changes for jar
This commit is contained in:
fixminer
@@ -3,14 +3,14 @@ java:
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spinfer:
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home: /Users/anil.koyuncu/projects/spinfer/spinfer.native
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dataset:
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home: /Users/anil.koyuncu/projects/test/fixminer-data/patches/
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repo: /Users/anil.koyuncu/projects/test/fixminer-data/datasets
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# home: /data/fixminer-core/python/data/gumInputLinux/
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home: /Users/anil.koyuncu/projects/test/richedit-data/patches/
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repo: /Users/anil.koyuncu/projects/test/richedit-data/datasets
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# home: /data/richedit-core/python/data/gumInputLinux/
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coccinelle:
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home: /Users/anil.koyuncu/projects/spinfer/statics
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fixminer:
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datapath: /Users/anil.koyuncu/projects/test/fixminer-data/
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datapath: /Users/anil.koyuncu/projects/test/richedit-data/
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projectType : c
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# datapath: /data/fixminer-core/python/data/
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# datapath: /data/richedit-core/python/data/
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@@ -179,7 +179,7 @@ def clusterCore(clusterPath, level, match, pairsPath, root, s,action ,token=''):
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parallelRun(dumpFilesCore,workList)
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# for wl in workList:
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# dumpFilesCore(wl)
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# dumpFilesCore(('hive_d65d5c_96c1dc_ql#src#gen#protobuf#gen-java#org#apache#hadoop#hive#ql#io#orc#OrcProto.txt_31', 'ReturnStatement', 'tokens', '/Users/anil.koyuncu/projects/fixminer-all/enhancedASTDiff/python/data/tokens', '3', '1', '0', 10))
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# dumpFilesCore(('hive_d65d5c_96c1dc_ql#src#gen#protobuf#gen-java#org#apache#hadoop#hive#ql#io#orc#OrcProto.txt_31', 'ReturnStatement', 'tokens', '/Users/anil.koyuncu/projects/richedit-all/enhancedASTDiff/python/data/tokens', '3', '1', '0', 10))
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def dumpFilesCore(t):
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@@ -0,0 +1,13 @@
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2020-04-07 17:31:35,222 - 31200 - INFO - commons.py:setEnv - ROOT_DIR : /Users/anilkoyuncu/projects/release/test/fixminer_source/python
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2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - REPO_PATH : /Users/anilkoyuncu/projects/test/richedit-data/datasets
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2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - CODE_PATH : /Users/anilkoyuncu/projects/release/test/fixminer_source/python/code/
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2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - COMMIT_DFS : /Users/anilkoyuncu/projects/test/richedit-data/commitsDF/
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2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - BUG_POINT : /Users/anilkoyuncu/projects/test/richedit-data/bugPoints/
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2020-04-07 17:31:35,224 - 31200 - INFO - commons.py:setEnv - COMMIT_FOLDER : /Users/anilkoyuncu/projects/test/richedit-data/commits/
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2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - FEATURE_DIR : /Users/anilkoyuncu/projects/test/richedit-data/features/
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2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - CLASSIFIER_DIR : /Users/anilkoyuncu/projects/test/richedit-data/classifiers/
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2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - PREDICTION_DIR : /Users/anilkoyuncu/projects/test/richedit-data/predictions/
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2020-04-07 17:31:35,225 - 31200 - INFO - commons.py:setEnv - DATASET_DIR : /Users/anilkoyuncu/projects/test/richedit-data/datasets/
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2020-04-07 17:31:41,346 - 31200 - INFO - commons.py:shellCallTemplate - JAVA_HOME='/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home' java -jar /Users/anilkoyuncu/projects/release/test/fixminer_source/target/FixPatternMiner-1.0.0-jar-with-dependencies.jar /Users/anilkoyuncu/projects/release/test/fixminer_source/src/main/resources/config.yml RICHEDITSCRIPT
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2020-04-07 17:31:41,551 - 31200 - ERROR - commons.py:shellCallTemplate - Error: Could not find or load main class edu.lu.uni.serval.richedit.Launcher
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@@ -26,6 +26,8 @@ from collections import Counter
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import datetime
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import subprocess
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from pathlib import Path
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sourceCodeColumns = ['packageName', 'className', 'methodNames', 'formalParameter',
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@@ -72,13 +74,15 @@ def setEnv(args):
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import yaml
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if os.uname().nodename != '':
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with open(join(os.environ["ROOT_DIR"], os.uname().nodename + ".config.yml"), 'r') as ymlfile:
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cfg = yaml.load(ymlfile)
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else:
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with open(join(os.environ["ROOT_DIR"], "config.yml"), 'r') as ymlfile:
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cfg = yaml.load(ymlfile)
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# if os.uname().nodename != '':
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# with open(join(os.environ["ROOT_DIR"], os.uname().nodename + ".config.yml"), 'r') as ymlfile:
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# cfg = yaml.load(ymlfile)
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# else:
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# with open(join(os.environ["ROOT_DIR"], "config.yml"), 'r') as ymlfile:
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# cfg = yaml.load(ymlfile)
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with open(args.prop, 'r') as ymlfile:
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cfg = yaml.load(ymlfile)
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# for section in cfg:
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# print(section)
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# print(cfg['mysql'])
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@@ -88,10 +92,11 @@ def setEnv(args):
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os.environ["JDK8"] = cfg['java']['8home']
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os.environ["spinfer"] = cfg['spinfer']['home']
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os.environ["coccinelle"] = cfg['coccinelle']['home']
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os.environ["dataset"] = cfg['dataset']['home']
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os.environ["dataset"] = cfg['dataset']['inputPath']
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os.environ["REPO_PATH"] = cfg['dataset']['repo']
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os.environ["DATA_PATH"] = cfg['fixminer']['datapath']
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os.environ["PROJECT_TYPE"] = cfg['fixminer']['projectType']
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os.environ["PROJECT_LIST"] = cfg['fixminer']['projectList']
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# import yaml
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#
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@@ -160,11 +165,12 @@ def getRun():
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# parser.add_argument('-subject', dest='subject', help='Environment')
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parser.add_argument('-root', dest='root', help='root folder')
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parser.add_argument('-job',dest='job',help='job name')
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parser.add_argument('-prop',dest='prop',help='property file')
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args = parser.parse_args()
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if args.root is None or args.job is None:
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if args.root is None or args.job is None or args.prop is None:
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parser.print_help()
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raise AttributeError
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return args
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+6
-6
@@ -1,17 +1,17 @@
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java:
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8home: /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
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spinfer:
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home: /Users/anil.koyuncu/projects/fixminer/spinfer/spinfer.native
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home: /Users/anil.koyuncu/projects/richedit/spinfer/spinfer.native
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#home: /Users/anil.koyuncu/projects/spinfer/spinfer.native
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dataset:
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# home: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/
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home: /data/fixminer-core/python/data/gumInputLinux/
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# home: /Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/
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home: /data/richedit-core/python/data/gumInputLinux/
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coccinelle:
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home: /Users/anil.koyuncu/projects/fixminer/spinfer/statics
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home: /Users/anil.koyuncu/projects/richedit/spinfer/statics
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#home: /Users/anil.koyuncu/projects/spinfer/statics
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fixminer:
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# datapath: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/
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datapath: /data/fixminer-core/python/data/
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# datapath: /Users/anil.koyuncu/projects/test/richedit-core/python/data/
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datapath: /data/richedit-core/python/data/
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@@ -0,0 +1,46 @@
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Group,Subject,Repo,GitRepo,Branch
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Apache,CAMEL,camel,https://github.com/apache/camel.git,master
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Apache,HBASE,hbase,https://github.com/apache/hbase.git,master
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Apache,HIVE,hive,https://github.com/apache/hive.git,master
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Commons,CODEC,commons-codec,https://github.com/apache/commons-codec.git,trunk
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Commons,COLLECTIONS,commons-collections,https://github.com/apache/commons-collections.git,master
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Commons,COMPRESS,commons-compress,https://github.com/apache/commons-compress.git,master
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Commons,CONFIGURATION,commons-configuration,https://github.com/apache/commons-configuration.git,trunk
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Commons,CRYPTO,commons-crypto,https://github.com/apache/commons-crypto.git,master
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Commons,CSV,commons-csv,https://github.com/apache/commons-csv.git,master
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Commons,IO,commons-io,https://github.com/apache/commons-io.git,master
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Commons,WEAVER,commons-weaver,https://github.com/apache/commons-weaver.git,master
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JBoss,ENTESB,fuse,https://github.com/jboss-fuse/fuse.git,6.3.0.redhat
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JBoss,JBMETA,metadata,https://github.com/jboss/metadata.git,master
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Wildfly,ELY,wildfly-elytron,https://github.com/wildfly-security/wildfly-elytron.git,master
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Wildfly,SWARM,wildfly-swarm,https://github.com/wildfly-swarm/wildfly-swarm.git,master
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Wildfly,WFARQ,wildfly-arquillian,https://github.com/wildfly/wildfly-arquillian.git,master
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Wildfly,WFCORE,wildfly-core,https://github.com/wildfly/wildfly-core.git,master
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Wildfly,WFLY,wildfly,https://github.com/wildfly/wildfly.git,master
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Wildfly,WFMP,wildfly-maven-plugin,https://github.com/wildfly/wildfly-maven-plugin.git,master
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Spring,AMQP,spring-amqp,https://github.com/spring-projects/spring-amqp,master
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Spring,ANDROID,spring-android,https://github.com/spring-projects/spring-android,master
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Spring,BATCH,spring-batch,https://github.com/spring-projects/spring-batch,master
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Spring,BATCHADM,spring-batch-admin,https://github.com/spring-projects/spring-batch-admin,master
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Spring,DATACMNS,spring-data-commons,https://github.com/spring-projects/spring-data-commons,master
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Spring,DATAGRAPH,spring-data-neo4j,https://github.com/spring-projects/spring-data-neo4j,master
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Spring,DATAJPA,spring-data-jpa,https://github.com/spring-projects/spring-data-jpa,master
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Spring,DATAMONGO,spring-data-mongodb,https://github.com/spring-projects/spring-data-mongodb,master
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Spring,DATAREDIS,spring-data-redis,https://github.com/spring-projects/spring-data-redis,master
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Spring,DATAREST,spring-data-rest,https://github.com/spring-projects/spring-data-rest,master
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Spring,LDAP,spring-ldap,https://github.com/spring-projects/spring-ldap,master
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Spring,MOBILE,spring-mobile,https://github.com/spring-projects/spring-mobile,master
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Spring,ROO,spring-roo,https://github.com/spring-projects/spring-roo,master
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Spring,SEC,spring-security,https://github.com/spring-projects/spring-security,master
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Spring,SECOAUTH,spring-security-oauth,https://github.com/spring-projects/spring-security-oauth,master
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Spring,SGF,spring-data-gemfire,https://github.com/spring-projects/spring-data-gemfire,master
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Spring,SHDP,spring-hadoop,https://github.com/spring-projects/spring-hadoop,master
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Spring,SHL,spring-shell,https://github.com/spring-projects/spring-shell,master
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Spring,SOCIAL,spring-social,https://github.com/spring-projects/spring-social,master
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Spring,SOCIALFB,spring-social-facebook,https://github.com/spring-projects/spring-social-facebook,master
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Spring,SOCIALLI,spring-social-linkedin,https://github.com/spring-projects/spring-social-linkedin,master
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Spring,SOCIALTW,spring-social-twitter,https://github.com/spring-projects/spring-social-twitter,master
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Spring,SPR,spring-framework,https://github.com/spring-projects/spring-framework,master
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Spring,SWF,spring-webflow,https://github.com/spring-projects/spring-webflow,master
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Spring,SWS,spring-ws,https://github.com/spring-projects/spring-ws,master
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+2
-2
@@ -1,6 +1,6 @@
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#!/bin/bash
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source activate redisEnv
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source activate fixminerEnv
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PYTHONPATH=$(pwd) python -u main.py -root $(pwd) -job $1
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PYTHONPATH=$(pwd) python -u main.py -root $(pwd) -job $1 -prop $2
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+20
-21
@@ -15,7 +15,6 @@ if __name__ == '__main__':
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setEnv(args)
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job = args.job
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job = 'indexClusters'
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ROOT_DIR = os.environ["ROOT_DIR"]
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REPO_PATH = os.environ["REPO_PATH"]
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CODE_PATH = os.environ["CODE_PATH"]
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@@ -36,24 +35,24 @@ if __name__ == '__main__':
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print(job)
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if job == 'dataset':
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if job == 'dataset4j':
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from javaDS import createDS
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createDS(subject)
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elif job == 'linuxDS':
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from linuxDataset import collectBugFixPatches
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collectBugFixPatches()
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elif job =='otherDS':
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# elif job == 'linuxDS':
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# from linuxDataset import collectBugFixPatches
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# collectBugFixPatches()
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elif job =='dataset4c':
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from otherDatasets import core
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core()
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elif job =='richEditScript':
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cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " RICHEDITSCRIPT " + 'L1'
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cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(Path(ROOT_DIR).parent, 'target','FixPatternMiner-1.0.0-jar-with-dependencies.jar') + " " + args.prop + " RICHEDITSCRIPT "
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output = shellCallTemplate(cmd)
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logging.info(output)
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elif job =='loadRES':
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cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " LOAD " + rootType
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output = shellCallTemplate(cmd)
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logging.info(output)
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# elif job =='loadRES':
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# cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " LOAD " + rootType
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# output = shellCallTemplate(cmd)
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# logging.info(output)
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elif job =='shapeSI':
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from pairs import shapePairs
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@@ -66,14 +65,14 @@ if __name__ == '__main__':
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importShape()
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elif job =='compareShapes':
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# cmd = "mvn exec:java -f '/data/fixminer_source/' -Dexec.mainClass='edu.lu.uni.serval.fixminer.akka.compare.CompareTrees' -Dexec.args='"+ " shape " + join(DATA_PATH,"redis") +" ALLdumps-gumInput.rdb " + "clusterl0-gumInputALL.rdb /data/fixminer-core/python/data/richEditScript'"
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cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(DATA_PATH, 'FixPatternMiner-1.0.1.jar') + " " + join(DATA_PATH, 'app.properties') + " COMPARE " + 'L1'
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# 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'"
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cmd = "JAVA_HOME='" + jdk8 + "' java -jar " + join(Path(ROOT_DIR).parent, 'target','FixPatternMiner-1.0.0-jar-with-dependencies.jar') + " " + args.prop + " COMPARE "
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output = shellCallTemplate(cmd)
|
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logging.info(output)
|
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|
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elif job == 'clusterAdditional':
|
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from addNewData import cluster
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cluster()
|
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# elif job == 'clusterAdditional':
|
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# from addNewData import cluster
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# cluster()
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|
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elif job == 'cluster':
|
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from abstractPatch import cluster
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@@ -125,11 +124,11 @@ if __name__ == '__main__':
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cluster(join(DATA_PATH, 'tokens'), join(DATA_PATH, 'pairsToken'),'tokens')
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stopDB(dbDir, "6380", "clusterl2-gumInputALL.rdb")
|
||||
|
||||
elif job == 'additional':
|
||||
from addNewData import core
|
||||
core()
|
||||
# from addNewData import checkWrongMembers
|
||||
# checkWrongMembers()
|
||||
# elif job == 'additional':
|
||||
# from addNewData import core
|
||||
# core()
|
||||
# # from addNewData import checkWrongMembers
|
||||
# # checkWrongMembers()
|
||||
|
||||
elif job == 'codeflaws':
|
||||
from otherDatasets import codeflaws
|
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|
||||
@@ -1,20 +1,20 @@
|
||||
java:
|
||||
8home: /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
|
||||
spinfer:
|
||||
home: /Users/anil.koyuncu/projects/fixminer/spinfer/spinfer.native
|
||||
home: /Users/anil.koyuncu/projects/richedit/spinfer/spinfer.native
|
||||
#home: /Users/anil.koyuncu/projects/spinfer/spinfer.native
|
||||
dataset:
|
||||
# home: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/
|
||||
home: /Users/anil.koyuncu/projects/fixminer/fixminer-data/patches/
|
||||
# home: /data/fixminer-core/python/data/gumInputLinux/
|
||||
# home: /Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/
|
||||
home: /Users/anil.koyuncu/projects/richedit/richedit-data/patches/
|
||||
# home: /data/richedit-core/python/data/gumInputLinux/
|
||||
repo: /Users/anil.koyuncu/projects/datasets
|
||||
|
||||
coccinelle:
|
||||
home: /Users/anil.koyuncu/projects/fixminer/spinfer/statics
|
||||
home: /Users/anil.koyuncu/projects/richedit/spinfer/statics
|
||||
#home: /Users/anil.koyuncu/projects/spinfer/statics
|
||||
|
||||
|
||||
fixminer:
|
||||
# datapath: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/
|
||||
datapath: /Users/anil.koyuncu/projects/fixminer/fixminer-data
|
||||
# datapath: /data/fixminer-core/python/data/
|
||||
# datapath: /Users/anil.koyuncu/projects/test/richedit-core/python/data/
|
||||
datapath: /Users/anil.koyuncu/projects/richedit/richedit-data
|
||||
# datapath: /data/richedit-core/python/data/
|
||||
|
||||
+18
-9
@@ -5,6 +5,7 @@ COMMIT_DFS = os.environ["COMMIT_DFS"]
|
||||
DATASET_PATH = os.environ["REPO_PATH"]
|
||||
DATASET = os.environ["dataset"]
|
||||
ROOT = os.environ["ROOT_DIR"]
|
||||
PROJECT_LIST = os.environ["PROJECT_LIST"]
|
||||
|
||||
def filetype_fileter(filename):
|
||||
# return filename.endswith(u'.java') and not bool(re.search('test.*\/', filename))
|
||||
@@ -266,16 +267,24 @@ def getAllCommits(datasetName):
|
||||
def core():
|
||||
datasets = pd.read_csv(join(ROOT,'data', 'datasets.csv'))
|
||||
# repoList = ['FFmpeg','curl','nginx','openssl','redis','tmux','vlc']
|
||||
pjs = listdir(DATASET_PATH)
|
||||
# newRepo = ['php-src','libtiff','cpython']
|
||||
pjs = [i for i in pjs if not (i.startswith('.') or i.startswith('codeflaws'))]
|
||||
# pjs = [i for i in pjs if (i in newRepo )]
|
||||
repoList = pjs
|
||||
|
||||
pjList = PROJECT_LIST.split(',')
|
||||
if not os.path.exists(DATASET_PATH):
|
||||
os.mkdir(DATASET_PATH)
|
||||
|
||||
for repo,src in datasets.values.tolist():
|
||||
cmd = 'git -C ' + DATASET_PATH + ' clone ' + src
|
||||
shellCallTemplate(cmd)
|
||||
logging.info(repo)
|
||||
collectBugFixPatches(repo)
|
||||
if(pjList != ['ALL']):
|
||||
if repo in pjList:
|
||||
print(repo)
|
||||
cmd = 'git -C ' + DATASET_PATH + ' clone ' + src
|
||||
shellCallTemplate(cmd)
|
||||
logging.info(repo)
|
||||
collectBugFixPatches(repo)
|
||||
else:
|
||||
cmd = 'git -C ' + DATASET_PATH + ' clone ' + src
|
||||
shellCallTemplate(cmd)
|
||||
logging.info(repo)
|
||||
collectBugFixPatches(repo)
|
||||
|
||||
def codeflaws():
|
||||
cf = listdir(join(DATASET_PATH,'codeflaws'))
|
||||
|
||||
@@ -1,21 +1,21 @@
|
||||
java:
|
||||
8home: /Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home
|
||||
spinfer:
|
||||
home: /Users/anilkoyuncu/projects/fixminer/spinfer/spinfer.native
|
||||
home: /Users/anilkoyuncu/projects/richedit/spinfer/spinfer.native
|
||||
#home: /Users/anil.koyuncu/projects/spinfer/spinfer.native
|
||||
dataset:
|
||||
# home: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/gumInputLinux/
|
||||
home: /Users/anilkoyuncu/projects/fixminer/fixminer-core/python/data/gumInputLinux
|
||||
# home: /data/fixminer-core/python/data/gumInputLinux/
|
||||
repo: /Users/anil.koyuncu/projects/datasets
|
||||
# home: /Users/anil.koyuncu/projects/test/richedit-core/python/data/gumInputLinux/
|
||||
home: /Users/anilkoyuncu/projects/richedit/richedit-core/python/data/gumInputLinux
|
||||
# home: /data/richedit-core/python/data/gumInputLinux/
|
||||
repo: /Users/anilkoyuncu/projects/datasets
|
||||
|
||||
coccinelle:
|
||||
home: /Users/anilkoyuncu/projects/fixminer/spinfer/statics
|
||||
home: /Users/anilkoyuncu/projects/richedit/spinfer/statics
|
||||
#home: /Users/anil.koyuncu/projects/spinfer/statics
|
||||
|
||||
|
||||
fixminer:
|
||||
# datapath: /Users/anil.koyuncu/projects/test/fixminer-core/python/data/
|
||||
datapath: /Users/anilkoyuncu/projects/fixminer/fixminer-data/
|
||||
# datapath: /Users/anil.koyuncu/projects/test/richedit-core/python/data/
|
||||
datapath: /Users/anilkoyuncu/projects/richedit/richedit-data/
|
||||
projectType : c
|
||||
# datapath: /data/fixminer-core/python/data/
|
||||
# datapath: /data/richedit-core/python/data/
|
||||
|
||||
Reference in New Issue
Block a user