clean up

.gitignore

@@ -1,5 +1,5 @@
-target
 .idea
+.DS_Store
 /output_diversify/
 /output_sosie/
 /result/

grid5000.sh

@@ -4,4 +4,4 @@ git pull
 mvn clean package
 java -jar target/Diversify-statements-1.0-SNAPSHOT-jar-with-dependencies.jar git repo
 
-sh runFromGit.sh 100 &
+sh script/runFromGit.sh 100 &

src/main/java/fr/inria/diversify/sosie/Logger/LogWriter.java

@@ -109,6 +109,35 @@ public static void writeError(int id,Thread thread, String className, String met
         }
     }
 
+    public static void writeException(int id,Thread thread, String className, String methodSignature, Object exception) {
+        FileWriter fileWriter = null;
+        try {
+            fileWriter = init(thread);
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+        try {
+            fileWriter.append("$$$\n");
+            fileWriter.append("ST");
+            fileWriter.append(separator);
+            fileWriter.append(id+"");
+            fileWriter.append(separator);
+            fileWriter.append(className);
+            fileWriter.append(separator);
+            fileWriter.append(methodSignature);
+
+            fileWriter.append(separator);
+            if(exception != null)
+                fileWriter.append(exception.toString());
+            else
+                fileWriter.append("NullException");
+
+        }
+        catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
     public static void close() {
         for (FileWriter flw : fileWriters.values())
             try {

src/main/java/fr/inria/diversify/sosie/Logger/processor/ConditionalLoggingInstrumenter.java

@@ -29,7 +29,7 @@ public boolean isToBeProcessed(CtStatement candidate) {
         return
                 CtIf.class.isAssignableFrom(candidate.getClass())
                         || CtLoop.class.isAssignableFrom(candidate.getClass())
-                        || CtTry.class.isAssignableFrom(candidate.getClass())
+                        || CtThrow.class.isAssignableFrom(candidate.getClass())
                 ;
     }
 
@@ -49,8 +49,8 @@ public boolean hasStaticParent(CtElement el) {
 
     public void process(CtStatement statement) {
         count++;
-        if (CtTry.class.isAssignableFrom(statement.getClass())) {
-            instruCatch((CtTry) statement);
+        if (CtThrow.class.isAssignableFrom(statement.getClass())) {
+            instruThrow((CtThrow) statement);
         } else {
             instruLoopOrIf(statement);
         }
@@ -105,9 +105,23 @@ private void instruLoopOrIf(CtStatement statement) {
         }
     }
 
+    private void instruThrow(CtThrow throwStmt) {
+        String snippet = "{\nfr.inria.diversify.sosie.logger.LogWriter.writeException(" + count + ",Thread.currentThread(),\"" +
+                getClass(throwStmt).getQualifiedName() + "\",\"" + getMethod(throwStmt).getSignature() + "\"," +
+                throwStmt.getThrownExpression() + ");\n";
+        SourcePosition sp = throwStmt.getPosition();
+        CompilationUnit compileUnit = sp.getCompilationUnit();
+        int index = compileUnit.beginOfLineIndex(sp.getSourceStart());
+        compileUnit.addSourceCodeFragment(new SourceCodeFragment(index, snippet, 0));
+
+        snippet = "\n}\n";
+
+        index = compileUnit.nextLineIndex(sp.getSourceEnd());
+        compileUnit.addSourceCodeFragment(new SourceCodeFragment(index, snippet, 0));
+    }
+
+
     private void instruCatch(CtTry tryStmt) {
-        Log.info("instruCath");
-        Log.info(tryStmt.toString());
         List<CtCatch> catchList = tryStmt.getCatchers();
         for (CtCatch catchStmt : catchList) {
             if(getMethod(tryStmt) != null) {

src/main/java/fr/inria/diversify/sosie/Logger/processor/TestLoggingInstrumenter.java

@@ -0,0 +1,20 @@
+package fr.inria.diversify.sosie.logger.processor;
+
+import spoon.processing.AbstractProcessor;
+import spoon.reflect.declaration.CtMethod;
+
+/**
+ * User: Simon
+ * Date: 10/21/13
+ * Time: 9:27 AM
+ */
+public class TestLoggingInstrumenter extends AbstractProcessor<CtMethod> {
+
+
+    @Override
+    public void process(CtMethod element) {
+
+        element.getAnnotation();
+        //To change body of implemented methods use File | Settings | File Templates.
+    }
+}

src/main/java/fr/inria/diversify/sosie/compare/CompareLogMain.java

@@ -58,7 +58,11 @@ protected void same() throws IOException {
 
     protected void diff() throws Exception {
         String startPointString = DiversifyProperties.getProperty("startPoint");
+        int count = 0;
+        int i =0;
         for(File f : (new File(dirSosie).listFiles())) {
+            i++;
+            Log.info("i {}",i);
             try {
 //            Log.info("log files {}",f);
             File startPoint = new File(f.getAbsolutePath()+"/"+startPointString);
@@ -75,14 +79,19 @@ protected void diff() throws Exception {
                 Log.info(f.getName());
                 Log.info(diff.report());
                 diff.toDot(f.getName()+".dot");
+                if(!diff.sameVar()) {
+                    count++;
+                Log.info("i: "+count);
+                }
             }
-                else
+            else
                 Log.info("same trace");
             } catch (Exception e) {
                 Log.error("error",e);
                 e.printStackTrace();
             }
 
+
         }
     }
 

src/main/java/fr/inria/diversify/sosie/compare/CompareSingleLogSequence.java

@@ -64,6 +64,8 @@ protected int[][] findDivergence(int syncroRange, int startOriginal, int startSo
      */
     protected int[][] findDivergence(int syncroRange, int start1, int start2, PointSequence ps1, PointSequence ps2) {
         int bound = Math.min(ps1.size(), ps2.size());
+        if(bound == 0)
+            return null;
         int[][] divergence = new int[bound][2];
         int i = 0;
         divergence[i][0] = start1;

src/main/java/fr/inria/diversify/sosie/compare/Diff.java

@@ -65,6 +65,15 @@ public boolean sameTraceAndVar() {
         return true;
     }
 
+    public boolean sameVar() {
+
+        for (Set<VariableDiff> vars : diffVar.values())
+            if (!vars.isEmpty())
+                return false;
+
+        return true;
+    }
+
     public boolean hasMatch(PointSequence original) {
         return match.containsKey(original);
     }
@@ -84,7 +93,6 @@ public String report() {
             }
 
         return report;
-
     }
 
     protected int findDiversificationIndex(PointSequence sequence) {
@@ -98,78 +106,74 @@ public void toDot(String fileName) throws IOException {
         FileWriter fw = new FileWriter(fileName);
         BufferedWriter bw = new BufferedWriter(fw);
 
+
         bw.write("digraph G {\n");
         for (PointSequence ps : match.keySet())
-            toDot(bw, ps);
+            bw.write(toDot(ps));
 
         bw.write("}");
         bw.close();
     }
 
 
-    protected void toDot(BufferedWriter writer, PointSequence original) throws IOException {
+    protected String toDot( PointSequence original) throws IOException {
         if(match.get(original) == null)
-            return;
+            return "";
 
+        StringBuilder builder = new StringBuilder();
         PointSequence sosie = match.get(original);
         int[][] div = divergence.get(original);
-        int y = 1;
-        Point precedent = original.get(0);
-        writer.write(original.toDot() +"\n");
-        writer.write(original.hashCode() + " -> " +precedent.hashCode()+"\n");
-        writer.write(precedent.toDot(1, y,getVariableDiffFor(original, 0))+"\n");
-
         int i = 0;
         int start1 = 0;
         int start2 = 0;
+        boolean toString = false;
+
+        Point precedent = original.get(0);
+        builder.append(original.toDot() + "\n");
+        builder.append(original.hashCode() + " -> " + precedent.hashCode() + "\n");
+        builder.append(precedent.toDot(getVariableDiffFor(original, 0)) + "\n");
 
         while(i < div.length) {
             Point next = original.get(start1);
+            Set<VariableDiff> varD = getVariableDiffFor(original, div[i][0]);
+            if(!varD.isEmpty())
+                toString = true;
+
             if(start1 == div[i][0] && start2 == div[i][1]) {
-                writer.write(precedent.hashCode() + " -> " + next.hashCode()+"\n");
+                builder.append(precedent.hashCode() + " -> " + next.hashCode()+"\n");
                 precedent = next;
-                writer.write(precedent.toDot(1,y,getVariableDiffFor(original, div[i][0]))+"\n");
+                builder.append(precedent.toDot(varD)+"\n");
                 start1++;
                 start2++;
                 i++;
             }
             else {
-                writeDotBranch(writer,precedent, original.get(div[i][0]),start1,div[i][0], original);
-                writeDotBranch(writer,precedent, original.get(div[i][0]),start2,div[i][1], sosie);
-//                Point branchNext = precedent;
-//                int j = start1;
-//                for(; j < div[i][0]; j++) {
-//                    writer.write(branchNext.hashCode() + " -> " + original.get(j).hashCode()+"\n");
-//                    branchNext = original.get(j);
-//                    writer.write(branchNext.toDot(1, y, new HashSet<VariableDiff>()));
-//                }
-//                writer.write(branchNext.hashCode() + " -> " + original.get(div[i][0]).hashCode()+"\n");
-//                branchNext = precedent;
-//                j = start2;
-//                for(; j < div[i][1]; j++) {
-//                    writer.write(branchNext.hashCode() + " -> " + sosie.get(j).hashCode()+"\n");
-//                    branchNext = sosie.get(j);
-//                    writer.write(branchNext.toDot(1,y,new HashSet<VariableDiff>()));
-//                }
-//                writer.write(branchNext.hashCode() + " -> " + original.get(div[i][0]).hashCode()+"\n");
-                precedent = original.get(div[i][0]);
-                writer.write(precedent.toDot(0,10,getVariableDiffFor(original, div[i][0])));
+                toString = true;
+                Point endBranch = original.get(div[i][0]);
+                writeDotBranch(builder,precedent, endBranch,start1,div[i][0], original);
+                writeDotBranch(builder,precedent, endBranch,start2,div[i][1], sosie);
+                precedent = endBranch;
+                builder.append(precedent.toDot(varD));
                 i++;
                 start1 = div[i][0];
                 start2 = div[i][1];
             }
         }
+        if(toString)
+            return builder.toString();
+        return "";
     }
 
-    protected void writeDotBranch(BufferedWriter writer, Point branchNext, Point endBranch, int i, int borne,  PointSequence ps) throws IOException {
+    protected void writeDotBranch(StringBuilder builder, Point branchNext, Point endBranch, int i, int borne,  PointSequence ps) throws IOException {
         for(; i < borne; i++) {
-            writer.write(branchNext.hashCode() + " -> " + ps.get(i).hashCode()+"\n");
+            builder.append(branchNext.hashCode() + " -> " + ps.get(i).hashCode() + "\n");
             branchNext = ps.get(i);
-            writer.write(branchNext.toDot(1, 0, new HashSet<VariableDiff>()));
+            builder.append(branchNext.toDot(new HashSet<VariableDiff>()));
         }
-        writer.write(branchNext.hashCode() + " -> " + endBranch.hashCode()+"\n");
+        builder.append(branchNext.hashCode() + " -> " + endBranch.hashCode() + "\n");
     }
 
+
     protected Set<VariableDiff> getVariableDiffFor(PointSequence ps, int index) {
         Set<VariableDiff> set = new HashSet<VariableDiff>();
         for (VariableDiff varD : diffVar.get(ps)) {
@@ -178,4 +182,4 @@ protected Set<VariableDiff> getVariableDiffFor(PointSequence ps, int index) {
         }
         return set;
     }
-}
+}

src/main/java/fr/inria/diversify/sosie/pointSequence/CatchPoint.java

@@ -37,8 +37,8 @@ protected void buildFrom(String string) {
     }
 
     @Override
-    public String toDot(int x, int y, Set<VariableDiff> varDiff) {
-        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    public String toDot(Set<VariableDiff> varDiff) {
+        return null;
     }
 
     public boolean sameValue(Point sPoint) {

src/main/java/fr/inria/diversify/sosie/pointSequence/ConditionalPoint.java

@@ -50,7 +50,7 @@ protected void buildFrom(String string) {
     }
 
     @Override
-    public String toDot(int x, int y,Set<VariableDiff> varsDiff) {
+    public String toDot(Set<VariableDiff> varsDiff) {
         String dot = hashCode() + "     ";
         dot += "[\n label =";
         if(varsDiff.isEmpty())
@@ -62,7 +62,7 @@ public String toDot(int x, int y,Set<VariableDiff> varsDiff) {
                 dot += "\\n"+vf.toDot();
             dot += "\"\n,color=\"red\",";
         }
-        dot += "\npos=\"" + x + "," + y + "!\"\n];";
+        dot += "\n];";
         return dot;
     }
 

src/main/java/fr/inria/diversify/sosie/pointSequence/Point.java

@@ -55,6 +55,6 @@ public int getId() {
         return id;
     }
 
-    public abstract String toDot(int x, int y, Set<VariableDiff> varDiff);
+    public abstract String toDot(Set<VariableDiff> varDiff);
 }
 

src/main/java/fr/inria/diversify/sosie/pointSequence/PointSequence.java

@@ -46,10 +46,8 @@ public void parseFile(File file) throws IOException {
         addPoint(tmp);
     }
 
-
-
     protected void addPoint(String stringPoint) {
-        if(stringPoint.startsWith("ST"))
+        if(stringPoint.startsWith("----------------------------------ST"))
             cacthPoints.add(new CatchPoint(stringPoint));
         else
             conditionalPoints.add(new ConditionalPoint(stringPoint));

src/main/java/fr/inria/diversify/transformation/RunMaven.java

@@ -66,7 +66,6 @@ public void run() {
         invoker.setOutputHandler(psh);
         invoker.setErrorHandler(psh);
         try {
-            Log.debug("invoke maven");
             invoker.execute(request);
             if(clojureTest)
                 parseClojureResult(os.toString());

src/main/java/fr/inria/diversify/transformation/TransformationParser.java

@@ -174,8 +174,6 @@ protected CodeFragment findCodeFragment(JSONObject jsonObject) throws Exception
         }
         if (cf  == null) {
             //TODO exception
-//            System.out.println(jsonObject.get("Position"));
-//            System.out.println(jsonObject.get("SourceCode"));
             throw new Exception();
         }
         return cf;