From 296120cf83ac8bae853a494ebdbe6bdcd78606e6 Mon Sep 17 00:00:00 2001
From: mimic <fse19@github.com>
Date: Mon, 8 Jun 2020 11:43:24 +0200
Subject: [PATCH 1/2] change

---
 .idea/encodings.xml                           |    8 +
 .idea/workspace.xml                           | 1232 ++---------------
 README.md                                     |    7 +
 fixminer.sh                                   |    6 +
 .../__pycache__/__init__.cpython-37.pyc       |  Bin 169 -> 165 bytes
 python/javaDS.py                              |    2 +
 .../main/java/edu/lu/uni/serval/Launcher.java |    3 +-
 .../serval/richedit/jobs/EnhancedASTDiff.java |   50 +-
 src/main/resources/config.yml                 |   12 +-
 9 files changed, 180 insertions(+), 1140 deletions(-)
 create mode 100644 fixminer.sh

diff --git a/.idea/encodings.xml b/.idea/encodings.xml
index 3b2fa6d..03b68ee 100644
--- a/.idea/encodings.xml
+++ b/.idea/encodings.xml
@@ -5,9 +5,17 @@
     <file url="file://$PROJECT_DIR$/gumtree" charset="UTF-8" />
     <file url="file://$PROJECT_DIR$/gumtree/client" charset="UTF-8" />
     <file url="file://$PROJECT_DIR$/gumtree/client.diff" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/gumtree/client.diff/src/main/java" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/gumtree/client.diff/src/main/resources" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/gumtree/client/src/main/java" charset="UTF-8" />
     <file url="file://$PROJECT_DIR$/gumtree/core" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/gumtree/core/src/main/java" charset="UTF-8" />
     <file url="file://$PROJECT_DIR$/gumtree/gen.jdt" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/gumtree/gen.jdt/src/main/java" charset="UTF-8" />
     <file url="file://$PROJECT_DIR$/gumtree/gen.srcml" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/gumtree/gen.srcml/src/main/java" charset="UTF-8" />
     <file url="file://$PROJECT_DIR$/richedit" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/richedit/src/main/java" charset="UTF-8" />
+    <file url="file://$PROJECT_DIR$/src/main/resources" charset="UTF-8" />
   </component>
 </project>
\ No newline at end of file
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index cbfff81..9f27d8d 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -2,36 +2,14 @@
 <project version="4">
   <component name="ChangeListManager">
     <list default="true" id="75ef5724-93bc-4ed4-82b2-ff12411188dc" name="Default Changelist" comment="">
+      <change beforePath="$PROJECT_DIR$/.idea/encodings.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/encodings.xml" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/com/github/gumtreediff/gen/jdt/AbstractJdtVisitor.java" beforeDir="false" afterPath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/com/github/gumtreediff/gen/jdt/AbstractJdtVisitor.java" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gen/jdt/exp/ExpJdtVisitor.java" beforeDir="false" afterPath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gen/jdt/exp/ExpJdtVisitor.java" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeComparer.java" beforeDir="false" afterPath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeComparer.java" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeGenerator.java" beforeDir="false" afterPath="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeGenerator.java" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/abstractPatch.py" beforeDir="false" afterPath="$PROJECT_DIR$/python/abstractPatch.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/bugReport.pdf" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/common/commons.py" beforeDir="false" afterPath="$PROJECT_DIR$/python/common/commons.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/data/FixPatternMiner-1.0.0.jar" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/data/FixPatternMiner-1.0.1.jar" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/data/bugReports.7z.001" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/data/bugReports.7z.002" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/data/bugReports.7z.003" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/data/gumInput.7z.001" beforeDir="false" />
-      <change beforePath="$PROJECT_DIR$/python/main.py" beforeDir="false" afterPath="$PROJECT_DIR$/python/main.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffParser.java" beforeDir="false" afterPath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffParser.java" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouper.java" beforeDir="false" afterPath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouper.java" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/BaseTest.java" beforeDir="false" afterPath="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/BaseTest.java" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/README.md" beforeDir="false" afterPath="$PROJECT_DIR$/README.md" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/python/javaDS.py" beforeDir="false" afterPath="$PROJECT_DIR$/python/javaDS.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/Launcher.java" beforeDir="false" afterPath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/Launcher.java" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java" beforeDir="false" afterPath="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/src/main/resources/config.yml" beforeDir="false" afterPath="$PROJECT_DIR$/src/main/resources/config.yml" afterDir="false" />
     </list>
-    <ignored path="$PROJECT_DIR$/classes/" />
-    <ignored path="$PROJECT_DIR$/target/" />
-    <ignored path="$PROJECT_DIR$/richedit/target/" />
-    <ignored path="$PROJECT_DIR$/gumtree/gen.srcml/target/" />
-    <ignored path="$PROJECT_DIR$/gumtree/core/target/" />
-    <ignored path="$PROJECT_DIR$/gumtree/client.diff/target/" />
-    <ignored path="$PROJECT_DIR$/gumtree/gen.jdt/target/" />
-    <ignored path="$PROJECT_DIR$/gumtree/client/target/" />
-    <ignored path="$PROJECT_DIR$/gumtree/target/" />
-    <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
     <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
@@ -40,94 +18,6 @@
   <component name="DefaultGradleProjectSettings">
     <option name="isMigrated" value="true" />
   </component>
-  <component name="FileEditorManager">
-    <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
-      <file pinned="false" current-in-tab="true">
-        <entry file="file://$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/TestJavaMiner.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="192">
-              <caret line="592" column="27" selection-start-line="592" selection-start-column="27" selection-end-line="592" selection-end-column="27" />
-              <folding>
-                <element signature="imports" expanded="true" />
-              </folding>
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/com/github/gumtreediff/gen/jdt/AbstractJdtTreeGenerator.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="375">
-              <caret line="67" selection-start-line="67" selection-end-line="67" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffParser.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="168">
-              <caret line="56" column="26" selection-start-line="56" selection-start-column="12" selection-end-line="56" selection-end-column="26" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeComparer.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="117">
-              <caret line="23" column="24" selection-start-line="23" selection-start-column="24" selection-end-line="23" selection-end-column="24" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalActionSet.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="-1273">
-              <caret line="15" column="13" selection-start-line="15" selection-start-column="13" selection-end-line="15" selection-end-column="13" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouper.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="286">
-              <caret line="111" selection-start-line="111" selection-end-line="111" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouperForC.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="212">
-              <caret line="91" column="12" selection-start-line="91" selection-start-column="12" selection-end-line="96" selection-end-column="13" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/utils/ListSorter.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="120">
-              <caret line="11" column="11" selection-start-line="11" selection-start-column="11" selection-end-line="11" selection-end-column="11" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file pinned="false" current-in-tab="false">
-        <entry file="jar:///Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/src.zip!/java/lang/Comparable.java">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="509">
-              <caret line="135" column="15" selection-start-line="135" selection-start-column="15" selection-end-line="135" selection-end-column="15" />
-            </state>
-          </provider>
-        </entry>
-      </file>
-    </leaf>
-  </component>
   <component name="FileTemplateManagerImpl">
     <option name="RECENT_TEMPLATES">
       <list>
@@ -175,63 +65,6 @@
   <component name="Git.Settings">
     <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
   </component>
-  <component name="IdeDocumentHistory">
-    <option name="CHANGED_PATHS">
-      <list>
-        <option value="$PROJECT_DIR$/src/main/java/edu/lu/uni/serval/fixminer/Launcher.java" />
-        <option value="$PROJECT_DIR$/src/main/java/edu/lu/uni/serval/richedit/Launcher.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.jdt/pom.xml" />
-        <option value="$PROJECT_DIR$/gumtree/core/pom.xml" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/utils/FileHelper.java" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffWorker.java" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/utils/EDiffHelper.java" />
-        <option value="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/FixPatternMiner/HunkParserTest.java" />
-        <option value="$PROJECT_DIR$/python/fixminer.sh" />
-        <option value="$PROJECT_DIR$/src/main/java/edu/lu/uni/serval/Launcher.java" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/Launcher.java" />
-        <option value="$PROJECT_DIR$/python/data/callJava.sh" />
-        <option value="$PROJECT_DIR$/python/data/redis/stopServer.sh" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java" />
-        <option value="$PROJECT_DIR$/python/javaDS.py" />
-        <option value="$PROJECT_DIR$/python/otherDatasets.py" />
-        <option value="$PROJECT_DIR$/.gitignore" />
-        <option value="$PROJECT_DIR$/gumtree/core/src/test/java/com/github/gumtreediff/test/TreeLoader.java" />
-        <option value="$PROJECT_DIR$/gumtree/core/src/main/java/com/github/gumtreediff/io/TreeIoUtils.java" />
-        <option value="$PROJECT_DIR$/gumtree/core/src/test/java/com/github/gumtreediff/test/TestActionGenerator.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/test/java/com/github/gumtreediff/gen/srcml/TestSrcmlCGenerator.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/test/java/com/github/gumtreediff/gen/srcml/TestSrcmlCppGenerator.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/test/java/com/github/gumtreediff/gen/srcml/TestSrcmlCsGenerator.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/test/java/com/github/gumtreediff/gen/srcml/TestSrcmlJavaGenerator.java" />
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-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/main/java/com/github/gumtreediff/gen/srcml/SrcmlCTreeGenerator.java" />
-        <option value="$PROJECT_DIR$/.travis_native_dependencies.sh" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouperForC.java" />
-        <option value="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/TestRealCases.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/main/java/com/github/gumtreediff/gen/srcml/NodeMap_new.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.srcml/src/main/java/com/github/gumtreediff/gen/srcml/AbstractSrcmlTreeGenerator.java" />
-        <option value="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/TestPredefinedCases.java" />
-        <option value="$PROJECT_DIR$/gumtree/core/src/test/java/com/github/gumtreediff/test/TestActionIo.java" />
-        <option value="$PROJECT_DIR$/richedit/pom.xml" />
-        <option value="$PROJECT_DIR$/pom.xml" />
-        <option value="$PROJECT_DIR$/.travis.yml" />
-        <option value="$PROJECT_DIR$/gumtree/pom.xml" />
-        <option value="$PROJECT_DIR$/gumtree/client.diff/pom.xml" />
-        <option value="$PROJECT_DIR$/README.md" />
-        <option value="$PROJECT_DIR$/python/abstractPatch.py" />
-        <option value="$PROJECT_DIR$/src/main/resources/config.yml" />
-        <option value="$PROJECT_DIR$/python/common/commons.py" />
-        <option value="$PROJECT_DIR$/python/main.py" />
-        <option value="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeComparer.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gumtree/GumTreeGenerator.java" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffParser.java" />
-        <option value="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/BaseTest.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/com/github/gumtreediff/gen/jdt/AbstractJdtVisitor.java" />
-        <option value="$PROJECT_DIR$/gumtree/gen.jdt/src/main/java/edu/lu/uni/serval/gen/jdt/exp/ExpJdtVisitor.java" />
-        <option value="$PROJECT_DIR$/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/HierarchicalRegrouper.java" />
-        <option value="$PROJECT_DIR$/richedit/src/test/java/edu/lu/uni/serval/TestJavaMiner.java" />
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   <component name="MavenImportPreferences">
     <option name="generalSettings">
       <MavenGeneralSettings>
@@ -244,135 +77,16 @@
       </MavenImportingSettings>
     </option>
   </component>
-  <component name="MavenProjectNavigator">
-    <treeState>
-      <expand>
-        <path>
-          <item name="" type="16c1761:MavenProjectsStructure$RootNode" />
-          <item name="RichEdit" type="9519ce18:MavenProjectsStructure$ProjectNode" />
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-          <item name="RichEdit" type="9519ce18:MavenProjectsStructure$ProjectNode" />
-          <item name="Lifecycle" type="58874e2:MavenProjectsStructure$LifecycleNode" />
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-      <select />
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-  <component name="ProjectFrameBounds" fullScreen="true">
-    <option name="width" value="1680" />
-    <option name="height" value="1050" />
-  </component>
-  <component name="ProjectView">
-    <navigator proportions="" version="1">
-      <foldersAlwaysOnTop value="true" />
-    </navigator>
-    <panes>
-      <pane id="Scope" />
-      <pane id="PackagesPane" />
-      <pane id="ProjectPane">
-        <subPane>
-          <expand>
-            <path>
-              <item name="gumtree" type="b2602c69:ProjectViewProjectNode" />
-              <item name="fixminer_source" type="462c0819:PsiDirectoryNode" />
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-              <item name="python" type="462c0819:PsiDirectoryNode" />
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-  <component name="masterDetails">
-    <states>
-      <state key="ArtifactsStructureConfigurable.UI">
-        <settings>
-          <artifact-editor />
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="FacetStructureConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="GlobalLibrariesConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="JdkListConfigurable.UI">
-        <settings>
-          <last-edited>Python 3.7 (fixminerEnv)</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.38275862" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ModuleStructureConfigurable.UI">
-        <settings>
-          <last-edited>fixminer_source</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.38275862" />
-                <option value="0.6" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ProjectJDKs.UI">
-        <settings>
-          <last-edited>1.8</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ProjectLibrariesConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-    </states>
-  </component>
   <component name="mavenExecuteGoalHistory">
     <option value="" />
   </component>
diff --git a/README.md b/README.md
index 0ffe7ec..22bf4c0 100644
--- a/README.md
+++ b/README.md
@@ -71,6 +71,10 @@ In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
 
 * Update [config file](src/main/resources/config.yml) with corresponding user paths.
 
+* Install the project with maven from root. (usage [pom.xml](pom.xml))
+  ```powershell
+  mvn clean install
+  ```
 * Active the conda environment from shell
   ```powershell
   source activate fixminerEnv
@@ -81,6 +85,9 @@ In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
     bash fixminer.sh [JOB] [CONFIG_FILE]
      e.g. bash fixminer.sh  dataset4c /Users/projects/release/fixminer_source/src/main/resources/config.yml
 
+#### Redis Commands
+hlen diffEntry
+To see number of patches / diff entries computed rich edit
     
 #### Job Types  
 
diff --git a/fixminer.sh b/fixminer.sh
new file mode 100644
index 0000000..6354738
--- /dev/null
+++ b/fixminer.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+
+source activate fixminerEnv
+
+PYTHONPATH=$(pwd) python -u python/main.py -root $(pwd)/python -job $2 -prop $1
diff --git a/python/common/__pycache__/__init__.cpython-37.pyc b/python/common/__pycache__/__init__.cpython-37.pyc
index 46bb90d518aa8c4fae580d0802d9b9ac5a106195..5496b708cdefc04a236491f52c7a846aa572e2ff 100644
GIT binary patch
delta 39
tcmZ3<xRjCGiI<m)0SJ13+?~j6!Rx0VTAW%`te=>dnWHz+Uvgru4FJ-w3&;Qf

delta 43
xcmZ3=xRR0EiI<m)0SL63x+ij5@C50H7N-^!>nG-A=1dHbWGP84E}58N3jpKn3^M=#

diff --git a/python/javaDS.py b/python/javaDS.py
index 444e93b..10a6913 100644
--- a/python/javaDS.py
+++ b/python/javaDS.py
@@ -17,6 +17,8 @@ def createDS():
     pjList = PROJECT_LIST.split(',')
     if not os.path.exists(DATASET_PATH):
         os.mkdir(DATASET_PATH)
+    if not os.path.exists(COMMIT_DFS):
+        os.mkdir(COMMIT_DFS)
 
     subjects = pd.read_csv(join(ROOT,'data', 'dataset.csv'))
 
diff --git a/richedit/src/main/java/edu/lu/uni/serval/Launcher.java b/richedit/src/main/java/edu/lu/uni/serval/Launcher.java
index 823bf77..d3da760 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/Launcher.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/Launcher.java
@@ -135,7 +135,8 @@ public class Launcher {
 
             }
         } catch (Exception e) {
-            log.error(e.getMessage());
+//            log.error(e.getMessage());
+            e.printStackTrace();
 //            e.printStackTrace();
 
         }
diff --git a/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java b/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java
index c7d4ada..74e44ca 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java
@@ -29,37 +29,36 @@ public class EnhancedASTDiff {
 	public static void main(String inputPath, String portInner, String dbDir, String chunkName,String srcMLPath,String parameter,String hunkLimit,String[] projectList,String patchSize,String projectType) throws Exception {
 
 
-		String parameters = String.format("\nInput path %s",inputPath);
+		String parameters = String.format("\nInput path %s", inputPath);
 		log.info(parameters);
 
 		CallShell cs = new CallShell();
-		String cmd = "bash "+dbDir + "/" + "startServer.sh" +" %s %s %s";
+		String cmd = "bash " + dbDir + "/" + "startServer.sh" + " %s %s %s";
 
-		cmd = String.format(cmd, dbDir,chunkName,Integer.valueOf(portInner));
+		cmd = String.format(cmd, dbDir, chunkName, Integer.valueOf(portInner));
 
 		cs.runShell(cmd, portInner);
 
-		JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1",Integer.valueOf(portInner),20000000);
+		JedisPool innerPool = new JedisPool(PoolBuilder.getPoolConfig(), "127.0.0.1", Integer.valueOf(portInner), 20000000);
 
 		boolean isJava = false;
-		if (projectType.equals("java")){
-			isJava =true;
+		if (projectType.equals("java")) {
+			isJava = true;
 		}
 		File folder = new File(inputPath);
 		File[] listOfFiles = folder.listFiles();
-		if(listOfFiles == null){
+		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("")){
+		if (projectList.length == 1 && projectList[0].equals("")) {
 			folders = stream
 					.filter(x -> !x.getName().startsWith("."))
 					.filter(x -> !x.getName().startsWith("cocci"))
 					.filter(x -> !x.getName().endsWith(".index"))
 					.collect(Collectors.toList());
-		}
-		else {
+		} else {
 			List<Predicate<File>> allPredicates = new ArrayList<Predicate<File>>();
 			for (String s : projectList) {
 				Predicate<File> predicate = x -> x.getName().endsWith(s);
@@ -69,20 +68,16 @@ public class EnhancedASTDiff {
 					.filter(x -> !x.getName().startsWith("."))
 					.filter(x -> !x.getName().startsWith("cocci"))
 					.filter(x -> !x.getName().endsWith(".index"))
-					.filter(allPredicates.stream().reduce(x->false, Predicate::or))
+					.filter(allPredicates.stream().reduce(x -> false, Predicate::or))
 					.collect(Collectors.toList());
 		}
 
 
-
-
-
-
 		String project = folder.getName();
 		List<MessageFile> allMessageFiles = new ArrayList<>();
-        for (File target : folders) {
+		for (File target : folders) {
 
-			List<MessageFile> msgFiles = getMessageFiles(target.toString() + "/",project,patchSize,isJava); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/"
+			List<MessageFile> msgFiles = getMessageFiles(target.toString() + "/", project, patchSize, isJava); //"/Users/anilkoyuncu/bugStudy/code/python/GumTreeInput/Apache/CAMEL/"
 
 //			msgFiles = msgFiles.subList(0,3000);
 			if (msgFiles == null)
@@ -104,16 +99,25 @@ public class EnhancedASTDiff {
 			log.info("{} files to process ...", allMessageFiles.size());
 		}
 		boolean finalIsJava = isJava;
-		ProgressBar.wrap(allMessageFiles.stream().
-				parallel(),"Task").
+//		ProgressBar.wrap(allMessageFiles.stream().
+//				parallel(),"Task").
+//				forEach(m ->
+//						{
+//							EDiffHunkParser parser =  new EDiffHunkParser();
+//							parser.parseFixPatterns(m.getPrevFile(),m.getRevFile(), m.getDiffEntryFile(),project,innerPool,srcMLPath,hunkLimit, finalIsJava);
+//						}
+//				);
+//
+//        }
+		allMessageFiles.stream().
+				parallel().
 				forEach(m ->
 						{
-							EDiffHunkParser parser =  new EDiffHunkParser();
-							parser.parseFixPatterns(m.getPrevFile(),m.getRevFile(), m.getDiffEntryFile(),project,innerPool,srcMLPath,hunkLimit, finalIsJava);
+							EDiffHunkParser parser = new EDiffHunkParser();
+							parser.parseFixPatterns(m.getPrevFile(), m.getRevFile(), m.getDiffEntryFile(), project, innerPool, srcMLPath, hunkLimit, finalIsJava);
 						}
 				);
-
-        }
+	}
 
 	
 
diff --git a/src/main/resources/config.yml b/src/main/resources/config.yml
index 7131ddc..ed2c912 100644
--- a/src/main/resources/config.yml
+++ b/src/main/resources/config.yml
@@ -7,12 +7,12 @@ coccinelle:
 
 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
+    inputPath : /Users/anil.koyuncu/projects/release/fixminer-data/patches
+    repo:   /Users/anil.koyuncu/projects/release/fixminer-data/datasets
 
 fixminer:
     projectType : java
-    datapath: /Users/anilkoyuncu/projects/test/fixminer-data/
+    datapath: /Users/anil.koyuncu/projects/release/fixminer-data/
 
 
     pjName : patches
@@ -22,7 +22,7 @@ fixminer:
     hunkLimit : 2
     patchSize : 50
 
-    projectList : spring-shell,fuse,metadata,commons-codec,commons-collections,commons-compress,commons-configuration,commons-crypto,commons-csv
-    inputPath : /Users/anilkoyuncu/projects/test/fixminer-data/patches
-    redisPath : /Users/anilkoyuncu/projects/release/test/fixminer_source/python/data/redis
+    projectList : fuse
+    inputPath : /Users/anil.koyuncu/projects/release/fixminer-data/patches
+    redisPath : /Users/anil.koyuncu/projects/release/fixminer_source/python/data/redis
     srcMLPath :  /usr/local/bin/srcml

From a26275cf4a9af911137b38b4e108216bd29dbc87 Mon Sep 17 00:00:00 2001
From: mimic <fse19@github.com>
Date: Tue, 9 Jun 2020 14:51:19 +0200
Subject: [PATCH 2/2] enabled back token iteration

---
 README.md                                     |  60 +++---
 python/abstractPatch.py                       |  47 ++---
 python/main.py                                |  82 ++-------
 python/pairs.py                               | 174 +++---------------
 python/stats.py                               |  45 ++---
 python/tokens.py                              |   4 +-
 .../main/java/edu/lu/uni/serval/Launcher.java |  56 +++---
 .../edu/lu/uni/serval/richedit/Launcher2.java | 134 --------------
 .../richedit/ediff/EDiffHunkParser.java       |   4 +
 .../serval/richedit/jobs/CompareTrees.java    |  80 +++++++-
 .../serval/richedit/jobs/EnhancedASTDiff.java |   2 +-
 .../edu/lu/uni/serval/utils/EDiffHelper.java  |  32 +++-
 12 files changed, 256 insertions(+), 464 deletions(-)
 delete mode 100755 richedit/src/main/java/edu/lu/uni/serval/richedit/Launcher2.java

diff --git a/README.md b/README.md
index 3e8645d..7e2524b 100644
--- a/README.md
+++ b/README.md
@@ -34,6 +34,10 @@ You can cite FixMiner using the following bibtex:
 Fixminer is a systematic and automated approach to mine relevant and actionable fix patterns for automated program repair.
 ![The workflow of this technique.\label{workflow}](worflow.png)
 
+** This version of the Fixminer has some changes compared to the one published in the paper. 
+
+    - The iteration that was computing the shapes separetely is removed. Now the operation of the shape trees are performed together with the action trees. As a result of this change no shape clusters are generated separately anymore. The initial output of the pattern mining iteration is action trees (a.k.a patterns ) 
+
 ## II. Environment setup
 
 * OS: macOS Mojave (10.14.3)
@@ -82,8 +86,8 @@ In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
 
 In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
 
-    bash fixminer.sh [JOB] [CONFIG_FILE]
-     e.g. bash fixminer.sh  dataset4c /Users/projects/release/fixminer_source/src/main/resources/config.yml
+    bash fixminer.sh [CONFIG_FILE] [JOB]
+     e.g. bash fixminer.sh  /Users/projects/release/fixminer_source/src/main/resources/config.yml dataset4c
      
 A log file (app.log) is created after every execution of the [fixminer.sh]((python/fixminer.sh)). Please check this log file in order to access more information. 
  
@@ -91,30 +95,38 @@ A log file (app.log) is created after every execution of the [fixminer.sh]((pyth
     
 #### Job Types  
 
-*FixMiner* needs to specify a job to run.
+*FixMiner* needs to follow an execution, **in the order listed below** in order to create clusters of patches.
 
    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
       
-   2. __richEditScript__: Calls the jar file produced as the results as maven package to compute Rich edit scripts.
+   2. __richedit__: 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.
 
          ```powershell
          java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar  /Users/projects/release/fixminer_source/src/main/resources/config.yml RICHEDITSCRIPT
          ```   
-   3. __shapeSI__: Search index creation for shapes. The output of this step is written to __pairs__ folder which will be generated under __datapath__ in [config file](src/main/resources/config.yml)
+   3. __actionSI__: Search index creation for actions. The output of this step is written to __pairs__ folder which will be generated under __datapath__ in [config file](src/main/resources/config.yml)
     
    4. __compare__ : 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.
                              
-                           ```powershell
-                           java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar  /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARE
-                          
-                           ```     
-   5. __cluster__ : Forms clusters of identical trees. The output of this step is written to __shapes__ folder which will be generated under __datapath__ in [config file](src/main/resources/config.yml)
+        ```powershell
+        java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar  /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARE
+        ```       
+   5. __cluster__ : Forms clusters of identical trees. The output of this step is written to __actions__ folder which will be generated under __datapath__ in [config file](src/main/resources/config.yml)
    
-   6. __stats__: Calculate frequency statistics of the patterns under statsshapes.csv in datapath. The information is also written in app.log file.
+   6. __tokenSI__ : Search index creation for tokens. The output of this step is written to __pairsToken__ folder which will be generated under __datapath__ in [config file](src/main/resources/config.yml)
    
-   7. __exportPatterns__ : Export FixPatterns of APR integration under patterns folder located in datapath/
+   7. __compare__ : 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.
+                                   
+        ```powershell
+        java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar  /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARE
+        ```     
+   
+   8. __stats__: Calculate frequency statistics of the patterns under statsactions.csv in datapath. The information is also written in app.log file.
+   
+   7. __patterns__ : Export FixPatterns of APR integration under patterns folder located in datapath/
                                                                                                                    
    <!--
     
@@ -252,10 +264,11 @@ Connect to redis instance
      redis-cli -p 6399
   ```   
 
-We use 3 databases inside the redis, 0,1,2.
+We use 3 databases inside the redis, 0,1,2,3.
 DB 0 stores the richedit dumps, comparison indices
-DB 1 stores the filenames and their corresponding indices
-DB 2 stores the output of comparison, a.k.a same trees.
+DB 1 stores the filenames and their indices (used in comparison and stored in DB2, DB3) 
+DB 2 stores the output of comparison action trees.
+DB 3 stores the output of comparison token trees.
 
 In order to switch between these database use the following command
 
@@ -298,15 +311,18 @@ hgetall NAME_OF_THE_EXACT_KEY
 hgetall MethodDeclaration/40/fuse_67b14b_04e5b1_fabric#fabric-client#src#main#java#org#fusesource#fabric#jolokia#facade#facades#ProfileFacade.java.txt_1
 
 OUTPUT:
-1) "targetTree"
-2) "[(55@@[(31@@)][(31@@)][(31@@)][(31@@[(44@@)][(44@@)])][(31@@[(44@@[(74@@)][(74@@)][(74@@)])][(44@@)])][(31@@[(60@@[(74@@)][(74@@)][(74@@[(74@@)][(74@@)][(74@@)])])][(60@@[(59@@)][(59@@)])])][(31@@[(25@@[(27@@)][(27@@)][(27@@)])][(25@@[(8@@[(21@@[(32@@)][(32@@[(42@@)][(42@@)])])])][(8@@[(21@@[(32@@[(42@@)])])])])])])]"
-3) "actionTree"
-4) "[(100@@[(100@@)][(100@@)][(100@@)][(100@@[(100@@)][(100@@)])][(100@@[(100@@[(100@@)][(100@@)][(100@@)])][(100@@)])][(100@@[(100@@[(100@@)][(100@@)][(100@@[(100@@)][(100@@)][(100@@)])])][(100@@[(100@@)][(100@@)])])][(100@@[(100@@[(100@@)][(100@@)][(100@@)])][(100@@[(100@@[(100@@[(100@@)][(100@@[(100@@)][(100@@)])])])][(100@@[(100@@[(100@@[(100@@)])])])])])])]"
-5) "shapeTree"
-6) "[(31@@[(83@@)][(39@@)][(42@@)][(44@@[(43@@)][(42@@)])][(44@@[(74@@[(43@@)][(43@@)][(43@@)])][(42@@)])][(60@@[(74@@[(43@@)][(43@@)][(74@@[(43@@)][(43@@)][(43@@)])])][(59@@[(42@@)][(32@@)])])][(25@@[(27@@[(42@@)][(-1@@)][(33@@)])][(8@@[(21@@[(32@@[(42@@)][(42@@[(42@@)][(42@@)])])])][(21@@[(32@@[(42@@[(42@@)])])])])])])]"
+1) "tokens"
+2) "public  void  MethodName:setConfiguration  String  pid  Map  String  String  configuration  Map  String  Map  String  String  configurations  MethodName:getConfigurations:[]  configurations  !=  null  Name:configurations  pid  configuration  configurations "
+3) "targetTree"
+4) "[(55@@[(31@@)][(31@@)][(31@@)][(31@@[(44@@)][(44@@)])][(31@@[(44@@[(74@@)][(74@@)][(74@@)])][(44@@)])][(31@@[(60@@[(74@@)][(74@@)][(74@@[(74@@)][(74@@)][(74@@)])])][(60@@[(59@@)][(59@@)])])][(31@@[(25@@[(27@@)][(27@@)][(27@@)])][(25@@[(8@@[(21@@[(32@@)][(32@@[(42@@)][(42@@)])])])][(8@@[(21@@[(32@@[(42@@)])])])])])])]"
+5) "actionTree"
+6) "[(100@@[(100@@)][(100@@)][(100@@)][(100@@[(100@@)][(100@@)])][(100@@[(100@@[(100@@)][(100@@)][(100@@)])][(100@@)])][(100@@[(100@@[(100@@)][(100@@)][(100@@[(100@@)][(100@@)][(100@@)])])][(100@@[(100@@)][(100@@)])])][(100@@[(100@@[(100@@)][(100@@)][(100@@)])][(100@@[(100@@[(100@@[(100@@)][(100@@[(100@@)][(100@@)])])])][(100@@[(100@@[(100@@[(100@@)])])])])])])]"
+7) "shapeTree"
+8) "[(31@@[(83@@)][(39@@)][(42@@)][(44@@[(43@@)][(42@@)])][(44@@[(74@@[(43@@)][(43@@)][(43@@)])][(42@@)])][(60@@[(74@@[(43@@)][(43@@)][(74@@[(43@@)][(43@@)][(43@@)])])][(59@@[(42@@)][(32@@)])])][(25@@[(27@@[(42@@)][(-1@@)][(33@@)])][(8@@[(21@@[(32@@[(42@@)][(42@@[(42@@)][(42@@)])])])][(21@@[(32@@[(42@@[(42@@)])])])])])])]"
   ```  
 
-After executing the shapeSI step, the rich edit scripts to be compared are stored in a key in DB 0. Use the following command to verify number of comparison to be made.
+After executing the actionSI / tokenSI steps, the rich edit scripts to be compared are stored in a key in DB 0. Use the following command to verify number of comparison to be made. 
+The trees that are labelled to be same are stored in DB2 for action trees and,in DB3 for token trees. 
 
 This command can also be used in order to progress the compare step. When the comparison is completed the following command will return 0.
  ```powershell
diff --git a/python/abstractPatch.py b/python/abstractPatch.py
index 2a7bea9..3d682f1 100644
--- a/python/abstractPatch.py
+++ b/python/abstractPatch.py
@@ -6,6 +6,8 @@ from common.commons import *
 DATA_PATH = os.environ["DATA_PATH"]
 DATASET = os.environ["dataset"]
 jdk8 = os.environ["JDK8"]
+REDIS_PORT = os.environ["REDIS_PORT"]
+
 # def localPairCore(aTuple):
 #     redis_db = redis.StrictRedis(host="localhost", port=6380, db=1)
 #     idx, key = aTuple
@@ -54,12 +56,15 @@ def loadPairMulti(root,clusterPath,level):
 
     # root = 'BreakStatement'
     logging.info(root)
-    port = 6399
+    port = REDIS_PORT
     # if isfile(clusterPath +"/"+root+".pickle"):
     #     return load_zipped_pickle(clusterPath +"/"+root+".pickle")
     # else:
         # redis_db = redis.StrictRedis(host="localhost", port=port, db=1)  #L1
-    redis_db = redis.StrictRedis(host="localhost", port=port, db=2)
+    if level == 'tokens':
+        redis_db = redis.StrictRedis(host="localhost", port=port, db=3)
+    else:
+        redis_db = redis.StrictRedis(host="localhost", port=port, db=2)
     keys = redis_db.scan(0, match=root+'-*', count='100000000')
     # keys = redis_db.hkeys("dump")
 
@@ -81,11 +86,11 @@ def loadPairMulti(root,clusterPath,level):
     matches['path2']=matches['pairs'].apply(lambda x:x[1])
     # matches['sizes']=matches['pairs_key'].apply(lambda x:x.split('_')[0].split('-')[1])
     matches['sizes']=matches['pairs_key'].apply(lambda x:x.split(root)[1].split('/')[0].split('-')[1])
-    if level == 'actions':
-        matches['actions']=matches['pairs_key'].apply(lambda x:x.split('/')[0].split('-')[2])
     if level == 'tokens':
-        matches['actions'] = matches['pairs_key'].apply(lambda x: x.split('/')[0].split('-')[2])
-        matches['tokens']=matches['pairs_key'].apply(lambda x:x.split('/')[0].split('-')[3])
+        matches['tokens']=matches['pairs_key'].apply(lambda x:x.split('/')[0].split('-')[2])
+    # if level == 'tokens':
+    #     matches['actions'] = matches['pairs_key'].apply(lambda x: x.split('/')[0].split('-')[2])
+    #     matches['tokens']=matches['pairs_key'].apply(lambda x:x.split('/')[0].split('-')[3])
 
 
     # save_zipped_pickle(matches,clusterPath +"/"+root+".pickle")
@@ -119,19 +124,19 @@ def cluster(clusterPath,pairsPath, level):
                 for s in sizes:
                     match = matches[matches['sizes'] == s]
 
-                    if level == 'actions':
-                        actions = match['actions'].unique().tolist()
+                    if level == 'tokens':
+                        actions = match['tokens'].unique().tolist()
                         for action in actions:
-                            match = match[match['actions'] == action]
+                            match = match[match['tokens'] == action]
                             clusterCore(clusterPath,  level, match, pairsPath, root, s,action)
-                    elif level == 'tokens':
-                        actions = match['actions'].unique().tolist()
-                        for action in actions:
-                            match = match[match['actions'] == action]
-                            tokens = match['tokens'].unique().tolist()
-                            for token in tokens:
-                                match = match[match['tokens']==token]
-                                clusterCore(clusterPath, level, match, pairsPath, root, s, action,token)
+                    # elif level == 'tokens':
+                    #     actions = match['actions'].unique().tolist()
+                    #     for action in actions:
+                    #         match = match[match['actions'] == action]
+                    #         tokens = match['tokens'].unique().tolist()
+                    #         for token in tokens:
+                    #             match = match[match['tokens']==token]
+                    #             clusterCore(clusterPath, level, match, pairsPath, root, s, action,token)
                     else:
                         clusterCore(clusterPath,  level, match, pairsPath, root, s,'')
 
@@ -158,12 +163,12 @@ def clusterCore(clusterPath, level, match, pairsPath, root, s,action ,token=''):
         cluster.append(subgraph.nodes())
     cluster
     pathMapping = dict()
-    if level == 'actions':
+    if level == 'tokens':
         indexFile = join(pairsPath, root, s,action+'.index')
-    elif level == 'shapes':
+    elif level == 'actions':
         indexFile = join(pairsPath, root, s + '.index')
-    else:
-        indexFile =join(pairsPath, root, s,action,token+'.index')
+    # else:
+    #     indexFile =join(pairsPath, root, s,action,token+'.index')
     df = pd.read_csv(indexFile, header=None, usecols=[0, 1], index_col=[0])
     pathMapping = df.to_dict()
 
diff --git a/python/main.py b/python/main.py
index d632bbc..f7c7651 100644
--- a/python/main.py
+++ b/python/main.py
@@ -40,9 +40,7 @@ if __name__ == '__main__':
         if job == 'dataset4j':
             from javaDS import createDS
             createDS()
-        # elif job == 'linuxDS':
-        #     from linuxDataset import collectBugFixPatches
-        #     collectBugFixPatches()
+
         elif job =='dataset4c':
             from otherDatasets import core
             core()
@@ -53,20 +51,16 @@ if __name__ == '__main__':
             output = shellCallTemplate(cmd)
             logging.info(output)
 
-        # elif job =='loadRES':
-        #     cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " LOAD " + rootType
-        #     output = shellCallTemplate(cmd)
-        #     logging.info(output)
 
-        elif job =='shapeSI':
-            from pairs import shapePairs
-            matches = shapePairs()
+        elif job =='actionSI':
+            from pairs import actionPairs
+            matches = actionPairs()
 
             from pairs import createPairs
             createPairs(matches)
 
-            from pairs import importShape
-            importShape()
+            from pairs import importAction
+            importAction()
 
         elif job =='compare':
              # 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'"
@@ -74,65 +68,28 @@ if __name__ == '__main__':
             output = shellCallTemplate4jar(cmd)
             logging.info(output)
 
-        # elif job == 'clusterAdditional':
-        #     from addNewData import cluster
-        #     cluster()
 
         elif job == 'cluster':
             from abstractPatch import cluster
 
             dbDir = join(DATA_PATH, 'redis')
-            startDB(dbDir, "6399", PROJECT_TYPE)
-            cluster(join(DATA_PATH,'shapes'),join(DATA_PATH, 'pairs'),'shapes')
+            startDB(dbDir, REDIS_PORT, PROJECT_TYPE)
+            cluster(join(DATA_PATH,'actions'),join(DATA_PATH, 'pairs'),'actions')
 
-        # elif job =='actionSI':
-        #     from pairs import actionPairs
-        #     actionPairs(rootType)
-        #
-        # # elif job =='importActionPairs':
-        #     from pairs import importAction
-        #     importAction(rootType)
-        #
-        # elif job =='compareActions':
-        #     # cmd = "JAVA_HOME='"+jdk8+"' java -Xmx8096m -Djava.util.concurrent.ForkJoinPool.common.parallelism=64 -jar "+  join(DATA_PATH,'CompareTrees.jar') + " action " + join(DATA_PATH,"redis") +" ALLdumps-gumInput.rdb " + "clusterl1-gumInputALL.rdb"
-        #
-        #     cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " COMPARE " + 'L2'
-        #     output = shellCallTemplate(cmd)
-        #     logging.info(output)
-        #
-        # elif job == 'clusterActions':
-        #     from abstractPatch import cluster
-        #
-        #     dbDir = join(DATA_PATH, 'redis')
-        #     startDB(dbDir, "6399", PROJECT_TYPE)
-        #     cluster( join(DATA_PATH, 'actions'),join(DATA_PATH, 'pairsAction'),'actions',rootType)
-
-        elif job == 'tokenSI':
+        elif job =='tokenSI':
             from pairs import tokenPairs
             tokenPairs()
-            from pairs import importToken
-            importToken()
 
-        elif job == 'compareTokens':
-            # cmd = "JAVA_HOME='"+jdk8+"' java -jar "+  join(DATA_PATH,'CompareTrees.jar') + " token " + join(DATA_PATH,"redis") +" ALLdumps-gumInput.rdb " + "clusterl2-gumInputALL.rdb"
-            cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " COMPARE " + 'L3'
-            output = shellCallTemplate(cmd)
-            logging.info(output)
+            from pairs import importTokens
+            importTokens()
 
         elif job == 'clusterTokens':
             from abstractPatch import cluster
 
             dbDir = join(DATA_PATH, 'redis')
-            startDB(dbDir, "6399", PROJECT_TYPE)
-            startDB(dbDir, "6380", "clusterl2-gumInputALL.rdb")
-            cluster(join(DATA_PATH, 'tokens'), join(DATA_PATH, 'pairsToken'),'tokens')
-            stopDB(dbDir, "6380", "clusterl2-gumInputALL.rdb")
+            startDB(dbDir, REDIS_PORT, PROJECT_TYPE)
+            cluster( join(DATA_PATH, 'tokens'),join(DATA_PATH, 'pairsToken'),'tokens')
 
-        # elif job == 'additional':
-        #     from addNewData import core
-        #     core()
-        #     # from addNewData import checkWrongMembers
-        #     # checkWrongMembers()
 
         elif job == 'codeflaws':
             from otherDatasets import codeflaws
@@ -218,19 +175,10 @@ if __name__ == '__main__':
         elif job == 'defects4j':
             from stats import defects4jStats
             defects4jStats()
-        elif job == 'exportPatterns':
+        elif job == 'patterns':
             from stats import exportAbstractPatterns
             exportAbstractPatterns()
-        elif job =='export':
-            patternPath = join(DATA_PATH,'actions','ExpressionStatement','3','0','0')
-            patterns = listdir(patternPath)
-            for pattern in patterns:
-                repo = pattern.split('_')[0]
-                file = pattern.replace(repo+'_','')
-                print(file)
-                filename = file.rsplit('_',1)[0]
-                print(join(DATA_PATH,'gumInput',repo,'DiffEntries',filename))
-                break
+
 
         else:
             logging.error('Unknown job %s',job)
diff --git a/python/pairs.py b/python/pairs.py
index 11a81d8..f339a69 100644
--- a/python/pairs.py
+++ b/python/pairs.py
@@ -3,50 +3,20 @@ DATA_PATH = os.environ["DATA_PATH"]
 ROOT = os.environ["ROOT_DIR"]
 INNER_DATA_PATH = join(ROOT,'data')
 PROJECT_TYPE = os.environ["PROJECT_TYPE"]
-def importToken():
-    # global dbDir, portInner, redis_db, pairs, cluster, action, e, idx, v, key
-    dbDir = join(INNER_DATA_PATH, 'redis')
-    portInner = '6380'
-    dbDir = join(INNER_DATA_PATH, 'redis')
-    startDB(dbDir, portInner, "clusterl2-gumInputALL.rdb")
-    import redis
-    pairsToken = join(DATA_PATH, 'pairsToken')
-    redis_db = redis.StrictRedis(host="localhost", port=portInner, db=1)
-    pairs = get_filepaths(pairsToken, '.txt')
-    for pair in pairs:
-        split = pair.split("/")
+REDIS_PORT = os.environ["REDIS_PORT"]
 
-        shapeName = split[-4]
-        shapeSize = split[-3]
-        cluster = split[-2]
-        action = split[-1].replace('.txt', '')
 
-        # cmd ="bash " + join(DATA_PATH,'redisSingleImport.sh') + " " +  pair + " 6380 " +  shapeName + "-"+sizeCluster+"-"+actionCluster ;#+, portInner,f.getName()+"-"+pair.getName().split("\\.")[0]);
-        cmd = "bash " + join(INNER_DATA_PATH,
-                             'redisSingleImport.sh') + " " + pair + " 6380 " + shapeName + "-" + shapeSize + "-" + cluster + "-" + action;  # +, portInner,f.getName()+"-"+pair.getName().split("\\.")[0]);
-
-        o, e = shellGitCheckout(cmd)
-        o
-        indexFile = pair.replace('.txt', '.index')
-        with open(indexFile, 'r') as iFile:
-            idx = iFile.readlines()
-        for i in idx:
-            k, v = i.split(',')
-            key = shapeName + "-" + shapeSize + "-" + cluster + "-" + action + "-" + k
-            # redis_db.set(key, v.strip())
-            redis_db.hset('filenames', key, v.strip())
-
-def importAction(rootType):
+def importTokens():
     # global dbDir, portInner, redis_db, pairs, pair, split, shapeName, shapeSize, cluster, cmd, o, e, indexFile, iFile, idx, i, k, v, key
     dbDir = join(INNER_DATA_PATH, 'redis')
     # portInner = '6380'
     # startDB(dbDir, portInner, "clusterl1-gumInputALL.rdb")
-    portInner = '6399'
+    portInner = REDIS_PORT
     startDB(dbDir, portInner, PROJECT_TYPE)
 
     import redis
     # import pairs
-    pairsAction = join(DATA_PATH, 'pairsAction',rootType)
+    pairsAction = join(DATA_PATH, 'pairsToken')
     redis_db = redis.StrictRedis(host="localhost", port=portInner, db=1)
     pairs = get_filepaths(pairsAction, '.txt')
     for pair in pairs:
@@ -55,7 +25,7 @@ def importAction(rootType):
         shapeSize = split[-2]
         cluster = split[-1].replace('.txt', '')
         cmd = "bash " + join(INNER_DATA_PATH,
-                             'redisSingleImport.sh') + " " + pair + " 6399 " + shapeName + "-" + shapeSize + "-" + cluster;  # +, portInner,f.getName()+"-"+pair.getName().split("\\.")[0]);
+                             'redisSingleImport.sh') + " " + pair + " "+REDIS_PORT+" " + shapeName + "-" + shapeSize + "-" + cluster;  # +, portInner,f.getName()+"-"+pair.getName().split("\\.")[0]);
 
         o, e = shellGitCheckout(cmd)
         print(o)
@@ -67,49 +37,17 @@ def importAction(rootType):
             key = shapeName + "-" + shapeSize + "-" + cluster + "-" + k
             # redis_db.set(key, v.strip())
             redis_db.hset('filenames', key, v.strip())
+    redis_db.set("level", "l2")
 
 
-# def importShape():
-#     # global dbDir, portInner, redis_db, pairs, pair, split, shapeName, cmd, o, e, indexFile, iFile, idx, i, k, v, key
-#     dbDir = join(DATA_PATH, 'redis')
-#     portInner = '6380'
-#     startDB(dbDir, portInner, "clusterl1-gumInputALL.rdb")
-#     import redis
-#     pairsShapes = join(DATA_PATH, 'pairs')
-#     redis_db = redis.StrictRedis(host="localhost", port=portInner, db=1)
-#     pairs = get_filepaths(pairsShapes, '.index')
-#     l = []
-#     for pair in pairs:
-#         # split = pair.split("/")
-#         # shapeName = split[-2]
-#         # sizeCluster = split[-1].replace('.txt', '')
-#         # cmd = "bash " + join(DATA_PATH, 'redisSingleImport.sh') + " " + pair + " 6380 " + shapeName + "-" + sizeCluster;
-#         #
-#         # o, e = shellGitCheckout(cmd)
-#         # print(o)
-#         # indexFile = pair.replace('.txt', '.index')
-#         with open(pair, 'r') as iFile:
-#             idx = iFile.readlines()
-#             idx = [i.split(',')[1] for i in idx]
-#             l.append(idx)
-#     l = list(itertools.chain.from_iterable(l))
-#     l = [i for i in l if not (i.startswith('commons-math') or i.startswith('commons-lang') or i.startswith(
-#         'closure-compiler') or i.startswith('joda-time') or i.startswith('mockito') or i.startswith('jfreechart'))]
-#     l
-#
-#         # for i in idx:
-#         #     k, v = i.split(',')
-#         #     key = shapeName + "-" + sizeCluster + "-" + k
-#         #     redis_db.set(key, v.strip())
 
-
-def importShape():
+def importAction():
     # global dbDir, portInner, redis_db, pairs, pair, split, shapeName, cmd, o, e, indexFile, iFile, idx, i, k, v, key
     dbDir = join(INNER_DATA_PATH, 'redis')
     # portInner = '6380'
     # startDB(dbDir, portInner, "clusterl0-gumInputALL.rdb")
 
-    portInner = '6399'
+    portInner = REDIS_PORT
     startDB(dbDir, portInner, PROJECT_TYPE)
 
     import redis
@@ -120,7 +58,7 @@ def importShape():
         split = pair.split("/")
         shapeName = split[-2]
         sizeCluster = split[-1].replace('.txt', '')
-        cmd = "bash " + join(INNER_DATA_PATH, 'redisSingleImport.sh') + " " + pair + " 6399 " + shapeName + "-" + sizeCluster;
+        cmd = "bash " + join(INNER_DATA_PATH, 'redisSingleImport.sh') + " " + pair + " "+REDIS_PORT+" " + shapeName + "-" + sizeCluster;
 
         o, e = shellGitCheckout(cmd)
         print(o)
@@ -132,43 +70,45 @@ def importShape():
             key = shapeName + "-" + sizeCluster + "-" + k
             #redis_db.set(key, v.strip())
             redis_db.hset('filenames',key,v.strip())
+    redis_db.set("level","l1")
 
 def tokenPairs():
-    global shapes, shape, sizes, clusters, cluster, actions, action, idx, val, pairs
+    # global shapes, shape, sizes, sf, clusters, cluster, files, indexCompared, out, idx, val, pairs, row, a, b
     shapes = listdir(join(DATA_PATH, 'actions'))
     shapes = [f for f in shapes if isdir(join(DATA_PATH, 'actions', f))]
+
+    if os.path.exists(join(DATA_PATH, 'pairsToken')):
+        import shutil
+        shutil.rmtree(join(DATA_PATH, 'pairsToken'))
+    # shapes = [rootType]
     for shape in shapes:
         sizes = listdir(join(DATA_PATH, 'actions', shape))
         sizes = [f for f in sizes if isdir(join(DATA_PATH, 'actions', shape, f))]
         for sf in sizes:
             if sf.startswith('.'):
                 continue
-            if sf == '1':
-                continue
             clusters = listdir(join(DATA_PATH, 'actions', shape, sf))
             for cluster in clusters:
                 if cluster.startswith('.'):
                     continue
-                actions = listdir(join(DATA_PATH, 'actions', shape, sf, cluster))
-                for action in actions:
-
-                    files = listdir(join(DATA_PATH, 'actions', shape, sf, cluster, action))
+                files = listdir(join(DATA_PATH, 'actions', shape, sf, cluster))
+                if len(files) > 1:
                     indexCompared = []
-                    if not os.path.exists(join(DATA_PATH, 'pairsToken', shape, sf, cluster)):
-                        os.makedirs(join(DATA_PATH, 'pairsToken', shape, sf, cluster))
+                    if not os.path.exists(join(DATA_PATH, 'pairsToken', shape, sf)):
+                        os.makedirs(join(DATA_PATH, 'pairsToken', shape, sf))
 
-                    infexFile = join(DATA_PATH, 'pairsToken', shape, sf, cluster, action + '.index')
-                    if isfile(infexFile):
-                        test = pd.read_csv(infexFile, header=None, index_col=0)
+                    indexFile = join(DATA_PATH, 'pairsToken', shape, sf, cluster + '.index')
+                    if isfile(indexFile):
+                        test = pd.read_csv(indexFile, header=None, index_col=0)
                         test.rename(columns={1: 'filename'}, inplace=True)
 
                         newFiles = [i for i in files if i not in test.filename.values.tolist()]
                         for newFile in newFiles:
                             test = test.append(pd.DataFrame(columns=['filename'], data=[newFile]), ignore_index=True)
                         indexCompared = test.index.values.tolist()
-                        test.to_csv(infexFile, header=None)
+                        test.to_csv(indexFile, header=None)
                     else:
-                        with open(infexFile, 'w') as out:
+                        with open(indexFile, 'w') as out:
                             # csv_out = csv.writer(out)
 
                             for idx, val in enumerate(files):
@@ -176,7 +116,8 @@ def tokenPairs():
                                 indexCompared.append(str(idx))
 
                     pairs = list(itertools.combinations(indexCompared, 2))
-                    pairsFile = join(DATA_PATH, 'pairsToken', shape, sf, cluster, action + '.txt')
+
+                    pairsFile = join(DATA_PATH, 'pairsToken', shape, sf, cluster + '.txt')
                     if isfile(pairsFile):
                         test = pd.read_csv(pairsFile, header=None)
                         test['pairs'] = test.apply(lambda x: tuple([x[0], x[1]]), axis=1)
@@ -193,69 +134,12 @@ def tokenPairs():
                                 a, b = row
                                 out.write(a + ',' + b + '\n')
 
-def actionPairs(rootType):
-    # global shapes, shape, sizes, sf, clusters, cluster, files, indexCompared, out, idx, val, pairs, row, a, b
-    # shapes = listdir(join(DATA_PATH, 'shapes'))
-    # shapes = [f for f in shapes if isdir(join(DATA_PATH, 'shapes', f))]
-    shapes = [rootType]
-    for shape in shapes:
-        sizes = listdir(join(DATA_PATH, 'shapes', shape))
-        sizes = [f for f in sizes if isdir(join(DATA_PATH, 'shapes', shape, f))]
-        for sf in sizes:
-            if sf.startswith('.'):
-                continue
-            clusters = listdir(join(DATA_PATH, 'shapes', shape, sf))
-            for cluster in clusters:
-                if cluster.startswith('.'):
-                    continue
-                files = listdir(join(DATA_PATH, 'shapes', shape, sf, cluster))
-                indexCompared = []
-                if not os.path.exists(join(DATA_PATH, 'pairsAction', shape, sf)):
-                    os.makedirs(join(DATA_PATH, 'pairsAction', shape, sf))
-
-                indexFile = join(DATA_PATH, 'pairsAction', shape, sf, cluster + '.index')
-                if isfile(indexFile):
-                    test = pd.read_csv(indexFile, header=None, index_col=0)
-                    test.rename(columns={1: 'filename'}, inplace=True)
-
-                    newFiles = [i for i in files if i not in test.filename.values.tolist()]
-                    for newFile in newFiles:
-                        test = test.append(pd.DataFrame(columns=['filename'], data=[newFile]), ignore_index=True)
-                    indexCompared = test.index.values.tolist()
-                    test.to_csv(indexFile, header=None)
-                else:
-                    with open(indexFile, 'w') as out:
-                        # csv_out = csv.writer(out)
-
-                        for idx, val in enumerate(files):
-                            out.write(str(idx) + ',' + val + '\n')
-                            indexCompared.append(str(idx))
-
-                pairs = list(itertools.combinations(indexCompared, 2))
-
-                pairsFile = join(DATA_PATH, 'pairsAction', shape, sf, cluster + '.txt')
-                if isfile(pairsFile):
-                    test = pd.read_csv(pairsFile, header=None)
-                    test['pairs'] = test.apply(lambda x: tuple([x[0], x[1]]), axis=1)
-                    newPairs = [i for i in pairs if i not in test['pairs'].values.tolist()]
-                    with open(pairsFile, 'w') as out:
-                        # csv_out = csv.writer(out)
-                        for row in newPairs:
-                            a, b = row
-                            out.write(a + ',' + b + '\n')
-                else:
-                    with open(pairsFile, 'w') as out:
-                        # csv_out = csv.writer(out)
-                        for row in pairs:
-                            a, b = row
-                            out.write(a + ',' + b + '\n')
-
-def shapePairs():
+def actionPairs():
     # global dbDir, portInner, redis_db, keys, matches, roots, sizes, sf, files, indexCompared, out, idx, val, pairs, row, a, b
     # if not (isfile(join(DATA_PATH, 'studyDataset.pickle'))):
     dbDir = join(INNER_DATA_PATH, 'redis')
 
-    portInner = '6399'
+    portInner = REDIS_PORT
     startDB(dbDir, portInner, PROJECT_TYPE)
 
     import redis
diff --git a/python/stats.py b/python/stats.py
index 17eedf3..b2f11e3 100644
--- a/python/stats.py
+++ b/python/stats.py
@@ -1,12 +1,13 @@
 from common.commons import *
 DATA_PATH = os.environ["DATA_PATH"]
 PROJECT_TYPE = os.environ["PROJECT_TYPE"]
+REDIS_PORT = os.environ["REDIS_PORT"]
 
 def statsNormal(isFixminer=True):
     # tokens = join(DATA_PATH, 'tokens')
     # actions = join(DATA_PATH, 'actions')
     import redis
-    redis_db = redis.StrictRedis(host="localhost", port=6399, db=0)
+    redis_db = redis.StrictRedis(host="localhost", port=REDIS_PORT, db=0)
     # keys = redis_db.scan(0, match='*', count='1000000')
     keys = redis_db.hkeys("dump")  # hkeys "dump"
     matches = pd.DataFrame(keys, columns=['pairs_key'])
@@ -95,7 +96,7 @@ def statsNormal(isFixminer=True):
 
 
     # for type in ['tokens', 'actions', 'shapes']:
-    for type in ['shapes']:
+    for type in ['actions']:
         statsS,clusterDF = stats(type,isFixminer)
         if isFixminer:
             clusterDF = clusterDF[clusterDF.members.str.len() > 1]
@@ -136,25 +137,7 @@ def statsNormal(isFixminer=True):
         matches
         if isFixminer:
             matches.to_csv(join(DATA_PATH, "stats" + type + ".csv"), index=False)
-            if type == 'actions':
-                clusterDF['ms'] = clusterDF.members.str.len()
-                clusterDF.sort_values(by='ms', ascending=False, inplace=True)
-                top50 = clusterDF.head(50)
-                top50['member'] = top50.members.apply(lambda x: x[0])
-                top50['cid'] = top50.cid.apply(lambda x: x[0])
-                top50['path'] = top50.apply(lambda x:x['cid'].replace('-','/')+'/'+x['member'],axis=1)
-                def readFile(x):
-                    with open(join(DATA_PATH,'actions',x), 'r', encoding='utf-8') as writeFile:
-                        lines = writeFile.read()
-                        return lines
-                        # if lines.startswith('UPD'):
-                        #     return lines
-                        # else:
-                        #     return ''
-                    # return lines
 
-                top50['pattern'] = top50.path.apply(lambda x:readFile(x))
-                top50[['cid','pattern']].to_csv('actionsPattern2verify.csv',index=False,header=None)
 
 
 
@@ -253,7 +236,7 @@ def stats(type,isFixminer=True):
                     continue
                 cs = listdir(join(shapesPath, shape, size, cluster))
 
-                if shapesPath.endswith('shapes'):
+                if shapesPath.endswith('actions'):
                     cs = listdir(join(shapesPath, shape, size, cluster))
                     statsCore(cs)
                 else:
@@ -262,14 +245,14 @@ def stats(type,isFixminer=True):
                         if action.startswith('.'):
                             continue
                         tokens = listdir(join(shapesPath, shape, size, cluster, action))
-                        if shapesPath.endswith('actions'):
+                        if shapesPath.endswith('tokens'):
                             statsCore(tokens)
-                        else:
-                            for token in tokens:
-                                if token.startswith('.'):
-                                    continue
-                                cs = listdir(join(shapesPath, shape, size, cluster, action, token))
-                                statsCore(cs)
+                        # else:
+                        #     for token in tokens:
+                        #         if token.startswith('.'):
+                        #             continue
+                        #         cs = listdir(join(shapesPath, shape, size, cluster, action, token))
+                        #         statsCore(cs)
     return statsS,clustersDF
 
 
@@ -282,7 +265,7 @@ def defects4jStats(isFixminer=False):
         mapping.rename(columns={0: 'repo', 1: "commit", 2: 'defects4jID'}, inplace=True)
         dbDir = join(DATA_PATH, 'redis')
 
-        portInner = '6399'
+        portInner = REDIS_PORT
         startDB(dbDir, portInner, PROJECT_TYPE )
 
         import redis
@@ -474,8 +457,8 @@ cAst = ["unit","comment","literal","operator","modifier","name","type","conditio
 
 
 def exportAbstractPatterns():
-    clusterStats,df = stats('shapes')
-    port = 6399
+    clusterStats,df = stats('actions')
+    port = REDIS_PORT
     import redis
     redis_db = redis.StrictRedis(host="localhost", port=port, db=0)
     isJava = False
diff --git a/python/tokens.py b/python/tokens.py
index 3ceeb51..0f6f16c 100644
--- a/python/tokens.py
+++ b/python/tokens.py
@@ -1,5 +1,5 @@
 from common.commons import *
-
+REDIS_PORT = os.environ["REDIS_PORT"]
 DATA_PATH = os.environ["DATA_PATH"]
 ast = ["AnonymousClassDeclaration", "ArrayAccess", "ArrayCreation", "ArrayInitializer", "ArrayType", "AssertStatement",
        "Assignment", "Block", "BooleanLiteral", "BreakStatement", "CastExpression", "CatchClause", "CharacterLiteral",
@@ -31,7 +31,7 @@ redis_db = redis.StrictRedis(host="localhost", port=port, db=0)
 redis_db1 = redis.StrictRedis(host="localhost", port=port, db=1)
 redis_db2 = redis.StrictRedis(host="localhost", port=port, db=2)
 
-redis_out  = redis.StrictRedis(host="localhost", port=6399, db=0)
+redis_out  = redis.StrictRedis(host="localhost", port=REDIS_PORT, db=0)
 
 def getTokens(prefix, i):
     dist2load = redis_db1.get(prefix + "-" + i);
diff --git a/richedit/src/main/java/edu/lu/uni/serval/Launcher.java b/richedit/src/main/java/edu/lu/uni/serval/Launcher.java
index d3da760..960cfac 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/Launcher.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/Launcher.java
@@ -73,18 +73,18 @@ public class Launcher {
         String srcMLPath = (String) fixminer.get("srcMLPath");
 
 //        String parameter = args[2];
-        String parameter = "L1";
+//        String parameter = "L1";
         String jobType = args[1];
 //        String jobType = "RICHEDITSCRIPT";
-//        String jobType = "COMPARE";
+//        jobType = "COMPARE";
 
 
-        mainLaunch( numOfWorkers, jobType, portDumps,projectType,input,redisPath,parameter, srcMLPath,hunkLimit,projectList,patchSize);
+        mainLaunch( numOfWorkers, jobType, portDumps,projectType,input,redisPath, srcMLPath,hunkLimit,projectList,patchSize);
 
 
     }
 
-    public static void mainLaunch(String numOfWorkers, String jobType, String portDumps, String projectType, String input, String redisPath,String parameter,String srcMLPath,String hunkLimit,String[] projectList,String patchSize){
+    public static void mainLaunch(String numOfWorkers, String jobType, String portDumps, String projectType, String input, String redisPath,String srcMLPath,String hunkLimit,String[] projectList,String patchSize){
 
 
         String dbDir;
@@ -100,36 +100,36 @@ public class Launcher {
         try {
             switch (jobType) {
                 case "RICHEDITSCRIPT":
-                    EnhancedASTDiff.main(gumInput, portDumps, dbDir, dumpsName, srcMLPath,parameter,hunkLimit,projectList,patchSize,projectType);
+                    EnhancedASTDiff.main(gumInput, portDumps, dbDir, dumpsName, srcMLPath,hunkLimit,projectList,patchSize,projectType);
                     break;
 
                 case "COMPARE":
-                    String job;
-                    String compareDBName;
-                    switch (parameter){
-                        case "L1":
-//                            job = "shape";
-                            job = "single";
-                            compareDBName = "clusterl0-gumInputALL.rdb";
-                            break;
-                        case "L2":
-                            job = "action";
-                            compareDBName = "clusterl1-gumInputALL.rdb";
-                            break;
-                        case "L3":
-                            job = "token";
-                            compareDBName = "clusterl2-gumInputALL.rdb";
-                            break;
-                        default:
-                            throw new Error("unknown level please specify L1,L2,L3");
-                    }
+//                    String job;
+//                    String compareDBName;
+//                    switch (parameter){
+//                        case "L1":
+////                            job = "shape";
+//                            job = "single";
+//                            compareDBName = "clusterl0-gumInputALL.rdb";
+//                            break;
+//                        case "L2":
+//                            job = "action";
+//                            compareDBName = "clusterl1-gumInputALL.rdb";
+//                            break;
+//                        case "L3":
+//                            job = "token";
+//                            compareDBName = "clusterl2-gumInputALL.rdb";
+//                            break;
+//                        default:
+//                            throw new Error("unknown level please specify L1,L2,L3");
+//                    }
 
 
-                    CompareTrees.main(redisPath, portDumps,dumpsName, job,numOfWorkers);
-                    break;
-                case "PATTERN":
-                    ClusterToPattern.main(portDumps,redisPath, dumpsName, parameter);
+                    CompareTrees.main(redisPath, portDumps,dumpsName, numOfWorkers);
                     break;
+//                case "PATTERN":
+//                    ClusterToPattern.main(portDumps,redisPath, dumpsName, parameter);
+//                    break;
                 default:
                     throw new Error("unknown Job");
 
diff --git a/richedit/src/main/java/edu/lu/uni/serval/richedit/Launcher2.java b/richedit/src/main/java/edu/lu/uni/serval/richedit/Launcher2.java
deleted file mode 100755
index 24cbdc0..0000000
--- a/richedit/src/main/java/edu/lu/uni/serval/richedit/Launcher2.java
+++ /dev/null
@@ -1,134 +0,0 @@
-package edu.lu.uni.serval.richedit;
-
-import edu.lu.uni.serval.richedit.jobs.CompareTrees;
-import edu.lu.uni.serval.richedit.jobs.EnhancedASTDiff;
-import edu.lu.uni.serval.utils.ClusterToPattern;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-import java.util.Properties;
-
-/**
- * Created by anilkoyuncu on 14/04/2018.
- */
-public class Launcher2 {
-
-    private static Logger log = LoggerFactory.getLogger(Launcher2.class);
-
-    public static void main(String[] args) throws IOException {
-
-
-        Properties appProps = new Properties();
-
-        String hostname = "Unknown";
-        try
-        {
-            InetAddress addr;
-            addr = InetAddress.getLocalHost();
-            hostname = addr.getHostName();
-        }
-        catch (UnknownHostException ex)
-        {
-            System.out.println("Hostname can not be resolved");
-        }
-        String appConfigPath;
-        if (hostname.equals("Unknown")){
-             appConfigPath = "src/main/resource/app.properties";
-        }
-        else{
-             appConfigPath = "src/main/resource/"+hostname+".app.properties";
-        }
-//        String appConfigPath = args[0];
-        appProps.load(new FileInputStream(appConfigPath));
-
-        String numOfWorkers = appProps.getProperty("numOfWorkers", "10");
-        String portDumps = appProps.getProperty("portDumps","6399");
-        String projectType = appProps.getProperty("projectType","java");
-
-        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 redisPath = appProps.getProperty("redisPath","FORKJOIN");
-        String srcMLPath = appProps.getProperty("srcMLPath","FORKJOIN");
-
-//        String parameter = args[2];
-        String parameter = "L1";
-//        String jobType = args[1];
-//        String jobType = "RICHEDITSCRIPT";
-        String jobType = "COMPARE";
-
-
-        mainLaunch( numOfWorkers, jobType, portDumps,projectType,input,redisPath,parameter, srcMLPath,hunkLimit,projectList,patchSize);
-
-
-    }
-
-    public static void mainLaunch(String numOfWorkers, String jobType, String portDumps, String projectType, String input, String redisPath,String parameter,String srcMLPath,String hunkLimit,String[] projectList,String patchSize){
-
-
-        String dbDir;
-        String dumpsName;
-        String gumInput;
-
-        dumpsName = "dumps-"+projectType+".rdb";
-
-        gumInput = input;
-        dbDir = redisPath;
-
-
-        try {
-            switch (jobType) {
-                case "RICHEDITSCRIPT":
-                    EnhancedASTDiff.main(gumInput, portDumps, dbDir, dumpsName, srcMLPath,parameter,hunkLimit,projectList,patchSize,projectType);
-                    break;
-
-                case "COMPARE":
-                    String job;
-                    String compareDBName;
-                    switch (parameter){
-                        case "L1":
-//                            job = "shape";
-                            job = "single";
-                            compareDBName = "clusterl0-gumInputALL.rdb";
-                            break;
-                        case "L2":
-                            job = "action";
-                            compareDBName = "clusterl1-gumInputALL.rdb";
-                            break;
-                        case "L3":
-                            job = "token";
-                            compareDBName = "clusterl2-gumInputALL.rdb";
-                            break;
-                        default:
-                            throw new Error("unknown level please specify L1,L2,L3");
-                    }
-
-
-                    CompareTrees.main(redisPath, portDumps,dumpsName, job,numOfWorkers);
-                    break;
-                case "PATTERN":
-                    ClusterToPattern.main(portDumps,redisPath, dumpsName, parameter);
-                    break;
-                default:
-                    throw new Error("unknown Job");
-
-            }
-        } catch (Exception e) {
-            e.printStackTrace();
-
-        }
-
-
-
-
-        }
-
-}
-
-
diff --git a/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffHunkParser.java b/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffHunkParser.java
index 56f2cf4..5348144 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffHunkParser.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/richedit/ediff/EDiffHunkParser.java
@@ -62,12 +62,16 @@ public class EDiffHunkParser extends EDiffParser {
 							ITree targetTree = EDiffHelper.getTargets(actionSet, isJava);
 							ITree actionTree = EDiffHelper.getActionTrees(actionSet);
 							ITree shapeTree = EDiffHelper.getShapeTree(actionSet, isJava);
+							ITree tokenTree = EDiffHelper.getTokenTree(actionSet,isJava);
+							String tokens = EDiffHelper.getNames2(tokenTree);
+//						EDiffHelper.getTokenTree(actionSet, parent, children, tc);
 							try (Jedis inner = innerPool.getResource()) {
 
 								inner.hset("dump", key, actionSet.toString());
 								inner.hset(key, "actionTree", actionTree.toStaticHashString());
 								inner.hset(key, "targetTree", targetTree.toStaticHashString());
 								inner.hset(key, "shapeTree", shapeTree.toStaticHashString());
+								inner.hset(key, "tokens", tokens);
 							}
 //						File f = new File(root+"dumps/"+astNodeType+"/"+String.valueOf(size)+"/");
 //						f.mkdirs();
diff --git a/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/CompareTrees.java b/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/CompareTrees.java
index 07a31a2..79770bb 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/CompareTrees.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/CompareTrees.java
@@ -4,6 +4,7 @@ import edu.lu.uni.serval.utils.CallShell;
 import edu.lu.uni.serval.utils.EDiffHelper;
 import edu.lu.uni.serval.utils.PoolBuilder;
 import me.tongfei.progressbar.ProgressBar;
+import org.apache.commons.text.similarity.JaroWinklerDistance;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import redis.clients.jedis.Jedis;
@@ -28,7 +29,7 @@ public class CompareTrees {
     private static Logger log = LoggerFactory.getLogger(CompareTrees.class);
 
 
-    public static void main(String redisPath, String portDumps, String dumpsName, String job,String numOfWorkers) throws Exception {
+    public static void main(String redisPath, String portDumps, String dumpsName, String numOfWorkers) throws Exception {
 
         // 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
 
@@ -55,6 +56,7 @@ public class CompareTrees {
 
 //        List<String> listOfPairs = AkkaTreeParser.getMessages(innerPool,Integer.valueOf(numOfWorkers));
         HashMap<String, String> filenames = getFilenames(outerPool);
+        String job= getLevel(outerPool);
 //        List<String> listOfPairs = AkkaTreeParser.files2compare(outerPool);
 
 
@@ -69,12 +71,13 @@ public class CompareTrees {
         }
         IntStream stream = IntStream.range(0, compare.intValue());
 
+        String finalJob = job;
         ProgressBar.wrap(stream.
                 parallel(),"Task").
 
                 forEach(m ->
                         {
-                            newCoreCompare(job, errorPairs, filenames, outerPool);
+                            newCoreCompare(finalJob, errorPairs, filenames, outerPool);
                         }
                 );
 
@@ -164,14 +167,16 @@ public class CompareTrees {
             String keyName = split[0];
             matchKey = keyName + "/" + (String.valueOf(i)) + "/" + String.valueOf(j);
 
+            if (matchKey == null){
+                return false;
+            }
+            Map<String, String> oldTreeString = EDiffHelper.getTreeString(keyName, i, outerPool, filenames);
+            Map<String, String> newTreeString = EDiffHelper.getTreeString(keyName, j, outerPool, filenames);
+
             switch (treeType) {
                 case "single":
 
-                    if (matchKey == null){
-                        return false;
-                    }
-                    Map<String, String> oldTreeString = EDiffHelper.getTreeString(keyName, i, outerPool, filenames);
-                    Map<String, String> newTreeString = EDiffHelper.getTreeString(keyName, j, outerPool, filenames);
+
 
                     String oldShapeTree =oldTreeString.get("shapeTree");
                     String newShapeTree =newTreeString.get("shapeTree");
@@ -196,6 +201,35 @@ public class CompareTrees {
                         }
                     }
                     return true;
+                case "token":
+
+                    String oldTokens = oldTreeString.get("tokens");
+                    String newTokens = newTreeString.get("tokens");
+//                    EDiffHelper.getTokens(keyName, i, outerPool, filenames);
+//                    newTree = EDiffHelper.getTokens(keyName, j, outerPool, innerPool);
+
+//                    String oldTokens = EDiffHelper.getNames2(oldTree);
+//                    String newTokens = EDiffHelper.getNames2(newTree);
+//
+                    JaroWinklerDistance jwd = new JaroWinklerDistance();
+//
+//
+                    Double overallSimi = Double.valueOf(0);
+//
+                    if (!(oldTokens.trim().isEmpty() || newTokens.trim().isEmpty())) {
+                        overallSimi = jwd.apply(oldTokens, newTokens);
+
+                    }
+                    int retval = Double.compare(overallSimi, Double.valueOf(1));
+
+                    if (retval >= 0) {
+                        try (Jedis jedis = outerPool.getResource()) {
+                            jedis.select(3);
+                            jedis.set(matchKey, "1");
+                        }
+
+                    }
+                    return true;
                 default:
                     return true;
 //                    break;
@@ -212,6 +246,35 @@ public class CompareTrees {
     }
 
 
+    public static String  getLevel(JedisPool innerPool){
+
+
+        HashMap<String, String> fileMap =new HashMap<String, String>();
+
+        try (Jedis inner = innerPool.getResource()) {
+            while (!inner.ping().equals("PONG")){
+                log.info("wait");
+            }
+
+            inner.select(1);
+            String level = inner.get("level");
+
+            switch (level){
+                case "l1":
+                    return "single";
+                case "l2":
+                    return "token";
+                default:
+                    return "";
+            }
+
+
+
+
+
+
+        }
+    }
 
     public static HashMap<String, String>  getFilenames(JedisPool innerPool){
 
@@ -244,4 +307,7 @@ public class CompareTrees {
 
 
 
+
+
+
 }
diff --git a/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java b/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java
index 486fcf3..dca2c5b 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/richedit/jobs/EnhancedASTDiff.java
@@ -26,7 +26,7 @@ public class EnhancedASTDiff {
 
 	private static Logger log = LoggerFactory.getLogger(EnhancedASTDiff.class);
 
-	public static void main(String inputPath, String portInner, String dbDir, String chunkName,String srcMLPath,String parameter,String hunkLimit,String[] projectList,String patchSize,String projectType) throws Exception {
+	public static void main(String inputPath, String portInner, String dbDir, String chunkName,String srcMLPath,String hunkLimit,String[] projectList,String patchSize,String projectType) throws Exception {
 
 
 		String parameters = String.format("\nInput path %s", inputPath);
diff --git a/richedit/src/main/java/edu/lu/uni/serval/utils/EDiffHelper.java b/richedit/src/main/java/edu/lu/uni/serval/utils/EDiffHelper.java
index 2b1a2f4..503cdd0 100755
--- a/richedit/src/main/java/edu/lu/uni/serval/utils/EDiffHelper.java
+++ b/richedit/src/main/java/edu/lu/uni/serval/utils/EDiffHelper.java
@@ -71,15 +71,22 @@ public class EDiffHelper {
     }
 
 
-    public static ITree getTokenTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc){
+    public static ITree getTokenTree(HierarchicalActionSet actionSet, ITree parent, ITree children,TreeContext tc,boolean isJava){
 
         int newType = 0;
 
         String astNodeType = actionSet.getAstNodeType();
 
         String label = actionSet.getAction().toString();
+
+        Map<Integer, String> nodeMap;
+        if(isJava){
+            nodeMap = ASTNodeMap.map;
+        }else{
+            nodeMap = NodeMap_new.map;
+        }
 //        List<Integer> keysByValue = getKeysByValue(ASTNodeMap.map, astNodeType);
-        List<Integer> keysByValue = getKeysByValue(NodeMap_new.map, astNodeType);
+        List<Integer> keysByValue = getKeysByValue(nodeMap, astNodeType);
 
         if(keysByValue.size() != 1){
             log.error("More than 1");
@@ -102,7 +109,7 @@ public class EDiffHelper {
                 if(actionSet.getParent() == null){
                     children = parent;
                 }
-                getTokenTree(subAction,children,null,tc);
+                getTokenTree(subAction,children,null,tc,isJava);
 
             }
 
@@ -307,6 +314,17 @@ public class EDiffHelper {
         return tree;
     }
 
+    public static ITree getTokenTree(HierarchicalActionSet actionSet,boolean isJava) {
+        ITree tree = null;
+        ITree parent = null;
+        ITree children = null;
+        TreeContext tc = new TreeContext();
+        tree = EDiffHelper.getTokenTree(actionSet, parent, children, tc,isJava);
+        //tree.setParent(null);
+        tc.validate();
+        return tree;
+    }
+
 
     public static ITree getTargets(HierarchicalActionSet actionSet,boolean isJava) {
 
@@ -420,13 +438,15 @@ public class EDiffHelper {
 //                String[] split = prefix.split("-");
 //                String key = split[0] + "/"+split[1]+"/" + dist2load;
 //
-//                byte[] s = outer.hget("dump".getBytes(), key.getBytes());
-//                actionSet = (HierarchicalActionSet) EDiffHelper.kryoDeseerialize(s);
+//                String s = outer.hget("dump", key);
+//                actionSet = (HierarchicalActionSet) EDiffHelper.fromString(s);
+//
+////                actionSet = (HierarchicalActionSet) EDiffHelper.kryoDeseerialize(s);
 //
 //                ITree parent = null;
 //                ITree children = null;
 //                TreeContext tc = new TreeContext();
-//                tree = EDiffHelper.getTokenTree(actionSet, parent, children, tc);
+//                tree = EDiffHelper.getTokenTree(actionSet, parent, children, tc,is);
 //                tree.setParent(null);
 //                tc.validate();
 ////            getLeaves(tree);