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Posted to notifications@ctakes.apache.org by Apache Jenkins Server <je...@builds.apache.org> on 2017/10/26 11:13:25 UTC
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #17
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/17/display/redirect>
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[...truncated 43.20 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-26 11:04:48,249 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-26 11:04:48,258 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-26 11:04:48,897 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-26 11:04:48,993 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-26 11:04:49,010 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-26 11:04:49,893 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,894 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,895 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,896 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,897 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,898 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,899 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,901 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,902 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,903 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,905 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,906 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,907 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,908 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,909 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-26 11:04:49,910 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-26 11:04:50,991 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-26 11:04:51,001 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-26 11:04:51,007 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex987922290.sql
26 Oct 2017 11:04:51 INFO ENGINE - open start - state not modified
26 Oct 2017 11:04:51 INFO ENGINE - dataFileCache open start
26 Oct 2017 11:04:51 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex987922290.sql
26 Oct 2017 11:04:51 INFO ENGINE - dataFileCache commit start
26 Oct 2017 11:04:51 INFO ENGINE - dataFileCache commit end
26 Oct 2017 11:04:51 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex987922290.sql
[delete] Deleting: /tmp/ytex130266774use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-26 11:04:56,048 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-26 11:04:56,059 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-26 11:04:56,587 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-26 11:04:56,668 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-26 11:04:56,686 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-26 11:04:56,773 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-26 11:04:56,796 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-26 11:04:56,804 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-26 11:04:56,807 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex629111785.sql
26 Oct 2017 11:04:57 INFO ENGINE - open start - state not modified
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache open start
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex629111785.sql
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache commit start
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache commit end
26 Oct 2017 11:04:57 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex629111785.sql
[delete] Deleting: /tmp/ytex389431894use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1783272285.sql
26 Oct 2017 11:04:57 INFO ENGINE - open start - state not modified
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache open start
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1783272285.sql
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache commit start
26 Oct 2017 11:04:57 INFO ENGINE - dataFileCache commit end
26 Oct 2017 11:04:57 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1783272285.sql
[delete] Deleting: /tmp/ytex2085043900use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
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T E S T S
-------------------------------------------------------
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T E S T S
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Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-26 11:04:58,650 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Thu Oct 26 11:04:58 UTC 2017]; root of context hierarchy
2017-10-26 11:04:58,701 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-26 11:04:58,945 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-26 11:04:58,953 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-26 11:04:58,970 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-26 11:04:59,042 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Thu Oct 26 11:04:59 UTC 2017]; root of context hierarchy
2017-10-26 11:04:59,044 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-26 11:04:59,296 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-26 11:04:59,343 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-26 11:04:59,568 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-26 11:04:59,569 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-26 11:04:59,569 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-26 11:04:59,625 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-26 11:04:59,692 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-26 11:05:00,636 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-26 11:05:00,643 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-26 11:05:00,645 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-26 11:05:00,647 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-26 11:05:01,495 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-26 11:05:01,617 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-26 11:05:01,626 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-26 11:05:01,748 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-26 11:05:01,750 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-26 11:05:01,752 INFO hsqldb.db..ENGINE - Database closed
2017-10-26 11:05:01,893 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-26 11:05:01,951 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-26 11:05:01,952 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-26 11:05:02,002 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-26 11:05:02,106 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-26 11:05:02,111 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-26 11:05:02,291 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-26 11:05:02,296 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-26 11:05:03,001 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-26 11:05:03,327 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-26 11:05:03,372 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-26 11:05:03,374 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-26 11:05:03,376 INFO hsqldb.db..ENGINE - Database closed
2017-10-26 11:05:03,477 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.109 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-26 11:05:04,252 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Thu Oct 26 11:05:04 UTC 2017]; root of context hierarchy
2017-10-26 11:05:04,305 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-26 11:05:04,531 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-26 11:05:04,540 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-26 11:05:04,557 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-26 11:05:04,625 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Thu Oct 26 11:05:04 UTC 2017]; root of context hierarchy
2017-10-26 11:05:04,628 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-26 11:05:04,844 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-26 11:05:04,873 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-26 11:05:05,055 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-26 11:05:05,056 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-26 11:05:05,056 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-26 11:05:05,103 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-26 11:05:05,163 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-26 11:05:05,971 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-26 11:05:05,980 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-26 11:05:05,984 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-26 11:05:05,993 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-26 11:05:06,974 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-26 11:05:07,088 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-26 11:05:07,099 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-26 11:05:07,242 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-26 11:05:07,243 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-26 11:05:07,246 INFO hsqldb.db..ENGINE - Database closed
2017-10-26 11:05:07,391 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-26 11:05:07,456 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-26 11:05:07,457 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-26 11:05:07,510 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-26 11:05:07,646 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-26 11:05:07,655 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-26 11:05:07,817 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-26 11:05:07,821 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-26 11:05:08,518 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-26 11:05:08,822 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-26 11:05:08,838 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-26 11:05:08,849 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-26 11:05:08,853 INFO hsqldb.db..ENGINE - Database closed
2017-10-26 11:05:08,954 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.026 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.678 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.767 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.593 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.728 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-26 11:05:17,210 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-26 11:05:17,247 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.743 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.168 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.607 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.648 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Jenkins build is back to normal : cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #26
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See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/26/display/redirect?page=changes>
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #25
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/25/display/redirect>
------------------------------------------
[...truncated 74.59 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-13 18:49:08,933 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-11-13 18:49:08,943 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-11-13 18:49:09,616 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-13 18:49:09,702 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-13 18:49:09,732 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-13 18:49:09,851 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,853 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,854 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,856 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,857 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,859 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,861 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,863 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,865 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,866 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,870 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,872 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,874 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,875 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,876 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-13 18:49:09,877 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-11-13 18:49:09,951 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-13 18:49:10,060 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-13 18:49:10,128 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1089789233.sql
13 Nov 2017 18:49:10 INFO ENGINE - open start - state not modified
13 Nov 2017 18:49:10 INFO ENGINE - dataFileCache open start
13 Nov 2017 18:49:10 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1089789233.sql
13 Nov 2017 18:49:10 INFO ENGINE - dataFileCache commit start
13 Nov 2017 18:49:10 INFO ENGINE - dataFileCache commit end
13 Nov 2017 18:49:11 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1089789233.sql
[delete] Deleting: /tmp/ytex1583906206use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-13 18:49:15,836 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-11-13 18:49:15,847 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-11-13 18:49:16,499 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-13 18:49:16,621 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-13 18:49:16,645 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-13 18:49:16,817 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-11-13 18:49:16,898 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-13 18:49:17,016 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-13 18:49:17,083 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1530424806.sql
13 Nov 2017 18:49:17 INFO ENGINE - open start - state not modified
13 Nov 2017 18:49:17 INFO ENGINE - dataFileCache open start
13 Nov 2017 18:49:17 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1530424806.sql
13 Nov 2017 18:49:17 INFO ENGINE - dataFileCache commit start
13 Nov 2017 18:49:17 INFO ENGINE - dataFileCache commit end
13 Nov 2017 18:49:17 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1530424806.sql
[delete] Deleting: /tmp/ytex371307974use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1523429978.sql
13 Nov 2017 18:49:18 INFO ENGINE - open start - state not modified
13 Nov 2017 18:49:18 INFO ENGINE - dataFileCache open start
13 Nov 2017 18:49:18 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1523429978.sql
13 Nov 2017 18:49:18 INFO ENGINE - dataFileCache commit start
13 Nov 2017 18:49:18 INFO ENGINE - dataFileCache commit end
13 Nov 2017 18:49:18 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1523429978.sql
[delete] Deleting: /tmp/ytex1587001795use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-13 18:49:19,451 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Mon Nov 13 18:49:19 UTC 2017]; root of context hierarchy
2017-11-13 18:49:19,506 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-13 18:49:19,749 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-13 18:49:19,759 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-13 18:49:19,780 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-13 18:49:19,844 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Mon Nov 13 18:49:19 UTC 2017]; root of context hierarchy
2017-11-13 18:49:19,851 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-13 18:49:20,092 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-13 18:49:20,123 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-13 18:49:20,322 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-13 18:49:20,323 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-13 18:49:20,324 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-13 18:49:20,378 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-13 18:49:20,436 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-13 18:49:21,193 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-13 18:49:21,200 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-13 18:49:21,203 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-13 18:49:21,204 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-13 18:49:22,045 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-13 18:49:22,176 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-13 18:49:22,187 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-13 18:49:22,364 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-13 18:49:22,398 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-13 18:49:22,465 INFO hsqldb.db..ENGINE - Database closed
2017-11-13 18:49:22,609 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-13 18:49:22,670 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-13 18:49:22,671 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-13 18:49:22,718 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-13 18:49:22,850 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-13 18:49:22,856 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-13 18:49:23,022 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-13 18:49:23,026 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-13 18:49:23,817 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-13 18:49:24,091 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-13 18:49:24,222 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-13 18:49:24,262 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-13 18:49:24,358 INFO hsqldb.db..ENGINE - Database closed
2017-11-13 18:49:24,460 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.322 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-13 18:49:25,165 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Mon Nov 13 18:49:25 UTC 2017]; root of context hierarchy
2017-11-13 18:49:25,255 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-13 18:49:25,476 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-13 18:49:25,489 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-13 18:49:25,513 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-13 18:49:25,581 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Mon Nov 13 18:49:25 UTC 2017]; root of context hierarchy
2017-11-13 18:49:25,583 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-13 18:49:25,839 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-13 18:49:25,869 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-13 18:49:26,076 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-13 18:49:26,077 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-13 18:49:26,078 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-13 18:49:26,134 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-13 18:49:26,178 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-13 18:49:27,050 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-13 18:49:27,057 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-13 18:49:27,059 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-13 18:49:27,060 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-13 18:49:27,875 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-13 18:49:27,989 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-13 18:49:28,003 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-13 18:49:28,303 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-13 18:49:28,345 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-13 18:49:28,413 INFO hsqldb.db..ENGINE - Database closed
2017-11-13 18:49:28,563 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-13 18:49:28,621 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-13 18:49:28,621 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-13 18:49:28,664 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-13 18:49:28,783 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-13 18:49:28,787 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-13 18:49:28,938 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-13 18:49:28,943 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-13 18:49:29,709 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-13 18:49:29,918 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-13 18:49:30,038 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-13 18:49:30,073 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-13 18:49:30,139 INFO hsqldb.db..ENGINE - Database closed
2017-11-13 18:49:30,241 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.364 sec <<< FAILURE!
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.625 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.682 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.819 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-13 18:49:34,638 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-11-13 18:49:34,678 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.757 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.429 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.368 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.766 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.84 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.782 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.641 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #24
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/24/display/redirect>
------------------------------------------
[...truncated 43.25 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-09 18:37:42,401 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-11-09 18:37:42,410 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-11-09 18:37:42,984 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-09 18:37:43,100 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-09 18:37:43,117 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-09 18:37:43,159 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,160 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,160 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,161 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,162 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,163 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,164 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,165 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,166 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,167 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,169 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,170 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,171 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,172 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,172 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 18:37:43,173 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-11-09 18:37:43,185 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-09 18:37:43,193 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-09 18:37:43,196 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex553160567.sql
09 Nov 2017 18:37:43 INFO ENGINE - open start - state not modified
09 Nov 2017 18:37:43 INFO ENGINE - dataFileCache open start
09 Nov 2017 18:37:43 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex553160567.sql
09 Nov 2017 18:37:43 INFO ENGINE - dataFileCache commit start
09 Nov 2017 18:37:43 INFO ENGINE - dataFileCache commit end
09 Nov 2017 18:37:43 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex553160567.sql
[delete] Deleting: /tmp/ytex364324706use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-09 18:37:48,376 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-11-09 18:37:48,388 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-11-09 18:37:48,908 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-09 18:37:49,002 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-09 18:37:49,032 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-09 18:37:49,128 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-11-09 18:37:49,136 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-09 18:37:49,144 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-09 18:37:49,147 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1902997275.sql
09 Nov 2017 18:37:49 INFO ENGINE - open start - state not modified
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache open start
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1902997275.sql
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache commit start
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache commit end
09 Nov 2017 18:37:49 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1902997275.sql
[delete] Deleting: /tmp/ytex730666983use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex609525201.sql
09 Nov 2017 18:37:49 INFO ENGINE - open start - state not modified
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache open start
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex609525201.sql
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache commit start
09 Nov 2017 18:37:49 INFO ENGINE - dataFileCache commit end
09 Nov 2017 18:37:49 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex609525201.sql
[delete] Deleting: /tmp/ytex945328930use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-09 18:37:51,180 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Thu Nov 09 18:37:51 UTC 2017]; root of context hierarchy
2017-11-09 18:37:51,250 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 18:37:51,474 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 18:37:51,488 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-09 18:37:51,506 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-09 18:37:51,602 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Thu Nov 09 18:37:51 UTC 2017]; root of context hierarchy
2017-11-09 18:37:51,604 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-09 18:37:51,832 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-09 18:37:51,866 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-09 18:37:52,056 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-09 18:37:52,057 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 18:37:52,057 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-09 18:37:52,102 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 18:37:52,160 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 18:37:52,886 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-09 18:37:52,895 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-09 18:37:52,897 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-09 18:37:52,899 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-09 18:37:53,762 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 18:37:53,859 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 18:37:53,872 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 18:37:53,985 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 18:37:53,986 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 18:37:53,989 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 18:37:54,159 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 18:37:54,204 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 18:37:54,204 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 18:37:54,252 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-09 18:37:54,362 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-09 18:37:54,366 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-09 18:37:54,532 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-09 18:37:54,538 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-09 18:37:55,230 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-09 18:37:55,570 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 18:37:55,606 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 18:37:55,607 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 18:37:55,610 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 18:37:55,711 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.821 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-09 18:37:56,395 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Thu Nov 09 18:37:56 UTC 2017]; root of context hierarchy
2017-11-09 18:37:56,456 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 18:37:56,652 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 18:37:56,664 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-09 18:37:56,684 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-09 18:37:56,749 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Thu Nov 09 18:37:56 UTC 2017]; root of context hierarchy
2017-11-09 18:37:56,751 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-09 18:37:56,977 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-09 18:37:57,010 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-09 18:37:57,163 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-09 18:37:57,164 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 18:37:57,164 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-09 18:37:57,214 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 18:37:57,268 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 18:37:57,951 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-09 18:37:57,956 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-09 18:37:57,958 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-09 18:37:57,960 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-09 18:37:58,827 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 18:37:58,920 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 18:37:58,933 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 18:37:59,024 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 18:37:59,025 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 18:37:59,033 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 18:37:59,193 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 18:37:59,250 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 18:37:59,250 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 18:37:59,289 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-09 18:37:59,440 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-09 18:37:59,445 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-09 18:37:59,600 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-09 18:37:59,605 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-09 18:38:00,438 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-09 18:38:00,697 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 18:38:00,714 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 18:38:00,715 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 18:38:00,717 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 18:38:00,818 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.68 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.712 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.713 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.366 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.427 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.767 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.49 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.731 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-09 18:38:08,831 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-11-09 18:38:08,852 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.682 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.579 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.559 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #23
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/23/display/redirect>
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[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-09 16:38:07,193 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-11-09 16:38:07,203 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-11-09 16:38:07,782 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-09 16:38:07,880 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-09 16:38:07,904 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-09 16:38:07,947 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,948 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,949 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,949 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,950 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,951 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,952 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,954 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,954 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,955 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,957 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,958 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,959 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,959 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,960 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-09 16:38:07,960 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-11-09 16:38:07,969 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-09 16:38:07,974 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-09 16:38:07,976 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex2027177025.sql
09 Nov 2017 16:38:08 INFO ENGINE - open start - state not modified
09 Nov 2017 16:38:08 INFO ENGINE - dataFileCache open start
09 Nov 2017 16:38:08 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex2027177025.sql
09 Nov 2017 16:38:08 INFO ENGINE - dataFileCache commit start
09 Nov 2017 16:38:08 INFO ENGINE - dataFileCache commit end
09 Nov 2017 16:38:08 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex2027177025.sql
[delete] Deleting: /tmp/ytex262028346use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-09 16:38:12,944 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-11-09 16:38:12,952 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-11-09 16:38:13,620 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-09 16:38:13,700 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-09 16:38:13,727 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-09 16:38:13,845 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-11-09 16:38:13,855 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-09 16:38:13,866 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-09 16:38:13,869 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1003837360.sql
09 Nov 2017 16:38:14 INFO ENGINE - open start - state not modified
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache open start
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1003837360.sql
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache commit start
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache commit end
09 Nov 2017 16:38:14 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1003837360.sql
[delete] Deleting: /tmp/ytex1625252798use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1573713767.sql
09 Nov 2017 16:38:14 INFO ENGINE - open start - state not modified
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache open start
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1573713767.sql
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache commit start
09 Nov 2017 16:38:14 INFO ENGINE - dataFileCache commit end
09 Nov 2017 16:38:14 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1573713767.sql
[delete] Deleting: /tmp/ytex1064097810use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-09 16:38:15,720 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Thu Nov 09 16:38:15 UTC 2017]; root of context hierarchy
2017-11-09 16:38:15,785 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 16:38:16,033 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 16:38:16,044 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-09 16:38:16,063 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-09 16:38:16,155 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Thu Nov 09 16:38:16 UTC 2017]; root of context hierarchy
2017-11-09 16:38:16,157 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-09 16:38:16,449 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-09 16:38:16,482 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-09 16:38:16,726 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-09 16:38:16,727 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 16:38:16,727 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-09 16:38:16,783 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 16:38:16,843 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 16:38:17,697 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-09 16:38:17,704 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-09 16:38:17,707 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-09 16:38:17,708 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-09 16:38:18,625 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 16:38:18,743 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 16:38:18,765 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 16:38:18,852 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 16:38:18,853 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 16:38:18,856 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 16:38:19,000 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 16:38:19,060 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 16:38:19,060 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 16:38:19,105 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-09 16:38:19,209 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-09 16:38:19,214 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-09 16:38:19,357 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-09 16:38:19,363 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-09 16:38:20,038 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-09 16:38:20,306 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 16:38:20,320 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 16:38:20,322 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 16:38:20,324 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 16:38:20,425 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.008 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-09 16:38:21,256 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Thu Nov 09 16:38:21 UTC 2017]; root of context hierarchy
2017-11-09 16:38:21,335 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 16:38:21,557 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-09 16:38:21,574 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-09 16:38:21,597 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-09 16:38:21,679 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Thu Nov 09 16:38:21 UTC 2017]; root of context hierarchy
2017-11-09 16:38:21,682 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-09 16:38:21,918 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-09 16:38:21,937 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-09 16:38:22,109 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-09 16:38:22,110 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 16:38:22,110 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-09 16:38:22,158 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 16:38:22,195 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-09 16:38:23,091 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-09 16:38:23,101 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-09 16:38:23,104 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-09 16:38:23,106 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-09 16:38:23,897 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 16:38:23,983 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 16:38:23,994 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 16:38:24,086 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 16:38:24,087 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 16:38:24,092 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 16:38:24,230 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-09 16:38:24,315 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-09 16:38:24,315 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-09 16:38:24,361 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-09 16:38:24,491 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-09 16:38:24,496 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-09 16:38:24,696 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-09 16:38:24,702 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-09 16:38:25,447 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-09 16:38:25,670 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-09 16:38:25,688 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-09 16:38:25,690 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-09 16:38:25,692 INFO hsqldb.db..ENGINE - Database closed
2017-11-09 16:38:25,794 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.841 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.757 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.686 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.295 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.711 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.608 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.696 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-09 16:38:33,799 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-11-09 16:38:33,842 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.761 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.583 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.619 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #22
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/22/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-08 17:37:37,066 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-11-08 17:37:37,074 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-11-08 17:37:37,543 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-08 17:37:37,611 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-08 17:37:37,627 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-08 17:37:37,671 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,672 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,673 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,674 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,674 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,675 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,676 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,678 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,678 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,679 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,681 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,682 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,683 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,683 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,684 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 17:37:37,684 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-11-08 17:37:37,693 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-08 17:37:37,699 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-08 17:37:37,702 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1751788231.sql
08 Nov 2017 17:37:38 INFO ENGINE - open start - state not modified
08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache open start
08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1751788231.sql
08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache commit start
08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache commit end
08 Nov 2017 17:37:38 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1751788231.sql
[delete] Deleting: /tmp/ytex2144289946use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-08 17:37:42,633 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-11-08 17:37:42,641 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-11-08 17:37:43,165 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-08 17:37:43,235 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-08 17:37:43,251 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-08 17:37:43,328 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-11-08 17:37:43,336 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-08 17:37:43,346 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-08 17:37:43,349 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1642712519.sql
08 Nov 2017 17:37:43 INFO ENGINE - open start - state not modified
08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache open start
08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1642712519.sql
08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache commit start
08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache commit end
08 Nov 2017 17:37:43 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1642712519.sql
[delete] Deleting: /tmp/ytex348288983use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex702157901.sql
08 Nov 2017 17:37:44 INFO ENGINE - open start - state not modified
08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache open start
08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex702157901.sql
08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache commit start
08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache commit end
08 Nov 2017 17:37:44 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex702157901.sql
[delete] Deleting: /tmp/ytex227994778use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-08 17:37:45,064 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 17:37:45 UTC 2017]; root of context hierarchy
2017-11-08 17:37:45,126 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 17:37:45,339 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 17:37:45,354 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 17:37:45,376 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 17:37:45,451 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 17:37:45 UTC 2017]; root of context hierarchy
2017-11-08 17:37:45,458 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 17:37:45,661 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 17:37:45,688 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 17:37:45,834 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 17:37:45,835 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 17:37:45,835 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 17:37:45,875 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 17:37:45,918 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 17:37:46,708 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-08 17:37:46,720 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 17:37:46,723 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-08 17:37:46,724 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-08 17:37:47,461 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 17:37:47,536 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 17:37:47,545 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 17:37:47,602 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 17:37:47,604 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 17:37:47,607 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 17:37:47,745 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 17:37:47,794 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 17:37:47,794 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 17:37:47,829 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 17:37:47,946 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 17:37:47,950 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 17:37:48,087 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 17:37:48,092 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 17:37:48,637 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-08 17:37:48,822 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 17:37:48,834 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 17:37:48,836 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 17:37:48,839 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 17:37:48,940 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.117 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-08 17:37:49,664 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 17:37:49 UTC 2017]; root of context hierarchy
2017-11-08 17:37:49,723 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 17:37:49,916 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 17:37:49,929 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 17:37:49,947 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 17:37:50,017 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 17:37:50 UTC 2017]; root of context hierarchy
2017-11-08 17:37:50,019 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 17:37:50,224 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 17:37:50,249 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 17:37:50,413 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 17:37:50,414 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 17:37:50,414 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 17:37:50,461 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 17:37:50,509 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 17:37:51,292 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-08 17:37:51,302 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 17:37:51,304 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-08 17:37:51,306 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-08 17:37:52,033 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 17:37:52,134 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 17:37:52,143 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 17:37:52,231 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 17:37:52,232 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 17:37:52,236 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 17:37:52,366 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 17:37:52,402 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 17:37:52,402 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 17:37:52,434 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 17:37:52,549 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 17:37:52,553 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 17:37:52,681 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 17:37:52,685 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 17:37:53,278 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-08 17:37:53,501 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 17:37:53,513 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 17:37:53,515 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 17:37:53,518 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 17:37:53,619 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.208 sec <<< FAILURE!
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.514 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.487 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.646 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.346 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.582 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.637 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.5 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-08 17:38:02,236 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-11-08 17:38:02,258 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.651 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #21
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/21/display/redirect>
------------------------------------------
[...truncated 43.94 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-08 16:46:27,469 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-11-08 16:46:27,479 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-11-08 16:46:28,061 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-08 16:46:28,141 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-08 16:46:28,160 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-08 16:46:28,252 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,254 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,255 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,256 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,258 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,259 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,261 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,263 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,265 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,266 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,268 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,270 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,272 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,272 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,273 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 16:46:28,274 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-11-08 16:46:28,435 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-08 16:46:28,653 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-08 16:46:28,781 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1328227159.sql
08 Nov 2017 16:46:29 INFO ENGINE - open start - state not modified
08 Nov 2017 16:46:29 INFO ENGINE - dataFileCache open start
08 Nov 2017 16:46:29 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1328227159.sql
08 Nov 2017 16:46:29 INFO ENGINE - dataFileCache commit start
08 Nov 2017 16:46:29 INFO ENGINE - dataFileCache commit end
08 Nov 2017 16:46:29 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1328227159.sql
[delete] Deleting: /tmp/ytex1315143500use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-08 16:46:34,191 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-11-08 16:46:34,200 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-11-08 16:46:34,731 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-08 16:46:34,817 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-08 16:46:34,845 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-08 16:46:35,009 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-11-08 16:46:35,145 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-08 16:46:35,371 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-08 16:46:35,482 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1264790108.sql
08 Nov 2017 16:46:36 INFO ENGINE - open start - state not modified
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache open start
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1264790108.sql
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache commit start
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache commit end
08 Nov 2017 16:46:36 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1264790108.sql
[delete] Deleting: /tmp/ytex2147318110use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1773679046.sql
08 Nov 2017 16:46:36 INFO ENGINE - open start - state not modified
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache open start
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1773679046.sql
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache commit start
08 Nov 2017 16:46:36 INFO ENGINE - dataFileCache commit end
08 Nov 2017 16:46:37 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1773679046.sql
[delete] Deleting: /tmp/ytex1549224809use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-08 16:46:37,929 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 16:46:37 UTC 2017]; root of context hierarchy
2017-11-08 16:46:37,985 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:38,171 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:38,180 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 16:46:38,199 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 16:46:38,262 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 16:46:38 UTC 2017]; root of context hierarchy
2017-11-08 16:46:38,264 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 16:46:38,466 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 16:46:38,493 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 16:46:38,653 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 16:46:38,654 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:38,654 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 16:46:38,709 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 16:46:38,752 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:39,446 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-08 16:46:39,452 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 16:46:39,454 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-08 16:46:39,455 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-08 16:46:40,161 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 16:46:40,255 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 16:46:40,268 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 16:46:40,538 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 16:46:40,580 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 16:46:40,690 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 16:46:40,823 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 16:46:40,860 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 16:46:40,861 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 16:46:40,895 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 16:46:41,004 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 16:46:41,009 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 16:46:41,152 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 16:46:41,156 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 16:46:41,743 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-08 16:46:41,910 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 16:46:42,469 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 16:46:42,520 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 16:46:42,638 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 16:46:42,739 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.056 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-08 16:46:43,308 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 16:46:43 UTC 2017]; root of context hierarchy
2017-11-08 16:46:43,370 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:43,557 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:43,566 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 16:46:43,584 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 16:46:43,658 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 16:46:43 UTC 2017]; root of context hierarchy
2017-11-08 16:46:43,661 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 16:46:43,890 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 16:46:43,912 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 16:46:44,054 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 16:46:44,055 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:44,055 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 16:46:44,091 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 16:46:44,129 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:44,859 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-08 16:46:44,882 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 16:46:44,887 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-08 16:46:44,891 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-08 16:46:45,599 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 16:46:45,698 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 16:46:45,709 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 16:46:45,959 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 16:46:46,015 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 16:46:46,150 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 16:46:46,283 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 16:46:46,323 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 16:46:46,324 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 16:46:46,361 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 16:46:46,483 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 16:46:46,491 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 16:46:46,641 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 16:46:46,646 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 16:46:47,259 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-08 16:46:47,434 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 16:46:47,611 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 16:46:47,653 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 16:46:47,771 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 16:46:47,872 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.791 sec <<< FAILURE!
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.429 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-08 16:46:51,245 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-11-08 16:46:51,272 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.456 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.575 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.345 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.579 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.467 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #20
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/20/display/redirect>
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[...truncated 43.19 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-08 15:39:21,119 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-11-08 15:39:21,126 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-11-08 15:39:21,587 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-08 15:39:21,652 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-08 15:39:21,669 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-08 15:39:21,710 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,711 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,711 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,712 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,713 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,714 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,715 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,716 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,717 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,717 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,719 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,720 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,721 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,722 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,722 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-11-08 15:39:21,722 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-11-08 15:39:21,731 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-08 15:39:21,738 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-08 15:39:21,741 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex838347098.sql
08 Nov 2017 15:39:22 INFO ENGINE - open start - state not modified
08 Nov 2017 15:39:22 INFO ENGINE - dataFileCache open start
08 Nov 2017 15:39:22 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex838347098.sql
08 Nov 2017 15:39:22 INFO ENGINE - dataFileCache commit start
08 Nov 2017 15:39:22 INFO ENGINE - dataFileCache commit end
08 Nov 2017 15:39:22 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex838347098.sql
[delete] Deleting: /tmp/ytex1955455492use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-11-08 15:39:26,296 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-11-08 15:39:26,303 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-11-08 15:39:26,792 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-11-08 15:39:26,866 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-11-08 15:39:26,882 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-11-08 15:39:26,967 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-11-08 15:39:26,982 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-11-08 15:39:26,994 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-11-08 15:39:26,997 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex423476875.sql
08 Nov 2017 15:39:27 INFO ENGINE - open start - state not modified
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache open start
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex423476875.sql
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache commit start
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache commit end
08 Nov 2017 15:39:27 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex423476875.sql
[delete] Deleting: /tmp/ytex1648126577use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex262933407.sql
08 Nov 2017 15:39:27 INFO ENGINE - open start - state not modified
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache open start
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex262933407.sql
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache commit start
08 Nov 2017 15:39:27 INFO ENGINE - dataFileCache commit end
08 Nov 2017 15:39:27 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex262933407.sql
[delete] Deleting: /tmp/ytex2097796996use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-08 15:39:28,730 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 15:39:28 UTC 2017]; root of context hierarchy
2017-11-08 15:39:28,801 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 15:39:29,004 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 15:39:29,020 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 15:39:29,038 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 15:39:29,109 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 15:39:29 UTC 2017]; root of context hierarchy
2017-11-08 15:39:29,111 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 15:39:29,318 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 15:39:29,347 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 15:39:29,513 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 15:39:29,513 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 15:39:29,514 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 15:39:29,562 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 15:39:29,609 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 15:39:30,392 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-08 15:39:30,402 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 15:39:30,404 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-08 15:39:30,406 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-08 15:39:31,129 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 15:39:31,213 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 15:39:31,222 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 15:39:31,312 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 15:39:31,313 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 15:39:31,321 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 15:39:31,469 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 15:39:31,512 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 15:39:31,513 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 15:39:31,558 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 15:39:31,667 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 15:39:31,671 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 15:39:31,801 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 15:39:31,804 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 15:39:32,344 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-08 15:39:32,535 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 15:39:32,549 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 15:39:32,551 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 15:39:32,554 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 15:39:32,655 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.186 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-08 15:39:33,304 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 15:39:33 UTC 2017]; root of context hierarchy
2017-11-08 15:39:33,364 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 15:39:33,562 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 15:39:33,576 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 15:39:33,593 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 15:39:33,665 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 15:39:33 UTC 2017]; root of context hierarchy
2017-11-08 15:39:33,668 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 15:39:33,878 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 15:39:33,906 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 15:39:34,071 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 15:39:34,072 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 15:39:34,072 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 15:39:34,117 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 15:39:34,171 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 15:39:34,953 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-11-08 15:39:34,962 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 15:39:34,965 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-11-08 15:39:34,966 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-11-08 15:39:35,737 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 15:39:35,818 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 15:39:35,827 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 15:39:35,887 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 15:39:35,888 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 15:39:35,891 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 15:39:36,036 INFO hsqldb.db..ENGINE - open start - state not modified
2017-11-08 15:39:36,085 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-11-08 15:39:36,085 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-11-08 15:39:36,118 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 15:39:36,214 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 15:39:36,219 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 15:39:36,342 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 15:39:36,346 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 15:39:36,989 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-11-08 15:39:37,262 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-11-08 15:39:37,295 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-11-08 15:39:37,298 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-11-08 15:39:37,302 INFO hsqldb.db..ENGINE - Database closed
2017-11-08 15:39:37,404 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.351 sec <<< FAILURE!
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.498 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.519 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.286 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.344 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.628 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.661 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.506 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.636 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-08 15:39:46,434 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-11-08 15:39:46,459 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.673 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #19
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/19/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-31 00:57:34,689 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-31 00:57:34,701 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-31 00:57:35,354 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-31 00:57:35,433 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-31 00:57:35,470 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-31 00:57:35,524 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,525 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,526 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,527 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,528 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,529 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,530 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,532 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,533 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,533 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,535 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,536 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,538 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,538 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,539 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-31 00:57:35,540 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-31 00:57:35,550 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-31 00:57:35,561 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-31 00:57:35,569 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1417254447.sql
31 Oct 2017 00:57:36 INFO ENGINE - open start - state not modified
31 Oct 2017 00:57:36 INFO ENGINE - dataFileCache open start
31 Oct 2017 00:57:36 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1417254447.sql
31 Oct 2017 00:57:36 INFO ENGINE - dataFileCache commit start
31 Oct 2017 00:57:36 INFO ENGINE - dataFileCache commit end
31 Oct 2017 00:57:36 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1417254447.sql
[delete] Deleting: /tmp/ytex1941765425use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-31 00:57:40,939 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-31 00:57:40,951 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-31 00:57:41,565 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-31 00:57:41,616 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-31 00:57:41,678 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-31 00:57:41,773 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-31 00:57:41,784 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-31 00:57:41,795 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-31 00:57:41,799 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1514183121.sql
31 Oct 2017 00:57:42 INFO ENGINE - open start - state not modified
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache open start
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1514183121.sql
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache commit start
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache commit end
31 Oct 2017 00:57:42 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1514183121.sql
[delete] Deleting: /tmp/ytex2050064787use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1557073590.sql
31 Oct 2017 00:57:42 INFO ENGINE - open start - state not modified
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache open start
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1557073590.sql
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache commit start
31 Oct 2017 00:57:42 INFO ENGINE - dataFileCache commit end
31 Oct 2017 00:57:42 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1557073590.sql
[delete] Deleting: /tmp/ytex1544232291use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-31 00:57:43,799 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Tue Oct 31 00:57:43 UTC 2017]; root of context hierarchy
2017-10-31 00:57:43,865 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-31 00:57:44,123 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-31 00:57:44,142 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-31 00:57:44,163 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-31 00:57:44,249 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Tue Oct 31 00:57:44 UTC 2017]; root of context hierarchy
2017-10-31 00:57:44,251 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-31 00:57:44,583 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-31 00:57:44,611 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-31 00:57:44,881 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-31 00:57:44,882 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-31 00:57:44,882 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-31 00:57:44,943 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-31 00:57:45,008 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-31 00:57:46,017 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-31 00:57:46,031 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-31 00:57:46,034 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-31 00:57:46,035 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-31 00:57:46,967 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-31 00:57:47,072 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-31 00:57:47,081 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-31 00:57:47,193 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-31 00:57:47,194 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-31 00:57:47,197 INFO hsqldb.db..ENGINE - Database closed
2017-10-31 00:57:47,334 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-31 00:57:47,385 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-31 00:57:47,385 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-31 00:57:47,446 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-31 00:57:47,592 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-31 00:57:47,598 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-31 00:57:47,759 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-31 00:57:47,764 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-31 00:57:48,546 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-31 00:57:49,016 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-31 00:57:49,104 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-31 00:57:49,107 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-31 00:57:49,111 INFO hsqldb.db..ENGINE - Database closed
2017-10-31 00:57:49,212 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.737 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-31 00:57:50,048 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Tue Oct 31 00:57:50 UTC 2017]; root of context hierarchy
2017-10-31 00:57:50,121 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-31 00:57:50,400 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-31 00:57:50,414 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-31 00:57:50,434 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-31 00:57:50,522 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Tue Oct 31 00:57:50 UTC 2017]; root of context hierarchy
2017-10-31 00:57:50,524 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-31 00:57:50,808 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-31 00:57:50,846 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-31 00:57:51,079 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-31 00:57:51,080 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-31 00:57:51,080 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-31 00:57:51,145 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-31 00:57:51,210 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-31 00:57:52,243 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-31 00:57:52,256 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-31 00:57:52,259 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-31 00:57:52,263 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-31 00:57:53,276 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-31 00:57:53,414 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-31 00:57:53,429 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-31 00:57:53,537 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-31 00:57:53,538 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-31 00:57:53,541 INFO hsqldb.db..ENGINE - Database closed
2017-10-31 00:57:53,685 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-31 00:57:53,746 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-31 00:57:53,746 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-31 00:57:53,799 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-31 00:57:53,957 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-31 00:57:53,964 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-31 00:57:54,203 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-31 00:57:54,207 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-31 00:57:55,100 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-31 00:57:55,358 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-31 00:57:55,388 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-31 00:57:55,390 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-31 00:57:55,395 INFO hsqldb.db..ENGINE - Database closed
2017-10-31 00:57:55,497 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.806 sec <<< FAILURE!
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.237 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.121 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.643 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.748 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-31 00:58:01,004 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-31 00:58:01,034 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.618 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.744 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.751 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.789 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.636 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #18
Posted by Apache Jenkins Server <je...@builds.apache.org>.
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/18/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-30 02:37:31,717 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-30 02:37:31,729 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-30 02:37:32,265 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-30 02:37:32,351 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-30 02:37:32,367 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-30 02:37:32,423 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,424 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,425 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,425 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,426 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,428 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,429 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,430 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,431 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,432 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,433 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,435 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,436 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,436 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,437 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-30 02:37:32,438 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-30 02:37:32,452 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-30 02:37:32,473 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-30 02:37:32,476 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex2145059090.sql
30 Oct 2017 02:37:33 INFO ENGINE - open start - state not modified
30 Oct 2017 02:37:33 INFO ENGINE - dataFileCache open start
30 Oct 2017 02:37:33 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex2145059090.sql
30 Oct 2017 02:37:33 INFO ENGINE - dataFileCache commit start
30 Oct 2017 02:37:33 INFO ENGINE - dataFileCache commit end
30 Oct 2017 02:37:33 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex2145059090.sql
[delete] Deleting: /tmp/ytex1270028177use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-30 02:37:37,479 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-30 02:37:37,491 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-30 02:37:38,113 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-30 02:37:38,204 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-30 02:37:38,227 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-30 02:37:38,357 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-30 02:37:38,364 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-30 02:37:38,373 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-30 02:37:38,375 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1612710776.sql
30 Oct 2017 02:37:38 INFO ENGINE - open start - state not modified
30 Oct 2017 02:37:38 INFO ENGINE - dataFileCache open start
30 Oct 2017 02:37:38 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1612710776.sql
30 Oct 2017 02:37:38 INFO ENGINE - dataFileCache commit start
30 Oct 2017 02:37:38 INFO ENGINE - dataFileCache commit end
30 Oct 2017 02:37:38 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1612710776.sql
[delete] Deleting: /tmp/ytex843853751use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex481372029.sql
30 Oct 2017 02:37:39 INFO ENGINE - open start - state not modified
30 Oct 2017 02:37:39 INFO ENGINE - dataFileCache open start
30 Oct 2017 02:37:39 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex481372029.sql
30 Oct 2017 02:37:39 INFO ENGINE - dataFileCache commit start
30 Oct 2017 02:37:39 INFO ENGINE - dataFileCache commit end
30 Oct 2017 02:37:39 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex481372029.sql
[delete] Deleting: /tmp/ytex1863120082use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-30 02:37:40,220 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Mon Oct 30 02:37:40 UTC 2017]; root of context hierarchy
2017-10-30 02:37:40,305 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-30 02:37:40,516 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-30 02:37:40,527 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-30 02:37:40,549 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-30 02:37:40,611 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Mon Oct 30 02:37:40 UTC 2017]; root of context hierarchy
2017-10-30 02:37:40,613 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-30 02:37:40,869 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-30 02:37:40,899 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-30 02:37:41,097 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-30 02:37:41,098 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-30 02:37:41,098 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-30 02:37:41,141 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-30 02:37:41,189 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-30 02:37:42,077 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-30 02:37:42,087 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-30 02:37:42,090 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-30 02:37:42,092 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-30 02:37:42,962 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-30 02:37:43,083 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-30 02:37:43,096 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-30 02:37:45,726 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-30 02:37:47,775 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-30 02:37:49,762 INFO hsqldb.db..ENGINE - Database closed
2017-10-30 02:37:49,907 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-30 02:37:49,943 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-30 02:37:49,943 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-30 02:37:49,991 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-30 02:37:50,148 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-30 02:37:50,153 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-30 02:37:50,330 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-30 02:37:50,336 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-30 02:37:51,032 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-30 02:37:51,294 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-30 02:37:51,310 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-30 02:37:51,312 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-30 02:37:51,315 INFO hsqldb.db..ENGINE - Database closed
2017-10-30 02:37:51,417 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 11.53 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-30 02:37:52,082 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66: startup date [Mon Oct 30 02:37:52 UTC 2017]; root of context hierarchy
2017-10-30 02:37:52,147 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-30 02:37:52,362 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-30 02:37:52,377 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'kernelApplicationContext': 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:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-30 02:37:52,395 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-30 02:37:52,470 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111: startup date [Mon Oct 30 02:37:52 UTC 2017]; root of context hierarchy
2017-10-30 02:37:52,473 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-30 02:37:52,741 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-30 02:37:52,777 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-30 02:37:52,963 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-30 02:37:52,963 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-30 02:37:52,963 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-30 02:37:53,017 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-30 02:37:53,073 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-30 02:37:53,931 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-30 02:37:53,937 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-30 02:37:53,939 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-30 02:37:53,940 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-30 02:37:54,757 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-30 02:37:54,848 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-30 02:37:54,860 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-30 02:37:54,970 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-30 02:37:54,971 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-30 02:37:54,979 INFO hsqldb.db..ENGINE - Database closed
2017-10-30 02:37:55,119 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-30 02:37:55,179 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-30 02:37:55,180 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-30 02:37:55,231 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-30 02:37:55,353 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-30 02:37:55,358 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-30 02:37:55,508 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-30 02:37:55,513 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-30 02:37:56,289 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-30 02:37:56,588 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,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]; root of factory hierarchy
2017-10-30 02:37:56,612 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-30 02:37:56,613 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-30 02:37:56,617 INFO hsqldb.db..ENGINE - Database closed
2017-10-30 02:37:56,718 INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312: defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.931 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.764 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.725 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.337 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.41 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.746 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.628 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.71 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-30 02:38:04,696 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-30 02:38:04,717 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.722 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.581 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.603 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled