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Posted to notifications@ctakes.apache.org by Apache Jenkins Server <je...@builds.apache.org> on 2017/10/08 22:32:45 UTC
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #12
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/12/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] 2017-10-08 22:22:05,003 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-08 22:22:05,010 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-08 22:22:05,584 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-08 22:22:05,657 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-08 22:22:05,673 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-08 22:22:05,717 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,718 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,719 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,719 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,720 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,721 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,722 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,724 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,725 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,725 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,727 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,728 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,729 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,730 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,731 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-08 22:22:05,731 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-08 22:22:05,740 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-08 22:22:05,757 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-08 22:22:05,760 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/ytex1608892790.sql
08 Oct 2017 22:22:06 INFO ENGINE - open start - state not modified
08 Oct 2017 22:22:06 INFO ENGINE - dataFileCache open start
08 Oct 2017 22:22:06 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1608892790.sql
08 Oct 2017 22:22:06 INFO ENGINE - dataFileCache commit start
08 Oct 2017 22:22:06 INFO ENGINE - dataFileCache commit end
08 Oct 2017 22:22:06 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1608892790.sql
[delete] Deleting: /tmp/ytex1116258534use.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] 2017-10-08 22:22:10,965 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-08 22:22:10,972 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-08 22:22:11,539 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-08 22:22:11,629 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-08 22:22:11,649 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-08 22:22:11,728 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-08 22:22:11,740 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-08 22:22:11,750 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-08 22:22:11,752 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/ytex1409723003.sql
08 Oct 2017 22:22:12 INFO ENGINE - open start - state not modified
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache open start
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1409723003.sql
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache commit start
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache commit end
08 Oct 2017 22:22:12 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1409723003.sql
[delete] Deleting: /tmp/ytex1065742959use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1730680987.sql
08 Oct 2017 22:22:12 INFO ENGINE - open start - state not modified
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache open start
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1730680987.sql
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache commit start
08 Oct 2017 22:22:12 INFO ENGINE - dataFileCache commit end
08 Oct 2017 22:22:12 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1730680987.sql
[delete] Deleting: /tmp/ytex2105924416use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-08 22:22:13,778 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Sun Oct 08 22:22:13 UTC 2017]; root of context hierarchy
2017-10-08 22:22:13,839 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-08 22:22:14,060 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-08 22:22:14,070 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]]>
2017-10-08 22:22:14,094 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
2017-10-08 22:22:14,197 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Sun Oct 08 22:22:14 UTC 2017]; root of context hierarchy
2017-10-08 22:22:14,200 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-08 22:22:14,458 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-08 22:22:14,498 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-08 22:22:14,692 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-08 22:22:14,693 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-08 22:22:14,693 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-08 22:22:14,738 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
2017-10-08 22:22:14,791 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-08 22:22:15,649 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-08 22:22:15,655 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-08 22:22:15,657 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-08 22:22:15,659 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-08 22:22:16,510 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-08 22:22:16,640 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-08 22:22:16,654 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-08 22:22:16,782 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-08 22:22:16,783 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-08 22:22:16,786 INFO hsqldb.db..ENGINE - Database closed
2017-10-08 22:22:16,937 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-08 22:22:16,983 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-08 22:22:16,983 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-08 22:22:17,020 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-08 22:22:17,122 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-08 22:22:17,126 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-08 22:22:17,286 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-08 22:22:17,291 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-08 22:22:17,961 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-08 22:22:18,287 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
2017-10-08 22:22:18,308 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-08 22:22:18,309 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-08 22:22:18,312 INFO hsqldb.db..ENGINE - Database closed
2017-10-08 22:22:18,414 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: 4.915 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-08 22:22:19,151 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Sun Oct 08 22:22:19 UTC 2017]; root of context hierarchy
2017-10-08 22:22:19,214 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-08 22:22:19,420 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-08 22:22:19,431 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]]>
2017-10-08 22:22:19,457 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
2017-10-08 22:22:19,542 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Sun Oct 08 22:22:19 UTC 2017]; root of context hierarchy
2017-10-08 22:22:19,544 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-08 22:22:19,787 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-08 22:22:19,818 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-08 22:22:20,000 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-08 22:22:20,001 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-08 22:22:20,001 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-08 22:22:20,057 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
2017-10-08 22:22:20,103 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-08 22:22:20,841 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-08 22:22:20,849 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-08 22:22:20,853 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-08 22:22:20,861 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-08 22:22:21,770 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-08 22:22:21,874 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-08 22:22:21,888 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-08 22:22:22,007 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-08 22:22:22,008 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-08 22:22:22,011 INFO hsqldb.db..ENGINE - Database closed
2017-10-08 22:22:22,156 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-08 22:22:22,227 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-08 22:22:22,227 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-08 22:22:22,272 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-08 22:22:22,401 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-08 22:22:22,406 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-08 22:22:22,592 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-08 22:22:22,597 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-08 22:22:23,409 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-08 22:22:23,667 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
2017-10-08 22:22:23,687 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-08 22:22:23,689 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-08 22:22:23,692 INFO hsqldb.db..ENGINE - Database closed
2017-10-08 22:22:23,793 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: 4.908 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.717 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.701 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.748 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.549 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.709 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-08 22:22:31,644 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-08 22:22:31,675 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.597 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.596 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 #14
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/14/display/redirect>
------------------------------------------
[...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] 2017-10-24 04:36:43,237 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-24 04:36:43,245 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-24 04:36:43,707 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-24 04:36:43,767 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-24 04:36:43,784 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-24 04:36:43,831 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,832 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,833 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,833 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,834 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,835 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,836 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,837 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,839 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,839 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,841 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,842 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,843 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,843 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,844 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-24 04:36:43,844 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-24 04:36:43,853 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-24 04:36:43,859 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-24 04:36:43,862 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/ytex1998016020.sql
24 Oct 2017 04:36:44 INFO ENGINE - open start - state not modified
24 Oct 2017 04:36:44 INFO ENGINE - dataFileCache open start
24 Oct 2017 04:36:44 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1998016020.sql
24 Oct 2017 04:36:44 INFO ENGINE - dataFileCache commit start
24 Oct 2017 04:36:44 INFO ENGINE - dataFileCache commit end
24 Oct 2017 04:36:44 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1998016020.sql
[delete] Deleting: /tmp/ytex1716414692use.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] 2017-10-24 04:36:48,051 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-24 04:36:48,059 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-24 04:36:48,565 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-24 04:36:48,629 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-24 04:36:48,654 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-24 04:36:48,752 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-24 04:36:48,762 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-24 04:36:48,771 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-24 04:36:48,775 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/ytex714450541.sql
24 Oct 2017 04:36:49 INFO ENGINE - open start - state not modified
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache open start
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex714450541.sql
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache commit start
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache commit end
24 Oct 2017 04:36:49 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex714450541.sql
[delete] Deleting: /tmp/ytex1400603832use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex865868782.sql
24 Oct 2017 04:36:49 INFO ENGINE - open start - state not modified
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache open start
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex865868782.sql
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache commit start
24 Oct 2017 04:36:49 INFO ENGINE - dataFileCache commit end
24 Oct 2017 04:36:49 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex865868782.sql
[delete] Deleting: /tmp/ytex1463961292use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.403 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.532 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-24 04:36:53,884 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-24 04:36:53,906 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.503 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.412 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.549 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.292 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.49 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.411 sec
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-24 04:36:58,998 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Tue Oct 24 04:36:58 UTC 2017]; root of context hierarchy
2017-10-24 04:36:59,051 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-24 04:36:59,218 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-24 04:36:59,227 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]]>
2017-10-24 04:36:59,243 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
2017-10-24 04:36:59,301 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Tue Oct 24 04:36:59 UTC 2017]; root of context hierarchy
2017-10-24 04:36:59,303 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-24 04:36:59,485 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-24 04:36:59,504 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-24 04:36:59,663 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-24 04:36:59,664 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-24 04:36:59,665 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-24 04:36:59,697 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
2017-10-24 04:36:59,731 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-24 04:37:00,266 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-24 04:37:00,271 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-24 04:37:00,272 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-24 04:37:00,274 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-24 04:37:00,869 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-24 04:37:00,952 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-24 04:37:00,961 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-24 04:37:01,019 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-24 04:37:01,019 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-24 04:37:01,022 INFO hsqldb.db..ENGINE - Database closed
2017-10-24 04:37:01,154 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-24 04:37:01,205 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-24 04:37:01,206 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-24 04:37:01,243 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-24 04:37:01,358 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-24 04:37:01,363 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-24 04:37:01,496 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-24 04:37:01,500 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-24 04:37:02,122 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-24 04:37:02,289 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
2017-10-24 04:37:02,303 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-24 04:37:02,305 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-24 04:37:02,307 INFO hsqldb.db..ENGINE - Database closed
2017-10-24 04:37:02,408 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: 3.616 sec <<< FAILURE!
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-24 04:37:02,990 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Tue Oct 24 04:37:02 UTC 2017]; root of context hierarchy
2017-10-24 04:37:03,039 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-24 04:37:03,199 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-24 04:37:03,206 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]]>
2017-10-24 04:37:03,222 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
2017-10-24 04:37:03,283 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Tue Oct 24 04:37:03 UTC 2017]; root of context hierarchy
2017-10-24 04:37:03,284 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-24 04:37:03,451 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-24 04:37:03,470 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-24 04:37:03,592 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-24 04:37:03,592 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-24 04:37:03,592 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-24 04:37:03,626 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
2017-10-24 04:37:03,661 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-24 04:37:04,184 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-24 04:37:04,189 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-24 04:37:04,192 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-24 04:37:04,194 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-24 04:37:04,798 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-24 04:37:04,876 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-24 04:37:04,886 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-24 04:37:04,968 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-24 04:37:04,969 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-24 04:37:04,971 INFO hsqldb.db..ENGINE - Database closed
2017-10-24 04:37:05,102 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-24 04:37:05,140 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-24 04:37:05,140 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-24 04:37:05,172 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-24 04:37:05,271 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-24 04:37:05,276 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-24 04:37:05,405 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-24 04:37:05,409 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-24 04:37:05,951 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-24 04:37:06,110 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
2017-10-24 04:37:06,125 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-24 04:37:06,127 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-24 04:37:06,129 INFO hsqldb.db..ENGINE - Database closed
2017-10-24 04:37:06,230 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: 3.45 sec <<< FAILURE!
Results :
Tests in error:
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$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$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
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 #13
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/13/display/redirect>
------------------------------------------
[...truncated 43.93 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] 2017-10-17 22:18:54,084 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-17 22:18:54,092 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-17 22:18:54,656 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-17 22:18:54,734 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-17 22:18:54,754 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-17 22:18:54,799 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,800 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,801 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,802 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,803 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,804 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,805 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,806 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,807 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,808 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,809 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,810 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,811 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,812 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,812 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-17 22:18:54,813 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-17 22:18:54,822 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-17 22:18:54,831 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-17 22:18:54,835 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/ytex1672192884.sql
17 Oct 2017 22:18:55 INFO ENGINE - open start - state not modified
17 Oct 2017 22:18:55 INFO ENGINE - dataFileCache open start
17 Oct 2017 22:18:55 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1672192884.sql
17 Oct 2017 22:18:55 INFO ENGINE - dataFileCache commit start
17 Oct 2017 22:18:55 INFO ENGINE - dataFileCache commit end
17 Oct 2017 22:18:55 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1672192884.sql
[delete] Deleting: /tmp/ytex1366903143use.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] 2017-10-17 22:18:59,970 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-17 22:18:59,978 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-17 22:19:00,566 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-17 22:19:00,647 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-17 22:19:00,665 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-17 22:19:00,746 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-17 22:19:00,755 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-17 22:19:00,764 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-17 22:19:00,766 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/ytex1927076944.sql
17 Oct 2017 22:19:01 INFO ENGINE - open start - state not modified
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache open start
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1927076944.sql
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache commit start
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache commit end
17 Oct 2017 22:19:01 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1927076944.sql
[delete] Deleting: /tmp/ytex1535306732use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex60945300.sql
17 Oct 2017 22:19:01 INFO ENGINE - open start - state not modified
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache open start
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex60945300.sql
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache commit start
17 Oct 2017 22:19:01 INFO ENGINE - dataFileCache commit end
17 Oct 2017 22:19:01 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex60945300.sql
[delete] Deleting: /tmp/ytex1783473453use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-17 22:19:02,572 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Tue Oct 17 22:19:02 UTC 2017]; root of context hierarchy
2017-10-17 22:19:02,635 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-17 22:19:02,864 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-17 22:19:02,875 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]]>
2017-10-17 22:19:02,899 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
2017-10-17 22:19:02,974 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Tue Oct 17 22:19:02 UTC 2017]; root of context hierarchy
2017-10-17 22:19:02,976 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-17 22:19:03,210 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-17 22:19:03,237 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-17 22:19:03,410 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-17 22:19:03,411 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-17 22:19:03,411 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-17 22:19:03,458 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
2017-10-17 22:19:03,508 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-17 22:19:04,366 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-17 22:19:04,372 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-17 22:19:04,374 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-17 22:19:04,380 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-17 22:19:05,101 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-17 22:19:05,181 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-17 22:19:05,190 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-17 22:19:06,699 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-17 22:19:06,930 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-17 22:19:07,758 INFO hsqldb.db..ENGINE - Database closed
2017-10-17 22:19:07,904 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-17 22:19:07,986 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-17 22:19:07,987 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-17 22:19:08,027 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-17 22:19:08,155 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-17 22:19:08,160 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-17 22:19:08,312 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-17 22:19:08,317 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-17 22:19:08,929 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-17 22:19:09,224 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
2017-10-17 22:19:12,636 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-17 22:19:13,277 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-17 22:19:15,190 INFO hsqldb.db..ENGINE - Database closed
2017-10-17 22:19:15,292 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: 12.994 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-17 22:19:15,987 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Tue Oct 17 22:19:15 UTC 2017]; root of context hierarchy
2017-10-17 22:19:16,054 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-17 22:19:16,272 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-17 22:19:16,281 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]]>
2017-10-17 22:19:16,306 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
2017-10-17 22:19:16,380 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Tue Oct 17 22:19:16 UTC 2017]; root of context hierarchy
2017-10-17 22:19:16,382 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-17 22:19:16,612 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-17 22:19:16,638 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-17 22:19:16,804 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-17 22:19:16,804 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-17 22:19:16,805 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-17 22:19:16,854 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
2017-10-17 22:19:16,903 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-17 22:19:17,839 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-17 22:19:17,845 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-17 22:19:17,847 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-17 22:19:17,854 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-17 22:19:18,667 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-17 22:19:18,781 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-17 22:19:18,793 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-17 22:19:18,886 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-17 22:19:18,887 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-17 22:19:18,891 INFO hsqldb.db..ENGINE - Database closed
2017-10-17 22:19:19,029 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-17 22:19:19,064 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-17 22:19:19,065 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-17 22:19:19,097 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-17 22:19:19,216 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-17 22:19:19,222 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-17 22:19:19,359 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-17 22:19:19,364 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-17 22:19:19,943 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-17 22:19:20,224 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
2017-10-17 22:19:20,709 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-17 22:19:20,710 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-17 22:19:20,713 INFO hsqldb.db..ENGINE - Database closed
2017-10-17 22:19:20,815 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: 5.091 sec <<< FAILURE!
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.521 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.65 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.625 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.342 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.504 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.605 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-17 22:19:28,571 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-17 22:19:28,600 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.628 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.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 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.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.492 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 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