LENGTH@ 19\n" +
+                "---------MOV MethodInvocation@@tmp.renameTo(file) @TO@ PrefixExpression@@!tmp.renameTo(file) @AT@ 4209 @LENGTH@ 18\n" +
+                "---------INS Operator@@! @TO@ PrefixExpression@@!tmp.renameTo(file) @AT@ 4609 @LENGTH@ 1\n" +
+                "------INS Block@@ThenBody:{  throw new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString());} @TO@ IfStatement@@if (!tmp.renameTo(file)) {  throw new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString());} @AT@ 4630 @LENGTH@ 132\n" +
+                "---------INS ThrowStatement@@ClassInstanceCreation:new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString()) @TO@ Block@@ThenBody:{  throw new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString());} @AT@ 4652 @LENGTH@ 92\n" +
+                "------------INS ClassInstanceCreation@@IOException[\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString()] @TO@ ThrowStatement@@ClassInstanceCreation:new IOException(\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString()) @AT@ 4658 @LENGTH@ 85\n" +
+                "---------------INS New@@new @TO@ ClassInstanceCreation@@IOException[\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString()] @AT@ 4658 @LENGTH@ 3\n" +
+                "---------------INS SimpleType@@IOException @TO@ ClassInstanceCreation@@IOException[\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString()] @AT@ 4662 @LENGTH@ 11\n" +
+                "---------------INS InfixExpression@@\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString() @TO@ ClassInstanceCreation@@IOException[\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString()] @AT@ 4674 @LENGTH@ 68\n" +
+                "------------------INS StringLiteral@@\"Unable to rename file \" @TO@ InfixExpression@@\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString() @AT@ 4674 @LENGTH@ 24\n" +
+                "------------------INS Operator@@+ @TO@ InfixExpression@@\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString() @AT@ 4698 @LENGTH@ 1\n" +
+                "------------------INS MethodInvocation@@tmp.toString() @TO@ InfixExpression@@\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString() @AT@ 4701 @LENGTH@ 14\n" +
+                "---------------------MOV SimpleName@@Name:tmp @TO@ MethodInvocation@@tmp.toString() @AT@ 4041 @LENGTH@ 3\n" +
+                "---------------------MOV SimpleName@@MethodName:mkdirs:[] @TO@ MethodInvocation@@tmp.toString() @AT@ 4061 @LENGTH@ 8\n" +
+                "------------------INS StringLiteral@@\" to \" @TO@ InfixExpression@@\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString() @AT@ 4718 @LENGTH@ 6\n" +
+                "------------------INS MethodInvocation@@file.toString() @TO@ InfixExpression@@\"Unable to rename file \" + tmp.toString() + \" to \"+ file.toString() @AT@ 4727 @LENGTH@ 15\n" +
+                "---------------------MOV SimpleName@@Name:file @TO@ MethodInvocation@@file.toString() @AT@ 4178 @LENGTH@ 4\n" +
+                "---------------------MOV SimpleName@@MethodName:delete:[] @TO@ MethodInvocation@@file.toString() @AT@ 4183 @LENGTH@ 8\n");
+    }
+
+
+    //commons-collections_2d6bc8_506966_src#java#org#apache#commons#collections#ExtendedProperties.java
+    @Test
+    public void test_collections_2d6bc8_506966() throws IOException {
+        //TODO seems ok but
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_2d6bc8_506966_src#java#org#apache#commons#collections#ExtendedProperties.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),3);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"DEL MethodDeclaration@@private, void, MethodName:init, ExtendedProperties exp, IOException,  @AT@ 13436 @LENGTH@ 104\n" +
+                "---DEL Modifier@@private @AT@ 13436 @LENGTH@ 7\n" +
+                "---DEL PrimitiveType@@void @AT@ 13444 @LENGTH@ 4\n" +
+                "---DEL SimpleName@@MethodName:init @AT@ 13449 @LENGTH@ 4\n" +
+                "---DEL SingleVariableDeclaration@@ExtendedProperties exp @AT@ 13455 @LENGTH@ 22\n" +
+                "------DEL SimpleType@@ExtendedProperties @AT@ 13455 @LENGTH@ 18\n" +
+                "------DEL SimpleName@@exp @AT@ 13474 @LENGTH@ 3\n" +
+                "---DEL SimpleType@@IOException @AT@ 13487 @LENGTH@ 11\n");
+        Assert.assertEquals(hierarchicalActionSets.get(1).toString(),"MOV ExpressionStatement@@Assignment:isInitialized=true @TO@ MethodDeclaration@@public, void, MethodName:addProperty, String key, Object token,  @AT@ 13513 @LENGTH@ 21\n");
+        Assert.assertEquals(hierarchicalActionSets.get(2).toString(),"UPD TryStatement@@try {  while (true) {    String line=reader.readProperty();    int equalSign=line.indexOf('=');    if (equalSign > 0) {      String key=line.substring(0,equalSign).trim();      String value=line.substring(equalSign + 1).trim();      if (\"\".equals(value))       continue;      if (getInclude() != null && key.equalsIgnoreCase(getInclude())) {        File file=null;        if (value.startsWith(fileSeparator)) {          file=new File(value);        } else {          if (value.startsWith(\".\" + fileSeparator)) {            value=value.substring(2);          }          file=new File(basePath + value);        }        if (file != null && file.exists() && file.canRead()) {          load(new FileInputStream(file));        }      } else {        addProperty(key,value);      }    }  }} catch (NullPointerException e) {  return;} @TO@ try {  while (true) {    String line=reader.readProperty();    int equalSign=line.indexOf('=');    if (equalSign > 0) {      String key=line.substring(0,equalSign).trim();      String value=line.substring(equalSign + 1).trim();      if (\"\".equals(value))       continue;      if (getInclude() != null && key.equalsIgnoreCase(getInclude())) {        File file=null;        if (value.startsWith(fileSeparator)) {          file=new File(value);        } else {          if (value.startsWith(\".\" + fileSeparator)) {            value=value.substring(2);          }          file=new File(basePath + value);        }        if (file != null && file.exists() && file.canRead()) {          load(new FileInputStream(file));        }      } else {        addProperty(key,value);      }    }  }} catch (NullPointerException e) {  return;} finally {  isInitialized=true;} @AT@ 15296 @LENGTH@ 2508\n" +
+                "---INS Block@@FinallyBody:{  isInitialized=true;} @TO@ TryStatement@@try {  while (true) {    String line=reader.readProperty();    int equalSign=line.indexOf('=');    if (equalSign > 0) {      String key=line.substring(0,equalSign).trim();      String value=line.substring(equalSign + 1).trim();      if (\"\".equals(value))       continue;      if (getInclude() != null && key.equalsIgnoreCase(getInclude())) {        File file=null;        if (value.startsWith(fileSeparator)) {          file=new File(value);        } else {          if (value.startsWith(\".\" + fileSeparator)) {            value=value.substring(2);          }          file=new File(basePath + value);        }        if (file != null && file.exists() && file.canRead()) {          load(new FileInputStream(file));        }      } else {        addProperty(key,value);      }    }  }} catch (NullPointerException e) {  return;} @AT@ 17503 @LENGTH@ 115\n" +
+                "------INS ExpressionStatement@@Assignment:isInitialized=true @TO@ Block@@FinallyBody:{  isInitialized=true;} @AT@ 17587 @LENGTH@ 21\n" +
+                "---------INS Assignment@@isInitialized=true @TO@ ExpressionStatement@@Assignment:isInitialized=true @AT@ 17587 @LENGTH@ 20\n" +
+                "------------INS SimpleName@@isInitialized @TO@ Assignment@@isInitialized=true @AT@ 17587 @LENGTH@ 13\n" +
+                "------------INS Operator@@= @TO@ Assignment@@isInitialized=true @AT@ 17600 @LENGTH@ 1\n" +
+                "------------INS BooleanLiteral@@true @TO@ Assignment@@isInitialized=true @AT@ 17603 @LENGTH@ 4\n");
+    }
+
+
+    //commons-compress_b7de91_5273bd_src#main#java#org#apache#commons#compress#archivers#sevenz#SevenZFile.java
+    @Test
+    public void test_compress_b7de91_5273bd() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-compress_b7de91_5273bd_src#main#java#org#apache#commons#compress#archivers#sevenz#SevenZFile.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ForStatement@@for (int i=0; i < files.length; i++) {  files[i].setHasAcessDate(timesDefined.get(i));  if (files[i].getHasAcessDate()) {    files[i].setAccessDate(Long.reverseBytes(header.readLong()));  }} @TO@ for (int i=0; i < files.length; i++) {  files[i].setHasAccessDate(timesDefined.get(i));  if (files[i].getHasAccessDate()) {    files[i].setAccessDate(Long.reverseBytes(header.readLong()));  }} @AT@ 27930 @LENGTH@ 327\n" +
+                "---UPD ExpressionStatement@@MethodInvocation:files[i].setHasAcessDate(timesDefined.get(i)) @TO@ MethodInvocation:files[i].setHasAccessDate(timesDefined.get(i)) @AT@ 27999 @LENGTH@ 46\n" +
+                "------UPD MethodInvocation@@files[i].setHasAcessDate(timesDefined.get(i)) @TO@ files[i].setHasAccessDate(timesDefined.get(i)) @AT@ 27999 @LENGTH@ 45\n" +
+                "---------UPD SimpleName@@MethodName:setHasAcessDate:[timesDefined.get(i)] @TO@ MethodName:setHasAccessDate:[timesDefined.get(i)] @AT@ 28008 @LENGTH@ 36\n" +
+                "---UPD IfStatement@@if (files[i].getHasAcessDate()) {  files[i].setAccessDate(Long.reverseBytes(header.readLong()));} @TO@ if (files[i].getHasAccessDate()) {  files[i].setAccessDate(Long.reverseBytes(header.readLong()));} @AT@ 28074 @LENGTH@ 157\n" +
+                "------UPD MethodInvocation@@files[i].getHasAcessDate() @TO@ files[i].getHasAccessDate() @AT@ 28078 @LENGTH@ 26\n" +
+                "---------UPD SimpleName@@MethodName:getHasAcessDate:[] @TO@ MethodName:getHasAccessDate:[] @AT@ 28087 @LENGTH@ 17\n");
+    }
+
+    //metadata_017a3f_580eac_web#src#main#java#org#jboss#metadata#parser#jbossweb#ContainerListenerMetaDataParser.java
+    @Test
+    public void test_metadata_017a3f_580eac() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("metadata_017a3f_580eac_web#src#main#java#org#jboss#metadata#parser#jbossweb#ContainerListenerMetaDataParser.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD SwitchStatement@@switch (element) {case CLASS_NAME:  containerListener.setListenerClass(getElementText(reader));break;case MODULE:containerListener.setModule(getElementText(reader));break;case LISTENER_TYPE:containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));break;case PARAM:List<ParamValueMetaData> params=containerListener.getParams();if (params == null) {params=new ArrayList<ParamValueMetaData>();containerListener.setParams(params);}params.add(ParamValueMetaDataParser.parse(reader));break;default :throw unexpectedElement(reader);} @TO@ switch (element) {case CLASS_NAME:  containerListener.setListenerClass(getElementText(reader));break;case MODULE:containerListener.setModule(getElementText(reader));break;case LISTENER_TYPE:try {containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));} catch (IllegalArgumentException e) {throw unexpectedValue(reader,e);}break;case PARAM:List<ParamValueMetaData> params=containerListener.getParams();if (params == null) {params=new ArrayList<ParamValueMetaData>();containerListener.setParams(params);}params.add(ParamValueMetaDataParser.parse(reader));break;default :throw unexpectedElement(reader);} @AT@ 1995 @LENGTH@ 924\n" +
+                "---INS TryStatement@@try {  containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));} catch (IllegalArgumentException e) {  throw unexpectedValue(reader,e);} @TO@ SwitchStatement@@switch (element) {case CLASS_NAME:  containerListener.setListenerClass(getElementText(reader));break;case MODULE:containerListener.setModule(getElementText(reader));break;case LISTENER_TYPE:containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));break;case PARAM:List<ParamValueMetaData> params=containerListener.getParams();if (params == null) {params=new ArrayList<ParamValueMetaData>();containerListener.setParams(params);}params.add(ParamValueMetaDataParser.parse(reader));break;default :throw unexpectedElement(reader);} @AT@ 2333 @LENGTH@ 258\n" +
+                "------MOV ExpressionStatement@@MethodInvocation:containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader))) @TO@ TryStatement@@try {  containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));} catch (IllegalArgumentException e) {  throw unexpectedValue(reader,e);} @AT@ 2330 @LENGTH@ 89\n" +
+                "------INS CatchClause@@catch (IllegalArgumentException e) {  throw unexpectedValue(reader,e);} @TO@ TryStatement@@try {  containerListener.setListenerType(ContainerListenerType.valueOf(getElementText(reader)));} catch (IllegalArgumentException e) {  throw unexpectedValue(reader,e);} @AT@ 2475 @LENGTH@ 116\n" +
+                "---------INS SingleVariableDeclaration@@IllegalArgumentException e @TO@ CatchClause@@catch (IllegalArgumentException e) {  throw unexpectedValue(reader,e);} @AT@ 2482 @LENGTH@ 26\n" +
+                "------------INS SimpleType@@IllegalArgumentException @TO@ SingleVariableDeclaration@@IllegalArgumentException e @AT@ 2482 @LENGTH@ 24\n" +
+                "------------INS SimpleName@@e @TO@ SingleVariableDeclaration@@IllegalArgumentException e @AT@ 2507 @LENGTH@ 1\n" +
+                "---------INS ThrowStatement@@MethodInvocation:unexpectedValue(reader,e) @TO@ CatchClause@@catch (IllegalArgumentException e) {  throw unexpectedValue(reader,e);} @AT@ 2536 @LENGTH@ 33\n" +
+                "------------INS MethodInvocation@@unexpectedValue(reader,e) @TO@ ThrowStatement@@MethodInvocation:unexpectedValue(reader,e) @AT@ 2542 @LENGTH@ 26\n" +
+                "---------------INS SimpleName@@MethodName:unexpectedValue:[reader, e] @TO@ MethodInvocation@@unexpectedValue(reader,e) @AT@ 2542 @LENGTH@ 26\n" +
+                "------------------INS SimpleName@@reader @TO@ SimpleName@@MethodName:unexpectedValue:[reader, e] @AT@ 2558 @LENGTH@ 6\n" +
+                "------------------INS SimpleName@@e @TO@ SimpleName@@MethodName:unexpectedValue:[reader, e] @AT@ 2566 @LENGTH@ 1\n");
+    }
+
+    //metadata_674226_73eff3_common#src#main#java#org#jboss#metadata#parser#ee#ServiceReferenceMetaDataParser.java
+    @Test
+    public void test_metadata_674226_73eff3() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("metadata_674226_73eff3_common#src#main#java#org#jboss#metadata#parser#ee#ServiceReferenceMetaDataParser.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ExpressionStatement@@MethodInvocation:serviceReference.setServiceQname(QName.valueOf(getElementText(reader))) @TO@ MethodInvocation:serviceReference.setServiceQname(parseQName(reader,getElementText(reader))) @AT@ 4613 @LENGTH@ 72\n" +
+                "---UPD MethodInvocation@@serviceReference.setServiceQname(QName.valueOf(getElementText(reader))) @TO@ serviceReference.setServiceQname(parseQName(reader,getElementText(reader))) @AT@ 4613 @LENGTH@ 71\n" +
+                "------UPD SimpleName@@MethodName:setServiceQname:[QName.valueOf(getElementText(reader))] @TO@ MethodName:setServiceQname:[parseQName(reader,getElementText(reader))] @AT@ 4630 @LENGTH@ 54\n" +
+                "---------UPD MethodInvocation@@QName.valueOf(getElementText(reader)) @TO@ parseQName(reader,getElementText(reader)) @AT@ 4646 @LENGTH@ 37\n" +
+                "------------DEL SimpleName@@Name:QName @AT@ 4646 @LENGTH@ 5\n" +
+                "------------UPD SimpleName@@MethodName:valueOf:[getElementText(reader)] @TO@ MethodName:parseQName:[reader, getElementText(reader)] @AT@ 4652 @LENGTH@ 31\n" +
+                "---------------INS SimpleName@@reader @TO@ SimpleName@@MethodName:valueOf:[getElementText(reader)] @AT@ 4657 @LENGTH@ 6\n");
+    }
+
+    //commons-configuration_bad272_1c720e_src#java#org#apache#commons#configuration#DataConfiguration.java
+    @Test
+    public void test_configuration_bad272_1c720e() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-configuration_bad272_1c720e_src#java#org#apache#commons#configuration#DataConfiguration.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),2);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ThrowStatement@@ClassInstanceCreation:new IllegalArgumentException(\"The type of the default value (\" + defaultValue.getClass() + \") is not an array of the specified class (\"+ cls+ \")\") @TO@ ClassInstanceCreation:new IllegalArgumentException(\"The type of the default value (\" + defaultValue.getClass() + \")\"+ \" is not an array of the specified class (\"+ cls+ \")\") @AT@ 13001 @LENGTH@ 155\n" +
+                "---UPD ClassInstanceCreation@@IllegalArgumentException[\"The type of the default value (\" + defaultValue.getClass() + \") is not an array of the specified class (\"+ cls+ \")\"] @TO@ IllegalArgumentException[\"The type of the default value (\" + defaultValue.getClass() + \")\"+ \" is not an array of the specified class (\"+ cls+ \")\"] @AT@ 13007 @LENGTH@ 148\n" +
+                "------UPD InfixExpression@@\"The type of the default value (\" + defaultValue.getClass() + \") is not an array of the specified class (\"+ cls+ \")\" @TO@ \"The type of the default value (\" + defaultValue.getClass() + \")\"+ \" is not an array of the specified class (\"+ cls+ \")\" @AT@ 13036 @LENGTH@ 118\n" +
+                "---------UPD StringLiteral@@\") is not an array of the specified class (\" @TO@ \" is not an array of the specified class (\" @AT@ 13098 @LENGTH@ 44\n" +
+                "---------INS StringLiteral@@\")\" @TO@ InfixExpression@@\"The type of the default value (\" + defaultValue.getClass() + \") is not an array of the specified class (\"+ cls+ \")\" @AT@ 13122 @LENGTH@ 3\n");
+        Assert.assertEquals(hierarchicalActionSets.get(1).toString(),"UPD ThrowStatement@@ClassInstanceCreation:new ConversionException('\\'' + key + \"' (\"+ arrayType+ \") doesn't map to a compatible array of \"+ cls) @TO@ ClassInstanceCreation:new ConversionException('\\'' + key + \"' (\"+ arrayType+ \")\"+ \" doesn't map to a compatible array of \"+ cls) @AT@ 15560 @LENGTH@ 112\n" +
+                "---UPD ClassInstanceCreation@@ConversionException['\\'' + key + \"' (\"+ arrayType+ \") doesn't map to a compatible array of \"+ cls] @TO@ ConversionException['\\'' + key + \"' (\"+ arrayType+ \")\"+ \" doesn't map to a compatible array of \"+ cls] @AT@ 15566 @LENGTH@ 105\n" +
+                "------UPD InfixExpression@@'\\'' + key + \"' (\"+ arrayType+ \") doesn't map to a compatible array of \"+ cls @TO@ '\\'' + key + \"' (\"+ arrayType+ \")\"+ \" doesn't map to a compatible array of \"+ cls @AT@ 15590 @LENGTH@ 80\n" +
+                "---------UPD StringLiteral@@\") doesn't map to a compatible array of \" @TO@ \" doesn't map to a compatible array of \" @AT@ 15623 @LENGTH@ 41\n" +
+                "---------INS StringLiteral@@\")\" @TO@ InfixExpression@@'\\'' + key + \"' (\"+ arrayType+ \") doesn't map to a compatible array of \"+ cls @AT@ 15672 @LENGTH@ 3\n");
+    }
+
+    //commons-compress_4ac67b_0eccda_src#main#java#org#apache#commons#compress#compressors#snappy#SnappyCompressorInputStream.java
+    @Test
+    public void test_compress_4ac67b_0eccda() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-compress_4ac67b_0eccda_src#main#java#org#apache#commons#compress#compressors#snappy#SnappyCompressorInputStream.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD SwitchStatement@@switch (state) {case NO_BLOCK:  fill();return read(b,off,len);case IN_LITERAL:int litLen=readLiteral(b,off,len);if (!hasMoreDataInBlock()) {state=State.NO_BLOCK;}return litLen;case IN_BACK_REFERENCE:int backReferenceLen=readBackReference(b,off,len);if (!hasMoreDataInBlock()) {state=State.NO_BLOCK;}return backReferenceLen;default :throw new IOException(\"Unknown stream state \" + state);} @TO@ switch (state) {case NO_BLOCK:  fill();return read(b,off,len);case IN_LITERAL:int litLen=readLiteral(b,off,len);if (!hasMoreDataInBlock()) {state=State.NO_BLOCK;}return litLen > 0 ? litLen : read(b,off,len);case IN_BACK_REFERENCE:int backReferenceLen=readBackReference(b,off,len);if (!hasMoreDataInBlock()) {state=State.NO_BLOCK;}return backReferenceLen > 0 ? backReferenceLen : read(b,off,len);default :throw new IOException(\"Unknown stream state \" + state);} @AT@ 3346 @LENGTH@ 621\n" +
+                "---UPD ReturnStatement@@SimpleName:litLen @TO@ ConditionalExpression:litLen > 0 ? litLen : read(b,off,len) @AT@ 3627 @LENGTH@ 14\n" +
+                "------INS ConditionalExpression@@litLen > 0 ? litLen : read(b,off,len) @TO@ ReturnStatement@@SimpleName:litLen @AT@ 3634 @LENGTH@ 39\n" +
+                "---------INS InfixExpression@@litLen > 0 @TO@ ConditionalExpression@@litLen > 0 ? litLen : read(b,off,len) @AT@ 3634 @LENGTH@ 10\n" +
+                "------------INS SimpleName@@litLen @TO@ InfixExpression@@litLen > 0 @AT@ 3634 @LENGTH@ 6\n" +
+                "------------INS Operator@@> @TO@ InfixExpression@@litLen > 0 @AT@ 3640 @LENGTH@ 1\n" +
+                "------------INS NumberLiteral@@0 @TO@ InfixExpression@@litLen > 0 @AT@ 3643 @LENGTH@ 1\n" +
+                "---------INS SimpleName@@litLen @TO@ ConditionalExpression@@litLen > 0 ? litLen : read(b,off,len) @AT@ 3647 @LENGTH@ 6\n" +
+                "---------INS MethodInvocation@@read(b,off,len) @TO@ ConditionalExpression@@litLen > 0 ? litLen : read(b,off,len) @AT@ 3656 @LENGTH@ 17\n" +
+                "------------INS SimpleName@@MethodName:read:[b, off, len] @TO@ MethodInvocation@@read(b,off,len) @AT@ 3656 @LENGTH@ 17\n" +
+                "---------------INS SimpleName@@b @TO@ SimpleName@@MethodName:read:[b, off, len] @AT@ 3661 @LENGTH@ 1\n" +
+                "---------------INS SimpleName@@off @TO@ SimpleName@@MethodName:read:[b, off, len] @AT@ 3664 @LENGTH@ 3\n" +
+                "---------------INS SimpleName@@len @TO@ SimpleName@@MethodName:read:[b, off, len] @AT@ 3669 @LENGTH@ 3\n" +
+                "------DEL SimpleName@@litLen @AT@ 3634 @LENGTH@ 6\n" +
+                "---UPD ReturnStatement@@SimpleName:backReferenceLen @TO@ ConditionalExpression:backReferenceLen > 0 ? backReferenceLen : read(b,off,len) @AT@ 3848 @LENGTH@ 24\n" +
+                "------DEL SimpleName@@backReferenceLen @AT@ 3855 @LENGTH@ 16\n" +
+                "------INS ConditionalExpression@@backReferenceLen > 0 ? backReferenceLen : read(b,off,len) @TO@ ReturnStatement@@SimpleName:backReferenceLen @AT@ 3888 @LENGTH@ 59\n" +
+                "---------INS InfixExpression@@backReferenceLen > 0 @TO@ ConditionalExpression@@backReferenceLen > 0 ? backReferenceLen : read(b,off,len) @AT@ 3888 @LENGTH@ 20\n" +
+                "------------INS SimpleName@@backReferenceLen @TO@ InfixExpression@@backReferenceLen > 0 @AT@ 3888 @LENGTH@ 16\n" +
+                "------------INS Operator@@> @TO@ InfixExpression@@backReferenceLen > 0 @AT@ 3904 @LENGTH@ 1\n" +
+                "------------INS NumberLiteral@@0 @TO@ InfixExpression@@backReferenceLen > 0 @AT@ 3907 @LENGTH@ 1\n" +
+                "---------INS SimpleName@@backReferenceLen @TO@ ConditionalExpression@@backReferenceLen > 0 ? backReferenceLen : read(b,off,len) @AT@ 3911 @LENGTH@ 16\n" +
+                "---------INS MethodInvocation@@read(b,off,len) @TO@ ConditionalExpression@@backReferenceLen > 0 ? backReferenceLen : read(b,off,len) @AT@ 3930 @LENGTH@ 17\n" +
+                "------------INS SimpleName@@MethodName:read:[b, off, len] @TO@ MethodInvocation@@read(b,off,len) @AT@ 3930 @LENGTH@ 17\n" +
+                "---------------INS SimpleName@@b @TO@ SimpleName@@MethodName:read:[b, off, len] @AT@ 3935 @LENGTH@ 1\n" +
+                "---------------INS SimpleName@@off @TO@ SimpleName@@MethodName:read:[b, off, len] @AT@ 3938 @LENGTH@ 3\n" +
+                "---------------INS SimpleName@@len @TO@ SimpleName@@MethodName:read:[b, off, len] @AT@ 3943 @LENGTH@ 3\n");
+    }
+
+
+    //commons-collections_b6d038_4bdb89_src#java#org#apache#commons#collections#iterators#ArrayListIterator.java
+    @Test
+    public void test_collections_b6d038_4bdb89() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_b6d038_4bdb89_src#java#org#apache#commons#collections#iterators#ArrayListIterator.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),2);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD ReturnStatement@@FieldAccess:this.index @TO@ InfixExpression:this.index - this.startIndex @AT@ 7714 @LENGTH@ 18\n" +
+                "---DEL FieldAccess@@this.index @AT@ 7721 @LENGTH@ 10\n" +
+                "---INS InfixExpression@@this.index - this.startIndex @TO@ ReturnStatement@@FieldAccess:this.index @AT@ 7740 @LENGTH@ 28\n" +
+                "------INS FieldAccess@@this.index @TO@ InfixExpression@@this.index - this.startIndex @AT@ 7740 @LENGTH@ 10\n" +
+                "---------MOV ThisExpression@@this @TO@ FieldAccess@@this.index @AT@ 7721 @LENGTH@ 4\n" +
+                "---------MOV SimpleName@@index @TO@ FieldAccess@@this.index @AT@ 7726 @LENGTH@ 5\n" +
+                "------INS Operator@@- @TO@ InfixExpression@@this.index - this.startIndex @AT@ 7750 @LENGTH@ 1\n" +
+                "------INS FieldAccess@@this.startIndex @TO@ InfixExpression@@this.index - this.startIndex @AT@ 7753 @LENGTH@ 15\n" +
+                "---------INS ThisExpression@@this @TO@ FieldAccess@@this.startIndex @AT@ 7753 @LENGTH@ 4\n" +
+                "---------INS SimpleName@@startIndex @TO@ FieldAccess@@this.startIndex @AT@ 7758 @LENGTH@ 10\n");
+        Assert.assertEquals(hierarchicalActionSets.get(1).toString(),"UPD ReturnStatement@@InfixExpression:this.index - 1 @TO@ InfixExpression:this.index - this.startIndex - 1 @AT@ 7947 @LENGTH@ 22\n" +
+                "---UPD InfixExpression@@this.index - 1 @TO@ this.index - this.startIndex - 1 @AT@ 7954 @LENGTH@ 14\n" +
+                "------INS FieldAccess@@this.startIndex @TO@ InfixExpression@@this.index - 1 @AT@ 8004 @LENGTH@ 15\n" +
+                "---------INS ThisExpression@@this @TO@ FieldAccess@@this.startIndex @AT@ 8004 @LENGTH@ 4\n" +
+                "---------INS SimpleName@@startIndex @TO@ FieldAccess@@this.startIndex @AT@ 8009 @LENGTH@ 10\n");
+    }
+
+    //commons-collections_3761b5_3639ab_src#java#org#apache#commons#collections#FastHashMap.java
+    @Test
+    public void test_collections_3761b5_3639ab() throws IOException {
+        //TODO can be different
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("commons-collections_3761b5_3639ab_src#java#org#apache#commons#collections#FastHashMap.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD IfStatement@@if (fast) {  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Entry e=(Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} else {synchronized (map) {    if (mo.size() != map.size())     return (false);    Iterator i=map.entrySet().iterator();    while (i.hasNext()) {      Entry e=(Entry)i.next();      Object key=e.getKey();      Object value=e.getValue();      if (value == null) {        if (!(mo.get(key) == null && mo.containsKey(key)))         return (false);      } else {        if (!value.equals(mo.get(key)))         return (false);      }    }    return (true);  }} @TO@ if (fast) {  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Map.Entry e=(Map.Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} else {synchronized (map) {    if (mo.size() != map.size())     return (false);    Iterator i=map.entrySet().iterator();    while (i.hasNext()) {      Map.Entry e=(Map.Entry)i.next();      Object key=e.getKey();      Object value=e.getValue();      if (value == null) {        if (!(mo.get(key) == null && mo.containsKey(key)))         return (false);      } else {        if (!value.equals(mo.get(key)))         return (false);      }    }    return (true);  }} @AT@ 8632 @LENGTH@ 1375\n" +
+                "---UPD Block@@ThenBody:{  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Entry e=(Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} @TO@ ThenBody:{  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Map.Entry e=(Map.Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} @AT@ 8642 @LENGTH@ 624\n" +
+                "------UPD WhileStatement@@while (i.hasNext()) {  Entry e=(Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @TO@ while (i.hasNext()) {  Map.Entry e=(Map.Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @AT@ 8781 @LENGTH@ 448\n" +
+                "---------UPD Block@@WhileBody:{  Entry e=(Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @TO@ WhileBody:{  Map.Entry e=(Map.Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @AT@ 8801 @LENGTH@ 428\n" +
+                "------------UPD VariableDeclarationStatement@@Entry e=(Entry)i.next(); @TO@ Map.Entry e=(Map.Entry)i.next(); @AT@ 8819 @LENGTH@ 27\n" +
+                "---------------UPD SimpleType@@Entry @TO@ Map.Entry @AT@ 8819 @LENGTH@ 5\n" +
+                "---------------UPD VariableDeclarationFragment@@e=(Entry)i.next() @TO@ e=(Map.Entry)i.next() @AT@ 8825 @LENGTH@ 20\n" +
+                "------------------UPD CastExpression@@(Entry)i.next() @TO@ (Map.Entry)i.next() @AT@ 8829 @LENGTH@ 16\n" +
+                "---------------------UPD SimpleType@@Entry @TO@ Map.Entry @AT@ 8830 @LENGTH@ 5\n" +
+                "---UPD Block@@ElseBody:{synchronized (map) {    if (mo.size() != map.size())     return (false);    Iterator i=map.entrySet().iterator();    while (i.hasNext()) {      Entry e=(Entry)i.next();      Object key=e.getKey();      Object value=e.getValue();      if (value == null) {        if (!(mo.get(key) == null && mo.containsKey(key)))         return (false);      } else {        if (!value.equals(mo.get(key)))         return (false);      }    }    return (true);  }} @TO@ ElseBody:{synchronized (map) {    if (mo.size() != map.size())     return (false);    Iterator i=map.entrySet().iterator();    while (i.hasNext()) {      Map.Entry e=(Map.Entry)i.next();      Object key=e.getKey();      Object value=e.getValue();      if (value == null) {        if (!(mo.get(key) == null && mo.containsKey(key)))         return (false);      } else {        if (!value.equals(mo.get(key)))         return (false);      }    }    return (true);  }} @AT@ 9272 @LENGTH@ 735\n" +
+                "------UPD SynchronizedStatement@@synchronized (map) {  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Entry e=(Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} @TO@ synchronized (map) {  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Map.Entry e=(Map.Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} @AT@ 9286 @LENGTH@ 711\n" +
+                "---------UPD Block@@SyncBody:{  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Entry e=(Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} @TO@ SyncBody:{  if (mo.size() != map.size())   return (false);  Iterator i=map.entrySet().iterator();  while (i.hasNext()) {    Map.Entry e=(Map.Entry)i.next();    Object key=e.getKey();    Object value=e.getValue();    if (value == null) {      if (!(mo.get(key) == null && mo.containsKey(key)))       return (false);    } else {      if (!value.equals(mo.get(key)))       return (false);    }  }  return (true);} @AT@ 9305 @LENGTH@ 692\n" +
+                "------------UPD WhileStatement@@while (i.hasNext()) {  Entry e=(Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @TO@ while (i.hasNext()) {  Map.Entry e=(Map.Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @AT@ 9460 @LENGTH@ 492\n" +
+                "---------------UPD Block@@WhileBody:{  Entry e=(Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @TO@ WhileBody:{  Map.Entry e=(Map.Entry)i.next();  Object key=e.getKey();  Object value=e.getValue();  if (value == null) {    if (!(mo.get(key) == null && mo.containsKey(key)))     return (false);  } else {    if (!value.equals(mo.get(key)))     return (false);  }} @AT@ 9480 @LENGTH@ 472\n" +
+                "------------------UPD VariableDeclarationStatement@@Entry e=(Entry)i.next(); @TO@ Map.Entry e=(Map.Entry)i.next(); @AT@ 9502 @LENGTH@ 27\n" +
+                "---------------------UPD SimpleType@@Entry @TO@ Map.Entry @AT@ 9502 @LENGTH@ 5\n" +
+                "---------------------UPD VariableDeclarationFragment@@e=(Entry)i.next() @TO@ e=(Map.Entry)i.next() @AT@ 9508 @LENGTH@ 20\n" +
+                "------------------------UPD CastExpression@@(Entry)i.next() @TO@ (Map.Entry)i.next() @AT@ 9512 @LENGTH@ 16\n" +
+                "---------------------------UPD SimpleType@@Entry @TO@ Map.Entry @AT@ 9513 @LENGTH@ 5\n");
+
+    }
+
+
+    //fuse_74c02c_a4658a_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#DataStoreManager.java
+    @Test
+    public void test_fuse_74c02c_a4658a() throws IOException {
+        //mov position
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_74c02c_a4658a_fabric#fabric-core#src#main#java#org#fusesource#fabric#service#DataStoreManager.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),2);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD IfStatement@@if (type.equals(dataStorePlugin.getName())) {  updateServiceRegistration();} @TO@ if (type != null && type.equals(dataStorePlugin.getName())) {  updateServiceRegistration();} @AT@ 5887 @LENGTH@ 104\n" +
+                "---INS InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @TO@ IfStatement@@if (type.equals(dataStorePlugin.getName())) {  updateServiceRegistration();} @AT@ 5891 @LENGTH@ 54\n" +
+                "------MOV MethodInvocation@@type.equals(dataStorePlugin.getName()) @TO@ InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @AT@ 5891 @LENGTH@ 38\n" +
+                "------INS InfixExpression@@type != null @TO@ InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @AT@ 5891 @LENGTH@ 12\n" +
+                "---------INS SimpleName@@type @TO@ InfixExpression@@type != null @AT@ 5891 @LENGTH@ 4\n" +
+                "---------INS Operator@@!= @TO@ InfixExpression@@type != null @AT@ 5895 @LENGTH@ 2\n" +
+                "---------INS NullLiteral@@null @TO@ InfixExpression@@type != null @AT@ 5899 @LENGTH@ 4\n" +
+                "------INS Operator@@&& @TO@ InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @AT@ 5903 @LENGTH@ 2\n");
+        Assert.assertEquals(hierarchicalActionSets.get(1).toString(),"UPD IfStatement@@if (type.equals(dataStorePlugin.getName())) {  updateServiceRegistration();} @TO@ if (type != null && type.equals(dataStorePlugin.getName())) {  updateServiceRegistration();} @AT@ 6204 @LENGTH@ 104\n" +
+                "---INS InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @TO@ IfStatement@@if (type.equals(dataStorePlugin.getName())) {  updateServiceRegistration();} @AT@ 6224 @LENGTH@ 54\n" +
+                "------MOV MethodInvocation@@type.equals(dataStorePlugin.getName()) @TO@ InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @AT@ 6208 @LENGTH@ 38\n" +
+                "------INS InfixExpression@@type != null @TO@ InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @AT@ 6224 @LENGTH@ 12\n" +
+                "---------INS SimpleName@@type @TO@ InfixExpression@@type != null @AT@ 6224 @LENGTH@ 4\n" +
+                "---------INS Operator@@!= @TO@ InfixExpression@@type != null @AT@ 6228 @LENGTH@ 2\n" +
+                "---------INS NullLiteral@@null @TO@ InfixExpression@@type != null @AT@ 6232 @LENGTH@ 4\n" +
+                "------INS Operator@@&& @TO@ InfixExpression@@type != null && type.equals(dataStorePlugin.getName()) @AT@ 6236 @LENGTH@ 2\n");
+    }
+
+    //fuse_cb3362_cfb295_fabric#fabric-features-service#src#main#java#org#fusesource#fabric#features#FabricFeaturesServiceImpl.java
+    @Test
+    public void test_fuse_cb3362_cfb295() throws IOException {
+        //todo maye wrong but also true
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("fuse_cb3362_cfb295_fabric#fabric-features-service#src#main#java#org#fusesource#fabric#features#FabricFeaturesServiceImpl.java");
+        Assert.assertEquals(hierarchicalActionSets.size(),2);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"UPD EnhancedForStatement@@for (Repository repository : repositories) {  for (  Feature feature : repository.getFeatures()) {    if (!allfeatures.contains(feature)) {      allfeatures.add(feature);    }  }} @TO@ for (Repository repository : repositories) {  try {    for (    Feature feature : repository.getFeatures()) {      if (!allfeatures.contains(feature)) {        allfeatures.add(feature);      }    }  } catch (  Exception ex) {    LOGGER.debug(\"Could not load features from %s.\",repository.getURI());  }} @AT@ 8535 @LENGTH@ 273\n" +
+                "---INS TryStatement@@try {  for (  Feature feature : repository.getFeatures()) {    if (!allfeatures.contains(feature)) {      allfeatures.add(feature);    }  }} catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repository.getURI());} @TO@ EnhancedForStatement@@for (Repository repository : repositories) {  for (  Feature feature : repository.getFeatures()) {    if (!allfeatures.contains(feature)) {      allfeatures.add(feature);    }  }} @AT@ 8596 @LENGTH@ 390\n" +
+                "------MOV EnhancedForStatement@@for (Feature feature : repository.getFeatures()) {  if (!allfeatures.contains(feature)) {    allfeatures.add(feature);  }} @TO@ TryStatement@@try {  for (  Feature feature : repository.getFeatures()) {    if (!allfeatures.contains(feature)) {      allfeatures.add(feature);    }  }} catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repository.getURI());} @AT@ 8596 @LENGTH@ 198\n" +
+                "------INS CatchClause@@catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repository.getURI());} @TO@ TryStatement@@try {  for (  Feature feature : repository.getFeatures()) {    if (!allfeatures.contains(feature)) {      allfeatures.add(feature);    }  }} catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repository.getURI());} @AT@ 8855 @LENGTH@ 131\n" +
+                "---------INS SingleVariableDeclaration@@Exception ex @TO@ CatchClause@@catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repository.getURI());} @AT@ 8862 @LENGTH@ 12\n" +
+                "------------INS SimpleType@@Exception @TO@ SingleVariableDeclaration@@Exception ex @AT@ 8862 @LENGTH@ 9\n" +
+                "------------INS SimpleName@@ex @TO@ SingleVariableDeclaration@@Exception ex @AT@ 8872 @LENGTH@ 2\n" +
+                "---------INS ExpressionStatement@@MethodInvocation:LOGGER.debug(\"Could not load features from %s.\",repository.getURI()) @TO@ CatchClause@@catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repository.getURI());} @AT@ 8898 @LENGTH@ 70\n" +
+                "------------INS MethodInvocation@@LOGGER.debug(\"Could not load features from %s.\",repository.getURI()) @TO@ ExpressionStatement@@MethodInvocation:LOGGER.debug(\"Could not load features from %s.\",repository.getURI()) @AT@ 8898 @LENGTH@ 69\n" +
+                "---------------INS SimpleName@@Name:LOGGER @TO@ MethodInvocation@@LOGGER.debug(\"Could not load features from %s.\",repository.getURI()) @AT@ 8898 @LENGTH@ 6\n" +
+                "---------------INS SimpleName@@MethodName:debug:[\"Could not load features from %s.\", repository.getURI()] @TO@ MethodInvocation@@LOGGER.debug(\"Could not load features from %s.\",repository.getURI()) @AT@ 8905 @LENGTH@ 62\n" +
+                "------------------INS StringLiteral@@\"Could not load features from %s.\" @TO@ SimpleName@@MethodName:debug:[\"Could not load features from %s.\", repository.getURI()] @AT@ 8911 @LENGTH@ 34\n" +
+                "------------------INS MethodInvocation@@repository.getURI() @TO@ SimpleName@@MethodName:debug:[\"Could not load features from %s.\", repository.getURI()] @AT@ 8947 @LENGTH@ 19\n" +
+                "---------------------INS SimpleName@@Name:repository @TO@ MethodInvocation@@repository.getURI() @AT@ 8947 @LENGTH@ 10\n" +
+                "---------------------INS SimpleName@@MethodName:getURI:[] @TO@ MethodInvocation@@repository.getURI() @AT@ 8958 @LENGTH@ 8\n");
+        Assert.assertEquals(hierarchicalActionSets.get(1).toString(),"UPD EnhancedForStatement@@for (Repository repo : repositories) {  for (  Feature f : repo.getFeatures()) {    if (features.get(f.getName()) == null) {      Map<String,Feature> versionMap=new TreeMap<String,Feature>();      versionMap.put(f.getVersion(),f);      features.put(f.getName(),versionMap);    } else {      features.get(f.getName()).put(f.getVersion(),f);    }  }} @TO@ for (Repository repo : repositories) {  try {    for (    Feature f : repo.getFeatures()) {      if (features.get(f.getName()) == null) {        Map<String,Feature> versionMap=new TreeMap<String,Feature>();        versionMap.put(f.getVersion(),f);        features.put(f.getName(),versionMap);      } else {        features.get(f.getName()).put(f.getVersion(),f);      }    }  } catch (  Exception ex) {    LOGGER.debug(\"Could not load features from %s.\",repo.getURI());  }} @AT@ 11093 @LENGTH@ 483\n" +
+                "---INS TryStatement@@try {  for (  Feature f : repo.getFeatures()) {    if (features.get(f.getName()) == null) {      Map<String,Feature> versionMap=new TreeMap<String,Feature>();      versionMap.put(f.getVersion(),f);      features.put(f.getName(),versionMap);    } else {      features.get(f.getName()).put(f.getVersion(),f);    }  }} catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repo.getURI());} @TO@ EnhancedForStatement@@for (Repository repo : repositories) {  for (  Feature f : repo.getFeatures()) {    if (features.get(f.getName()) == null) {      Map<String,Feature> versionMap=new TreeMap<String,Feature>();      versionMap.put(f.getVersion(),f);      features.put(f.getName(),versionMap);    } else {      features.get(f.getName()).put(f.getVersion(),f);    }  }} @AT@ 11336 @LENGTH@ 608\n" +
+                "------MOV EnhancedForStatement@@for (Feature f : repo.getFeatures()) {  if (features.get(f.getName()) == null) {    Map<String,Feature> versionMap=new TreeMap<String,Feature>();    versionMap.put(f.getVersion(),f);    features.put(f.getName(),versionMap);  } else {    features.get(f.getName()).put(f.getVersion(),f);  }} @TO@ TryStatement@@try {  for (  Feature f : repo.getFeatures()) {    if (features.get(f.getName()) == null) {      Map<String,Feature> versionMap=new TreeMap<String,Feature>();      versionMap.put(f.getVersion(),f);      features.put(f.getName(),versionMap);    } else {      features.get(f.getName()).put(f.getVersion(),f);    }  }} catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repo.getURI());} @AT@ 11144 @LENGTH@ 422\n" +
+                "------INS CatchClause@@catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repo.getURI());} @TO@ TryStatement@@try {  for (  Feature f : repo.getFeatures()) {    if (features.get(f.getName()) == null) {      Map<String,Feature> versionMap=new TreeMap<String,Feature>();      versionMap.put(f.getVersion(),f);      features.put(f.getName(),versionMap);    } else {      features.get(f.getName()).put(f.getVersion(),f);    }  }} catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repo.getURI());} @AT@ 11827 @LENGTH@ 117\n" +
+                "---------INS SingleVariableDeclaration@@Exception ex @TO@ CatchClause@@catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repo.getURI());} @AT@ 11834 @LENGTH@ 12\n" +
+                "------------INS SimpleType@@Exception @TO@ SingleVariableDeclaration@@Exception ex @AT@ 11834 @LENGTH@ 9\n" +
+                "------------INS SimpleName@@ex @TO@ SingleVariableDeclaration@@Exception ex @AT@ 11844 @LENGTH@ 2\n" +
+                "---------INS ExpressionStatement@@MethodInvocation:LOGGER.debug(\"Could not load features from %s.\",repo.getURI()) @TO@ CatchClause@@catch (Exception ex) {  LOGGER.debug(\"Could not load features from %s.\",repo.getURI());} @AT@ 11866 @LENGTH@ 64\n" +
+                "------------INS MethodInvocation@@LOGGER.debug(\"Could not load features from %s.\",repo.getURI()) @TO@ ExpressionStatement@@MethodInvocation:LOGGER.debug(\"Could not load features from %s.\",repo.getURI()) @AT@ 11866 @LENGTH@ 63\n" +
+                "---------------INS SimpleName@@Name:LOGGER @TO@ MethodInvocation@@LOGGER.debug(\"Could not load features from %s.\",repo.getURI()) @AT@ 11866 @LENGTH@ 6\n" +
+                "---------------INS SimpleName@@MethodName:debug:[\"Could not load features from %s.\", repo.getURI()] @TO@ MethodInvocation@@LOGGER.debug(\"Could not load features from %s.\",repo.getURI()) @AT@ 11873 @LENGTH@ 56\n" +
+                "------------------INS StringLiteral@@\"Could not load features from %s.\" @TO@ SimpleName@@MethodName:debug:[\"Could not load features from %s.\", repo.getURI()] @AT@ 11879 @LENGTH@ 34\n" +
+                "------------------INS MethodInvocation@@repo.getURI() @TO@ SimpleName@@MethodName:debug:[\"Could not load features from %s.\", repo.getURI()] @AT@ 11915 @LENGTH@ 13\n" +
+                "---------------------INS SimpleName@@Name:repo @TO@ MethodInvocation@@repo.getURI() @AT@ 11915 @LENGTH@ 4\n" +
+                "---------------------INS SimpleName@@MethodName:getURI:[] @TO@ MethodInvocation@@repo.getURI() @AT@ 11920 @LENGTH@ 8\n");
+    }
+
+    @Ignore
+    @Test
+    public void test_() throws IOException {
+
+        List<HierarchicalActionSet> hierarchicalActionSets = getHierarchicalActionSets4java("");
+        Assert.assertEquals(hierarchicalActionSets.size(),1);
+        Assert.assertEquals(hierarchicalActionSets.get(0).toString(),"");
+    }
+}

src/main/resources/config.yml

@@ -19,10 +19,10 @@ fixminer:
     portDumps : 6399
     numOfWorkers : 14
     hostname : localhost
-    hunkLimit : 10
+    hunkLimit : 2
     patchSize : 50
 
-    projectList : spring-shell,fuse,metadata
+    projectList : spring-shell,fuse,metadata,commons-codec,commons-collections,commons-compress,commons-configuration,commons-crypto,commons-csv
     inputPath : /Users/anilkoyuncu/projects/test/fixminer-data/patches
     redisPath : /Users/anilkoyuncu/projects/release/test/fixminer_source/python/data/redis
     srcMLPath :  /usr/local/bin/srcml