changes

src/main/java/edu/lu/uni/serval/fixminer/Launcher.java

@@ -22,8 +22,8 @@ public class Launcher {
 
         Properties appProps = new Properties();
 
-//        String appConfigPath = "/Users/anil.koyuncu/projects/test/fixminerC/src/main/resource/app.properties";
+        String appConfigPath = "/Users/anil.koyuncu/projects/fixminer/fixminer_source/src/main/resource/app.properties";
-        String appConfigPath = args[0];
+//        String appConfigPath = args[0];
         appProps.load(new FileInputStream(appConfigPath));
 
         String portInner = appProps.getProperty("portInner","6380");
@@ -38,12 +38,12 @@ public class Launcher {
         String redisPath = appProps.getProperty("redisPath","FORKJOIN");
         String srcMLPath = appProps.getProperty("srcMLPath","FORKJOIN");
 
-        String parameter = args[2];
+//        String parameter = args[2];
-//        String parameter = null;
+        String parameter = null;
-//        String parameter = "decl";
+//        String parameter = "if";
-//        String parameter = "L2";
+//        String parameter = "L1";
-        String jobType = args[1];
+//        String jobType = args[1];
-//        String jobType = "RICHEDITSCRIPT";
+        String jobType = "RICHEDITSCRIPT";
 //        String jobType = "LOAD";
 //        String jobType = "COMPARE";
 
@@ -89,7 +89,8 @@ public class Launcher {
                     String compareDBName;
                     switch (parameter){
                         case "L1":
-                            job = "shape";
+//                            job = "shape";
+                            job = "single";
                             compareDBName = "clusterl0-gumInputALL.rdb";
                             break;
                         case "L2":

src/main/java/edu/lu/uni/serval/fixminer/akka/compare/CompareTrees.java

@@ -42,7 +42,7 @@ public class CompareTrees {
 //        log.info(cmdInner);
 //        cs.runShell(cmdInner, portInner);
 
-        String numOfWorkers = "100000000";//args[4];
+//        String numOfWorkers = "100000000";//args[4];
         String host = "localhost";//args[5];
 //  -Djava.util.concurrent.ForkJoinPool.common.parallelism=256
 
@@ -63,7 +63,11 @@ public class CompareTrees {
         listOfPairs.stream().parallel().forEach(m->coreCompare(m, job,null, samePairs,errorPairs,filenames,outerPool));
 
         try (Jedis jedis = outerPool.getResource()) {
-
+            jedis.select(2);
+            for (String samePair : samePairs) {
+//                jedis.hset("compare", errorPair, "1");
+                jedis.set(samePair, "1");
+            }
             jedis.select(0);
 //            jedis.flushDB();
             jedis.del("compare");
@@ -108,6 +112,32 @@ public class CompareTrees {
 //                    jedis.srem("pairs",matchKey);
 //                JedisPool outerPool = null;
                 switch (treeType) {
+                    case "single":
+                        oldPair = EDiffHelper.getActions(keyName, i, outerPool, filenames);
+                        newPair = EDiffHelper.getActions(keyName, j, outerPool, filenames);
+                        ITree oldActionTree = oldPair.getValue0();
+                        ITree newActionTree = newPair.getValue0();
+                        HierarchicalActionSet oldProject = oldPair.getValue1();
+                        HierarchicalActionSet newProject = newPair.getValue1();
+
+
+                        ITree oldShapeTree = EDiffHelper.getShapeTree(oldProject);
+                        ITree newShapeTree = EDiffHelper.getShapeTree(newProject);
+
+                        ITree oldTargetTree = EDiffHelper.getTargets(oldProject);
+                        ITree newTargetTree = EDiffHelper.getTargets(newProject);
+
+                        if(oldShapeTree.toStaticHashString().equals(newShapeTree.toStaticHashString())){
+                            if(oldActionTree.toStaticHashString().equals(newActionTree.toStaticHashString())){
+                                if(oldTargetTree.toStaticHashString().equals(newTargetTree.toStaticHashString())){
+                                    samePairs.add(matchKey);
+                                }
+                            }
+                        }
+                        return;
+//                        break;
+
+
                     case "shape":
                         oldTree = EDiffHelper.getShapes(keyName, i,  outerPool,filenames);
                         newTree = EDiffHelper.getShapes(keyName, j,  outerPool,filenames);
@@ -145,12 +175,12 @@ public class CompareTrees {
                             String result = i + "," + j + "," + String.join(",", oldTokens);
 //                            jedis.select(2);
 //                            jedis.set(matchKey, result);
-                            try (Jedis jedis = innerPool.getResource()) {
+//                            try (Jedis jedis = innerPool.getResource()) {
-//                            jedis.del(matchKey);
+////                            jedis.del(matchKey);
-                                jedis.select(2);
+//                                jedis.select(2);
-                                jedis.set(matchKey, result);
+//                                jedis.set(matchKey, result);
-                            }
+//                            }
-//                            samePairs.add(matchKey);
+                            samePairs.add(matchKey);
 //                            try (Jedis jedis = innerPool.getResource()) {
 ////                                jedis.del(matchKey);
 //                                jedis.select(2);
@@ -180,18 +210,22 @@ public class CompareTrees {
                             oldTree = EDiffHelper.getTargets(oldProject);
                             newTree = EDiffHelper.getTargets(newProject);
                             if (oldTree.toStaticHashString().equals(newTree.toStaticHashString())) {
-                                try (Jedis jedis = innerPool.getResource()) {
+                                samePairs.add(matchKey);
-//                                    jedis.del(matchKey);
+//                                try (Jedis jedis = innerPool.getResource()) {
-                                    jedis.select(2);
+////                                    jedis.del(matchKey);
-                                    jedis.set(matchKey, result);
+//                                    jedis.select(2);
-                                }
+//                                    jedis.set(matchKey, result);
+//
+//                                }
                             }
                         } else {
-                            try (Jedis jedis = innerPool.getResource()) {
+                            samePairs.add(matchKey);
-//                            jedis.del(matchKey);
+//                            try (Jedis jedis = innerPool.getResource()) {
-                                jedis.select(2);
+////                            jedis.del(matchKey);
-                                jedis.set(matchKey, result);
+//                                jedis.select(2);
-                            }
+//                                jedis.set(matchKey, result);
+//
+//                            }
                         }
                     }
 

src/main/java/edu/lu/uni/serval/fixminer/akka/ediff/DefaultKryoContext.java

@@ -3,10 +3,7 @@ package edu.lu.uni.serval.fixminer.akka.ediff;
 import java.io.ByteArrayOutputStream;
 
 import com.esotericsoftware.kryo.Kryo;
-import com.esotericsoftware.kryo.io.Input;
+import com.esotericsoftware.kryo.io.*;
-import com.esotericsoftware.kryo.io.Output;
-import com.esotericsoftware.kryo.io.UnsafeInput;
-import com.esotericsoftware.kryo.io.UnsafeOutput;
 import com.esotericsoftware.kryo.pool.KryoFactory;
 import com.esotericsoftware.kryo.pool.KryoPool;
 import org.objenesis.strategy.SerializingInstantiatorStrategy;
@@ -51,7 +48,7 @@ public class DefaultKryoContext implements KryoContext{
     public byte[] serialze(Object obj, int bufferSize)
     {
         ByteArrayOutputStream base = new ByteArrayOutputStream();
-        Output output = new Output(base, bufferSize);
+        UnsafeMemoryOutput output = new UnsafeMemoryOutput(base, bufferSize);
 
         Kryo kryo = pool.borrow();
 
@@ -75,7 +72,7 @@ public class DefaultKryoContext implements KryoContext{
 
         Kryo kryo = pool.borrow();
 
-        Input input = new Input(serialized);
+        UnsafeMemoryInput input = new UnsafeMemoryInput(serialized);
         obj = kryo.readObject(input, clazz);
 
         pool.release(kryo);

src/main/java/edu/lu/uni/serval/fixminer/akka/ediff/EDiffHunkParser.java

@@ -62,6 +62,8 @@ public class EDiffHunkParser extends EDiffParser {
 						f = new File(root+"dumps/"+key);
 
 						FileUtils.writeByteArrayToFile(f,EDiffHelper.kryoSerialize(actionSet));
+//						FileUtils.writeByteArrayToFile(f,EDiffHelper.commonsSerialize(actionSet));
+//						FileUtils.writeByteArrayToFile(f,actionSet.toString().getBytes());
 //						FileOutputStream fos = new FileOutputStream(f);
 //						ObjectOutputStream oos = new ObjectOutputStream(fos);
 //						oos.writeObject(EDiffHelper.kryoSerialize(actionSet));

src/main/java/edu/lu/uni/serval/fixminer/akka/ediff/FileHelper.java

@@ -0,0 +1,383 @@
+package edu.lu.uni.serval.fixminer.akka.ediff;
+import java.io.BufferedInputStream;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class FileHelper {
+
+    /**
+     * @param filePath
+     */
+    public static void createDirectory(String filePath) {
+        File file = new File(filePath);
+        if (file.exists()) {
+            deleteDirectory(filePath);
+        }
+        file.mkdirs();
+    }
+
+    public static void createFile(File file, String content) {
+        FileWriter writer = null;
+        BufferedWriter bw = null;
+
+        try {
+            if (!file.getParentFile().exists()) {
+                file.getParentFile().mkdirs();
+            }
+            if (!file.exists()) file.createNewFile();
+            writer = new FileWriter(file);
+            bw = new BufferedWriter(writer);
+            bw.write(content);
+            bw.flush();
+        } catch (IOException e) {
+            e.printStackTrace();
+        } finally {
+            close(bw);
+            close(writer);
+        }
+    }
+
+    public static void deleteDirectory(String dir) {
+        File file = new File(dir);
+
+        if (file.exists()) {
+            if (file.isDirectory()) {
+                File[] files = file.listFiles();
+                if (files.length > 0) {
+                    for (File f : files) {
+                        if (f.isFile()) {
+                            deleteFile(f.getAbsolutePath());
+                        } else {
+                            deleteDirectory(f.getAbsolutePath());
+                        }
+                    }
+                }
+                file.delete();
+            } else {
+                deleteFile(dir);
+            }
+        }
+    }
+
+    public static void deleteFiles(String dir) {
+        File file = new File(dir);
+
+        if (file.exists()) {
+            if (file.isDirectory()) {
+                File[] files = file.listFiles();
+                if (files.length > 0) {
+                    for (File f : files) {
+                        if (f.isFile()) {
+                            deleteFile(f.getAbsolutePath());
+                        } else {
+                            deleteFiles(f.getAbsolutePath());
+                        }
+                    }
+                }
+            } else {
+                deleteFile(dir);
+            }
+        }
+    }
+
+    public static void deleteFile(String fileName) {
+        File file = new File(fileName);
+
+        if (file.exists()) {
+            if (file.isFile()) {
+                file.delete();
+            } else {
+                deleteDirectory(fileName);
+            }
+        }
+    }
+
+    public static List<File> getAllDirectories(String filePath) {
+        return listAllDirectories(new File(filePath));
+    }
+
+    /**
+     * List all files in the directory.
+     *
+     * @param filePath
+     * @param type
+     * @return
+     */
+    public static List<File> getAllFiles(String filePath, String type) {
+        return listAllFiles(new File(filePath), type);
+    }
+
+    public static List<File> getAllFilesInCurrentDiectory(String filePath, String type) {
+        return getAllFilesInCurrentDiectory(new File(filePath), type);
+    }
+
+    public static List<File> getAllFilesInCurrentDiectory(File directory, String type) {
+        List<File> fileList = new ArrayList<>();
+
+        if (!directory.exists()) {
+            return null;
+        }
+
+        File[] files = directory.listFiles();
+
+        for (File file : files) {
+            if (file.isFile()) {
+                if (file.toString().endsWith(type)) {
+                    fileList.add(file);
+                }
+            }
+        }
+
+        return fileList;
+    }
+
+    public static String getFileName(String filePath) {
+        File file = new File(filePath);
+
+        if (file.exists()) {
+            return file.getName();
+        } else {
+            return null;
+        }
+    }
+
+    public static String getFileNameWithoutExtension(File file) {
+        if (file.exists()) {
+            String fileName = file.getName();
+            fileName = fileName.substring(0, fileName.lastIndexOf("."));
+            return fileName;
+        } else {
+            return null;
+        }
+    }
+
+    public static String getFileExtension(File file) {
+        String fileName = file.getName();
+        String extension = fileName.substring(fileName.lastIndexOf("."));
+        return extension;
+    }
+
+    public static String getFileParentPath(String filePath) {
+        File file = new File(filePath);
+
+        if (file.exists()) {
+            return file.getParent() + "/";
+        }
+        return "";
+    }
+
+    /**
+     * Check whether a file path is valid or not.
+     *
+     * @param path, file path.
+     * @return true, the file path is valid.
+     * false, the file path is invalid.
+     */
+    public static boolean isValidPath(String path) {
+        File file = new File(path);
+
+        if (file.exists()) {
+            return true;
+        }
+
+        return false;
+    }
+
+    /**
+     * Recursively list all files in file.
+     *
+     * @param file
+     * @return
+     */
+    private static List<File> listAllFiles(File file, String type) {
+        List<File> fileList = new ArrayList<>();
+
+        if (!file.exists()) {
+            return null;
+        }
+
+        File[] files = file.listFiles();
+
+        for (File f : files) {
+            if (f.isFile()) {
+                if (f.toString().endsWith(type)) {
+                    fileList.add(f);
+                }
+            } else {
+                List<File> fl = listAllFiles(f, type);
+                if (fl != null && fl.size() > 0) {
+                    fileList.addAll(fl);
+                }
+            }
+        }
+
+        return fileList;
+    }
+
+    /**
+     * Recursively list all directories in file.
+     *
+     * @param file
+     * @return
+     */
+    private static List<File> listAllDirectories(File file) {
+        List<File> fileList = new ArrayList<>();
+
+        File[] files = file.listFiles();
+
+        for (File f : files) {
+            if (f.isDirectory()) {
+                fileList.add(f);
+                fileList.addAll(listAllDirectories(f));
+            }
+        }
+
+        return fileList;
+    }
+
+    public static void makeDirectory(String fileName) {
+        deleteFile(fileName);
+        File file = new File(fileName).getParentFile();
+        if (!file.exists()) {
+            file.mkdirs();
+        }
+    }
+
+    /**
+     * Read the content of a file.
+     *
+     * @param fileName
+     * @return String, the content of a file.
+     */
+    public static String readFile(String fileName) {
+        return readFile(new File(fileName));
+    }
+
+    /**
+     * Read the content of a file.
+     *
+     * @param file
+     * @return String, the content of a file.
+     */
+    public static String readFile(File file) {
+        byte[] input = null;
+        BufferedInputStream bis = null;
+
+        try {
+
+            bis = new BufferedInputStream(new FileInputStream(file));
+            input = new byte[bis.available()];
+            bis.read(input);
+
+        } catch (FileNotFoundException e) {
+            e.printStackTrace();
+        } catch (IOException e) {
+            e.printStackTrace();
+        } finally {
+            close(bis);
+        }
+
+        String sourceCode = null;
+        if (input != null) {
+            sourceCode = new String(input);
+        }
+
+        return sourceCode;
+    }
+
+    /**
+     * Output output into a file.
+     *
+     * @param fileName, output file name.
+     * @param data,     output data.
+     * @param append,   the output data will be appended previous data in the file or not.
+     */
+    public static void outputToFile(String fileName, StringBuilder data, boolean append) {
+        outputToFile(fileName, data.toString(), append);
+    }
+
+    public static void outputToFile(File file, StringBuilder data, boolean append) {
+        outputToFile(file, data.toString(), append);
+    }
+
+    public static void outputToFile(String fileName, String data, boolean append) {
+        File file = new File(fileName);
+        outputToFile(file, data, append);
+    }
+
+    public static void outputToFile(File file, String data, boolean append) {
+        FileWriter writer = null;
+        BufferedWriter bw = null;
+
+        try {
+            if (!file.getParentFile().exists()) {
+                file.getParentFile().mkdirs();
+            }
+            if (!file.exists()) {
+                file.createNewFile();
+            }
+            writer = new FileWriter(file, append);
+            bw = new BufferedWriter(writer);
+            bw.write(data);
+            bw.flush();
+        } catch (IOException e) {
+            e.printStackTrace();
+        } finally {
+            close(bw);
+            close(writer);
+        }
+    }
+
+    private static void close(FileWriter writer) {
+        try {
+            if (writer != null) {
+                writer.close();
+                writer = null;
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    private static void close(BufferedWriter bw) {
+        try {
+            if (bw != null) {
+                bw.close();
+                bw = null;
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    private static void close(BufferedInputStream bis) {
+        try {
+            if (bis != null) {
+                bis.close();
+                bis = null;
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static List<File> getAllSubDirectories(String fileName) {
+        File file = new File(fileName);
+        List<File> subDirectories = new ArrayList<>();
+        if (file.exists()) {
+            File[] files = file.listFiles();
+            for (File f : files) {
+                if (f.isDirectory()) {
+                    subDirectories.add(f);
+                }
+            }
+        }
+        return subDirectories;
+    }
+}

src/main/java/edu/lu/uni/serval/fixminer/akka/ediff/HunkParserTest.java

@@ -1,9 +1,14 @@
 package edu.lu.uni.serval.fixminer.akka.ediff;
 
+import com.github.gumtreediff.gen.srcml.NodeMap_new;
+import com.github.gumtreediff.tree.ITree;
+import com.github.gumtreediff.tree.TreeContext;
+import edu.lu.uni.serval.fixminer.akka.compare.AkkaTreeParser;
 import edu.lu.uni.serval.fixminer.akka.ediff.EDiffHunkParser;
 import edu.lu.uni.serval.utils.EDiffHelper;
 import edu.lu.uni.serval.utils.PoolBuilder;
 import org.apache.commons.io.FileUtils;
+import org.javatuples.Pair;
 import org.junit.Test;
 import redis.clients.jedis.Jedis;
 import redis.clients.jedis.JedisPool;
@@ -13,6 +18,9 @@ import java.io.IOException;
 import java.lang.instrument.Instrumentation;
 import java.time.Duration;
 import java.time.Instant;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 public class HunkParserTest {
 
@@ -89,18 +97,77 @@ public class HunkParserTest {
         final JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "localhost",Integer.valueOf("6399"),20000000);
 
         EDiffHunkParser parser = new EDiffHunkParser();
-        String root = "/Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/linux/";
+        String root = "/Users/anil.koyuncu/projects/fixminer/gumInputLinux/linux/";
-        String filename = "bb67dd_0922c7_sound#soc#sof#intel#hda.c";
+        String filename = "43f8987_f596c8_drivers#acpi#nfit#core.c";
         File revFile = new File(root + "revFiles/"+ filename);
         File prevFile =new File(root + "prevFiles/prev_"+filename);
         File diffFile = new File(root + "DiffEntries/"+filename+".txt");
         String srcMLPath = "/Users/anil.koyuncu/Downloads/srcML/src2srcml";
         parser.parseFixPatterns(prevFile,revFile,diffFile,"gumInputLinux",outerPool,srcMLPath,"if");
         String key = "if/3/linux_bb67dd_0922c7_sound#soc#sof#intel#hda.c.txt_0";
-        File file2load = new File("/Users/anil.koyuncu/projects/test/fixminer-core/python/data/dumps/"+ key);
+        File file2load = new File("/Users/anil.koyuncu/projects/fixminer/dumps/"+ key);
         byte[] dump = FileUtils.readFileToByteArray(file2load);
 
+//        String line = FileHelper.readFile(file2load);
+//        ITree parent = null;
+//        ITree children = null;
+////        if(line.isEmpty())
+////            continue;
+//        TreeContext tc = new TreeContext();
+//        line = line.replace("\"", "");
+//        String[] split1 = line.split("\n");
+//        int length = split1.length;
+//        List<String> strings = new LinkedList<String>(Arrays.asList(split1));
+//        ITree treeFromString = null;
+//        int prevLev = 0;
+//        int childPosition = 0;
+//        for (String l:strings) {
+//            int level = 0;
+//            Pattern pattern = Pattern.compile("---");
+//            Matcher matcher = pattern.matcher(l);
+//            while (matcher.find())
+//                level++;
+//
+//            l = l.replace("---","");
+//            l = l.trim();
+//
+//            String[] split2;
+//            List<Integer> keysByValue;
+//            split2 = l.split(" ");
+//            keysByValue = NodeMap_new.getKeysByValue(NodeMap_new.map, split2[1]);
+//
+//
+//
+//            if(level == 0){
+//                parent = tc.createTree(keysByValue.get(0), split2[0], null);
+//                tc.setRoot(parent);
+//
+//            }else if (level > prevLev) {
+//                if (children == null) {
+//                    children = tc.createTree(keysByValue.get(0), split2[0], null);
+//                    children.setParentAndUpdateChildren(parent);
+//                } else {
+//
+//                    ITree tree = tc.createTree(keysByValue.get(0), split2[0], null);
+//                    tree.setParentAndUpdateChildren(children);
+//                    children = tree;
+//                }
+//            }else if (level == prevLev){
+//                ITree innerParent = children.getParent();
+//                children = tc.createTree(keysByValue.get(0), split2[0], null);
+//                children.setParentAndUpdateChildren(innerParent);
+//            }else {
+//                ITree innerParent = children.getParent();
+//                children = tc.createTree(keysByValue.get(0), split2[0], null);
+//                children.setParentAndUpdateChildren(innerParent.getParent());
+//            }
+//            prevLev = level;
+//        }
+//        tc.validate();
+//        parent.getLength();
+
         HierarchicalActionSet actionSet = (HierarchicalActionSet)  EDiffHelper.kryoDeseerialize(dump);
+//        HierarchicalActionSet actionSet = (HierarchicalActionSet)  EDiffHelper.commonsDeserialize(dump);
         actionSet.toString();
 
 
@@ -122,5 +189,43 @@ public class HunkParserTest {
 //            }
 //        }
     }
+    @Test
+    public void testCompare(){
+        final JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "localhost",Integer.valueOf("6399"),20000000);
+
+        Pair<ITree, HierarchicalActionSet> oldPair = null;
+        Pair<ITree, HierarchicalActionSet> newPair = null;
+        String matchKey = null;
+        ArrayList<String> samePairs = new ArrayList<>();
+
+        String keyName = "if-3";
+        String i = "2";
+        String j = "21";
+        HashMap<String, String> filenames = AkkaTreeParser.filenames(outerPool);
+
+        oldPair = EDiffHelper.getActions(keyName, i, outerPool, filenames);
+        newPair = EDiffHelper.getActions(keyName, j, outerPool, filenames);
+        ITree oldActionTree = oldPair.getValue0();
+        ITree newActionTree = newPair.getValue0();
+        HierarchicalActionSet oldProject = oldPair.getValue1();
+        HierarchicalActionSet newProject = newPair.getValue1();
+
+        ITree oldShapeTree = EDiffHelper.getShapeTree(oldProject);
+        ITree newShapeTree = EDiffHelper.getShapeTree(newProject);
+
+        ITree oldTargetTree = EDiffHelper.getTargets(oldProject);
+        ITree newTargetTree = EDiffHelper.getTargets(newProject);
+        String oldShape = oldShapeTree.toStaticHashString();
+        String newShape = newShapeTree.toStaticHashString();
+
+        if(oldShape.equals(newShape)){
+            if(oldActionTree.toStaticHashString().equals(newActionTree.toStaticHashString())){
+                if(oldTargetTree.toStaticHashString().equals(newTargetTree.toStaticHashString())){
+                    samePairs.add(matchKey);
+                }
+            }
+        }
+    }
+
 
 }

src/main/java/edu/lu/uni/serval/fixminer/jobs/EnhancedASTDiff.java

@@ -57,7 +57,7 @@ public class EnhancedASTDiff {
 
 			List<MessageFile> msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/"
 
-//			msgFiles = msgFiles.subList(0,10000);
+//			msgFiles = msgFiles.subList(0,1000);
 			if (msgFiles == null)
 				continue;
 			allMessageFiles.addAll(msgFiles);

src/main/java/edu/lu/uni/serval/utils/EDiffHelper.java

@@ -8,6 +8,7 @@ import com.github.gumtreediff.tree.TreeUtils;
 import edu.lu.uni.serval.fixminer.akka.ediff.DefaultKryoContext;
 import edu.lu.uni.serval.fixminer.akka.ediff.HierarchicalActionSet;
 import edu.lu.uni.serval.fixminer.akka.ediff.KryoContext;
+import org.apache.commons.lang3.SerializationUtils;
 import org.javatuples.Pair;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -64,6 +65,14 @@ public class EDiffHelper {
         return baos.toByteArray();
     }
 
+    public static byte[] commonsSerialize(Serializable o){
+        return SerializationUtils.serialize(o);
+    }
+
+    public static Object commonsDeserialize(byte[] data){
+        return SerializationUtils.deserialize(data);
+    }
+
 
     public static byte[] kryoSerialize(Serializable o ){
         KryoContext kryoContext = DefaultKryoContext.newKryoContextFactory();
@@ -279,12 +288,7 @@ public class EDiffHelper {
                 byte[] s = outer.hget("dump".getBytes(), key.getBytes());
                 HierarchicalActionSet actionSet = (HierarchicalActionSet) EDiffHelper.kryoDeseerialize(s);
 
-                ITree parent = null;
+                tree = getShapeTree(actionSet);
-                ITree children = null;
-                TreeContext tc = new TreeContext();
-                tree = EDiffHelper.getASTTree(actionSet, parent, children, tc);
-                //tree.setParent(null);
-                tc.validate();
 
             } catch (Exception e) {
                 e.printStackTrace();
@@ -294,6 +298,17 @@ public class EDiffHelper {
 
     }
 
+    public static ITree getShapeTree(HierarchicalActionSet actionSet) {
+        ITree tree = null;
+        ITree parent = null;
+        ITree children = null;
+        TreeContext tc = new TreeContext();
+        tree = EDiffHelper.getASTTree(actionSet, parent, children, tc);
+        //tree.setParent(null);
+        tc.validate();
+        return tree;
+    }
+
 
     public static ITree getTargets(HierarchicalActionSet actionSet) {
 

src/main/resource/app.properties

@@ -5,10 +5,10 @@ portDumps = 6399
 parallelism = AKKA
 numOfWorkers = 14
 
-inputPath = /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux
+inputPath = /Users/anil.koyuncu/projects/fixminer/gumInputLinux
-redisPath = /Users/anil.koyuncu/projects/test/fixminer-core/python/data/redis
+redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
 srcMLPath=  /Users/anil.koyuncu/Downloads/srcML/src2srcml
-actionType =ALL
+actionType = ALL
 eDiffTimeout = 900
 
 #ENHANCEDASTDIFF,CACHE,LEVEL1,LEVEL2,LEVEL3