changes for jar

2020-04-07 18:06:53 +02:00
parent c5463f91f8
commit 40a8b0c290
57 changed files with 1180 additions and 301 deletions
@@ -21,7 +21,7 @@
      <module name="fixminer_source" target="1.8" />
      <module name="gen.jdt" target="1.8" />
      <module name="gen.srcml" target="1.8" />
-      <module name="gumtree (1) (com.github.gumtreediff)" target="1.8" />
+      <module name="gumtree" target="1.8" />
      <module name="RichEdit" target="1.8" />
    </bytecodeTargetLevel>
  </component>
@@ -24,7 +24,7 @@ Fixminer is a systematic and automated approach to mine relevant and actionable
 ## II. Environment setup
 * OS: macOS Mojave (10.14.3)
-* JDK8: Oracle jdk1.8 (**important!**)
+* JDK8: (**important!**)
 * Download and configure Anaconda
 * Create an python environment using the [environment file](environment.yml)
  ```powershell
@@ -32,7 +32,12 @@ Fixminer is a systematic and automated approach to mine relevant and actionable
  ```
 * After creating the environment, activate it. It is containing necessary dependencies for redis, and python.
  ```powershell
-  source activate redisEnv
+  source activate fixminerEnv
  ```
 * Update the config.yml file with the corresponding paths in your computer. An example config.yml file could be found under
  ```powershell
  fixminer_source/src/main/resources/config.yml
  ```
 <!---
 [fixminer.sh](python/fixminer.sh)
@@ -46,94 +51,51 @@ In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
    bash fixminer.sh /Users/..../enhancedASTDiff/python/ stats
 --->
 ## III. Replication Data
 Replication Data:
   [singleBR.pickle](python/data/singleBR.pickle)
    This pickle contains the list bug reports (i.e. bid) with the their corresponding fixes (i.e. commit) for each project in the dataset (i.e. project). 
   [bugReports.7z.00X](python/data/bugReports.7z.001)
    This is the dump of the bug reports archive extracted from each commit. These bug reports are not necessarily considered as BUG,CLOSED; this archive is the contins initial bug reports before identifying the fixes. 
   [gumInput.7z.001](python/data/gumInput.7z.001)
    This archive contains all the patches in our dataset, formatted in a way that can be processed by GumTree (i.e DiffEntries, prevFiles, revFiles)
   [ALLbugReportsComplete.pickle](python/data/ALLbugReportsComplete.pickle)
    The pickle object that represents the bug reports under the following columns 'bugReport', 'summary', 'description', 'created', 'updated', 'resolved', 'reporterDN', 'reporterEmail','hasAttachment', 'attachmentTime', 'hasPR', 'commentsCount'
 #### Data Viewer
 The data provided with replication package is listed in directory [python/data](python/data)
 The data is stored in different formats. (e.g. pickle, db, csv, etc..)
 The see content of the .pickle file the following script could be used.
  ```python
   import pickle as p
   import gzip
   def load_zipped_pickle(filename):
      with gzip.open(filename, 'rb') as f:
          loaded_object = p.load(f)
          return loaded_object
  ```
 Usage
  ```python
  result = load_zipped_pickle('code/LANGbugReportsComplete.pickle')
  # Result is pandas object which can be exported to several formats
  # Details on how to export is listed in offical library documentation
  # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
  ```
 ## IV. Step-by-Step execution
 #### Before running
-* Update [config file](python/config.yml) with corresponding user paths.
+* Update [config file](src/main/resources/config.yml) with corresponding user paths.
 * Active the conda environment from shell
  ```powershell
-  source activate redisEnv
+  source activate fixminerEnv
  ```
 In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
-    bash fixminer.sh [PATH_TO_PYTHON_FOLDER] [OPTIONS]
+    bash fixminer.sh [JOB] [CONFIG_FILE]
-     e.g. bash fixminer.sh Users/fixminer-core/python/ stats
+     e.g. bash fixminer.sh  dataset4c /Users/projects/release/fixminer_source/src/main/resources/config.yml
 #### Running Options 
-*FixMiner* needs to specify an option to run.
+#### Job Types  
-    1. 'dataset': Create a mining dataset from the project speficied in  [subjects.csv](python/data/subjects.csv)
+*FixMiner* needs to specify a job to run.
    Eventually dataset option is the execution of the following steps, which are merged under 'dataset' option 
    for this demo. Eventually single options can be activated by commenting out the corresponding option in [main.py](python/main.py)
-        `clone` : Clone target project repository.
+   1. __dataset4j__ / __dataset4c__: Create a java/c mining dataset from the projects listed in [subjects.csv](python/data/subjects.csv) or [datasets.csv](python/data/datasets.csv) for c
        `collect` : Collect all commit from repository.
-        `fix` : Collect commits linked to a bug report.
+   2. __richEditScript__: Calls the jar file produced as the results as maven package to compute Rich edit scripts.
   This step can be invoke natively from java or using the [Launcher](src/main/java/edu/lu/uni/serval/richedit/Launcher.java) with appropriate arguments.
-        `bugPoints` : Identify the snapshot of the repository before the bug fixing commit introducted.
+ ```powershell
 java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar  /Users/projects/release/fixminer_source/src/main/resources/config.yml RICHEDITSCRIPT
-        `brDownload` : Download bug reports recovered from commit log
+ ```   
        `brParser` : Parse bug reports to select the bug report where type labelled as BUG and status as RESOLVED or CLOSED
    2. 'richEditScript': Rich edit script computation step.    
-    3. 'shapeSI': Search index creation for shapes. The output of this step is written to [pairs](python/data/pairs)
+   3. __shapeSI__: Search index creation for shapes. The output of this step is written to __pairs__ which will be generated under __datapath__ in [config file](src/main/resources/config.yml)
-    4. 'compareShapes' : ShapeTree comparison
+   4. __compareShapes__ : Calls the jar file produced as the results as maven package to compare the trees.
                             This step can be invoke natively from java or using the [Launcher](src/main/java/edu/lu/uni/serval/richedit/Launcher.java) with appropriate arguments.
-    5. 'cluster': Forms clusters of identical shapetree. The output of this step is written to [shapes](python/data/shapes)
+                           ```powershell
                           java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar  /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARETREES
                           ```   
   5. 'cluster': Forms clusters of identical shapetree. The output of this step is written to [shapes](python/data/shapes)
    6. 'actionSI': Search index creation for actions. The output of this step is written to [pairs](python/data/pairsAction)
@@ -234,5 +196,50 @@ It is necessary to run the FixMiner, following the order.
 ## III. Replication Data
 Replication Data:
   [singleBR.pickle](python/data/singleBR.pickle)
    This pickle contains the list bug reports (i.e. bid) with the their corresponding fixes (i.e. commit) for each project in the dataset (i.e. project). 
   [bugReports.7z.00X](python/data/bugReports.7z.001)
    This is the dump of the bug reports archive extracted from each commit. These bug reports are not necessarily considered as BUG,CLOSED; this archive is the contins initial bug reports before identifying the fixes. 
   [gumInput.7z.001](python/data/gumInput.7z.001)
    This archive contains all the patches in our dataset, formatted in a way that can be processed by GumTree (i.e DiffEntries, prevFiles, revFiles)
   [ALLbugReportsComplete.pickle](python/data/ALLbugReportsComplete.pickle)
    The pickle object that represents the bug reports under the following columns 'bugReport', 'summary', 'description', 'created', 'updated', 'resolved', 'reporterDN', 'reporterEmail','hasAttachment', 'attachmentTime', 'hasPR', 'commentsCount'
 #### Data Viewer
 The data provided with replication package is listed in directory [python/data](python/data)
 The data is stored in different formats. (e.g. pickle, db, csv, etc..)
 The see content of the .pickle file the following script could be used.
  ```python
   import pickle as p
   import gzip
   def load_zipped_pickle(filename):
      with gzip.open(filename, 'rb') as f:
          loaded_object = p.load(f)
          return loaded_object
  ```
 Usage
  ```python
  result = load_zipped_pickle('code/LANGbugReportsComplete.pickle')
  # Result is pandas object which can be exported to several formats
  # Details on how to export is listed in offical library documentation
  # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
  ```
@@ -12,7 +12,12 @@
            <groupId>edu.lu.uni.serval</groupId>
            <artifactId>RichEdit</artifactId>
            <version>1.0.0</version>
-            <scope>compile</scope>
+<!--            <scope>compile</scope>-->
        </dependency>
        <dependency>
            <groupId>org.yaml</groupId>
            <artifactId>snakeyaml</artifactId>
            <version>1.21</version>
        </dependency>
    </dependencies>
    <packaging>pom</packaging>
@@ -24,6 +29,7 @@
    <build>
        <sourceDirectory>richedit/src/main/java/</sourceDirectory>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
@@ -47,10 +53,8 @@
                        <configuration>
                            <archive>
                                <manifest>
-                                    <mainClass>
+                                    <addClasspath>true</addClasspath>
-                                        <!--edu.lu.uni.serval.fixminer.jobs.CompareTrees-->
+                                    <mainClass>edu.lu.uni.serval.Launcher</mainClass>
                                        edu.lu.uni.serval.fixminer.Launcher
                                    </mainClass>
                                </manifest>
                            </archive>
                            <descriptorRefs>
@@ -3,14 +3,14 @@ java:
 spinfer:
    home:   /Users/anil.koyuncu/projects/spinfer/spinfer.native
 dataset:
-    home:   /Users/anil.koyuncu/projects/test/fixminer-data/patches/
+    home:   /Users/anil.koyuncu/projects/test/richedit-data/patches/
-    repo:   /Users/anil.koyuncu/projects/test/fixminer-data/datasets
+    repo:   /Users/anil.koyuncu/projects/test/richedit-data/datasets
-#    home:   /data/fixminer-core/python/data/gumInputLinux/
+#    home:   /data/richedit-core/python/data/gumInputLinux/
 coccinelle:
    home:   /Users/anil.koyuncu/projects/spinfer/statics
 fixminer:
-    datapath: /Users/anil.koyuncu/projects/test/fixminer-data/
+    datapath: /Users/anil.koyuncu/projects/test/richedit-data/
    projectType : c
-#    datapath: /data/fixminer-core/python/data/
+#    datapath: /data/richedit-core/python/data/
@@ -179,7 +179,7 @@ def clusterCore(clusterPath, level, match, pairsPath, root, s,action ,token=''):
    parallelRun(dumpFilesCore,workList)
    # for wl in workList:
    #     dumpFilesCore(wl)
-    # dumpFilesCore(('hive_d65d5c_96c1dc_ql#src#gen#protobuf#gen-java#org#apache#hadoop#hive#ql#io#orc#OrcProto.txt_31', 'ReturnStatement', 'tokens', '/Users/anil.koyuncu/projects/fixminer-all/enhancedASTDiff/python/data/tokens', '3', '1', '0', 10))
+    # dumpFilesCore(('hive_d65d5c_96c1dc_ql#src#gen#protobuf#gen-java#org#apache#hadoop#hive#ql#io#orc#OrcProto.txt_31', 'ReturnStatement', 'tokens', '/Users/anil.koyuncu/projects/richedit-all/enhancedASTDiff/python/data/tokens', '3', '1', '0', 10))
 def dumpFilesCore(t):
@@ -0,0 +1,13 @@
 2020-04-07 17:31:35,222 - 31200 - INFO - commons.py:setEnv - ROOT_DIR : /Users/anilkoyuncu/projects/release/test/fixminer_source/python
 2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - REPO_PATH : /Users/anilkoyuncu/projects/test/richedit-data/datasets
 2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - CODE_PATH : /Users/anilkoyuncu/projects/release/test/fixminer_source/python/code/
 2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - COMMIT_DFS : /Users/anilkoyuncu/projects/test/richedit-data/commitsDF/
 2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - BUG_POINT : /Users/anilkoyuncu/projects/test/richedit-data/bugPoints/
 2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - COMMIT_FOLDER : /Users/anilkoyuncu/projects/test/richedit-data/commits/
 2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - FEATURE_DIR : /Users/anilkoyuncu/projects/test/richedit-data/features/
 2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - CLASSIFIER_DIR : /Users/anilkoyuncu/projects/test/richedit-data/classifiers/
 2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - PREDICTION_DIR : /Users/anilkoyuncu/projects/test/richedit-data/predictions/
 2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - DATASET_DIR : /Users/anilkoyuncu/projects/test/richedit-data/datasets/
 2020-04-07 17:31:41,346 - 31200 - INFO - commons.py:shellCallTemplate - JAVA_HOME='/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home' java  -jar /Users/anilkoyuncu/projects/release/test/fixminer_source/target/FixPatternMiner-1.0.0-jar-with-dependencies.jar /Users/anilkoyuncu/projects/release/test/fixminer_source/src/main/resources/config.yml RICHEDITSCRIPT 
 2020-04-07 17:31:41,551 - 31200 - ERROR - commons.py:shellCallTemplate - Error: Could not find or load main class edu.lu.uni.serval.richedit.Launcher
@@ -26,6 +26,8 @@ from collections import Counter
 import datetime
 import subprocess
 from pathlib import Path
 sourceCodeColumns = ['packageName', 'className', 'methodNames', 'formalParameter',
@@ -72,13 +74,15 @@ def setEnv(args):
    import yaml
-    if os.uname().nodename != '':
+    # if os.uname().nodename != '':
-        with open(join(os.environ["ROOT_DIR"], os.uname().nodename + ".config.yml"), 'r') as ymlfile:
+    #     with open(join(os.environ["ROOT_DIR"], os.uname().nodename + ".config.yml"), 'r') as ymlfile:
-            cfg = yaml.load(ymlfile)
+    #         cfg = yaml.load(ymlfile)
-    else:
+    # else:
-        with open(join(os.environ["ROOT_DIR"], "config.yml"), 'r') as ymlfile:
+    #     with open(join(os.environ["ROOT_DIR"], "config.yml"), 'r') as ymlfile:
-            cfg = yaml.load(ymlfile)
+    #         cfg = yaml.load(ymlfile)
    with open(args.prop, 'r') as ymlfile:
        cfg = yaml.load(ymlfile)
    # for section in cfg:
    #     print(section)
    # print(cfg['mysql'])
@@ -88,10 +92,11 @@ def setEnv(args):
    os.environ["JDK8"] = cfg['java']['8home']
    os.environ["spinfer"] = cfg['spinfer']['home']
    os.environ["coccinelle"] = cfg['coccinelle']['home']
-    os.environ["dataset"] = cfg['dataset']['home']
+    os.environ["dataset"] = cfg['dataset']['inputPath']
    os.environ["REPO_PATH"] = cfg['dataset']['repo']
    os.environ["DATA_PATH"] = cfg['fixminer']['datapath']
    os.environ["PROJECT_TYPE"] = cfg['fixminer']['projectType']
    os.environ["PROJECT_LIST"] = cfg['fixminer']['projectList']
    # import yaml
    #
@@ -160,11 +165,12 @@ def getRun():
    # parser.add_argument('-subject', dest='subject', help='Environment')
    parser.add_argument('-root', dest='root', help='root folder')
    parser.add_argument('-job',dest='job',help='job name')
    parser.add_argument('-prop',dest='prop',help='property file')
    args = parser.parse_args()
-    if args.root is None or args.job is None:
+    if args.root is None or args.job is None or args.prop is None:
        parser.print_help()
        raise AttributeError
    return args
@@ -1,17 +1,17 @@
 java:
    8home:  /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
 spinfer:
-    home:   /Users/anil.koyuncu/projects/fixminer/spinfer/spinfer.native
+    home:   /Users/anil.koyuncu/projects/richedit/spinfer/spinfer.native
    #home:   /Users/anil.koyuncu/projects/spinfer/spinfer.native
 dataset:
-#    home:   /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/
+#    home:   /Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/
-    home:   /data/fixminer-core/python/data/gumInputLinux/
+    home:   /data/richedit-core/python/data/gumInputLinux/
 coccinelle:
-    home:   /Users/anil.koyuncu/projects/fixminer/spinfer/statics
+    home:   /Users/anil.koyuncu/projects/richedit/spinfer/statics
    #home:   /Users/anil.koyuncu/projects/spinfer/statics
 fixminer:
-#    datapath: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/
+#    datapath: /Users/anil.koyuncu/projects/test/richedit-core/python/data/
-    datapath: /data/fixminer-core/python/data/
+    datapath: /data/richedit-core/python/data/
@@ -0,0 +1,46 @@
 Group,Subject,Repo,GitRepo,Branch
 Apache,CAMEL,camel,https://github.com/apache/camel.git,master
 Apache,HBASE,hbase,https://github.com/apache/hbase.git,master
 Apache,HIVE,hive,https://github.com/apache/hive.git,master
 Commons,CODEC,commons-codec,https://github.com/apache/commons-codec.git,trunk
 Commons,COLLECTIONS,commons-collections,https://github.com/apache/commons-collections.git,master
 Commons,COMPRESS,commons-compress,https://github.com/apache/commons-compress.git,master
 Commons,CONFIGURATION,commons-configuration,https://github.com/apache/commons-configuration.git,trunk
 Commons,CRYPTO,commons-crypto,https://github.com/apache/commons-crypto.git,master
 Commons,CSV,commons-csv,https://github.com/apache/commons-csv.git,master
 Commons,IO,commons-io,https://github.com/apache/commons-io.git,master
 Commons,WEAVER,commons-weaver,https://github.com/apache/commons-weaver.git,master
 JBoss,ENTESB,fuse,https://github.com/jboss-fuse/fuse.git,6.3.0.redhat
 JBoss,JBMETA,metadata,https://github.com/jboss/metadata.git,master
 Wildfly,ELY,wildfly-elytron,https://github.com/wildfly-security/wildfly-elytron.git,master
 Wildfly,SWARM,wildfly-swarm,https://github.com/wildfly-swarm/wildfly-swarm.git,master
 Wildfly,WFARQ,wildfly-arquillian,https://github.com/wildfly/wildfly-arquillian.git,master
 Wildfly,WFCORE,wildfly-core,https://github.com/wildfly/wildfly-core.git,master
 Wildfly,WFLY,wildfly,https://github.com/wildfly/wildfly.git,master
 Wildfly,WFMP,wildfly-maven-plugin,https://github.com/wildfly/wildfly-maven-plugin.git,master
 Spring,AMQP,spring-amqp,https://github.com/spring-projects/spring-amqp,master
 Spring,ANDROID,spring-android,https://github.com/spring-projects/spring-android,master
 Spring,BATCH,spring-batch,https://github.com/spring-projects/spring-batch,master
 Spring,BATCHADM,spring-batch-admin,https://github.com/spring-projects/spring-batch-admin,master
 Spring,DATACMNS,spring-data-commons,https://github.com/spring-projects/spring-data-commons,master
 Spring,DATAGRAPH,spring-data-neo4j,https://github.com/spring-projects/spring-data-neo4j,master
 Spring,DATAJPA,spring-data-jpa,https://github.com/spring-projects/spring-data-jpa,master
 Spring,DATAMONGO,spring-data-mongodb,https://github.com/spring-projects/spring-data-mongodb,master
 Spring,DATAREDIS,spring-data-redis,https://github.com/spring-projects/spring-data-redis,master
 Spring,DATAREST,spring-data-rest,https://github.com/spring-projects/spring-data-rest,master
 Spring,LDAP,spring-ldap,https://github.com/spring-projects/spring-ldap,master
 Spring,MOBILE,spring-mobile,https://github.com/spring-projects/spring-mobile,master
 Spring,ROO,spring-roo,https://github.com/spring-projects/spring-roo,master
 Spring,SEC,spring-security,https://github.com/spring-projects/spring-security,master
 Spring,SECOAUTH,spring-security-oauth,https://github.com/spring-projects/spring-security-oauth,master
 Spring,SGF,spring-data-gemfire,https://github.com/spring-projects/spring-data-gemfire,master
 Spring,SHDP,spring-hadoop,https://github.com/spring-projects/spring-hadoop,master
 Spring,SHL,spring-shell,https://github.com/spring-projects/spring-shell,master
 Spring,SOCIAL,spring-social,https://github.com/spring-projects/spring-social,master
 Spring,SOCIALFB,spring-social-facebook,https://github.com/spring-projects/spring-social-facebook,master
 Spring,SOCIALLI,spring-social-linkedin,https://github.com/spring-projects/spring-social-linkedin,master
 Spring,SOCIALTW,spring-social-twitter,https://github.com/spring-projects/spring-social-twitter,master
 Spring,SPR,spring-framework,https://github.com/spring-projects/spring-framework,master
 Spring,SWF,spring-webflow,https://github.com/spring-projects/spring-webflow,master
 Spring,SWS,spring-ws,https://github.com/spring-projects/spring-ws,master
@@ -1,6 +1,6 @@
 #!/bin/bash
-source activate redisEnv
+source activate fixminerEnv
-PYTHONPATH=$(pwd) python -u main.py -root $(pwd) -job $1
+PYTHONPATH=$(pwd) python -u main.py -root $(pwd) -job $1 -prop $2
@@ -15,7 +15,6 @@ if __name__ == '__main__':
        setEnv(args)
        job = args.job
        job = 'indexClusters'
        ROOT_DIR = os.environ["ROOT_DIR"]
        REPO_PATH = os.environ["REPO_PATH"]
        CODE_PATH = os.environ["CODE_PATH"]
@@ -36,24 +35,24 @@ if __name__ == '__main__':
        print(job)
-        if job == 'dataset':
+        if job == 'dataset4j':
            from javaDS import createDS
            createDS(subject)
-        elif job == 'linuxDS':
+        # elif job == 'linuxDS':
-            from linuxDataset import collectBugFixPatches
+        #     from linuxDataset import collectBugFixPatches
-            collectBugFixPatches()
+        #     collectBugFixPatches()
-        elif job =='otherDS':
+        elif job =='dataset4c':
            from otherDatasets import core
            core()
        elif job =='richEditScript':
-            cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " RICHEDITSCRIPT " + 'L1'
+            cmd = "JAVA_HOME='" + jdk8 + "' java  -jar " + join(Path(ROOT_DIR).parent, 'target','FixPatternMiner-1.0.0-jar-with-dependencies.jar') + " " + args.prop + " RICHEDITSCRIPT "
            output = shellCallTemplate(cmd)
            logging.info(output)
-        elif job =='loadRES':
+        # elif job =='loadRES':
-            cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " LOAD " + rootType
+        #     cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " LOAD " + rootType
-            output = shellCallTemplate(cmd)
+        #     output = shellCallTemplate(cmd)
-            logging.info(output)
+        #     logging.info(output)
        elif job =='shapeSI':
            from pairs import shapePairs
@@ -66,14 +65,14 @@ if __name__ == '__main__':
            importShape()
        elif job =='compareShapes':
-             # cmd = "mvn exec:java -f '/data/fixminer_source/' -Dexec.mainClass='edu.lu.uni.serval.fixminer.akka.compare.CompareTrees' -Dexec.args='"+ " shape " + join(DATA_PATH,"redis") +" ALLdumps-gumInput.rdb " + "clusterl0-gumInputALL.rdb /data/fixminer-core/python/data/richEditScript'"
+             # cmd = "mvn exec:java -f '/data/fixminer_source/' -Dexec.mainClass='edu.lu.uni.serval.richedit.akka.compare.CompareTrees' -Dexec.args='"+ " shape " + join(DATA_PATH,"redis") +" ALLdumps-gumInput.rdb " + "clusterl0-gumInputALL.rdb /data/richedit-core/python/data/richEditScript'"
-            cmd = "JAVA_HOME='" + jdk8 + "' java  -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " COMPARE " + 'L1'
+            cmd = "JAVA_HOME='" + jdk8 + "' java  -jar " + join(Path(ROOT_DIR).parent, 'target','FixPatternMiner-1.0.0-jar-with-dependencies.jar') + " " + args.prop + " COMPARE "
            output = shellCallTemplate(cmd)
            logging.info(output)
-        elif job == 'clusterAdditional':
+        # elif job == 'clusterAdditional':
-            from addNewData import cluster
+        #     from addNewData import cluster
-            cluster()
+        #     cluster()
        elif job == 'cluster':
            from abstractPatch import cluster
@@ -125,11 +124,11 @@ if __name__ == '__main__':
            cluster(join(DATA_PATH, 'tokens'), join(DATA_PATH, 'pairsToken'),'tokens')
            stopDB(dbDir, "6380", "clusterl2-gumInputALL.rdb")
-        elif job == 'additional':
+        # elif job == 'additional':
-            from addNewData import core
+        #     from addNewData import core
-            core()
+        #     core()
-            # from addNewData import checkWrongMembers
+        #     # from addNewData import checkWrongMembers
-            # checkWrongMembers()
+        #     # checkWrongMembers()
        elif job == 'codeflaws':
            from otherDatasets import codeflaws
@@ -1,20 +1,20 @@
 java:
    8home:  /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
 spinfer:
-    home:   /Users/anil.koyuncu/projects/fixminer/spinfer/spinfer.native
+    home:   /Users/anil.koyuncu/projects/richedit/spinfer/spinfer.native
    #home:   /Users/anil.koyuncu/projects/spinfer/spinfer.native
 dataset:
-#    home:   /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/
+#    home:   /Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/
-    home:   /Users/anil.koyuncu/projects/fixminer/fixminer-data/patches/
+    home:   /Users/anil.koyuncu/projects/richedit/richedit-data/patches/
-#    home:   /data/fixminer-core/python/data/gumInputLinux/
+#    home:   /data/richedit-core/python/data/gumInputLinux/
    repo:   /Users/anil.koyuncu/projects/datasets
 coccinelle:
-    home:   /Users/anil.koyuncu/projects/fixminer/spinfer/statics
+    home:   /Users/anil.koyuncu/projects/richedit/spinfer/statics
    #home:   /Users/anil.koyuncu/projects/spinfer/statics
 fixminer:
-#    datapath: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/
+#    datapath: /Users/anil.koyuncu/projects/test/richedit-core/python/data/
-    datapath: /Users/anil.koyuncu/projects/fixminer/fixminer-data
+    datapath: /Users/anil.koyuncu/projects/richedit/richedit-data
-#    datapath: /data/fixminer-core/python/data/
+#    datapath: /data/richedit-core/python/data/
@@ -5,6 +5,7 @@ COMMIT_DFS = os.environ["COMMIT_DFS"]
 DATASET_PATH = os.environ["REPO_PATH"]
 DATASET = os.environ["dataset"]
 ROOT = os.environ["ROOT_DIR"]
 PROJECT_LIST = os.environ["PROJECT_LIST"]
 def filetype_fileter(filename):
    # return filename.endswith(u'.java') and not bool(re.search('test.*\/', filename))
@@ -266,16 +267,24 @@ def getAllCommits(datasetName):
 def core():
    datasets = pd.read_csv(join(ROOT,'data', 'datasets.csv'))
    # repoList = ['FFmpeg','curl','nginx','openssl','redis','tmux','vlc']
-    pjs = listdir(DATASET_PATH)
+
-    # newRepo = ['php-src','libtiff','cpython']
+    pjList = PROJECT_LIST.split(',')
-    pjs = [i for i in pjs if not (i.startswith('.') or i.startswith('codeflaws'))]
+    if not os.path.exists(DATASET_PATH):
-    # pjs = [i for i in pjs if (i in newRepo )]
+        os.mkdir(DATASET_PATH)
-    repoList = pjs
+
    for repo,src in datasets.values.tolist():
-        cmd = 'git -C ' + DATASET_PATH + ' clone ' + src
+        if(pjList != ['ALL']):
-        shellCallTemplate(cmd)
+            if repo in pjList:
-        logging.info(repo)
+                 print(repo)
-        collectBugFixPatches(repo)
+                 cmd = 'git -C ' + DATASET_PATH + ' clone ' + src
                 shellCallTemplate(cmd)
                 logging.info(repo)
                 collectBugFixPatches(repo)
        else:
            cmd = 'git -C ' + DATASET_PATH + ' clone ' + src
            shellCallTemplate(cmd)
            logging.info(repo)
            collectBugFixPatches(repo)
 def codeflaws():
    cf = listdir(join(DATASET_PATH,'codeflaws'))
@@ -1,21 +1,21 @@
 java:
    8home:  /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
 spinfer:
-    home:   /Users/anilkoyuncu/projects/fixminer/spinfer/spinfer.native
+    home:   /Users/anilkoyuncu/projects/richedit/spinfer/spinfer.native
    #home:   /Users/anil.koyuncu/projects/spinfer/spinfer.native
 dataset:
-#    home:   /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/
+#    home:   /Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/
-    home:   /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux
+    home:   /Users/anilkoyuncu/projects/richedit/richedit-core/python/data/gumInputLinux
-#    home:   /data/fixminer-core/python/data/gumInputLinux/
+#    home:   /data/richedit-core/python/data/gumInputLinux/
-    repo:   /Users/anil.koyuncu/projects/datasets
+    repo:   /Users/anilkoyuncu/projects/datasets
 coccinelle:
-    home:   /Users/anilkoyuncu/projects/fixminer/spinfer/statics
+    home:   /Users/anilkoyuncu/projects/richedit/spinfer/statics
    #home:   /Users/anil.koyuncu/projects/spinfer/statics
 fixminer:
-#    datapath: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/
+#    datapath: /Users/anil.koyuncu/projects/test/richedit-core/python/data/
-    datapath: /Users/anilkoyuncu/projects/fixminer/fixminer-data/
+    datapath: /Users/anilkoyuncu/projects/richedit/richedit-data/
    projectType : c
-#    datapath: /data/fixminer-core/python/data/
+#    datapath: /data/richedit-core/python/data/
@@ -5,7 +5,13 @@
 	<groupId>edu.lu.uni.serval</groupId>
 	<artifactId>RichEdit</artifactId>
 	<version>1.0.0</version>
-	<packaging>jar</packaging>
+
 <!--	<parent>-->
 <!--		<groupId>edu.lu.uni.serval</groupId>-->
 <!--		<artifactId>FixPatternMiner</artifactId>-->
 <!--		<version>1.0.0</version>-->
 <!--	</parent>-->
 <!--	<packaging>pom</packaging>-->
 	<name>RichEdit</name>
 	<url>http://maven.apache.org</url>
@@ -46,21 +52,21 @@
 		<dependency>
 			<groupId>com.github.gumtreediff</groupId>
 			<artifactId>core</artifactId>
-			<scope>compile</scope>
+<!--			<scope>compile</scope>-->
 			<version>${gumtree.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>com.github.gumtreediff</groupId>
 			<artifactId>gen.jdt</artifactId>
-			<scope>compile</scope>
+<!--			<scope>compile</scope>-->
 			<version>${gumtree.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>com.github.gumtreediff</groupId>
 			<artifactId>gen.srcml</artifactId>
-			<scope>compile</scope>
+<!--			<scope>compile</scope>-->
 			<version>${gumtree.version}</version>
 		</dependency>
@@ -110,6 +116,11 @@
 			<version>${commons-io.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.yaml</groupId>
 			<artifactId>snakeyaml</artifactId>
 			<version>1.21</version>
 		</dependency>
@@ -127,6 +138,19 @@
 					<target>1.8</target>
 				</configuration>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
 				<version>2.2.1</version>
 				<executions>
 					<execution>
 						<id>attach-sources</id>
 						<goals>
 							<goal>jar-no-fork</goal>
 						</goals>
 					</execution>
 				</executions>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
@@ -141,8 +165,8 @@
 							<archive>
 								<manifest>
 									<mainClass>
-										<!--edu.lu.uni.serval.fixminer.jobs.CompareTrees-->
+										<!--edu.lu.uni.serval.richedit.jobs.CompareTrees-->
-										edu.lu.uni.serval.fixminer.Launcher
+										edu.lu.uni.serval.Launcher
 									</mainClass>
 								</manifest>
 							</archive>
@@ -155,9 +179,11 @@
 			</plugin>
 		</plugins>
 	</build>
 </project>
-		<!--edu.lu.uni.serval.fixminer.Launcher
+		<!--edu.lu.uni.serval.richedit.Launcher
-		edu.lu.uni.serval.fixminer.jobs.CompareTrees
+		edu.lu.uni.serval.richedit.jobs.CompareTrees
 edu.lu.uni.serval.utils.ClusterToPattern
 		-->
@@ -1,16 +1,16 @@
-package edu.lu.uni.serval.fixminer;
+package edu.lu.uni.serval;
-import edu.lu.uni.serval.fixminer.jobs.CompareTrees;
+import edu.lu.uni.serval.richedit.jobs.CompareTrees;
-import edu.lu.uni.serval.fixminer.jobs.EnhancedASTDiff;
+import edu.lu.uni.serval.richedit.jobs.EnhancedASTDiff;
 import edu.lu.uni.serval.utils.ClusterToPattern;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.yaml.snakeyaml.Yaml;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.net.InetAddress;
+import java.util.Map;
 import java.net.UnknownHostException;
 import java.util.Properties;
 /**
@@ -43,26 +43,40 @@ public class Launcher {
 //        else{
 //             appConfigPath = "src/main/resource/"+hostname.split("\\.")[0]+".app.properties";
 //        }
        if(args.length != 2)
        {
            System.out.println("Proper Usage is: \n\tfirst argument full path to .properties file (e.g. an example is located under resources) \n\tsecond argument jobType (e.g RICHEDITSCRIPT, COMPARE)");
            System.exit(0);
        }
        String appConfigPath = args[0];
        Yaml yaml = new Yaml();
 //        InputStream inputStream = this.getClass()
 //                .getClassLoader()
 //                .getResourceAsStream("customer.yaml");
        Map<String, Object> obj = yaml.load(new FileInputStream(appConfigPath));
        appProps.load(new FileInputStream(appConfigPath));
        Map<String, Object> fixminer = (Map<String, Object>) obj.get("fixminer");
 //        String numOfWorkers = appProps.getProperty("numOfWorkers", "10");
        String numOfWorkers = String.valueOf(fixminer.get("numOfWorkers"));
        String portDumps = String.valueOf(fixminer.get("portDumps"));
        String projectType = (String) fixminer.get("projectType");
-        String numOfWorkers = appProps.getProperty("numOfWorkers", "10");
+        String hunkLimit = String.valueOf(fixminer.get("hunkLimit"));
-        String portDumps = appProps.getProperty("portDumps","6399");
+        String patchSize = String.valueOf(fixminer.get("patchSize"));
-        String projectType = appProps.getProperty("projectType","java");
+        String projectL = (String) fixminer.get("projectList");
        String hunkLimit = appProps.getProperty("hunkLimit","10");
        String patchSize = appProps.getProperty("patchSize","50");
        String projectL = appProps.getProperty("projectList","");
        String[] projectList = projectL.split(",");
-        String input = appProps.getProperty("inputPath","FORKJOIN");
+        String input = (String) fixminer.get("inputPath");
-        String redisPath = appProps.getProperty("redisPath","FORKJOIN");
+        String redisPath = (String) fixminer.get("redisPath");
-        String srcMLPath = appProps.getProperty("srcMLPath","FORKJOIN");
+        String srcMLPath = (String) fixminer.get("srcMLPath");
 //        String parameter = args[2];
        String parameter = "L1";
-//        String jobType = args[1];
+        String jobType = args[1];
 //        String jobType = "RICHEDITSCRIPT";
-        String jobType = "COMPARE";
+//        String jobType = "COMPARE";
        mainLaunch( numOfWorkers, jobType, portDumps,projectType,input,redisPath,parameter, srcMLPath,hunkLimit,projectList,patchSize);
@@ -121,7 +135,8 @@ public class Launcher {
            }
        } catch (Exception e) {
-            e.printStackTrace();
+            log.error(e.getMessage());
 //            e.printStackTrace();
        }
@@ -1,7 +1,7 @@
-package edu.lu.uni.serval.fixminer;
+package edu.lu.uni.serval.richedit;
-import edu.lu.uni.serval.fixminer.jobs.CompareTrees;
+import edu.lu.uni.serval.richedit.jobs.CompareTrees;
-import edu.lu.uni.serval.fixminer.jobs.EnhancedASTDiff;
+import edu.lu.uni.serval.richedit.jobs.EnhancedASTDiff;
 import edu.lu.uni.serval.utils.ClusterToPattern;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -15,9 +15,9 @@ import java.util.Properties;
 /**
 * Created by anilkoyuncu on 14/04/2018.
 */
-public class Launcher {
+public class Launcher2 {
-    private static Logger log = LoggerFactory.getLogger(Launcher.class);
+    private static Logger log = LoggerFactory.getLogger(Launcher2.class);
    public static void main(String[] args) throws IOException {
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 /**
 * Created by anilkoyuncu on 18/09/2018.
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import akka.actor.ActorRef;
 import akka.actor.Props;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import com.github.gumtreediff.tree.ITree;
 import edu.lu.uni.serval.utils.EDiffHelper;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import redis.clients.jedis.JedisPool;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import com.github.gumtreediff.actions.model.Action;
 import com.github.gumtreediff.gen.srcml.GumTreeCComparer;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import akka.actor.Props;
 import akka.actor.UntypedActor;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import com.github.gumtreediff.actions.model.Action;
 import com.github.gumtreediff.tree.ITree;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import com.github.gumtreediff.actions.model.*;
 import com.github.gumtreediff.tree.ITree;
@@ -1,7 +1,6 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import com.github.gumtreediff.actions.model.Action;
 import com.github.gumtreediff.actions.model.*;
 import com.github.gumtreediff.gen.srcml.NodeMap_new;
 import com.github.gumtreediff.tree.ITree;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import java.io.File;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import redis.clients.jedis.JedisPool;
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 public interface ParserInterface {
@@ -1,4 +1,4 @@
-package edu.lu.uni.serval.fixminer.ediff;
+package edu.lu.uni.serval.richedit.ediff;
 import redis.clients.jedis.JedisPool;
@@ -1,6 +1,5 @@
-package edu.lu.uni.serval.fixminer.jobs;
+package edu.lu.uni.serval.richedit.jobs;
 import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
 import edu.lu.uni.serval.utils.CallShell;
 import edu.lu.uni.serval.utils.EDiffHelper;
 import edu.lu.uni.serval.utils.PoolBuilder;
@@ -31,7 +30,7 @@ public class CompareTrees {
    public static void main(String redisPath, String portDumps, String dumpsName, String job,String numOfWorkers) throws Exception {
-        // shape /Users/anil.koyuncu/projects/test/fixminer-core/python/data/redis ALLdumps-gumInput.rdb clusterl0-gumInputALL.rdb /Users/anil.koyuncu/projects/test/fixminer-core/python/data/richEditScript
+        // shape /Users/anil.koyuncu/projects/test/richedit-core/python/data/redis ALLdumps-gumInput.rdb clusterl0-gumInputALL.rdb /Users/anil.koyuncu/projects/test/richedit-core/python/data/richEditScript
 //        String portInner = "6380";
        String port = portDumps; //"6399";
@@ -1,8 +1,8 @@
-package edu.lu.uni.serval.fixminer.jobs;
+package edu.lu.uni.serval.richedit.jobs;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
 import edu.lu.uni.serval.utils.FileHelper;
-import edu.lu.uni.serval.fixminer.ediff.MessageFile;
+import edu.lu.uni.serval.richedit.ediff.MessageFile;
 import edu.lu.uni.serval.utils.CallShell;
 import edu.lu.uni.serval.utils.PoolBuilder;
 import me.tongfei.progressbar.ProgressBar;
@@ -47,6 +47,9 @@ public class EnhancedASTDiff {
 		}
 		File folder = new File(inputPath);
 		File[] listOfFiles = folder.listFiles();
 		if(listOfFiles == null){
 			throw new Exception("No projects found, please verify the projects in the input path");
 		}
 		Stream<File> stream = Arrays.stream(listOfFiles);
 		List<File> folders;
 		if (projectList.length == 1 && projectList[0].equals("")){
@@ -5,7 +5,7 @@ import com.github.gumtreediff.gen.srcml.NodeMap_new;
 import com.github.gumtreediff.tree.ITree;
 import com.github.gumtreediff.tree.TreeContext;
 import com.github.gumtreediff.tree.TreeUtils;
-import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import org.apache.commons.lang3.SerializationUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -8,10 +8,10 @@ projectList =
 #projectList = libtiff,php-src,cpython,wireshark,gzip,gmp,lighttpd1.4,lighttpd2
 #inputPath = /Users/anilkoyuncu/projects/gumInputLinux
-#inputPath = /Users/anil.koyuncu/projects/fixminer/fixminer-data/gumInputLinux
+#inputPath = /Users/anil.koyuncu/projects/richedit/richedit-data/gumInputLinux
 inputPath = /Users/anil.koyuncu/projects/test/fixminer-data/patches
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
 redisPath = /Users/anil.koyuncu/projects/test/fixminer-core/python/data/redis
 #srcMLPath=  /Users/anil.koyuncu/Downloads/srcML.0.9.5/bin/srcml
 srcMLPath=  /Users/anil.koyuncu/projects/test/srcML/bin/srcml
@@ -9,10 +9,10 @@ patchSize = 50
 projectList = libtiff,php-src,cpython,wireshark,gzip,gmp,lighttpd1.4,lighttpd2
 #inputPath = /Users/anilkoyuncu/projects/gumInputLinux
-#inputPath = /Users/anil.koyuncu/projects/fixminer/fixminer-data/gumInputLinux
+#inputPath = /Users/anil.koyuncu/projects/richedit/richedit-data/gumInputLinux
 inputPath = /Users/anil.koyuncu/projects/test/fixminer-data/patches
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
 redisPath = /Users/anil.koyuncu/projects/test/fixminer-core/python/data/redis
 #srcMLPath=  /Users/anil.koyuncu/Downloads/srcML.0.9.5/bin/srcml
 srcMLPath=  /usr/local/bin/srcml
@@ -9,7 +9,7 @@ patchSize = 50
 projectList = codeflaws
 #inputPath = /Users/anilkoyuncu/projects/gumInputLinux
 inputPath = /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
 redisPath = /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/redis
 #srcMLPath=  /Users/anil.koyuncu/Downloads/srcML/src2srcml
 srcMLPath=  /usr/local/bin/srcml
@@ -1,7 +1,7 @@
 package edu.lu.uni.serval.FixPatternMiner;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
-import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import java.io.File;
 import java.io.FileInputStream;
@@ -33,7 +33,7 @@ public class BaseTest {
            List<HierarchicalActionSet> hierarchicalActionSets = parser.parseChangedSourceCodeWithGumTree2(prevFile, revFile, srcMLPath,false);
            return hierarchicalActionSets;
        }catch (NullPointerException n){
-//            String cmd = "cp /Users/anil.koyuncu/projects/test/fixminer-data/patches/codeflaws/"+n.getMessage().split(root)[1] + " /Users/anil.koyuncu/projects/test/fixminerC/"+n.getMessage();
+//            String cmd = "cp /Users/anil.koyuncu/projects/test/richedit-data/patches/codeflaws/"+n.getMessage().split(root)[1] + " /Users/anil.koyuncu/projects/test/fixminerC/"+n.getMessage();
 //            CallShell cs = new CallShell();
 //            try {
 //                cs.runShell(cmd);
@@ -1,8 +1,8 @@
 package edu.lu.uni.serval.FixPatternMiner;
 import com.github.gumtreediff.tree.ITree;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
-import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import edu.lu.uni.serval.utils.ClusterToPattern;
 import edu.lu.uni.serval.utils.EDiffHelper;
 import edu.lu.uni.serval.utils.PoolBuilder;
@@ -16,16 +16,17 @@ import java.io.File;
 import java.io.IOException;
 import java.time.Duration;
 import java.time.Instant;
-import java.util.*;
+import java.util.ArrayList;
@Ignore
 public class HunkParserTest extends BaseTest{
    @Test
    public void testSimple() throws IOException {
-//        String input = "/Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/revFiles/7f52f3_3845d29_drivers#pci#host#pcie-altera.c";
+//        String input = "/Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/revFiles/7f52f3_3845d29_drivers#pci#host#pcie-altera.c";
 //        String root = "//Users/anilkoyuncu/projects/gumInputLinux/";
-        String root = "/Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux/";
+        String root = "/Users/anilkoyuncu/projects/richedit/richedit-core/python/data/gumInputLinux/";
        String filename ="";
 //        filename ="freebsd_ceca9b8_b864ac4_sys#kern#sched_ule.c"; //too long
 //        filename ="openbsd_e592ec_39c81a_sys#arch#i386#pci#pci_machdep.c"; //not parseable 56 "parameter_list" "" () ( (57 "parameter" "" () ( (22 "decl" "" () ())))
@@ -91,7 +92,7 @@ public class HunkParserTest extends BaseTest{
    public void dumpFnction() throws Exception {
        String pattern = "function/20/gstreamer_0af74c_e8bae0_libs#gst#net#gstptpclock.c.txt_0";
 //        String pattern = "function/20/FFmpeg_4c9d1c_3da860_libavutil#file_open.c.txt_0";
-        ClusterToPattern.main("6399","/Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis","ALLdumps-gumInput.rdb ",pattern);
+        ClusterToPattern.main("6399","/Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis","ALLdumps-gumInput.rdb ",pattern);
    }
    @Test
@@ -112,7 +113,7 @@ public class HunkParserTest extends BaseTest{
    public void testSimpleJava() throws IOException {
-        String root = "/Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInput/spring-amqp/";
+        String root = "/Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInput/spring-amqp/";
        String filename = "5d6e02_e597c5_spring-rabbit#src#main#java#org#springframework#amqp#rabbit#connection#ConnectionFactoryUtils.java";
        File revFile = new File(root +"/revFiles/"+filename);
@@ -134,7 +135,7 @@ public class HunkParserTest extends BaseTest{
        final JedisPool outerPool = new JedisPool(PoolBuilder.getPoolConfig(), "localhost",Integer.valueOf("6399"),20000000);
        EDiffHunkParser parser = new EDiffHunkParser();
-        String root = "/Users/anil.koyuncu/projects/fixminer/gumInputLinux/linux/";
+        String root = "/Users/anil.koyuncu/projects/richedit/gumInputLinux/linux/";
        String filename = "43f8987_f596c8_drivers#acpi#nfit#core.c";
        File revFile = new File(root + "revFiles/"+ filename);
        File prevFile =new File(root + "prevFiles/prev_"+filename);
@@ -142,7 +143,7 @@ public class HunkParserTest extends BaseTest{
        String srcMLPath = "/Users/anil.koyuncu/Downloads/srcML/src2srcml";
        parser.parseFixPatterns(prevFile,revFile,diffFile,"gumInputLinux",outerPool,srcMLPath,"if",false);
        String key = "if/3/linux_bb67dd_0922c7_sound#soc#sof#intel#hda.c.txt_0";
-        File file2load = new File("/Users/anil.koyuncu/projects/fixminer/dumps/"+ key);
+        File file2load = new File("/Users/anil.koyuncu/projects/richedit/dumps/"+ key);
        byte[] dump = FileUtils.readFileToByteArray(file2load);
 //        String line = FileHelper.readFile(file2load);
@@ -1,9 +1,8 @@
 package edu.lu.uni.serval.FixPatternMiner;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
-import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import edu.lu.uni.serval.utils.CallShell;
 import edu.lu.uni.serval.utils.EDiffHelper;
 import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
@@ -1236,7 +1235,7 @@ public class TestInputCases {
        List<HierarchicalActionSet> hierarchicalActionSets = parser.parseChangedSourceCodeWithGumTree2(prevFile, revFile, srcMLPath,false);
        return hierarchicalActionSets;
    }catch (NullPointerException n){
-        String cmd = "cp /Users/anil.koyuncu/projects/test/fixminer-data/patches/"+project+"/"+n.getMessage().split(root)[1] + " /Users/anil.koyuncu/projects/test/fixminerC/"+n.getMessage();
+        String cmd = "cp /Users/anil.koyuncu/projects/test/richedit-data/patches/"+project+"/"+n.getMessage().split(root)[1] + " /Users/anil.koyuncu/projects/test/fixminerC/"+n.getMessage();
        CallShell cs = new CallShell();
        try {
            cs.runShell(cmd);
@@ -1,7 +1,7 @@
 package edu.lu.uni.serval.FixPatternMiner;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
-import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import org.apache.commons.lang3.StringUtils;
 import org.junit.Assert;
 import org.junit.Ignore;
@@ -1,8 +1,8 @@
 package edu.lu.uni.serval.FixPatternMiner;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.EDiffHunkParser;
-import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
@@ -1,8 +1,7 @@
 package edu.lu.uni.serval.FixPatternMiner;
 import com.github.gumtreediff.tree.ITree;
-import edu.lu.uni.serval.fixminer.ediff.EDiffHunkParser;
+import edu.lu.uni.serval.richedit.ediff.HierarchicalActionSet;
 import edu.lu.uni.serval.fixminer.ediff.HierarchicalActionSet;
 import edu.lu.uni.serval.utils.CallShell;
 import edu.lu.uni.serval.utils.EDiffHelper;
 import org.junit.Assert;
@@ -8,10 +8,10 @@ projectList =
 #projectList = libtiff,php-src,cpython,wireshark,gzip,gmp,lighttpd1.4,lighttpd2
 #inputPath = /Users/anilkoyuncu/projects/gumInputLinux
-#inputPath = /Users/anil.koyuncu/projects/fixminer/fixminer-data/gumInputLinux
+#inputPath = /Users/anil.koyuncu/projects/richedit/richedit-data/gumInputLinux
 inputPath = /Users/anil.koyuncu/projects/test/fixminer-data/patches
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
 redisPath = /Users/anil.koyuncu/projects/test/fixminer-core/python/data/redis
 #srcMLPath=  /Users/anil.koyuncu/Downloads/srcML.0.9.5/bin/srcml
 srcMLPath=  /Users/anil.koyuncu/projects/test/srcML/bin/srcml
@@ -9,10 +9,10 @@ patchSize = 50
 projectList = libtiff,php-src,cpython,wireshark,gzip,gmp,lighttpd1.4,lighttpd2
 #inputPath = /Users/anilkoyuncu/projects/gumInputLinux
-#inputPath = /Users/anil.koyuncu/projects/fixminer/fixminer-data/gumInputLinux
+#inputPath = /Users/anil.koyuncu/projects/richedit/richedit-data/gumInputLinux
 inputPath = /Users/anil.koyuncu/projects/test/fixminer-data/patches
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
 redisPath = /Users/anil.koyuncu/projects/test/fixminer-core/python/data/redis
 #srcMLPath=  /Users/anil.koyuncu/Downloads/srcML.0.9.5/bin/srcml
 srcMLPath=  /usr/local/bin/srcml
@@ -0,0 +1,28 @@
 java:
    8home:  /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
 spinfer:
    home:   /Users/anilkoyuncu/projects/fixminer/spinfer/spinfer.native
 coccinelle:
    home:   /Users/anilkoyuncu/projects/fixminer/spinfer/statics
 dataset:
 #    home:   /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux
    inputPath : /Users/anilkoyuncu/projects/test/fixminer-data/patches
    repo:   /Users/anilkoyuncu/projects/test/fixminer-data/datasets
 fixminer:
    projectType : c
    datapath: /Users/anilkoyuncu/projects/test/fixminer-data/
    pjName : patches
    portDumps : 6399
    numOfWorkers : 14
    hostname : localhost
    hunkLimit : 10
    patchSize : 50
    projectList : libtiff,gzip,gmp,lighttpd1.4,lighttpd2
    inputPath : /Users/anilkoyuncu/projects/test/fixminer-data/patches
    redisPath : /Users/anilkoyuncu/projects/test/fixminer-core/python/data/redis
    srcMLPath :  /usr/local/bin/srcml
@@ -9,7 +9,7 @@ patchSize = 50
 projectList = codeflaws
 #inputPath = /Users/anilkoyuncu/projects/gumInputLinux
 inputPath = /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux
-#redisPath = /Users/anil.koyuncu/projects/fixminer/fixminer-core/python/data/redis
+#redisPath = /Users/anil.koyuncu/projects/richedit/richedit-core/python/data/redis
 redisPath = /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/redis
 #srcMLPath=  /Users/anil.koyuncu/Downloads/srcML/src2srcml
 srcMLPath=  /usr/local/bin/srcml
`@@ -1,4 +1,4 @@`
	`package edu.lu.uni.serval.fixminer.ediff;`	`package edu.lu.uni.serval.richedit.ediff;`

	`import redis.clients.jedis.JedisPool;`	`import redis.clients.jedis.JedisPool;`