defects4j worked

src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/AkkaTreeLoader.java

@@ -93,7 +93,7 @@ public class AkkaTreeLoader {
     }
 
 //    public static void main(String[] args) {
-    public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port){
+    public static void main(String portInner,String serverWait,String dbDir,String chunkName,String port, String dumpsName){
 
 //        String inputPath;
 ////        String outputPath;
@@ -134,7 +134,7 @@ public class AkkaTreeLoader {
 //            numOfWorkers = "1";
 //
 //        }
-        String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",portInner,serverWait,chunkName,dbDir);
+        String parameters = String.format("\nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s \ndumpsName %s",portInner,serverWait,chunkName,dbDir,dumpsName);
         log.info(parameters);
 
 //        if (option.equals("CALC")) {
@@ -142,7 +142,7 @@ public class AkkaTreeLoader {
 //            log.info("Calculate pairs done");
 //        }else {
         String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
-        String cmd1 = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port));
+        String cmd1 = String.format(cmd, dbDir,dumpsName,Integer.valueOf(port));
         loadRedis(cmd1,serverWait);
 
         String cmdInner = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";

src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/CalculatePairs.java

@@ -30,7 +30,7 @@ import static edu.lu.uni.serval.FixPatternParser.cluster.TreeLoaderClusterL1.poo
 public class CalculatePairs {
     private static Logger log = LoggerFactory.getLogger(CalculatePairs.class);
 //    public static void main(String[] args) {
-    public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers,String port,String outputPath){
+    public static void main(String serverWait,String dbDir,String chunkName,String port,String outputPath,String pjName){
 
 //        String inputPath;
 //        String port;
@@ -62,12 +62,12 @@ public class CalculatePairs {
 //
 //
 //        }
-        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir);
+        String parameters = String.format("\nport %s \nserverWait %s \nchunkName %s \ndbDir %s",port,serverWait,chunkName,dbDir);
         log.info(parameters);
 
 
         String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
-        cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf(port));
+        cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(port));
         loadRedis(cmd,serverWait);
 
         FileHelper.createDirectory(outputPath);
@@ -99,7 +99,7 @@ public class CalculatePairs {
         String line = null;
         try {
 
-            FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +"textfile.txt", "rw").getChannel();
+            FileChannel rwChannel = new RandomAccessFile(outputPath + "/" +pjName +".txt", "rw").getChannel();
             ByteBuffer wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE);
             int fileCounter = 0;
 
@@ -116,7 +116,7 @@ public class CalculatePairs {
                     }else{
                         log.info("Next pair dump");
                         fileCounter++;
-                        rwChannel = new RandomAccessFile(outputPath+"/" +"textfile"+String.valueOf(fileCounter)+".txt", "rw").getChannel();
+                        rwChannel = new RandomAccessFile(outputPath+"/" +pjName+String.valueOf(fileCounter)+".txt", "rw").getChannel();
                         wrBuf = rwChannel.map(FileChannel.MapMode.READ_WRITE, 0, Integer.MAX_VALUE);
                     }
 

src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/Compare.java

@@ -27,6 +27,8 @@ public class Compare {
 
         Map<String, String> resultMap;
         Jedis jedis = null;
+        ITree oldTree = null;
+        ITree newTree = null;
 
         try {
             jedis = innerPool.getResource();
@@ -40,9 +42,9 @@ public class Compare {
             String firstValue = resultMap.get("0");
             String secondValue = resultMap.get("1");
 
-            ITree oldTree = getSimpliedTree(firstValue,outerPool);
+            oldTree = getSimpliedTree(firstValue,outerPool);
 
-            ITree newTree = getSimpliedTree(secondValue,outerPool);
+            newTree = getSimpliedTree(secondValue,outerPool);
 
             Matcher m = Matchers.getInstance().getMatcher(oldTree, newTree);
             m.match();
@@ -67,7 +69,7 @@ public class Compare {
             if (((Double) chawatheSimilarity1).equals(1.0) || ((Double) diceSimilarity1).equals(1.0)
                     || ((Double) jaccardSimilarity1).equals(1.0) || actions.size() == 0) {
                 String matchKey = "match_" + (String.valueOf(i)) + "_" + String.valueOf(j);
-                log.info(matchKey);
+//                log.info(matchKey);
 
                 jedis.select(1);
                 jedis.set(matchKey, result);
@@ -81,7 +83,8 @@ public class Compare {
 
 
         } catch (Exception e) {
-            log.error(e.toString() + " {}", (name));
+
+            log.error(e.toString() + " {}", name);
 
 
         }finally {

src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/ImportPairs2DB.java

@@ -21,7 +21,7 @@ public class ImportPairs2DB {
     private static Logger log = LoggerFactory.getLogger(ImportPairs2DB.class);
 //    public static void main(String[] args) {
 
-    public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers){
+    public static void main(String csvInputPath,String portInner,String serverWait,String dbDir,String numOfWorkers){
 
 //        String inputPath;
 //        String portInner;
@@ -44,11 +44,11 @@ public class ImportPairs2DB {
 //            dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis";
 //            numOfWorkers = "1";
 //        }
-        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir);
+        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nnumOfWorks %s \ndbDir %s",csvInputPath,portInner,serverWait,numOfWorkers,dbDir);
         log.info(parameters);
 
 
-        File folder = new File(inputPath);
+        File folder = new File(csvInputPath);
         File[] subFolders = folder.listFiles();
         Stream<File> stream = Arrays.stream(subFolders);
         List<File> pjs = stream
@@ -63,7 +63,7 @@ public class ImportPairs2DB {
             log.info(cmd);
             loadRedisWait(cmd);
 
-            cmd = "bash "+dbDir + "redisImportSingle.sh" +" %s %s";
+            cmd = "bash "+dbDir + "/redisImportSingle.sh" +" %s %s";
 
             cmd = String.format(cmd, pj.getPath(), portInt);
             log.info(cmd);

src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/StoreFile.java

@@ -26,7 +26,7 @@ public class StoreFile {
     private static Logger log = LoggerFactory.getLogger(StoreFile.class);
 
 //    public static void main(String[] args) {
-    public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName,String numOfWorkers){
+    public static void main(String inputPath,String portInner,String serverWait,String dbDir,String chunkName){
 //        String inputPath;
 //        String portInner;
 //        String serverWait;
@@ -48,7 +48,7 @@ public class StoreFile {
 //            dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis";
 //            numOfWorkers = "1";
 //        }
-        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,numOfWorkers,dbDir);
+        String parameters = String.format("\nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \ndbDir %s",inputPath,portInner,serverWait,chunkName,dbDir);
         log.info(parameters);
 
         String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
@@ -84,6 +84,11 @@ public class StoreFile {
                 .forEach(m -> storeCore(portInner, m.split(",")[1],m.split(",")[0]));
 
         log.info(parameters);
+
+        String stopServer = "bash "+dbDir + "/" + "stopServer.sh" +" %s";
+        String stopServer2 = String.format(stopServer,Integer.valueOf(portInner));
+        loadRedis(stopServer2,serverWait);
+
     }
 
     public static void storeCore(String portInner,String path,String key){

src/main/java/edu/lu/uni/serval/FixPatternParser/cluster/TreeLoaderClusterL1.java

@@ -38,7 +38,7 @@ public class TreeLoaderClusterL1 {
     private static Logger log = LoggerFactory.getLogger(TreeLoaderClusterL1.class);
 
 //    public static void main(String[] args){
-    public static void main(String portInner,String serverWait,String port,String inputPath){
+    public static void main(String portInner,String serverWait,String port,String inputPath,String level1DB,String level1Path){
 
 //        String inputPath;
 //        String outputPath;
@@ -67,13 +67,13 @@ public class TreeLoaderClusterL1 {
         log.info(parameters);
 
         String cmd = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s";
-        cmd = String.format(cmd, inputPath,"level1.rdb",Integer.valueOf(port));
+        cmd = String.format(cmd, inputPath,level1DB,Integer.valueOf(port));
         loadRedis(cmd,serverWait);
 
         JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
 
 
-        String level1Path = inputPath + "/level1";
+//        String level1Path = inputPath + "/level1";
         File chunks = new File(level1Path);
         File[] listFiles = chunks.listFiles();
         Stream<File> stream = Arrays.stream(listFiles);
@@ -81,8 +81,8 @@ public class TreeLoaderClusterL1 {
                 .filter(x -> x.getName().endsWith(".rdb"))
                 .collect(Collectors.toList());
         for (File db : dbs) {
-            String cmdInner = "bash "+level1Path + "/" + "startServer.sh" +" %s %s %s";
+            String cmdInner = "bash "+inputPath + "/" + "startServer.sh" +" %s %s %s";
-            cmdInner = String.format(cmdInner, level1Path,db.getName(),Integer.valueOf(portInner));
+            cmdInner = String.format(cmdInner, inputPath,db.getName(),Integer.valueOf(portInner));
             loadRedis(cmdInner,serverWait);
             JedisPool innerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
 

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

@@ -20,7 +20,7 @@ public class CommitPatchParser extends Parser{
 	@Override
 	public void parseFixPatterns(File prevFile, File revFile, File diffEntryFile) {
 	}
-	
+
 	protected DiffEntryHunk matchHunk(int startLine, int endLine, int startLine2, int endLine2, String actionStr, List<DiffEntryHunk> hunks) {
 		for (DiffEntryHunk hunk : hunks) {
 			int bugStartLine = hunk.getBugLineStartNum();

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

@@ -49,10 +49,11 @@ public class FixedViolationHunkParser extends FixedViolationParser {
 
 
 				FileOutputStream f = null;
+
 				try {
-					String pj = diffentryFile.getParent().split("GumTreeInputBug13April")[1];
+					String pj = diffentryFile.getParent().split("Defects4J")[1];
-					String root = diffentryFile.getParent().split("GumTreeInputBug13April")[0];
+					String root = diffentryFile.getParent().split("Defects4J")[0];
-					String hunkTreeFileName = root+"GumTreeOutput13April/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet);
+					String hunkTreeFileName = root+"GumTreeOutputDefects4J/" +pj.replace("DiffEntries","ActionSetDumps/") + diffentryFile.getName() + "_" + String.valueOf(hunkSet);
 					f = new FileOutputStream(new File(hunkTreeFileName));
 					ObjectOutputStream o = new ObjectOutputStream(f);
 					o.writeObject(actionSet);

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

@@ -88,7 +88,7 @@ public class MultiThreadTreeLoaderCluster {
         cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399"));
         edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"10000");
 
-        calculatePairsOfClusters(inputPath, outputPath);
+//        calculatePairsOfClusters(inputPath, outputPath);
 //        mainCompare(inputPath,port,pairsCSVPath,importScript);
         //        calculatePairs(inputPath, outputPath);
 //        processMessages(inputPath,outputPath);
@@ -119,15 +119,25 @@ public class MultiThreadTreeLoaderCluster {
         log.info("Load done");
     }
 
-    public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) {
+    public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner) {
 
-        String cmd;
+        String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
-        cmd = "bash " + importScript +" %s %s";
+        cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner));
+        edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000");
 
 
-        JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
+        String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
+        cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port));
+        edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000");
 
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf("6399"),20000000);
+
+        String cmd3;
+        cmd3 = "bash " + importScript +" %s %s";
+
+
+        JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+
+        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
 
 
         File folder = new File(pairsCSVPath);
@@ -139,7 +149,7 @@ public class MultiThreadTreeLoaderCluster {
 
         for (File f:folders){
 
-            if(f.getName().startsWith("cluster0")) {
+//            if(f.getName().startsWith("cluster0")) {
 
 
                 try (Jedis jedis = jedisPool.getResource()) {
@@ -153,7 +163,7 @@ public class MultiThreadTreeLoaderCluster {
                     int size = scan.getResult().size();
 
                     if (size == 0) {
-                        String comd = String.format(cmd,f.getPath(),port);
+                        String comd = String.format(cmd3,f.getPath(),portInner);
                         loadRedis(comd);
 
                         scan = jedis.scan("0", sc);
@@ -169,13 +179,13 @@ public class MultiThreadTreeLoaderCluster {
                     //76
 
                     scan.getResult().parallelStream()
-                            .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName,outerPool));
+                            .forEach(m -> coreCompare(m, jedisPool, clusterName,outerPool));
 
 
                     jedis.save();
 
                 }
-            }
+//            }
 
 
         }
@@ -224,23 +234,18 @@ public class MultiThreadTreeLoaderCluster {
         Jedis inner = null;
         String[] split2 = firstValue.split("/");
         String cluster = split2[1];
-
+        String fullFileName = split2[2];
-        File folder = new File("/Users/anilkoyuncu/bugStudy/code/python/cluster/"+cluster);
+        String[] split = fullFileName.split(".txt_");
-        File[] listOfFiles = folder.listFiles();
+        String pureFileName = split[0];
-        Stream<File> stream = Arrays.stream(listOfFiles);
+        String[] splitPJ = split[1].split("_");
-        List<File> folders = stream
-                .filter(x -> !x.getName().startsWith(".") && x.getName().startsWith(split2[2]))
-                .collect(Collectors.toList());
-
-        String[] split1 = folders.get(0).getName().split(".txt_");
-        String s = split1[0];
-        String[] splitPJ = split1[1].split("_");
         String project = splitPJ[1];
         String actionSetPosition = splitPJ[0];
 
+
+
         try {
             inner = outerPool.getResource();
-            String filename = project + "/ActionSetDumps/" + split2[2];
+            String filename = project + "/ActionSetDumps/" + pureFileName + ".txt_" + actionSetPosition;
             String si= inner.get(filename);
             HierarchicalActionSet actionSet = (HierarchicalActionSet) fromString(si);
 
@@ -400,7 +405,7 @@ public class MultiThreadTreeLoaderCluster {
 
 
     
-    private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName,JedisPool outerPool) {
+    private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool) {
 
 
         try (Jedis jedis = jedisPool.getResource()) {

src/main/java/edu/lu/uni/serval/FixPatternParser/violations/MultiThreadTreeLoaderCluster3.java

@@ -99,7 +99,7 @@ public class MultiThreadTreeLoaderCluster3 {
         cmd = String.format(cmd, dbDir,"dumps.rdb",Integer.valueOf("6399"));
         edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd,"1000");
 
-        mainCompare(inputPath,port,pairsCSVPath,importScript);
+//        mainCompare(inputPath,port,pairsCSVPath,importScript);
         //        calculatePairs(inputPath, outputPath);
 //        processMessages(inputPath,outputPath);
 //        evaluateResults(inputPath,outputPath);
@@ -160,13 +160,27 @@ public class MultiThreadTreeLoaderCluster3 {
         log.info("Load done");
     }
 
-    public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) {
+//    public static void mainCompare(String inputPath,String port,String pairsCSVPath,String importScript) {
+    public static void mainCompare(String port,String pairsCSVPath,String importScript,String dbDir,String chunkName,String dumpName,String portInner) {
 
-        String cmd;
+        String cmd1 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
-        cmd = "bash " + importScript +" %s %s";
+        cmd1 = String.format(cmd1, dbDir,chunkName,Integer.valueOf(portInner));
+        edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd1,"1000");
+
+
+        String cmd2 = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
+        cmd2 = String.format(cmd2, dbDir,dumpName,Integer.valueOf(port));
+        edu.lu.uni.serval.FixPatternParser.cluster.AkkaTreeLoader.loadRedis(cmd2,"10000");
+
+
+        String cmd3;
+        cmd3 = "bash " + importScript +" %s %s";
+
+
+        JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(portInner),20000000);
+
+        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
 
-        JedisPool jedisPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf(port),20000000);
-        JedisPool outerPool = new JedisPool(poolConfig, "127.0.0.1",Integer.valueOf("6399"),20000000);
 
 
         File folder = new File(pairsCSVPath);
@@ -192,7 +206,7 @@ public class MultiThreadTreeLoaderCluster3 {
                     int size = scan.getResult().size();
 
                     if (size == 0) {
-                        String comd = String.format(cmd, f.getPath(), port);
+                        String comd = String.format(cmd3, f.getPath(), portInner);
                         edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster.
                                 loadRedis(comd);
 
@@ -207,7 +221,7 @@ public class MultiThreadTreeLoaderCluster3 {
 
 
                     scan.getResult().parallelStream()
-                            .forEach(m -> coreCompare(m, inputPath, jedisPool, clusterName, outerPool));
+                            .forEach(m -> coreCompare(m, jedisPool, clusterName, outerPool));
 
 
                     jedis.save();
@@ -241,9 +255,9 @@ public class MultiThreadTreeLoaderCluster3 {
         String actionSetPosition = splitPJ[0];
 
         Integer asp = Integer.valueOf(actionSetPosition);
-        if (asp > 1){
+//        if (asp > 1){
-            return null;
+//            return null;
-        }
+//        }
 
 
         ITree tree = null;
@@ -464,6 +478,20 @@ public class MultiThreadTreeLoaderCluster3 {
                         oldTokens.add(hours.trim());
                         }
                     }
+                }else if(label.startsWith("MOV")  && upd == false){
+                    String timeRegex = "@@(.*)@TO@(.*)";
+                    Pattern pattern = Pattern.compile(timeRegex, Pattern.DOTALL);
+                    java.util.regex.Matcher matcher = pattern.matcher(split[1]);
+
+                    if (matcher.matches()) {
+                        String hours = matcher.group(1);
+                        if (hours.startsWith("MethodName:")){
+                            String methodName = hours.split(":")[1];
+                            oldTokens.add(methodName);
+                        }else {
+                            oldTokens.add(hours.trim());
+                        }
+                    }
                 }
                 boolean alreadyAddParentMethodName = false;
                 for (String s : m) {
@@ -536,13 +564,13 @@ public class MultiThreadTreeLoaderCluster3 {
             }
         }
 
-//        if (oldTokens.size() == 0 || oldTokens.size() > 3) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){
+        if (oldTokens.size() == 0 ) {// && (oldTree.getType() != 41 && oldTree.getType() != 21 && oldTree.getType() !=17 && oldTree.getType()!=60 && oldTree.getType() != 46)){
-//            log.info("dur bakalim nereye!???");
+            log.info("dur bakalim nereye!???");
-//        }
+        }
         return oldTokens;
     }
     
-    private static void coreCompare(String name , String inputPath, JedisPool jedisPool,String clusterName,JedisPool outerPool) {
+    private static void coreCompare(String name , JedisPool jedisPool,String clusterName,JedisPool outerPool) {
 
 
         try (Jedis jedis = jedisPool.getResource()) {

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

@@ -1,54 +1,45 @@
 package edu.lu.uni.serval.FixPatternParser.violations;
 
-import static java.lang.System.err;
+import akka.actor.ActorRef;
+import akka.actor.ActorSystem;
+import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
+import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor;
+import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
+import edu.lu.uni.serval.config.Configuration;
+import edu.lu.uni.serval.utils.FileHelper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.*;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import edu.lu.uni.serval.FixPatternParser.RunnableParser;
-import edu.lu.uni.serval.MultipleThreadsParser.AkkaParser;
-import edu.lu.uni.serval.MultipleThreadsParser.MessageFile;
-import edu.lu.uni.serval.MultipleThreadsParser.ParseFixPatternActor;
-import edu.lu.uni.serval.MultipleThreadsParser.WorkMessage;
-import edu.lu.uni.serval.config.Configuration;
-import edu.lu.uni.serval.utils.FileHelper;
-import org.eclipse.jgit.revwalk.RevCommit;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 public class TestHunkParser {
 
 	private static Logger log = LoggerFactory.getLogger(TestHunkParser.class);
-	public static void main(String[] args) {
+//	public static void main(String[] args) {
+	public static void main(String inputPath, String outputPath,String numOfWorkers) {
 		// input data
 
-//			String rootPath = "/Users/anilkoyuncu/bugStudy";
+////			String rootPath = "/Users/anilkoyuncu/bugStudy";
-        String inputPath;
+//        String inputPath;
-        String outputPath;
+//        String outputPath;
-        if(args.length > 0){
+//        if(args.length > 0){
-            inputPath = args[1];
+//            inputPath = args[1];
-            outputPath = args[0];
+//            outputPath = args[0];
-        }else{
+//        }else{
-//            inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4";
+////            inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug4";
-			inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug13April";
+//			inputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeInputBug13April";
-//            outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/";
+////            outputPath = "/Users/anilkoyuncu/bugStudy/code/python/GumTreeOutput2/";
-			outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput13April";
+//			outputPath = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutput13April";
-        }
+//        }
-
 
+		String parameters = String.format("\nInput path %s \nOutput path %s",inputPath,outputPath);
+		log.info(parameters);
 
 		File folder = new File(inputPath);
 		File[] listOfFiles = folder.listFiles();
@@ -74,7 +65,7 @@ public class TestHunkParser {
 //                continue;
 //            }
 
-            final List<MessageFile> msgFiles = getMessageFiles(target.toString() + "/"); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/"
+            final List<MessageFile> msgFiles = getMessageFiles(target.toString() + "/", outputPath); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/"
             System.out.println(msgFiles.size());
             if(msgFiles.size() == 0)
                 continue;
@@ -108,7 +99,7 @@ public class TestHunkParser {
 			try {
 				log.info("Akka begins...");
 				system = ActorSystem.create("Mining-FixPattern-System");
-				parsingActor = system.actorOf(ParseFixPatternActor.props(100, editScriptsFilePath,
+				parsingActor = system.actorOf(ParseFixPatternActor.props(Integer.valueOf(numOfWorkers), editScriptsFilePath,
 						patchesSourceCodeFilePath, buggyTokensFilePath, editScriptSizesFilePath), "mine-fix-pattern-actor");
 				parsingActor.tell(msg, ActorRef.noSender());
 			} catch (Exception e) {
@@ -178,7 +169,7 @@ public class TestHunkParser {
 	}
 	
 
-	private static List<MessageFile> getMessageFiles(String gumTreeInput) {
+	private static List<MessageFile> getMessageFiles(String gumTreeInput,String outputPath) {
 		String inputPath = gumTreeInput; // prevFiles  revFiles diffentryFile positionsFile
 		File revFilesPath = new File(inputPath + "revFiles/");
 		File[] revFiles = revFilesPath.listFiles();   // project folders

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

@@ -1,6 +1,9 @@
 package edu.lu.uni.serval;
 
 import edu.lu.uni.serval.FixPatternParser.cluster.*;
+import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster;
+import edu.lu.uni.serval.FixPatternParser.violations.MultiThreadTreeLoaderCluster3;
+import edu.lu.uni.serval.FixPatternParser.violations.TestHunkParser;
 
 /**
  * Created by anilkoyuncu on 14/04/2018.
@@ -9,7 +12,7 @@ public class Launcher {
 
     public static void main(String[] args) {
 
-        String inputPath;
+//        String inputPath;
         String portInner;
         String serverWait;
         String dbDir;
@@ -17,42 +20,74 @@ public class Launcher {
         String numOfWorkers;
         String jobType;
         String port;
-        String outputPath;
+        String pairsPath;
+        String csvInputPath;
+        String dumpsName;
+        String gumInput;
+        String gumOutput;
         if (args.length > 0) {
             jobType = args[0];
-            inputPath = args[1];
+            gumInput = args[1];
             portInner = args[2];
             serverWait = args[3];
             chunkName = args[4];
             numOfWorkers = args[5];
             dbDir = args[6];
             port = args[7];
-            outputPath = args[8];
+            pairsPath = args[8];
+            csvInputPath = args[9];
+            dumpsName = args[10];
+            gumOutput =args[12];
         } else {
-            inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs";
+//            inputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairs";
+            gumInput = "/Users/anilkoyuncu/bugStudy/dataset/Defects4J/";
             portInner = "6380";
             serverWait = "10000";
-            chunkName = "dumps.rdb";
+            chunkName = "textfile.txt.csv.rdb";
             dbDir = "/Users/anilkoyuncu/bugStudy/dataset/redis";
             numOfWorkers = "1";
-            jobType = "LEVEL1DB";
+            jobType = "L3PAIRDB";
             port = "6399";
-            outputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImport";
+            pairsPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J";
+            gumOutput = "/Users/anilkoyuncu/bugStudy/dataset/GumTreeOutputDefects4J";
+            csvInputPath = "/Users/anilkoyuncu/bugStudy/dataset/pairsImportDefects4J-CSV";
+            dumpsName = "dumpsDefect4J.rdb";
         }
-        String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir);
+//        String parameters = String.format("\nJob %s \nInput path %s \nportInner %s \nserverWait %s \nchunkName %s \nnumOfWorks %s \ndbDir %s", jobType, inputPath, portInner, serverWait, chunkName, numOfWorkers, dbDir);
 
 
         switch (jobType){
+            case "DUMPTREE":
+                TestHunkParser.main(gumInput,gumOutput,numOfWorkers);
+                break;
             case "STORE":
-                StoreFile.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers);
+                StoreFile.main(gumOutput,portInner,serverWait,dbDir,dumpsName);
+                break;
             case "CALCPAIRS":
-                CalculatePairs.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers,port,outputPath);
+                CalculatePairs.main(serverWait,dbDir,dumpsName,port,pairsPath,"DEFECT4J");
+                break;
             case "IMPORTPAIRS":
-                ImportPairs2DB.main(inputPath,portInner,serverWait,dbDir,chunkName,numOfWorkers);
+                ImportPairs2DB.main(csvInputPath,portInner,serverWait,dbDir,numOfWorkers);
+                break;
             case "AKKA":
-                AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port);
+                AkkaTreeLoader.main(portInner,serverWait,dbDir,chunkName,port,dumpsName);
+                break;
             case "LEVEL1DB":
-                TreeLoaderClusterL1.main(portInner,serverWait,port,inputPath);
+                TreeLoaderClusterL1.main(portInner,serverWait,port,dbDir,"level1-defect4j.rdb",dbDir+"/level1-defect4j/");
+                break;
+            //CALC python abstractPatch.py to from cluster folder
+            case "L2CALCPAIRS":
+                MultiThreadTreeLoaderCluster.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J","/Users/anilkoyuncu/bugStudy/dataset/");
+                break;
+            case "L2PAIRDB":
+                MultiThreadTreeLoaderCluster.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl1-d4j.rdb",dumpsName,"6301");
+                break;
+            case "L3CALCPAIRS":
+                MultiThreadTreeLoaderCluster3.calculatePairsOfClusters("/Users/anilkoyuncu/bugStudy/code/python/clusterDefect4J-2l","/Users/anilkoyuncu/bugStudy/dataset/");
+                break;
+            case "L3PAIRDB":
+                MultiThreadTreeLoaderCluster3.mainCompare("6300","/Users/anilkoyuncu/bugStudy/dataset/pairs-2l-csv","/Users/anilkoyuncu/bugStudy/dataset/redisSingleImport.sh",dbDir,"clusterl2-d4j.rdb",dumpsName,"6301");
+                break;
 
 
         }

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

@@ -85,6 +85,8 @@ public class ParseFixPatternWorker extends UntypedActor {
 				File revFile = msgFile.getRevFile();
 				File prevFile = msgFile.getPrevFile();
 				File diffentryFile = msgFile.getDiffEntryFile();
+
+
 //				File positionFile = msgFile.getPositionFile();
 				/*if (revFile.getName().toLowerCase().contains("test")) {
 					continue;