replace RMiner with GumTree for block tracking

.gitignore

@@ -28,4 +28,5 @@ hs_err_pid*
 
 # target folder
 target/
-result/
+result/
+tmp/

experiments/tracking-accuracy/block/gumtree/final.csv

@@ -0,0 +1,5 @@
+tool,oracle,level,processing_time_avg,processing_time_median,tp,fp,fn,precision,recall
+gumtree,training,change,23052.319502,14215,3928,498,1139,88.748305,77.521216
+gumtree,training,commit,23052.319502,14215,3871,222,841,94.576106,82.151952
+gumtree,test,change,5839.246835,3873,865,114,161,88.355465,84.307992
+gumtree,test,commit,5839.246835,3873,862,51,89,94.414020,90.641430

experiments/tracking-accuracy/block/gumtree/matcher-usage.csv

@@ -0,0 +1,3 @@
+Oracle,Analyzed Commits,Staged Tree Matching,Default Matching,No Matching,Staged Tree Percentage,Default Percentage,No Matching Percentage
+Training,57172,19,20681,36472,0.033233051,36.17330162,63.79346533
+Test,15152,11,2416,12725,0.072597677,15.94508976,83.98231257

pom.xml

@@ -5,7 +5,7 @@
     <groupId>io.github.jodavimehran</groupId>
     <artifactId>code-tracker</artifactId>
     <packaging>jar</packaging>
-    <version>1.1</version>
+    <version>1.1-SNAPSHOT</version>
     <name>Code Tracker</name>
     <description>A refactoring-aware tool that can generate the commit change history of code elements with a very high accuracy.</description>
     <url>https://github.com/jodavimehran/code-tracker</url>
@@ -36,7 +36,7 @@
         <dependency>
             <groupId>com.github.tsantalis</groupId>
             <artifactId>refactoring-miner</artifactId>
-            <version>2.3.2</version>
+            <version>2.4.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
@@ -119,6 +119,10 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.8.1</version>
+                <configuration>
+                    <source>9</source>
+                    <target>9</target>
+                </configuration>
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>

src/main/java/org/codetracker/BaseTracker.java

@@ -525,7 +525,7 @@ private CommitModel getCommitModel(RevCommit parentCommit1, RevCommit parentComm
 
         Map<String, String> fileContentsBeforeTrimmed = new HashMap<>(fileContentsBefore);
         Map<String, String> fileContentsCurrentTrimmed = new HashMap<>(fileContentsCurrent);
-        List<MoveSourceFolderRefactoring> moveSourceFolderRefactorings = GitHistoryRefactoringMinerImpl.processIdenticalFiles(fileContentsBeforeTrimmed, fileContentsCurrentTrimmed, renamedFilesHint);
+        List<MoveSourceFolderRefactoring> moveSourceFolderRefactorings = GitHistoryRefactoringMinerImpl.processIdenticalFiles(fileContentsBeforeTrimmed, fileContentsCurrentTrimmed, renamedFilesHint, false);
 
         return new CommitModel(repositoryDirectoriesBefore, fileContentsBefore, fileContentsBeforeTrimmed, repositoryDirectoriesCurrent, fileContentsCurrent, fileContentsCurrentTrimmed, renamedFilesHint, moveSourceFolderRefactorings);
     }

src/main/java/org/codetracker/BlockTrackerImpl.java

@@ -576,7 +576,7 @@ private Set<Block> analyseBlockRefactorings(Collection<Refactoring> refactorings
                     break;
                 }
             }
-            if (changeType != null) {
+            if (changeType != null && blockBefore != null) {
                 if (equalOperator.test(blockAfter)) {
                     blockChangeHistory.addChange(blockBefore, blockAfter, ChangeFactory.forBlock(changeType).refactoring(refactoring));
                     leftBlockSet.add(blockBefore);

src/main/java/org/codetracker/ChangeHistory.java

@@ -126,6 +126,8 @@ public Graph<T, Edge> findSubGraph(T start) {
         return GraphImpl.subGraph(changeHistoryGraph, start);
     }
 
+    public Graph<T, Edge> getCompleteGraph() {return GraphImpl.of(changeHistoryGraph);}
+
     public Set<T> predecessors(T codeElement) {
         return changeHistoryGraph.predecessors(codeElement);
     }

src/main/java/org/codetracker/HistoryImpl.java

@@ -154,6 +154,10 @@ public static class HistoryReportImpl implements HistoryReport {
     private int step3 = 0;
     private int step4 = 0;
     private int step5 = 0;
+    private int stagedTreeMatching = 0;
+    private int sameFileUnchanged = 0;
+    private int sameFileChanged = 0;
+
 
     public int getAnalysedCommits() {
       return analysedCommits;
@@ -202,5 +206,29 @@ public void step4PlusPlus() {
     public void step5PlusPlus() {
       step5++;
     }
+
+    public int getStagedTreeMatching() {
+      return stagedTreeMatching;
+    }
+
+    public void stagedTreeMatchingPlusPlus() {
+      stagedTreeMatching++;
+    }
+
+    public int getSameFileUnchanged() {
+      return sameFileUnchanged;
+    }
+
+    public void sameFileUnchangedPlusPlus() {
+      sameFileUnchanged++;
+    }
+
+    public int getSameFileChanged() {
+      return sameFileChanged;
+    }
+
+    public void sameFileChangedPlusPlus() {
+      sameFileChanged++;
+    }
   }
 }

src/main/java/org/codetracker/Main.java

@@ -3,8 +3,11 @@
 import org.codetracker.api.*;
 import org.codetracker.change.Change;
 import org.codetracker.element.Attribute;
+import org.codetracker.element.Block;
 import org.codetracker.element.Method;
 import org.codetracker.element.Variable;
+import org.codetracker.util.CodeElementLocator;
+import gr.uom.java.xmi.LocationInfo;
 import org.eclipse.jgit.lib.Repository;
 import org.refactoringminer.api.GitService;
 import org.refactoringminer.util.GitServiceImpl;
@@ -17,80 +20,25 @@ public class Main {
 
     public static void main(String args[]) throws Exception {
         GitService gitService = new GitServiceImpl();
-        // METHOD TRACKING EXAMPLE
-        try (Repository repository = gitService.cloneIfNotExists(FOLDER_TO_CLONE + "checkstyle\\checkstyle",
-                "https://github.com/checkstyle/checkstyle.git")){
-
-            MethodTracker methodTracker = CodeTracker.methodTracker()
-                    .repository(repository)
-                    .filePath("src/main/java/com/puppycrawl/tools/checkstyle/Checker.java")
-                    .startCommitId("119fd4fb33bef9f5c66fc950396669af842c21a3")
-                    .methodName("fireErrors")
-                    .methodDeclarationLineNumber(384)
-                    .build();
-
-            History<Method> methodHistory = methodTracker.track();
-
-            for (History.HistoryInfo<Method> historyInfo : methodHistory.getHistoryInfoList()) {
-                System.out.println("======================================================");
-                System.out.println("Commit ID: " + historyInfo.getCommitId());
-                System.out.println("Date: " +
-                        LocalDateTime.ofEpochSecond(historyInfo.getCommitTime(), 0, ZoneOffset.UTC));
-                System.out.println("Before: " + historyInfo.getElementBefore().getName());
-                System.out.println("After: " + historyInfo.getElementAfter().getName());
-
-                for (Change change : historyInfo.getChangeList()) {
-                    System.out.println(change.getType().getTitle() + ": " + change);
-                }
-            }
-            System.out.println("======================================================");
-        }
-        // VARIABLE TRACKING EXAMPLE
-        try (Repository repository = gitService.cloneIfNotExists(FOLDER_TO_CLONE + "checkstyle\\checkstyle",
-                "https://github.com/checkstyle/checkstyle.git")){
-
-            VariableTracker variableTracker = CodeTracker.variableTracker()
-                    .repository(repository)
-                    .filePath("src/main/java/com/puppycrawl/tools/checkstyle/Checker.java")
-                    .startCommitId("119fd4fb33bef9f5c66fc950396669af842c21a3")
-                    .methodName("fireErrors")
-                    .methodDeclarationLineNumber(384)
-                    .variableName("stripped")
-                    .variableDeclarationLineNumber(385)
-                    .build();
-
-            History<Variable> variableHistory = variableTracker.track();
-
-            for (History.HistoryInfo<Variable> historyInfo : variableHistory.getHistoryInfoList()) {
-                System.out.println("======================================================");
-                System.out.println("Commit ID: " + historyInfo.getCommitId());
-                System.out.println("Date: " +
-                        LocalDateTime.ofEpochSecond(historyInfo.getCommitTime(), 0, ZoneOffset.UTC));
-                System.out.println("Before: " + historyInfo.getElementBefore().getName());
-                System.out.println("After: " + historyInfo.getElementAfter().getName());
-
-                for (Change change : historyInfo.getChangeList()) {
-                    System.out.println(change.getType().getTitle() + ": " + change);
-                }
-            }
-            System.out.println("======================================================");
-        }
-
-        // ATTRIBUTE TRACKING EXAMPLE
+
+        // BLOCK TRACKING EXAMPLE
         try (Repository repository = gitService.cloneIfNotExists(FOLDER_TO_CLONE + "checkstyle\\checkstyle",
                 "https://github.com/checkstyle/checkstyle.git")) {
 
-            AttributeTracker attributeTracker = CodeTracker.attributeTracker()
+            BlockTrackerGumTree blockTracker = CodeTracker.blockTrackerGumTree()
                     .repository(repository)
-                    .filePath("src/main/java/com/puppycrawl/tools/checkstyle/Checker.java")
+                    .filePath("src/main/java/com/puppycrawl/tools/checkstyle/Main.java")
                     .startCommitId("119fd4fb33bef9f5c66fc950396669af842c21a3")
-                    .attributeName("cacheFile")
-                    .attributeDeclarationLineNumber(132)
+                    .methodName("main")
+                    .methodDeclarationLineNumber(174)
+                    .codeElementType(LocationInfo.CodeElementType.TRY_STATEMENT)
+                    .blockStartLineNumber(188)
+                    .blockEndLineNumber(243)
                     .build();
 
-            History<Attribute> attributeHistory = attributeTracker.track();
+            History<Block> blockHistory = blockTracker.track();
 
-            for (History.HistoryInfo<Attribute> historyInfo : attributeHistory.getHistoryInfoList()) {
+            for (History.HistoryInfo<Block> historyInfo : blockHistory.getHistoryInfoList()) {
                 System.out.println("======================================================");
                 System.out.println("Commit ID: " + historyInfo.getCommitId());
                 System.out.println("Date: " +

src/main/java/org/codetracker/api/BlockTrackerGumTree.java

@@ -0,0 +1,79 @@
+package org.codetracker.api;
+
+import gr.uom.java.xmi.LocationInfo.CodeElementType;
+import org.codetracker.element.Block;
+import org.codetracker.BlockTrackerGumTreeImpl;
+import org.codetracker.util.MethodCache;
+import org.eclipse.jgit.lib.Repository;
+
+public interface BlockTrackerGumTree extends CodeTracker {
+
+    History<Block> track() throws Exception;
+
+    class Builder {
+        private Repository repository;
+        private String startCommitId;
+        private String filePath;
+        private String methodName;
+        private int methodDeclarationLineNumber;
+        private CodeElementType codeElementType;
+        private int blockStartLineNumber;
+        private int blockEndLineNumber;
+        private MethodCache cache;
+
+        public BlockTrackerGumTree.Builder repository(Repository repository) {
+            this.repository = repository;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder startCommitId(String startCommitId) {
+            this.startCommitId = startCommitId;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder filePath(String filePath) {
+            this.filePath = filePath;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder methodName(String methodName) {
+            this.methodName = methodName;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder methodDeclarationLineNumber(int methodDeclarationLineNumber) {
+            this.methodDeclarationLineNumber = methodDeclarationLineNumber;
+            return this;
+        }
+
+        public Builder codeElementType(CodeElementType codeElementType) {
+            this.codeElementType = codeElementType;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder blockStartLineNumber(int blockStartLineNumber) {
+            this.blockStartLineNumber = blockStartLineNumber;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder blockEndLineNumber(int blockEndLineNumber) {
+            this.blockEndLineNumber = blockEndLineNumber;
+            return this;
+        }
+
+        public BlockTrackerGumTree.Builder cache(MethodCache cache) {
+            this.cache = cache;
+            return this;
+        }
+
+        private void checkInput() {
+
+        }
+
+        public BlockTrackerGumTree build() {
+            checkInput();
+            return new BlockTrackerGumTreeImpl(repository, startCommitId, filePath, methodName, methodDeclarationLineNumber,
+                    codeElementType, blockStartLineNumber, blockEndLineNumber, cache);
+        }
+    }
+}

src/main/java/org/codetracker/api/CodeTracker.java

@@ -17,6 +17,10 @@ static BlockTracker.Builder blockTracker() {
         return new BlockTracker.Builder();
     }
 
+    static BlockTrackerGumTree.Builder blockTrackerGumTree() {
+        return new BlockTrackerGumTree.Builder();
+    }
+
     static ClassTracker.Builder classTracker() {
         return new ClassTracker.Builder();
     }

src/main/java/org/codetracker/api/History.java

@@ -24,6 +24,12 @@ interface HistoryReport {
     int getStep4();
 
     int getStep5();
+
+    int getStagedTreeMatching();
+
+    int getSameFileUnchanged();
+
+    int getSameFileChanged();
   }
 
   interface HistoryInfo<C extends CodeElement> extends Comparable<HistoryInfo<C>> {

src/main/java/org/codetracker/experiment/AbstractExperimentStarter.java

@@ -32,7 +32,7 @@
 import static org.codetracker.util.FileUtil.writeToFile;
 
 public abstract class AbstractExperimentStarter {
-    protected final static String FOLDER_TO_CLONE = "tmp/";
+    protected final static String FOLDER_TO_CLONE = "../CodeTracker-API/tmp/";
     protected static final String SUMMARY_RESULT_FILE_NAME_FORMAT = "experiments/tracking-accuracy/%s/%s/summary-%s-%s.csv";
     protected final static String SUMMARY_RESULT_HEADER;
     protected static final String DETAILED_RESULT_HEADER = "file_name, repository,element_key,parent_commit_id,commit_id,commit_time, change_type,element_file_before,element_file_after,element_name_before,element_name_after,result,comment" + System.lineSeparator();
@@ -47,7 +47,7 @@ public abstract class AbstractExperimentStarter {
 
     static {
         StringBuilder header = new StringBuilder();
-        header.append("instance,processing_time,analysed_commits,git_log_command_calls,step2,step3,step4,step5,");
+        header.append("instance,processing_time,analysed_commits,stagedTreeMatching,sameFileChanged,sameFileUnchanged,");
         for (Change.Type changeType : Change.Type.values()) {
             if (Change.Type.NO_CHANGE.equals(changeType) || Change.Type.MULTI_CHANGE.equals(changeType) || Change.Type.REMOVED.equals(changeType))
                 continue;
@@ -282,11 +282,9 @@ protected <H extends AbstractHistoryInfo, E extends CodeElement> void codeTracke
                 content.append("\"").append(historyInfo.getElementKey()).append("\",")
                         .append(refactoringMinerProcessingTime).append(",")
                         .append(historyReport.getAnalysedCommits()).append(",")
-                        .append(historyReport.getGitLogCommandCalls()).append(",")
-                        .append(historyReport.getStep2()).append(",")
-                        .append(historyReport.getStep3()).append(",")
-                        .append(historyReport.getStep4()).append(",")
-                        .append(historyReport.getStep5()).append(",")
+                        .append(historyReport.getStagedTreeMatching()).append(",")
+                        .append(historyReport.getSameFileChanged()).append(",")
+                        .append(historyReport.getSameFileUnchanged()).append(",")
                 ;
 
                 for (Change.Type changeType : Change.Type.values()) {