See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/36/display/redirect>
------------------------------------------ [...truncated 203.47 KB...] 2017-11-17 19:19:44,202 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 19:19:44,202 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 19:19:44,211 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 19:19:44,211 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 19:19:44,217 INFO org.hibernate.id.enhanced.TableGenerator - HHH000398: Explicit segment value for id generator [PUBLIC.hibernate_sequences.sequence_name] suggested; using default [default] 2017-11-17 19:19:44,268 WARN org.hibernate.cache.ehcache.AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults. 2017-11-17 19:19:44,270 WARN org.hibernate.cache.ehcache.internal.strategy.EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType] 2017-11-17 19:19:44,522 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@4130955c] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 19:19:44,628 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 19:19:44,636 WARN net.sf.ehcache.CacheManager - Creating a new instance of CacheManager using the diskStorePath "/tmp" which is already used by an existing CacheManager. The source of the configuration was net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@5e99b9c. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510946384636. To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. 2017-11-17 19:19:44,835 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: test 2017-11-17 19:19:44,836 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - loading concept graph from <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/test.gz> 2017-11-17 19:19:44,838 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - concept graph test, vertices: 7 2017-11-17 19:19:44,839 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - initializing similarity measures 2017-11-17 19:19:44,843 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: test 2017-11-17 19:19:45,216 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 19:19:45,334 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 19:19:45,337 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 19:19:45,363 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - listConcept: [[dog], [animal, e coli], [cat]] 2017-11-17 19:19:45,363 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - i: 1, conceptSenses: [animal, e coli] 2017-11-17 19:19:45,384 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - i: 1, concept: animal Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.457 sec Running org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexTest 2017-11-17 19:19:46,134 DEBUG org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator - NamedEntityRegex [code=C00TEST, regex=(?i)COUGH] [cough] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.311 sec Running org.apache.ctakes.ytex.uima.annotators.DBCollectionReaderTest 2017-11-17 19:19:48,779 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - loading ytex.properties from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/ytex.properties> 2017-11-17 19:19:48,780 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 2017-11-17 19:19:48,852 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@47af7f3d: startup date [Fri Nov 17 19:19:48 UTC 2017]; root of context hierarchy 2017-11-17 19:19:48,901 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] 2017-11-17 19:19:48,971 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml] 2017-11-17 19:19:48,981 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'ytexApplicationContext': replacing [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [jar:file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]] 2017-11-17 19:19:49,012 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5f683daf: defining beans [ytexApplicationContext]; root of factory hierarchy 2017-11-17 19:19:49,079 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@6283d8b8: startup date [Fri Nov 17 19:19:49 UTC 2017]; root of context hierarchy 2017-11-17 19:19:49,083 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml] 2017-11-17 19:19:49,315 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 2017-11-17 19:19:49,422 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xml] 2017-11-17 19:19:49,445 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml] 2017-11-17 19:19:49,474 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao.xml] 2017-11-17 19:19:49,513 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml] 2017-11-17 19:19:49,544 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'mapperOperation': replacing [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null] with [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null] 2017-11-17 19:19:49,701 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-17 19:19:49,702 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 19:19:49,702 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-17 19:19:49,763 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5167f57d: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService]; root of factory hierarchy 2017-11-17 19:19:49,828 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 19:19:50,830 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-17 19:19:50,846 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final} 2017-11-17 19:19:50,850 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found 2017-11-17 19:19:50,852 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist 2017-11-17 19:19:51,847 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache open start 2017-11-17 19:19:51,862 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache open end 2017-11-17 19:19:51,997 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache commit start 2017-11-17 19:19:52,000 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache commit end 2017-11-17 19:19:52,003 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - Database closed 2017-11-17 19:19:52,167 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache open start 2017-11-17 19:19:52,167 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache open end 2017-11-17 19:19:52,273 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 19:19:52,416 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 19:19:52,417 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 19:19:52,421 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 19:19:52,426 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 19:19:52,584 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 19:19:52,592 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 19:19:52,609 INFO org.hibernate.id.enhanced.TableGenerator - HHH000398: Explicit segment value for id generator [PUBLIC.hibernate_sequences.sequence_name] suggested; using default [default] 2017-11-17 19:19:52,811 WARN org.hibernate.cache.ehcache.AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults. 2017-11-17 19:19:52,814 WARN org.hibernate.cache.ehcache.internal.strategy.EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType] 2017-11-17 19:19:53,468 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@53a5e217] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 19:19:54,091 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 19:19:54,100 WARN net.sf.ehcache.CacheManager - Creating a new instance of CacheManager using the diskStorePath "/tmp" which is already used by an existing CacheManager. The source of the configuration was net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@35e8316e. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510946394100. To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. 2017-11-17 19:19:55,107 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: sct-rxnorm 2017-11-17 19:19:55,300 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph from classpath, attempt to load from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> 2017-11-17 19:19:55,307 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> not found, cannot load concept graph 2017-11-17 19:19:55,307 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph: sct-rxnorm 2017-11-17 19:19:55,394 WARN org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - concept graph null, name: sct-rxnorm 2017-11-17 19:19:55,395 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: sct-rxnorm 2017-11-17 19:19:55,844 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 19:19:56,095 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 19:19:56,098 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 19:19:56,635 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=0} 2017-11-17 19:19:56,659 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=1} 2017-11-17 19:19:56,662 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=2} 2017-11-17 19:19:56,664 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=3} 2017-11-17 19:19:56,667 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=4} 2017-11-17 19:19:56,669 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=5} 2017-11-17 19:19:56,671 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=6} 2017-11-17 19:19:56,673 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=7} 2017-11-17 19:19:56,674 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=8} 2017-11-17 19:19:56,676 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=9} 2017-11-17 19:19:56,677 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=10} 2017-11-17 19:19:56,679 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=11} 2017-11-17 19:19:56,681 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=12} 2017-11-17 19:19:56,685 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=13} 2017-11-17 19:19:56,688 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=14} 2017-11-17 19:19:56,691 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=15} 2017-11-17 19:19:56,694 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=16} 2017-11-17 19:19:56,696 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=17} 2017-11-17 19:19:56,698 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=18} 2017-11-17 19:19:56,699 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=19} 2017-11-17 19:19:56,701 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=20} 2017-11-17 19:19:56,702 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=21} 2017-11-17 19:19:56,703 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=22} 2017-11-17 19:19:56,704 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=23} 2017-11-17 19:19:56,705 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=24} 2017-11-17 19:19:56,707 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=25} 2017-11-17 19:19:56,708 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=26} 2017-11-17 19:19:56,710 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=27} 2017-11-17 19:19:56,711 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=28} 2017-11-17 19:19:56,712 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=29} 2017-11-17 19:19:56,713 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=30} Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.953 sec Running org.apache.ctakes.ytex.uima.annotators.DictionaryLookupAnnotatorTest 2017-11-17 19:19:58,619 INFO org.apache.ctakes.chunker.ae.Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 2017-11-17 19:20:00,523 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 19:20:00,542 INFO org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator - Finite state machines loaded. 2017-11-17 19:20:00,548 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - loading ytex.properties from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/ytex.properties> 2017-11-17 19:20:00,548 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 2017-11-17 19:20:00,978 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache open start 2017-11-17 19:20:00,989 INFO hsqldb.db.HSQLDB5FCB6B2545.ENGINE - dataFileCache open end 2017-11-17 19:20:01,099 INFO org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl - Connection established to: jdbc:hsqldb:file:///tmp/ctakes-test-hsqldb/ctakes/ctakes;shutdown=true 2017-11-17 19:20:01,102 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - Parsing descriptor: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.xml> 2017-11-17 19:20:01,191 INFO org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl - Exclusion tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc, cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp] 2017-11-17 19:20:01,228 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - [SegmentsToSkip, SentenceModelFile] 2017-11-17 19:20:01,228 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 2017-11-17 19:20:01,392 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@9573584: startup date [Fri Nov 17 19:20:01 UTC 2017]; root of context hierarchy 2017-11-17 19:20:01,440 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] 2017-11-17 19:20:01,497 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml] 2017-11-17 19:20:01,508 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'ytexApplicationContext': replacing [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [jar:file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]] 2017-11-17 19:20:01,535 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@4c51cf28: defining beans [ytexApplicationContext]; root of factory hierarchy 2017-11-17 19:20:01,594 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@ff684e1: startup date [Fri Nov 17 19:20:01 UTC 2017]; root of context hierarchy 2017-11-17 19:20:01,597 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml] 2017-11-17 19:20:03,479 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 2017-11-17 19:20:03,597 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xml] 2017-11-17 19:20:03,615 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml] 2017-11-17 19:20:03,654 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao.xml] 2017-11-17 19:20:03,698 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml] 2017-11-17 19:20:03,721 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'mapperOperation': replacing [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null] with [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null] 2017-11-17 19:20:03,849 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-17 19:20:03,850 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 19:20:03,850 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-17 19:20:03,910 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@27305e6: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService]; root of factory hierarchy 2017-11-17 19:20:03,964 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 19:20:04,697 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-17 19:20:04,706 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final} 2017-11-17 19:20:04,709 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found 2017-11-17 19:20:04,711 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist 2017-11-17 19:20:05,035 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 19:20:05,173 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 19:20:05,173 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 19:20:05,179 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 19:20:05,186 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 19:20:05,357 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 19:20:05,364 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 19:20:05,381 INFO org.hibernate.id.enhanced.TableGenerator - HHH000398: Explicit segment value for id generator [PUBLIC.hibernate_sequences.sequence_name] suggested; using default [default] 2017-11-17 19:20:05,638 WARN org.hibernate.cache.ehcache.AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults. 2017-11-17 19:20:05,641 WARN org.hibernate.cache.ehcache.internal.strategy.EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType] 2017-11-17 19:20:07,065 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@76889e60] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 19:20:07,558 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 19:20:07,568 WARN net.sf.ehcache.CacheManager - Creating a new instance of CacheManager using the diskStorePath "/tmp" which is already used by an existing CacheManager. The source of the configuration was net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@24db6ce. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510946407568. To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. 2017-11-17 19:20:08,037 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: sct-rxnorm 2017-11-17 19:20:08,145 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph from classpath, attempt to load from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> 2017-11-17 19:20:08,145 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> not found, cannot load concept graph 2017-11-17 19:20:08,145 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph: sct-rxnorm 2017-11-17 19:20:08,189 WARN org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - concept graph null, name: sct-rxnorm 2017-11-17 19:20:08,189 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: sct-rxnorm 2017-11-17 19:20:08,633 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 19:20:08,719 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 19:20:08,722 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 19:20:08,752 WARN org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - Concept Graph was not loaded - word sense disambiguation disabled 2017-11-17 19:20:08,801 INFO org.apache.ctakes.postagger.POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 2017-11-17 19:20:09,830 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator - segmentsAdded: 0 2017-11-17 19:20:09,834 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Starting processing. 2017-11-17 19:20:09,842 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 19:20:09,866 INFO org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator - process(JCas) 2017-11-17 19:20:09,882 INFO org.apache.ctakes.postagger.POSTagger - process(JCas) 2017-11-17 19:20:09,898 INFO org.apache.ctakes.chunker.ae.Chunker - process(JCas) 2017-11-17 19:20:09,922 INFO org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster - process(JCas) 2017-11-17 19:20:09,925 INFO org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster - process(JCas) 2017-11-17 19:20:09,928 INFO org.apache.ctakes.core.ae.CopyAnnotator - process(JCas) 2017-11-17 19:20:09,930 INFO org.apache.ctakes.core.ae.OverlapAnnotator - process(JCas) 2017-11-17 19:20:09,933 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - process(JCas) NP [Dr. Doolitle] VP [asked] NP [patient] VP [ to take] O [ ] NP [a deep breath ] NP [ ] PP [ ] O [and] ADJP [exhale] ADVP [slowly] NP [Patient] VP [coughed] O [and] VP [complained] PP [of] NP [abdominal pain] NP [Patient] VP [was administered] NP [acetaminophen] LookupWindowAnnotation [Dr. Doolitle] LookupWindowAnnotation [patient] LookupWindowAnnotation [a deep breath ] LookupWindowAnnotation [Patient] LookupWindowAnnotation [abdominal pain] LookupWindowAnnotation [Patient] LookupWindowAnnotation [acetaminophen] EntityMention [abdominal] EntityMention [pain] EntityMention [acetaminophen] 2017-11-17 19:20:10,239 INFO org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl - Connection established to: jdbc:hsqldb:file:///tmp/ctakes-test-hsqldb/ctakes/ctakes;shutdown=true 2017-11-17 19:20:10,240 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - Parsing descriptor: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.xml> 2017-11-17 19:20:10,243 INFO org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl - Exclusion tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc, cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp] 2017-11-17 19:20:10,283 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - process(JCas) EntityMention [acetaminophen] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.965 sec Running org.apache.ctakes.ytex.tools.SetupAuiFirstWordTest 2017-11-17 19:20:10,978 WARN org.apache.ctakes.ytex.tools.SetupAuiFirstWord - classpath:ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml not available, attempting to load from file system 2017-11-17 19:20:11,193 INFO org.apache.ctakes.ytex.tools.SetupAuiFirstWord - loading lvg.properties from:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties ** Configuration Error: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/file>:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties (No such file or directory) ** Error: problem of opening/reading config file: '<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/file>:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg//file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'. Use -x option to specify the config file path. UmlsAuiFirstWord [aui=1tok, fword=heart] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.471 sec Results : Failed tests: testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest) Tests run: 13, Failures: 1, Errors: 0, Skipped: 0 [JENKINS] Recording test results [JENKINS] Archiving disabled
