See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/35/display/redirect>
------------------------------------------ [...truncated 195.78 KB...] 2017-11-17 17:08:46,199 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@24d61e4: 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 17:08:46,210 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 17:08:46,450 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open start 2017-11-17 17:08:46,450 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open end 2017-11-17 17:08:46,630 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit start 2017-11-17 17:08:46,664 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit end 2017-11-17 17:08:46,731 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - Database closed 2017-11-17 17:08:46,866 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open start 2017-11-17 17:08:46,867 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open end 2017-11-17 17:08:46,899 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 17:08:46,923 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 17:08:46,923 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 17:08:46,924 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 17:08:46,924 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 17:08:46,933 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 17:08:46,933 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 17:08:46,937 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 17:08:46,982 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 17:08:46,984 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 17:08:47,283 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@17e9bc9e] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 17:08:47,407 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 17:08:47,415 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@7fd987ef. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510938527415. 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 17:08:47,627 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: test 2017-11-17 17:08:47,628 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 17:08:47,629 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - concept graph test, vertices: 7 2017-11-17 17:08:47,630 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - initializing similarity measures 2017-11-17 17:08:47,636 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: test 2017-11-17 17:08:47,950 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 17:08:48,029 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 17:08:48,031 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 17:08:48,050 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - listConcept: [[dog], [animal, e coli], [cat]] 2017-11-17 17:08:48,050 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - i: 1, conceptSenses: [animal, e coli] 2017-11-17 17:08:48,067 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - i: 1, concept: animal Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.655 sec Running org.apache.ctakes.ytex.uima.annotators.SentenceDetectorTest 2017-11-17 17:08:49,683 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 17:08:49,692 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - [SegmentsToSkip, SentenceModelFile] 2017-11-17 17:08:49,805 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 2017-11-17 17:08:50,345 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 17:08:50,361 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Starting processing. [Dr. Doolitle asked patient to take a deep breath and exhale slowly.] [Patient coughed.] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.829 sec Running org.apache.ctakes.ytex.uima.annotators.DBConsumerTest 2017-11-17 17:08:50,988 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 17:08:50,991 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 2017-11-17 17:08:51,093 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@643b1d11: startup date [Fri Nov 17 17:08:51 UTC 2017]; root of context hierarchy 2017-11-17 17:08:51,172 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 17:08:51,430 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 17:08:51,446 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 17:08:51,476 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@12d3a4e9: defining beans [ytexApplicationContext]; root of factory hierarchy 2017-11-17 17:08:51,562 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@3eb7fc54: startup date [Fri Nov 17 17:08:51 UTC 2017]; root of context hierarchy 2017-11-17 17:08:51,566 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 17:08:51,844 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 17:08:51,954 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 17:08:51,975 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 17:08:52,001 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 17:08:52,039 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 17:08:52,076 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 17:08:52,223 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-17 17:08:52,224 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 17:08:52,224 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-17 17:08:52,268 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@623a8092: 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 17:08:52,327 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 17:08:53,164 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-17 17:08:53,173 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final} 2017-11-17 17:08:53,177 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found 2017-11-17 17:08:53,180 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist 2017-11-17 17:08:54,051 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open start 2017-11-17 17:08:54,063 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open end 2017-11-17 17:08:54,284 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit start 2017-11-17 17:08:54,309 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit end 2017-11-17 17:08:54,377 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - Database closed 2017-11-17 17:08:54,532 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open start 2017-11-17 17:08:54,533 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open end 2017-11-17 17:08:54,638 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 17:08:54,817 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 17:08:54,817 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 17:08:54,824 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 17:08:54,835 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 17:08:55,034 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 17:08:55,040 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 17:08:55,059 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 17:08:55,274 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 17:08:55,276 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 17:08:55,872 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@2e3cdec2] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 17:08:56,298 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 17:08:56,309 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$InputStreamConfigurationSource@4c4f4365. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510938536309. To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. 2017-11-17 17:08:56,787 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: sct-rxnorm 2017-11-17 17:08:56,858 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph from classpath, attempt to load from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> 2017-11-17 17:08:56,858 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 17:08:56,858 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph: sct-rxnorm 2017-11-17 17:08:56,906 WARN org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - concept graph null, name: sct-rxnorm 2017-11-17 17:08:56,906 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: sct-rxnorm 2017-11-17 17:08:57,271 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 17:08:57,364 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 17:08:57,368 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 17:08:58,190 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - [SegmentsToSkip, SentenceModelFile] 2017-11-17 17:08:58,283 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 2017-11-17 17:08:58,478 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 17:08:58,953 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator - segmentsAdded: 0 2017-11-17 17:08:58,955 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Starting processing. 2017-11-17 17:08:58,959 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 17:08:58,975 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveDocument 2017-11-17 17:08:59,169 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnotationsHib 2017-11-17 17:08:59,170 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoBaseHib 2017-11-17 17:08:59,219 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveAnnoBaseHib 2017-11-17 17:08:59,219 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin insertAnnotationContainmentLinks 2017-11-17 17:08:59,247 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end insertAnnotationContainmentLinks 2017-11-17 17:08:59,275 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoPrimitive 2017-11-17 17:08:59,353 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoPrimitive 2017-11-17 17:08:59,356 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - sql insert for type org.apache.ctakes.typesystem.type.textspan.Segment: insert into anno_segment(anno_base_id, "ID") values (?, ?) 2017-11-17 17:08:59,356 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - initMapInfo(segment): AnnoMappingInfo [mapField={ID=ColumnMappingInfo [columnName=ID]}, tableName=anno_segment] 2017-11-17 17:08:59,365 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveAnnoPrimitive 2017-11-17 17:08:59,365 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoPrimitive 2017-11-17 17:08:59,368 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - sql insert for type org.apache.ctakes.typesystem.type.textspan.Sentence: insert into anno_sentence(anno_base_id, "SEGMENTID", "SENTENCENUMBER") values (?, ?, ?) 2017-11-17 17:08:59,368 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - initMapInfo(sentence): AnnoMappingInfo [mapField={SEGMENTID=ColumnMappingInfo [columnName=SEGMENTID], SENTENCENUMBER=ColumnMappingInfo [columnName=SENTENCENUMBER]}, tableName=anno_sentence] 2017-11-17 17:08:59,369 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveAnnoPrimitive 2017-11-17 17:08:59,369 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoPrimitive 2017-11-17 17:08:59,371 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoPrimitive 2017-11-17 17:08:59,374 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - sql insert for type org.apache.ctakes.typesystem.type.syntax.WordToken: insert into anno_token(anno_base_id, coveredText, "CANONICALFORM", "CAPITALIZATION", "NORMALIZEDFORM", "NUMPOSITION", "PARTOFSPEECH", "SUGGESTION", "TOKENNUMBER") values (?, ?, ?, ?, ?, ?, ?, ?, ?) 2017-11-17 17:08:59,374 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - initMapInfo(wordtoken): AnnoMappingInfo [mapField={CANONICALFORM=ColumnMappingInfo [columnName=CANONICALFORM], CAPITALIZATION=ColumnMappingInfo [columnName=CAPITALIZATION], NORMALIZEDFORM=ColumnMappingInfo [columnName=NORMALIZEDFORM], NUMPOSITION=ColumnMappingInfo [columnName=NUMPOSITION], PARTOFSPEECH=ColumnMappingInfo [columnName=PARTOFSPEECH], SUGGESTION=ColumnMappingInfo [columnName=SUGGESTION], TOKENNUMBER=ColumnMappingInfo [columnName=TOKENNUMBER]}, tableName=anno_token] 2017-11-17 17:08:59,385 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveAnnoPrimitive 2017-11-17 17:08:59,396 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - begin saveAnnoLinks 2017-11-17 17:08:59,396 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveAnnoLinks 2017-11-17 17:08:59,396 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveAnnotationsHib 2017-11-17 17:08:59,409 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - end saveDocument 2017-11-17 17:08:59,428 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Closing ApplicationContext 'ytexApplicationContext': startup date [Fri Nov 17 17:08:51 UTC 2017]; root of context hierarchy 2017-11-17 17:08:59,430 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@623a8092: 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 17:08:59,431 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Shutting down EHCache CacheManager 2017-11-17 17:08:59,529 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit start 2017-11-17 17:09:00,737 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit end 2017-11-17 17:09:00,805 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - Database closed Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.131 sec Running org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.319 sec <<< FAILURE! Running org.apache.ctakes.ytex.uima.annotators.DBCollectionReaderTest 2017-11-17 17:09:04,020 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 17:09:04,023 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 2017-11-17 17:09:04,095 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@47af7f3d: startup date [Fri Nov 17 17:09:04 UTC 2017]; root of context hierarchy 2017-11-17 17:09:04,156 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 17:09:04,244 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 17:09:04,256 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 17:09:04,286 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 17:09:04,354 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@6283d8b8: startup date [Fri Nov 17 17:09:04 UTC 2017]; root of context hierarchy 2017-11-17 17:09:04,356 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 17:09:04,585 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 17:09:04,664 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 17:09:04,695 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 17:09:04,718 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 17:09:04,747 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 17:09:04,776 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 17:09:04,885 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-17 17:09:04,886 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 17:09:04,886 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-17 17:09:04,926 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 17:09:04,985 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 17:09:05,703 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-17 17:09:05,710 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final} 2017-11-17 17:09:05,713 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found 2017-11-17 17:09:05,715 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist 2017-11-17 17:09:06,623 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open start 2017-11-17 17:09:06,637 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open end 2017-11-17 17:09:06,886 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit start 2017-11-17 17:09:06,919 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache commit end 2017-11-17 17:09:06,987 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - Database closed 2017-11-17 17:09:07,148 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open start 2017-11-17 17:09:07,149 INFO hsqldb.db.HSQLDB5FCAF32979.ENGINE - dataFileCache open end 2017-11-17 17:09:07,261 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 17:09:07,423 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 17:09:07,423 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 17:09:07,430 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 17:09:07,435 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 17:09:07,625 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 17:09:07,633 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 17:09:07,654 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 17:09:07,876 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 17:09:07,878 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 17:09:08,503 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@53a5e217] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 17:09:09,012 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 17:09:09,032 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$InputStreamConfigurationSource@35e8316e. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510938549032. To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. 2017-11-17 17:09:09,465 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: sct-rxnorm 2017-11-17 17:09:09,537 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph from classpath, attempt to load from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> 2017-11-17 17:09:09,540 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 17:09:09,540 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph: sct-rxnorm 2017-11-17 17:09:09,622 WARN org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - concept graph null, name: sct-rxnorm 2017-11-17 17:09:09,622 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: sct-rxnorm 2017-11-17 17:09:09,958 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 17:09:10,179 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 17:09:10,182 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 17:09:10,748 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=0} 2017-11-17 17:09:10,772 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=1} 2017-11-17 17:09:10,773 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=2} 2017-11-17 17:09:10,775 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=3} 2017-11-17 17:09:10,776 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=4} 2017-11-17 17:09:10,777 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=5} 2017-11-17 17:09:10,779 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=6} 2017-11-17 17:09:10,780 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=7} 2017-11-17 17:09:10,782 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=8} 2017-11-17 17:09:10,784 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=9} 2017-11-17 17:09:10,787 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=10} 2017-11-17 17:09:10,790 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=11} 2017-11-17 17:09:10,792 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=12} 2017-11-17 17:09:10,795 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=13} 2017-11-17 17:09:10,797 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=14} 2017-11-17 17:09:10,799 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=15} 2017-11-17 17:09:10,802 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=16} 2017-11-17 17:09:10,803 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=17} 2017-11-17 17:09:10,804 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=18} 2017-11-17 17:09:10,806 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=19} 2017-11-17 17:09:10,808 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=20} 2017-11-17 17:09:10,809 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=21} 2017-11-17 17:09:10,810 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=22} 2017-11-17 17:09:10,812 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=23} 2017-11-17 17:09:10,813 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=24} 2017-11-17 17:09:10,814 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=25} 2017-11-17 17:09:10,815 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=26} 2017-11-17 17:09:10,816 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=27} 2017-11-17 17:09:10,817 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=28} 2017-11-17 17:09:10,818 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=29} 2017-11-17 17:09:10,819 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: 7.778 sec Running org.apache.ctakes.ytex.tools.SetupAuiFirstWordTest 2017-11-17 17:09:11,602 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 17:09:11,817 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: 0.483 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
