See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/33/display/redirect>
------------------------------------------ [...truncated 203.47 KB...] 2017-11-17 13:47:23,315 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 13:47:23,315 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 13:47:23,324 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 13:47:23,324 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 13:47:23,327 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 13:47:23,389 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 13:47:23,391 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 13:47:23,662 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@4130955c] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 13:47:23,768 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 13:47:23,775 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_1510926443775. 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 13:47:23,982 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: test 2017-11-17 13:47:23,984 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$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/test.gz> 2017-11-17 13:47:23,985 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - concept graph test, vertices: 7 2017-11-17 13:47:23,986 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - initializing similarity measures 2017-11-17 13:47:23,989 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: test 2017-11-17 13:47:24,353 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 13:47:24,451 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 13:47:24,454 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 13:47:24,481 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - listConcept: [[dog], [animal, e coli], [cat]] 2017-11-17 13:47:24,482 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - i: 1, conceptSenses: [animal, e coli] 2017-11-17 13:47:24,506 TRACE org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - i: 1, concept: animal Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.97 sec Running org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexTest 2017-11-17 13:47:25,199 DEBUG org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator - NamedEntityRegex [code=C00TEST, regex=(?i)COUGH] [cough] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.331 sec Running org.apache.ctakes.ytex.uima.annotators.DBCollectionReaderTest 2017-11-17 13:47:27,702 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - loading ytex.properties from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/ytex.properties> 2017-11-17 13:47:27,704 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 2017-11-17 13:47:27,779 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@47af7f3d: startup date [Fri Nov 17 13:47:27 UTC 2017]; root of context hierarchy 2017-11-17 13:47:27,836 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 13:47:27,909 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 13:47:27,920 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 13:47:27,951 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 13:47:28,020 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@6283d8b8: startup date [Fri Nov 17 13:47:28 UTC 2017]; root of context hierarchy 2017-11-17 13:47:28,023 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 13:47:28,297 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 13:47:28,407 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 13:47:28,430 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 13:47:28,451 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 13:47:28,488 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 13:47:28,516 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 13:47:28,648 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-17 13:47:28,650 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 13:47:28,650 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-17 13:47:28,714 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 13:47:28,791 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 13:47:29,557 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-17 13:47:29,566 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final} 2017-11-17 13:47:29,569 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found 2017-11-17 13:47:29,571 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist 2017-11-17 13:47:30,574 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache open start 2017-11-17 13:47:30,583 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache open end 2017-11-17 13:47:30,685 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache commit start 2017-11-17 13:47:30,686 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache commit end 2017-11-17 13:47:30,688 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - Database closed 2017-11-17 13:47:30,841 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache open start 2017-11-17 13:47:30,842 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache open end 2017-11-17 13:47:30,967 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 13:47:31,107 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 13:47:31,108 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 13:47:31,114 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 13:47:31,120 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 13:47:31,294 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 13:47:31,301 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 13:47:31,319 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 13:47:31,553 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 13:47:31,555 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 13:47:32,216 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@53a5e217] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 13:47:32,889 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 13:47:32,899 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$InputStreamConfigurationSource@35e8316e. The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510926452899. To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. 2017-11-17 13:47:33,454 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: sct-rxnorm 2017-11-17 13:47:33,567 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph from classpath, attempt to load from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> 2017-11-17 13:47:33,567 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 13:47:33,567 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph: sct-rxnorm 2017-11-17 13:47:33,733 WARN org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - concept graph null, name: sct-rxnorm 2017-11-17 13:47:33,733 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: sct-rxnorm 2017-11-17 13:47:34,192 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 13:47:34,292 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 13:47:34,295 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 13:47:34,968 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=0} 2017-11-17 13:47:34,986 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=1} 2017-11-17 13:47:34,988 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=2} 2017-11-17 13:47:34,989 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=3} 2017-11-17 13:47:34,990 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=4} 2017-11-17 13:47:34,992 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=5} 2017-11-17 13:47:34,994 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=6} 2017-11-17 13:47:34,996 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=7} 2017-11-17 13:47:34,997 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=8} 2017-11-17 13:47:34,999 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=9} 2017-11-17 13:47:35,001 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=10} 2017-11-17 13:47:35,003 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=11} 2017-11-17 13:47:35,005 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=12} 2017-11-17 13:47:35,008 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=13} 2017-11-17 13:47:35,011 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=14} 2017-11-17 13:47:35,013 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=15} 2017-11-17 13:47:35,016 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=16} 2017-11-17 13:47:35,019 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=17} 2017-11-17 13:47:35,020 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=18} 2017-11-17 13:47:35,021 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=19} 2017-11-17 13:47:35,039 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=20} 2017-11-17 13:47:35,043 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=21} 2017-11-17 13:47:35,044 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=22} 2017-11-17 13:47:35,045 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=23} 2017-11-17 13:47:35,046 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=24} 2017-11-17 13:47:35,047 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=25} 2017-11-17 13:47:35,049 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=26} 2017-11-17 13:47:35,050 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=27} 2017-11-17 13:47:35,051 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=28} 2017-11-17 13:47:35,052 INFO org.apache.ctakes.ytex.uima.DBCollectionReader - loading document with id = {INSTANCE_ID=29} 2017-11-17 13:47:35,053 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: 8.347 sec Running org.apache.ctakes.ytex.uima.annotators.DictionaryLookupAnnotatorTest 2017-11-17 13:47:37,070 INFO org.apache.ctakes.chunker.ae.Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 2017-11-17 13:47:39,128 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 13:47:39,157 INFO org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator - Finite state machines loaded. 2017-11-17 13:47:39,164 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 13:47:39,165 INFO org.apache.ctakes.ytex.uima.ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 2017-11-17 13:47:39,652 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache open start 2017-11-17 13:47:39,664 INFO hsqldb.db.HSQLDB5FCA3ADB4F.ENGINE - dataFileCache open end 2017-11-17 13:47:39,802 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 13:47:39,806 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - Parsing descriptor: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.xml> 2017-11-17 13:47:39,877 INFO org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl - Exclusion tagset loaded: [pp, pdt, prp$, 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 13:47:39,930 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - [SegmentsToSkip, SentenceModelFile] 2017-11-17 13:47:39,931 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 2017-11-17 13:47:40,137 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@9573584: startup date [Fri Nov 17 13:47:40 UTC 2017]; root of context hierarchy 2017-11-17 13:47:40,202 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 13:47:40,282 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 13:47:40,290 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 13:47:40,319 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 13:47:40,378 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@ff684e1: startup date [Fri Nov 17 13:47:40 UTC 2017]; root of context hierarchy 2017-11-17 13:47:40,380 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 13:47:42,071 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 13:47:42,163 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 13:47:42,188 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 13:47:42,210 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 13:47:42,236 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 13:47:42,283 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 13:47:42,395 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-17 13:47:42,395 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 13:47:42,396 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-17 13:47:42,437 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 13:47:42,482 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 2017-11-17 13:47:43,239 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-17 13:47:43,246 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final} 2017-11-17 13:47:43,249 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found 2017-11-17 13:47:43,250 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist 2017-11-17 13:47:43,616 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 13:47:43,739 WARN org.hibernate.mapping.RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 13:47:43,739 WARN org.hibernate.mapping.RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 2017-11-17 13:47:43,745 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 2017-11-17 13:47:43,751 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-17 13:47:43,915 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 2017-11-17 13:47:43,922 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 2017-11-17 13:47:43,942 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 13:47:44,193 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 13:47:44,195 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 13:47:45,590 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@76889e60] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-17 13:47:46,077 INFO org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing EHCache CacheManager 2017-11-17 13:47:46,105 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_1510926466105. 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 13:47:46,672 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin initialization for concept graph: sct-rxnorm 2017-11-17 13:47:46,840 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$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> 2017-11-17 13:47:46,840 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz> not found, cannot load concept graph 2017-11-17 13:47:46,841 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl - could not load conceptGraph: sct-rxnorm 2017-11-17 13:47:46,901 WARN org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - concept graph null, name: sct-rxnorm 2017-11-17 13:47:46,902 INFO org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end initialization for concept graph: sct-rxnorm 2017-11-17 13:47:47,309 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect 2017-11-17 13:47:47,404 INFO org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - document table name = PUBLIC.document 2017-11-17 13:47:47,407 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl - docTableCols: {} 2017-11-17 13:47:47,435 WARN org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator - Concept Graph was not loaded - word sense disambiguation disabled 2017-11-17 13:47:47,503 INFO org.apache.ctakes.postagger.POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 2017-11-17 13:47:48,674 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator - segmentsAdded: 0 2017-11-17 13:47:48,677 INFO org.apache.ctakes.ytex.uima.annotators.SentenceDetector - Starting processing. 2017-11-17 13:47:48,682 INFO org.apache.ctakes.core.ae.TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 2017-11-17 13:47:48,698 INFO org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator - process(JCas) 2017-11-17 13:47:48,708 INFO org.apache.ctakes.postagger.POSTagger - process(JCas) 2017-11-17 13:47:48,724 INFO org.apache.ctakes.chunker.ae.Chunker - process(JCas) 2017-11-17 13:47:48,749 INFO org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster - process(JCas) 2017-11-17 13:47:48,770 INFO org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster - process(JCas) 2017-11-17 13:47:48,774 INFO org.apache.ctakes.core.ae.CopyAnnotator - process(JCas) 2017-11-17 13:47:48,775 INFO org.apache.ctakes.core.ae.OverlapAnnotator - process(JCas) 2017-11-17 13:47:48,778 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 13:47:49,045 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 13:47:49,045 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - Parsing descriptor: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.xml> 2017-11-17 13:47:49,048 INFO org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl - Exclusion tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc, cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp] 2017-11-17 13:47:49,093 INFO org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator - process(JCas) EntityMention [acetaminophen] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.454 sec Running org.apache.ctakes.ytex.tools.SetupAuiFirstWordTest 2017-11-17 13:47:49,785 WARN org.apache.ctakes.ytex.tools.SetupAuiFirstWord - classpath:ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml not available, attempting to load from file system 2017-11-17 13:47:49,977 INFO org.apache.ctakes.ytex.tools.SetupAuiFirstWord - loading lvg.properties from:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties ** Configuration Error: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$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: 0.447 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
