enabled back token iteration
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mimic
@@ -34,6 +34,10 @@ You can cite FixMiner using the following bibtex:
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Fixminer is a systematic and automated approach to mine relevant and actionable fix patterns for automated program repair.
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** This version of the Fixminer has some changes compared to the one published in the paper.
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- 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 )
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## II. Environment setup
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* OS: macOS Mojave (10.14.3)
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@@ -82,8 +86,8 @@ In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
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In order to launch FixMiner, execute [fixminer.sh](python/fixminer.sh)
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bash fixminer.sh [JOB] [CONFIG_FILE]
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e.g. bash fixminer.sh dataset4c /Users/projects/release/fixminer_source/src/main/resources/config.yml
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bash fixminer.sh [CONFIG_FILE] [JOB]
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e.g. bash fixminer.sh /Users/projects/release/fixminer_source/src/main/resources/config.yml dataset4c
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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.
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@@ -91,30 +95,38 @@ A log file (app.log) is created after every execution of the [fixminer.sh]((pyth
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#### Job Types
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*FixMiner* needs to specify a job to run.
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*FixMiner* needs to follow an execution, **in the order listed below** in order to create clusters of patches.
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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
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2. __richEditScript__: Calls the jar file produced as the results as maven package to compute Rich edit scripts.
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2. __richedit__: Calls the jar file produced as the results as maven package to compute Rich edit scripts.
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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.
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```powershell
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java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar /Users/projects/release/fixminer_source/src/main/resources/config.yml RICHEDITSCRIPT
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```
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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)
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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)
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4. __compare__ : Calls the jar file produced as the results as maven package to compare the trees.
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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.
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```powershell
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java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARE
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```
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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)
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```powershell
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java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARE
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```
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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)
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6. __stats__: Calculate frequency statistics of the patterns under statsshapes.csv in datapath. The information is also written in app.log file.
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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)
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7. __exportPatterns__ : Export FixPatterns of APR integration under patterns folder located in datapath/
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7. __compare__ : Calls the jar file produced as the results as maven package to compare the trees.
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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.
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```powershell
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java -jar FixPatternMiner-1.0.0-jar-with-dependencies.jar /Users/projects/release/fixminer_source/src/main/resources/config.yml COMPARE
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```
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8. __stats__: Calculate frequency statistics of the patterns under statsactions.csv in datapath. The information is also written in app.log file.
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7. __patterns__ : Export FixPatterns of APR integration under patterns folder located in datapath/
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<!--
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@@ -252,10 +264,11 @@ Connect to redis instance
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redis-cli -p 6399
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```
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We use 3 databases inside the redis, 0,1,2.
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We use 3 databases inside the redis, 0,1,2,3.
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DB 0 stores the richedit dumps, comparison indices
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DB 1 stores the filenames and their corresponding indices
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DB 2 stores the output of comparison, a.k.a same trees.
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DB 1 stores the filenames and their indices (used in comparison and stored in DB2, DB3)
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DB 2 stores the output of comparison action trees.
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DB 3 stores the output of comparison token trees.
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In order to switch between these database use the following command
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@@ -298,15 +311,18 @@ hgetall NAME_OF_THE_EXACT_KEY
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hgetall MethodDeclaration/40/fuse_67b14b_04e5b1_fabric#fabric-client#src#main#java#org#fusesource#fabric#jolokia#facade#facades#ProfileFacade.java.txt_1
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OUTPUT:
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1) "targetTree"
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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@@)])])])])])])]"
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3) "actionTree"
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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@@)])])])])])])]"
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5) "shapeTree"
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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@@)])])])])])])]"
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1) "tokens"
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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 "
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3) "targetTree"
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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@@)])])])])])])]"
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5) "actionTree"
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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@@)])])])])])])]"
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7) "shapeTree"
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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@@)])])])])])])]"
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```
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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.
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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.
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The trees that are labelled to be same are stored in DB2 for action trees and,in DB3 for token trees.
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This command can also be used in order to progress the compare step. When the comparison is completed the following command will return 0.
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```powershell
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