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Posted to notifications@ctakes.apache.org by Apache Jenkins Server <je...@builds.apache.org> on 2017/09/28 23:01:23 UTC
Build failed in Jenkins: cTAKES-trunk » Apache cTAKES YTEX #3
See <https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/3/display/redirect>
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[...truncated 41.99 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] 2017-09-28 22:59:45,909 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-09-28 22:59:45,930 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-09-28 22:59:47,095 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-09-28 22:59:47,208 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-09-28 22:59:47,254 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-09-28 22:59:47,354 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,355 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,357 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,358 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,359 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,361 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,362 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,364 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,365 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,367 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,369 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,370 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,372 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,373 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,374 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-28 22:59:47,375 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-09-28 22:59:47,394 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-09-28 22:59:47,454 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-09-28 22:59:47,461 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/ytex1705115784.sql
28 Sep 2017 22:59:48 INFO ENGINE - open start - state not modified
28 Sep 2017 22:59:48 INFO ENGINE - dataFileCache open start
28 Sep 2017 22:59:48 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1705115784.sql
28 Sep 2017 22:59:48 INFO ENGINE - dataFileCache commit start
28 Sep 2017 22:59:48 INFO ENGINE - dataFileCache commit end
28 Sep 2017 22:59:48 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1705115784.sql
[delete] Deleting: /tmp/ytex1401723433use.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] 2017-09-28 22:59:56,418 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-09-28 22:59:56,438 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-09-28 22:59:57,598 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-09-28 22:59:57,711 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-09-28 22:59:57,758 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-09-28 22:59:57,923 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-09-28 22:59:57,942 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-09-28 22:59:58,004 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-09-28 22:59:58,011 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/ytex677611562.sql
28 Sep 2017 22:59:58 INFO ENGINE - open start - state not modified
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache open start
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex677611562.sql
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache commit start
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache commit end
28 Sep 2017 22:59:58 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex677611562.sql
[delete] Deleting: /tmp/ytex2008409978use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex629840965.sql
28 Sep 2017 22:59:58 INFO ENGINE - open start - state not modified
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache open start
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex629840965.sql
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache commit start
28 Sep 2017 22:59:58 INFO ENGINE - dataFileCache commit end
28 Sep 2017 22:59:58 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex629840965.sql
[delete] Deleting: /tmp/ytex1630091994use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-09-28 23:00:00,284 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Thu Sep 28 23:00:00 UTC 2017]; root of context hierarchy
2017-09-28 23:00:00,407 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-28 23:00:00,790 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-28 23:00:00,807 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/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-09-28 23:00:00,849 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
2017-09-28 23:00:00,981 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Thu Sep 28 23:00:00 UTC 2017]; root of context hierarchy
2017-09-28 23:00:00,986 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-09-28 23:00:01,390 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-09-28 23:00:01,444 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-09-28 23:00:01,750 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-09-28 23:00:01,752 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-28 23:00:01,752 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-09-28 23:00:01,830 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
2017-09-28 23:00:01,918 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-28 23:00:03,130 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-09-28 23:00:03,141 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-09-28 23:00:03,145 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-09-28 23:00:03,148 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-09-28 23:00:04,306 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-28 23:00:04,445 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-28 23:00:04,464 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-28 23:00:04,593 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-28 23:00:04,596 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-28 23:00:04,603 INFO hsqldb.db..ENGINE - Database closed
2017-09-28 23:00:04,762 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-28 23:00:04,836 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-28 23:00:04,837 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-28 23:00:04,905 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-09-28 23:00:05,119 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-09-28 23:00:05,128 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-09-28 23:00:05,426 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-09-28 23:00:05,435 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-09-28 23:00:06,534 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-09-28 23:00:06,902 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
2017-09-28 23:00:06,928 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-28 23:00:06,931 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-28 23:00:06,937 INFO hsqldb.db..ENGINE - Database closed
2017-09-28 23:00:07,039 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: 7.267 sec <<< FAILURE!
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-09-28 23:00:08,174 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Thu Sep 28 23:00:08 UTC 2017]; root of context hierarchy
2017-09-28 23:00:08,292 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-28 23:00:08,676 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-28 23:00:08,693 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/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]> with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-09-28 23:00:08,733 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
2017-09-28 23:00:08,862 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Thu Sep 28 23:00:08 UTC 2017]; root of context hierarchy
2017-09-28 23:00:08,867 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-09-28 23:00:09,257 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-09-28 23:00:09,304 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-09-28 23:00:09,601 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-09-28 23:00:09,602 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-28 23:00:09,602 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-09-28 23:00:09,677 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
2017-09-28 23:00:09,756 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-28 23:00:11,011 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-09-28 23:00:11,022 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-09-28 23:00:11,026 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-09-28 23:00:11,029 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-09-28 23:00:12,195 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-28 23:00:12,347 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-28 23:00:12,367 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-28 23:00:12,527 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-28 23:00:12,529 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-28 23:00:12,534 INFO hsqldb.db..ENGINE - Database closed
2017-09-28 23:00:12,699 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-28 23:00:12,788 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-28 23:00:12,788 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-28 23:00:12,856 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-09-28 23:00:13,085 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-09-28 23:00:13,097 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-09-28 23:00:13,422 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-09-28 23:00:13,433 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-09-28 23:00:14,745 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-09-28 23:00:15,177 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
2017-09-28 23:00:15,200 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-28 23:00:15,203 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-28 23:00:15,208 INFO hsqldb.db..ENGINE - Database closed
2017-09-28 23:00:15,310 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: 7.633 sec <<< FAILURE!
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.976 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.661 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.178 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.142 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.196 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.966 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-09-28 23:00:30,296 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-09-28 23:00:30,345 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.174 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.159 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.923 sec
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/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$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
Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #12
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/12/display/redirect>
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[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-08 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 #11
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/11/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-05 14:52:28,810 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-05 14:52:28,825 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-05 14:52:29,863 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-05 14:52:30,023 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-05 14:52:30,075 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-05 14:52:30,162 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,166 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,167 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,168 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,169 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,170 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,171 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,173 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,174 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,175 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,176 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,177 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,179 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,189 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,191 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-05 14:52:30,191 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-05 14:52:30,212 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-05 14:52:30,222 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-05 14:52:30,225 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/ytex159664894.sql
05 Oct 2017 14:52:30 INFO ENGINE - open start - state not modified
05 Oct 2017 14:52:30 INFO ENGINE - dataFileCache open start
05 Oct 2017 14:52:30 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex159664894.sql
05 Oct 2017 14:52:30 INFO ENGINE - dataFileCache commit start
05 Oct 2017 14:52:30 INFO ENGINE - dataFileCache commit end
05 Oct 2017 14:52:30 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex159664894.sql
[delete] Deleting: /tmp/ytex1868754528use.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] 2017-10-05 14:52:36,461 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-05 14:52:36,469 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-05 14:52:37,329 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-05 14:52:37,453 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-05 14:52:37,483 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-05 14:52:37,598 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-05 14:52:37,618 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-05 14:52:37,664 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-05 14:52:37,667 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/ytex2121545254.sql
05 Oct 2017 14:52:38 INFO ENGINE - open start - state not modified
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache open start
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex2121545254.sql
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache commit start
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache commit end
05 Oct 2017 14:52:38 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex2121545254.sql
[delete] Deleting: /tmp/ytex1911537010use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1096015810.sql
05 Oct 2017 14:52:38 INFO ENGINE - open start - state not modified
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache open start
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1096015810.sql
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache commit start
05 Oct 2017 14:52:38 INFO ENGINE - dataFileCache commit end
05 Oct 2017 14:52:38 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1096015810.sql
[delete] Deleting: /tmp/ytex1243256993use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-05 14:52:40,065 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Thu Oct 05 14:52:40 UTC 2017]; root of context hierarchy
2017-10-05 14:52:40,152 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-05 14:52:40,448 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-05 14:52:40,458 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]]>
2017-10-05 14:52:40,483 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
2017-10-05 14:52:40,577 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Thu Oct 05 14:52:40 UTC 2017]; root of context hierarchy
2017-10-05 14:52:40,579 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-05 14:52:40,906 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-05 14:52:40,931 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-05 14:52:41,162 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-05 14:52:41,163 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-05 14:52:41,164 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-05 14:52:41,224 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
2017-10-05 14:52:41,291 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-05 14:52:42,297 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-05 14:52:42,305 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-05 14:52:42,308 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-05 14:52:42,311 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-05 14:52:43,539 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-05 14:52:43,688 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-05 14:52:43,701 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-05 14:52:43,823 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-05 14:52:43,825 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-05 14:52:43,828 INFO hsqldb.db..ENGINE - Database closed
2017-10-05 14:52:44,017 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-05 14:52:44,072 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-05 14:52:44,073 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-05 14:52:44,158 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-05 14:52:44,349 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-05 14:52:44,370 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-05 14:52:44,599 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-05 14:52:44,617 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-05 14:52:45,776 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-05 14:52:46,141 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
2017-10-05 14:52:46,179 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-05 14:52:46,181 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-05 14:52:46,184 INFO hsqldb.db..ENGINE - Database closed
2017-10-05 14:52:46,286 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: 6.674 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-05 14:52:47,256 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Thu Oct 05 14:52:47 UTC 2017]; root of context hierarchy
2017-10-05 14:52:47,325 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-05 14:52:47,606 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-05 14:52:47,616 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]]>
2017-10-05 14:52:47,635 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
2017-10-05 14:52:47,719 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Thu Oct 05 14:52:47 UTC 2017]; root of context hierarchy
2017-10-05 14:52:47,721 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-05 14:52:48,050 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-05 14:52:48,080 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-05 14:52:48,335 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-05 14:52:48,336 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-05 14:52:48,336 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-05 14:52:48,408 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
2017-10-05 14:52:48,480 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-05 14:52:49,481 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-05 14:52:49,488 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-05 14:52:49,490 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-05 14:52:49,492 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-05 14:52:50,697 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-05 14:52:50,890 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-05 14:52:50,908 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-05 14:52:51,054 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-05 14:52:51,055 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-05 14:52:51,059 INFO hsqldb.db..ENGINE - Database closed
2017-10-05 14:52:51,225 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-05 14:52:51,266 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-05 14:52:51,267 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-05 14:52:51,347 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-05 14:52:51,526 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-05 14:52:51,532 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-05 14:52:51,809 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-05 14:52:51,814 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-05 14:52:52,902 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-05 14:52:53,224 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
2017-10-05 14:52:53,262 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-05 14:52:53,263 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-05 14:52:53,266 INFO hsqldb.db..ENGINE - Database closed
2017-10-05 14:52:53,367 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: 6.531 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.05 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.941 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.415 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.593 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.97 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.778 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.93 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-05 14:53:04,347 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-05 14:53:04,382 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.997 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.263 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 sec
Running org.apache.ctakes.jdl.AppTest
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: 0.673 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.734 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 #10
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/10/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-03 15:38:00,373 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-03 15:38:00,380 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-03 15:38:00,980 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-03 15:38:01,082 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-03 15:38:01,101 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-03 15:38:01,140 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,141 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,142 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,143 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,143 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,144 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,145 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,147 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,147 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,148 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,150 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,151 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,152 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,153 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,153 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-03 15:38:01,154 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-03 15:38:01,162 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-03 15:38:01,168 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-03 15:38:01,170 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/ytex660755700.sql
03 Oct 2017 15:38:01 INFO ENGINE - open start - state not modified
03 Oct 2017 15:38:01 INFO ENGINE - dataFileCache open start
03 Oct 2017 15:38:01 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex660755700.sql
03 Oct 2017 15:38:01 INFO ENGINE - dataFileCache commit start
03 Oct 2017 15:38:01 INFO ENGINE - dataFileCache commit end
03 Oct 2017 15:38:01 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex660755700.sql
[delete] Deleting: /tmp/ytex1566159714use.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] 2017-10-03 15:38:06,443 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-03 15:38:06,451 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-03 15:38:07,014 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-03 15:38:07,135 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-03 15:38:07,161 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-03 15:38:07,261 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-03 15:38:07,274 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-03 15:38:07,283 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-03 15:38:07,286 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/ytex1358934333.sql
03 Oct 2017 15:38:07 INFO ENGINE - open start - state not modified
03 Oct 2017 15:38:07 INFO ENGINE - dataFileCache open start
03 Oct 2017 15:38:07 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1358934333.sql
03 Oct 2017 15:38:07 INFO ENGINE - dataFileCache commit start
03 Oct 2017 15:38:07 INFO ENGINE - dataFileCache commit end
03 Oct 2017 15:38:07 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1358934333.sql
[delete] Deleting: /tmp/ytex1505386218use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1037189099.sql
03 Oct 2017 15:38:08 INFO ENGINE - open start - state not modified
03 Oct 2017 15:38:08 INFO ENGINE - dataFileCache open start
03 Oct 2017 15:38:08 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1037189099.sql
03 Oct 2017 15:38:08 INFO ENGINE - dataFileCache commit start
03 Oct 2017 15:38:08 INFO ENGINE - dataFileCache commit end
03 Oct 2017 15:38:08 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1037189099.sql
[delete] Deleting: /tmp/ytex841325908use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-03 15:38:09,234 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Tue Oct 03 15:38:09 UTC 2017]; root of context hierarchy
2017-10-03 15:38:09,297 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-03 15:38:09,523 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-03 15:38:09,532 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]]>
2017-10-03 15:38:09,554 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
2017-10-03 15:38:09,636 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Tue Oct 03 15:38:09 UTC 2017]; root of context hierarchy
2017-10-03 15:38:09,639 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-03 15:38:09,863 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-03 15:38:09,898 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-03 15:38:10,079 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-03 15:38:10,080 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-03 15:38:10,080 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-03 15:38:10,130 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
2017-10-03 15:38:10,186 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-03 15:38:11,280 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-03 15:38:11,287 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-03 15:38:11,289 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-03 15:38:11,291 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-03 15:38:12,136 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-03 15:38:12,243 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-03 15:38:12,256 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-03 15:38:12,368 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-03 15:38:12,370 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-03 15:38:12,379 INFO hsqldb.db..ENGINE - Database closed
2017-10-03 15:38:12,559 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-03 15:38:12,649 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-03 15:38:12,650 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-03 15:38:12,697 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-03 15:38:12,843 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-03 15:38:12,855 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-03 15:38:13,024 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-03 15:38:13,032 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-03 15:38:13,836 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-03 15:38:14,111 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
2017-10-03 15:38:14,129 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-03 15:38:14,130 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-03 15:38:14,133 INFO hsqldb.db..ENGINE - Database closed
2017-10-03 15:38:14,235 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: 5.299 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-03 15:38:15,047 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Tue Oct 03 15:38:15 UTC 2017]; root of context hierarchy
2017-10-03 15:38:15,108 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-03 15:38:15,291 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-03 15:38:15,302 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]]>
2017-10-03 15:38:15,327 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
2017-10-03 15:38:15,396 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Tue Oct 03 15:38:15 UTC 2017]; root of context hierarchy
2017-10-03 15:38:15,398 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-03 15:38:15,641 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-03 15:38:15,689 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-03 15:38:15,884 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-03 15:38:15,885 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-03 15:38:15,885 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-03 15:38:15,946 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
2017-10-03 15:38:16,005 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-03 15:38:16,995 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-03 15:38:17,003 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-03 15:38:17,006 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-03 15:38:17,020 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-03 15:38:17,882 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-03 15:38:18,029 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-03 15:38:18,042 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-03 15:38:18,135 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-03 15:38:18,136 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-03 15:38:18,138 INFO hsqldb.db..ENGINE - Database closed
2017-10-03 15:38:18,281 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-03 15:38:18,349 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-03 15:38:18,350 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-03 15:38:18,386 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-03 15:38:18,518 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-03 15:38:18,522 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-03 15:38:18,666 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-03 15:38:18,669 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-03 15:38:19,396 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-03 15:38:19,617 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
2017-10-03 15:38:19,632 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-03 15:38:19,634 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-03 15:38:19,637 INFO hsqldb.db..ENGINE - Database closed
2017-10-03 15:38:19,738 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: 5.007 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.691 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.913 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.334 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.774 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.65 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.741 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-03 15:38:27,975 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-03 15:38:28,013 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.495 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.563 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 #9
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/9/display/redirect>
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[...truncated 51.76 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] 2017-10-02 21:38:08,028 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-02 21:38:08,038 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-02 21:38:08,614 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-02 21:38:08,717 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-02 21:38:08,741 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-02 21:38:08,796 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,797 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,798 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,799 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,800 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,801 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,803 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,804 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,805 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,806 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,808 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,809 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,810 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,811 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,812 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,813 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-02 21:38:08,821 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-02 21:38:08,826 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-02 21:38:08,829 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/ytex265782330.sql
02 Oct 2017 21:38:09 INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex265782330.sql
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:09 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex265782330.sql
[delete] Deleting: /tmp/ytex1427625299use.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] 2017-10-02 21:38:13,573 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-02 21:38:13,589 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-02 21:38:14,181 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-02 21:38:14,262 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-02 21:38:14,288 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-02 21:38:14,385 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-02 21:38:14,400 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-02 21:38:14,410 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-02 21:38:14,413 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/ytex824337993.sql
02 Oct 2017 21:38:14 INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex824337993.sql
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:15 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex824337993.sql
[delete] Deleting: /tmp/ytex1487798293use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex177981942.sql
02 Oct 2017 21:38:15 INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex177981942.sql
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:15 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex177981942.sql
[delete] Deleting: /tmp/ytex621876601use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-02 21:38:16,266 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Mon Oct 02 21:38:16 UTC 2017]; root of context hierarchy
2017-10-02 21:38:16,328 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:16,546 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:16,555 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]]>
2017-10-02 21:38:16,576 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
2017-10-02 21:38:16,649 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Mon Oct 02 21:38:16 UTC 2017]; root of context hierarchy
2017-10-02 21:38:16,651 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 21:38:16,884 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 21:38:16,916 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 21:38:17,118 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 21:38:17,119 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:17,119 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 21:38:17,162 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
2017-10-02 21:38:17,206 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:18,134 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 21:38:18,141 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 21:38:18,144 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-02 21:38:18,146 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-02 21:38:18,986 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 21:38:19,095 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:19,104 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:19,165 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:19,166 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:19,169 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:19,330 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 21:38:19,368 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:19,369 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:19,403 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 21:38:19,543 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 21:38:19,550 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 21:38:19,719 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 21:38:19,726 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 21:38:20,539 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-02 21:38:20,784 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
2017-10-02 21:38:20,815 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:20,816 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:20,819 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:20,920 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: 4.945 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-02 21:38:21,720 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Mon Oct 02 21:38:21 UTC 2017]; root of context hierarchy
2017-10-02 21:38:21,789 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:21,985 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:21,994 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]]>
2017-10-02 21:38:22,025 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
2017-10-02 21:38:22,102 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Mon Oct 02 21:38:22 UTC 2017]; root of context hierarchy
2017-10-02 21:38:22,105 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 21:38:22,332 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 21:38:22,368 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 21:38:22,583 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 21:38:22,584 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:22,584 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 21:38:22,647 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
2017-10-02 21:38:22,705 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:23,557 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 21:38:23,565 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 21:38:23,568 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-02 21:38:23,574 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-02 21:38:24,406 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 21:38:24,502 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:24,514 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:24,630 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:24,632 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:24,641 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:24,803 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 21:38:24,852 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:24,853 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:24,903 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 21:38:25,017 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 21:38:25,023 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 21:38:25,196 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 21:38:25,200 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 21:38:25,928 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-02 21:38:26,231 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
2017-10-02 21:38:26,243 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:26,245 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:26,248 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:26,350 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: 4.918 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.754 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.713 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.388 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.607 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.573 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-02 21:38:34,320 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-02 21:38:34,348 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.547 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.594 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 #8
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/8/display/redirect>
------------------------------------------
[...truncated 43.25 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-02 15:37:16,656 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-02 15:37:16,663 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-02 15:37:17,206 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-02 15:37:17,295 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-02 15:37:17,316 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-02 15:37:17,391 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,392 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,393 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,394 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,395 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,396 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,397 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,399 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,400 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,400 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,402 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,403 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,405 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,406 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,407 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 15:37:17,407 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-02 15:37:17,416 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-02 15:37:17,422 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-02 15:37:17,424 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/ytex1063355916.sql
02 Oct 2017 15:37:17 INFO ENGINE - open start - state not modified
02 Oct 2017 15:37:18 INFO ENGINE - dataFileCache open start
02 Oct 2017 15:37:18 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1063355916.sql
02 Oct 2017 15:37:18 INFO ENGINE - dataFileCache commit start
02 Oct 2017 15:37:18 INFO ENGINE - dataFileCache commit end
02 Oct 2017 15:37:18 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1063355916.sql
[delete] Deleting: /tmp/ytex1337383923use.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] 2017-10-02 15:37:22,718 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-02 15:37:22,729 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-02 15:37:23,278 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-02 15:37:23,353 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-02 15:37:23,377 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-02 15:37:23,477 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-02 15:37:23,488 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-02 15:37:23,501 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-02 15:37:23,504 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/ytex108011702.sql
02 Oct 2017 15:37:24 INFO ENGINE - open start - state not modified
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache open start
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex108011702.sql
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache commit start
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache commit end
02 Oct 2017 15:37:24 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex108011702.sql
[delete] Deleting: /tmp/ytex325731354use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1429207758.sql
02 Oct 2017 15:37:24 INFO ENGINE - open start - state not modified
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache open start
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1429207758.sql
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache commit start
02 Oct 2017 15:37:24 INFO ENGINE - dataFileCache commit end
02 Oct 2017 15:37:24 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1429207758.sql
[delete] Deleting: /tmp/ytex1123332485use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-02 15:37:25,384 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Mon Oct 02 15:37:25 UTC 2017]; root of context hierarchy
2017-10-02 15:37:25,452 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 15:37:25,681 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 15:37:25,690 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]]>
2017-10-02 15:37:25,712 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
2017-10-02 15:37:25,778 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Mon Oct 02 15:37:25 UTC 2017]; root of context hierarchy
2017-10-02 15:37:25,780 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 15:37:26,010 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 15:37:26,034 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 15:37:26,220 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 15:37:26,221 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 15:37:26,221 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 15:37:26,267 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
2017-10-02 15:37:26,320 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 15:37:27,275 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 15:37:27,283 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 15:37:27,285 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-02 15:37:27,288 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-02 15:37:28,082 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 15:37:28,173 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 15:37:28,183 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 15:37:29,223 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 15:37:29,423 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 15:37:32,119 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 15:37:32,293 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 15:37:32,352 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 15:37:32,353 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 15:37:32,388 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 15:37:32,504 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 15:37:32,509 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 15:37:32,679 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 15:37:32,684 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 15:37:33,458 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-02 15:37:33,883 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
2017-10-02 15:37:33,938 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 15:37:33,941 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 15:37:33,944 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 15:37:34,047 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: 8.973 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-02 15:37:34,915 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Mon Oct 02 15:37:34 UTC 2017]; root of context hierarchy
2017-10-02 15:37:34,979 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 15:37:35,186 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 15:37:35,197 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]]>
2017-10-02 15:37:35,224 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
2017-10-02 15:37:35,287 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Mon Oct 02 15:37:35 UTC 2017]; root of context hierarchy
2017-10-02 15:37:35,289 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 15:37:35,570 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 15:37:35,600 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 15:37:35,787 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 15:37:35,788 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 15:37:35,788 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 15:37:35,835 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
2017-10-02 15:37:35,902 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 15:37:36,818 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 15:37:36,824 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 15:37:36,827 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-02 15:37:36,835 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-02 15:37:37,734 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 15:37:37,843 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 15:37:37,854 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 15:37:37,940 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 15:37:37,941 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 15:37:37,944 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 15:37:38,086 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 15:37:38,137 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 15:37:38,138 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 15:37:38,180 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 15:37:38,281 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 15:37:38,285 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 15:37:38,419 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 15:37:38,423 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 15:37:39,073 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-02 15:37:39,371 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
2017-10-02 15:37:39,393 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 15:37:39,399 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 15:37:39,403 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 15:37:39,505 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: 4.86 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.733 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.721 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.462 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.755 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.573 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.693 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-02 15:37:47,645 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-02 15:37:47,677 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.716 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.581 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.562 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 #7
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/7/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-02 12:30:15,719 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-02 12:30:15,727 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-02 12:30:16,292 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-02 12:30:16,389 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-02 12:30:16,408 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-02 12:30:16,457 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,458 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,459 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,459 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,460 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,461 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,462 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,463 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,464 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,465 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,466 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,467 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,468 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,469 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,470 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 12:30:16,470 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-02 12:30:16,478 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-02 12:30:16,483 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-02 12:30:16,486 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/ytex770167751.sql
02 Oct 2017 12:30:17 INFO ENGINE - open start - state not modified
02 Oct 2017 12:30:17 INFO ENGINE - dataFileCache open start
02 Oct 2017 12:30:17 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex770167751.sql
02 Oct 2017 12:30:17 INFO ENGINE - dataFileCache commit start
02 Oct 2017 12:30:17 INFO ENGINE - dataFileCache commit end
02 Oct 2017 12:30:17 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex770167751.sql
[delete] Deleting: /tmp/ytex1588518771use.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] 2017-10-02 12:30:21,269 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-02 12:30:21,276 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-02 12:30:21,830 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-02 12:30:21,904 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-02 12:30:21,922 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-02 12:30:22,016 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-02 12:30:22,030 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-02 12:30:22,041 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-02 12:30:22,045 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/ytex1321444660.sql
02 Oct 2017 12:30:22 INFO ENGINE - open start - state not modified
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache open start
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1321444660.sql
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache commit start
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache commit end
02 Oct 2017 12:30:22 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1321444660.sql
[delete] Deleting: /tmp/ytex1485605645use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex446460302.sql
02 Oct 2017 12:30:22 INFO ENGINE - open start - state not modified
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache open start
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex446460302.sql
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache commit start
02 Oct 2017 12:30:22 INFO ENGINE - dataFileCache commit end
02 Oct 2017 12:30:22 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex446460302.sql
[delete] Deleting: /tmp/ytex1116561346use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-02 12:30:23,903 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Mon Oct 02 12:30:23 UTC 2017]; root of context hierarchy
2017-10-02 12:30:23,974 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 12:30:24,181 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 12:30:24,192 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]]>
2017-10-02 12:30:24,217 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
2017-10-02 12:30:24,281 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Mon Oct 02 12:30:24 UTC 2017]; root of context hierarchy
2017-10-02 12:30:24,284 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 12:30:24,522 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 12:30:24,552 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 12:30:24,765 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 12:30:24,766 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 12:30:24,766 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 12:30:24,816 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
2017-10-02 12:30:24,874 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 12:30:25,734 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 12:30:25,740 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 12:30:25,742 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-02 12:30:25,749 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-02 12:30:26,620 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 12:30:26,700 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 12:30:26,709 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 12:30:26,846 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 12:30:26,847 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 12:30:26,852 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 12:30:26,988 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 12:30:27,043 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 12:30:27,044 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 12:30:27,090 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 12:30:27,215 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 12:30:27,219 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 12:30:27,391 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 12:30:27,397 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 12:30:28,120 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-02 12:30:28,485 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
2017-10-02 12:30:28,576 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 12:30:28,582 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 12:30:28,586 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 12:30:28,687 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: 5.086 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-02 12:30:29,457 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Mon Oct 02 12:30:29 UTC 2017]; root of context hierarchy
2017-10-02 12:30:29,507 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 12:30:29,691 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 12:30:29,700 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]]>
2017-10-02 12:30:29,717 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
2017-10-02 12:30:29,804 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Mon Oct 02 12:30:29 UTC 2017]; root of context hierarchy
2017-10-02 12:30:29,807 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 12:30:29,999 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 12:30:30,024 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 12:30:30,247 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 12:30:30,248 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 12:30:30,248 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 12:30:30,296 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
2017-10-02 12:30:30,356 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 12:30:31,262 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 12:30:31,268 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 12:30:31,270 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-02 12:30:31,277 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-02 12:30:32,139 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 12:30:32,240 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 12:30:32,254 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 12:30:32,312 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 12:30:32,313 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 12:30:32,316 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 12:30:32,451 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-02 12:30:32,544 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 12:30:32,548 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 12:30:32,587 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 12:30:32,746 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 12:30:32,752 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 12:30:32,929 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 12:30:32,935 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 12:30:33,676 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-02 12:30:33,884 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
2017-10-02 12:30:33,914 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 12:30:33,927 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 12:30:33,930 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 12:30:34,031 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: 4.841 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.73 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.814 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.417 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.756 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.553 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.746 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-02 12:30:42,011 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-02 12:30:42,040 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.677 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.232 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.533 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.586 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 #6
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/6/display/redirect>
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[...truncated 43.27 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] 2017-10-01 18:39:52,580 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-01 18:39:52,588 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-01 18:39:53,150 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-01 18:39:53,240 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-01 18:39:53,257 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-01 18:39:53,305 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,306 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,306 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,307 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,308 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,309 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,310 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,312 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,313 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,314 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,316 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,317 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,318 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,319 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,319 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-01 18:39:53,320 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-01 18:39:53,333 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-01 18:39:53,339 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-01 18:39:53,342 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/ytex1166934706.sql
01 Oct 2017 18:39:53 INFO ENGINE - open start - state not modified
01 Oct 2017 18:39:53 INFO ENGINE - dataFileCache open start
01 Oct 2017 18:39:53 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1166934706.sql
01 Oct 2017 18:39:53 INFO ENGINE - dataFileCache commit start
01 Oct 2017 18:39:53 INFO ENGINE - dataFileCache commit end
01 Oct 2017 18:39:53 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1166934706.sql
[delete] Deleting: /tmp/ytex1983276124use.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] 2017-10-01 18:39:58,286 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-01 18:39:58,297 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-10-01 18:39:58,849 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-10-01 18:39:58,926 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-10-01 18:39:58,942 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-10-01 18:39:59,038 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-01 18:39:59,051 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-10-01 18:39:59,061 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-10-01 18:39:59,065 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/ytex1758562859.sql
01 Oct 2017 18:39:59 INFO ENGINE - open start - state not modified
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache open start
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1758562859.sql
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache commit start
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache commit end
01 Oct 2017 18:39:59 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1758562859.sql
[delete] Deleting: /tmp/ytex1920501581use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex218024883.sql
01 Oct 2017 18:39:59 INFO ENGINE - open start - state not modified
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache open start
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex218024883.sql
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache commit start
01 Oct 2017 18:39:59 INFO ENGINE - dataFileCache commit end
01 Oct 2017 18:39:59 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex218024883.sql
[delete] Deleting: /tmp/ytex1481157183use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-01 18:40:00,937 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Sun Oct 01 18:40:00 UTC 2017]; root of context hierarchy
2017-10-01 18:40:01,018 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-01 18:40:01,234 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-01 18:40:01,247 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]]>
2017-10-01 18:40:01,269 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
2017-10-01 18:40:01,336 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Sun Oct 01 18:40:01 UTC 2017]; root of context hierarchy
2017-10-01 18:40:01,340 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-01 18:40:01,581 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-01 18:40:01,618 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-01 18:40:01,799 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-01 18:40:01,799 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-01 18:40:01,799 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-01 18:40:01,843 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
2017-10-01 18:40:01,897 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-01 18:40:02,850 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-01 18:40:02,858 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-01 18:40:02,861 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-01 18:40:02,870 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-01 18:40:03,665 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-01 18:40:03,778 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-01 18:40:03,787 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-01 18:40:03,893 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-01 18:40:03,894 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-01 18:40:03,901 INFO hsqldb.db..ENGINE - Database closed
2017-10-01 18:40:04,045 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-01 18:40:04,084 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-01 18:40:04,084 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-01 18:40:04,118 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-01 18:40:04,257 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-01 18:40:04,261 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-01 18:40:04,416 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-01 18:40:04,420 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-01 18:40:05,106 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-01 18:40:05,425 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
2017-10-01 18:40:05,444 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-01 18:40:05,445 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-01 18:40:05,447 INFO hsqldb.db..ENGINE - Database closed
2017-10-01 18:40:05,548 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: 4.976 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-01 18:40:06,263 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Sun Oct 01 18:40:06 UTC 2017]; root of context hierarchy
2017-10-01 18:40:06,348 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-01 18:40:06,572 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-01 18:40:06,582 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]]>
2017-10-01 18:40:06,605 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
2017-10-01 18:40:06,683 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Sun Oct 01 18:40:06 UTC 2017]; root of context hierarchy
2017-10-01 18:40:06,685 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-01 18:40:06,943 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-01 18:40:06,976 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-01 18:40:07,156 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-01 18:40:07,157 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-01 18:40:07,158 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-01 18:40:07,232 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
2017-10-01 18:40:07,279 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-01 18:40:08,131 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-01 18:40:08,137 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-01 18:40:08,139 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-10-01 18:40:08,145 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-10-01 18:40:08,974 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-01 18:40:09,088 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-01 18:40:09,097 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-01 18:40:09,194 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-01 18:40:09,195 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-01 18:40:09,197 INFO hsqldb.db..ENGINE - Database closed
2017-10-01 18:40:09,340 INFO hsqldb.db..ENGINE - open start - state not modified
2017-10-01 18:40:09,396 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-01 18:40:09,397 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-01 18:40:09,447 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-01 18:40:09,574 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-01 18:40:09,580 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-10-01 18:40:09,793 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-01 18:40:09,798 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-01 18:40:10,600 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-10-01 18:40:10,837 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
2017-10-01 18:40:10,852 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-01 18:40:10,854 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-01 18:40:10,856 INFO hsqldb.db..ENGINE - Database closed
2017-10-01 18:40:10,958 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: 4.999 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.757 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.626 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.398 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.726 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.619 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.735 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-01 18:40:18,986 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-10-01 18:40:19,015 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.742 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.195 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.535 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.574 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 #5
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/5/display/redirect>
------------------------------------------
[...truncated 43.26 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-09-29 19:10:06,589 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-09-29 19:10:06,600 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-09-29 19:10:07,218 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-09-29 19:10:07,289 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-09-29 19:10:07,324 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-09-29 19:10:07,381 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,382 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,383 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,384 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,385 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,386 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,387 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,389 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,389 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,390 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,392 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,393 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,403 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,404 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,405 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 19:10:07,406 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-09-29 19:10:07,421 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-09-29 19:10:07,428 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-09-29 19:10:07,432 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/ytex897090839.sql
29 Sep 2017 19:10:07 INFO ENGINE - open start - state not modified
29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache open start
29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex897090839.sql
29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache commit start
29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache commit end
29 Sep 2017 19:10:08 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex897090839.sql
[delete] Deleting: /tmp/ytex1929446082use.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] 2017-09-29 19:10:12,526 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-09-29 19:10:12,534 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-09-29 19:10:13,172 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-09-29 19:10:13,250 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-09-29 19:10:13,281 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-09-29 19:10:13,380 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-09-29 19:10:13,390 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-09-29 19:10:13,405 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-09-29 19:10:13,408 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/ytex1291228459.sql
29 Sep 2017 19:10:14 INFO ENGINE - open start - state not modified
29 Sep 2017 19:10:14 INFO ENGINE - dataFileCache open start
29 Sep 2017 19:10:14 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1291228459.sql
29 Sep 2017 19:10:15 INFO ENGINE - dataFileCache commit start
29 Sep 2017 19:10:16 INFO ENGINE - dataFileCache commit end
29 Sep 2017 19:10:16 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1291228459.sql
[delete] Deleting: /tmp/ytex564695223use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1195843211.sql
29 Sep 2017 19:10:16 INFO ENGINE - open start - state not modified
29 Sep 2017 19:10:16 INFO ENGINE - dataFileCache open start
29 Sep 2017 19:10:16 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1195843211.sql
29 Sep 2017 19:10:18 INFO ENGINE - dataFileCache commit start
29 Sep 2017 19:10:19 INFO ENGINE - dataFileCache commit end
29 Sep 2017 19:10:21 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1195843211.sql
[delete] Deleting: /tmp/ytex1363463702use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-09-29 19:10:23,222 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Fri Sep 29 19:10:23 UTC 2017]; root of context hierarchy
2017-09-29 19:10:23,289 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 19:10:23,526 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 19:10:23,543 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]]>
2017-09-29 19:10:23,576 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
2017-09-29 19:10:23,667 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Fri Sep 29 19:10:23 UTC 2017]; root of context hierarchy
2017-09-29 19:10:23,670 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-09-29 19:10:23,941 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-09-29 19:10:23,991 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-09-29 19:10:24,223 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-09-29 19:10:24,223 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 19:10:24,224 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-09-29 19:10:24,287 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
2017-09-29 19:10:24,345 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 19:10:25,288 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-09-29 19:10:25,294 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-09-29 19:10:25,296 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-09-29 19:10:25,299 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-09-29 19:10:26,259 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 19:10:26,381 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 19:10:26,395 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 19:10:26,493 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 19:10:26,494 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 19:10:26,497 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 19:10:26,639 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 19:10:26,724 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 19:10:26,725 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 19:10:26,817 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-09-29 19:10:26,924 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-09-29 19:10:26,929 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-09-29 19:10:27,115 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-09-29 19:10:27,121 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-09-29 19:10:27,910 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-09-29 19:10:28,207 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
2017-09-29 19:10:28,246 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 19:10:28,248 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 19:10:28,250 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 19:10:28,352 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: 5.439 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-09-29 19:10:29,193 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Fri Sep 29 19:10:29 UTC 2017]; root of context hierarchy
2017-09-29 19:10:29,255 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 19:10:29,472 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 19:10:29,481 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]]>
2017-09-29 19:10:29,504 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
2017-09-29 19:10:29,574 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Fri Sep 29 19:10:29 UTC 2017]; root of context hierarchy
2017-09-29 19:10:29,577 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-09-29 19:10:29,842 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-09-29 19:10:29,876 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-09-29 19:10:30,055 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-09-29 19:10:30,056 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 19:10:30,056 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-09-29 19:10:30,097 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
2017-09-29 19:10:30,149 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 19:10:30,956 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-09-29 19:10:30,962 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-09-29 19:10:30,965 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-09-29 19:10:30,972 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-09-29 19:10:31,891 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 19:10:32,007 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 19:10:32,019 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 19:10:32,159 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 19:10:32,159 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 19:10:32,162 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 19:10:32,321 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 19:10:32,405 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 19:10:32,406 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 19:10:32,453 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-09-29 19:10:32,594 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-09-29 19:10:32,600 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-09-29 19:10:32,783 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-09-29 19:10:32,790 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-09-29 19:10:33,615 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-09-29 19:10:33,893 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
2017-09-29 19:10:33,951 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 19:10:33,952 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 19:10:33,956 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 19:10:34,058 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: 5.172 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.846 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.936 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.512 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.832 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.621 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.867 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-09-29 19:10:43,011 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-09-29 19:10:43,128 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.893 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.782 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.62 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 #4
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/4/display/redirect>
------------------------------------------
[...truncated 51.22 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] 2017-09-29 18:10:29,447 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-09-29 18:10:29,454 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-09-29 18:10:30,013 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-09-29 18:10:30,073 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-09-29 18:10:30,116 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-09-29 18:10:30,176 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,177 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,178 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,179 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,180 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,181 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,182 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,184 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,185 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,186 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,187 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,189 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,190 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,191 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,192 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-09-29 18:10:30,192 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-09-29 18:10:30,203 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-09-29 18:10:30,227 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-09-29 18:10:30,231 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/ytex655576542.sql
29 Sep 2017 18:10:30 INFO ENGINE - open start - state not modified
29 Sep 2017 18:10:30 INFO ENGINE - dataFileCache open start
29 Sep 2017 18:10:30 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex655576542.sql
29 Sep 2017 18:10:30 INFO ENGINE - dataFileCache commit start
29 Sep 2017 18:10:30 INFO ENGINE - dataFileCache commit end
29 Sep 2017 18:10:30 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex655576542.sql
[delete] Deleting: /tmp/ytex688232860use.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] 2017-09-29 18:10:35,139 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-09-29 18:10:35,151 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?)
[java] 2017-09-29 18:10:35,757 INFO hsqldb.db..ENGINE - open start - state not modified
[java] 2017-09-29 18:10:35,833 INFO hsqldb.db..ENGINE - dataFileCache open start
[java] 2017-09-29 18:10:35,873 INFO hsqldb.db..ENGINE - dataFileCache open end
[java] 2017-09-29 18:10:35,968 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-09-29 18:10:35,975 INFO hsqldb.db..ENGINE - dataFileCache commit start
[java] 2017-09-29 18:10:35,984 INFO hsqldb.db..ENGINE - dataFileCache commit end
[java] 2017-09-29 18:10:35,987 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/ytex390349184.sql
29 Sep 2017 18:10:36 INFO ENGINE - open start - state not modified
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache open start
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex390349184.sql
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache commit start
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache commit end
29 Sep 2017 18:10:36 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex390349184.sql
[delete] Deleting: /tmp/ytex640409561use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1545831116.sql
29 Sep 2017 18:10:36 INFO ENGINE - open start - state not modified
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache open start
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1545831116.sql
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache commit start
29 Sep 2017 18:10:36 INFO ENGINE - dataFileCache commit end
29 Sep 2017 18:10:36 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1545831116.sql
[delete] Deleting: /tmp/ytex462831259use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-09-29 18:10:37,970 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Fri Sep 29 18:10:37 UTC 2017]; root of context hierarchy
2017-09-29 18:10:38,049 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 18:10:38,253 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 18:10:38,264 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]]>
2017-09-29 18:10:38,289 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
2017-09-29 18:10:38,351 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Fri Sep 29 18:10:38 UTC 2017]; root of context hierarchy
2017-09-29 18:10:38,353 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-09-29 18:10:38,589 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-09-29 18:10:38,623 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-09-29 18:10:38,800 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-09-29 18:10:38,801 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 18:10:38,801 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-09-29 18:10:38,847 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
2017-09-29 18:10:38,903 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 18:10:39,774 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-09-29 18:10:39,780 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-09-29 18:10:39,782 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-09-29 18:10:39,789 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-09-29 18:10:40,552 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 18:10:40,676 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 18:10:40,688 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 18:10:43,098 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 18:10:43,346 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 18:10:46,126 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 18:10:46,283 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 18:10:46,330 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 18:10:46,330 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 18:10:46,365 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-09-29 18:10:46,481 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-09-29 18:10:46,485 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-09-29 18:10:46,662 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-09-29 18:10:46,666 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-09-29 18:10:47,431 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-09-29 18:10:47,666 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
2017-09-29 18:10:47,714 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 18:10:47,717 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 18:10:47,720 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 18:10:47,842 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: 10.202 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-09-29 18:10:48,582 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199: startup date [Fri Sep 29 18:10:48 UTC 2017]; root of context hierarchy
2017-09-29 18:10:48,650 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 18:10:48,877 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-09-29 18:10:48,885 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]]>
2017-09-29 18:10:48,907 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
2017-09-29 18:10:48,973 INFO org.springframework.context.support.ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup date [Fri Sep 29 18:10:48 UTC 2017]; root of context hierarchy
2017-09-29 18:10:48,975 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-09-29 18:10:49,214 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-09-29 18:10:49,244 INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-09-29 18:10:49,436 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-09-29 18:10:49,437 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 18:10:49,437 INFO org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-09-29 18:10:49,494 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
2017-09-29 18:10:49,549 INFO org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-09-29 18:10:50,369 INFO org.hibernate.annotations.common.Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-09-29 18:10:50,376 INFO org.hibernate.Version - HHH000412: Hibernate Core {4.2.6.Final}
2017-09-29 18:10:50,379 INFO org.hibernate.cfg.Environment - HHH000206: hibernate.properties not found
2017-09-29 18:10:50,381 INFO org.hibernate.cfg.Environment - HHH000021: Bytecode provider name : javassist
2017-09-29 18:10:51,324 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 18:10:51,413 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 18:10:51,425 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 18:10:51,527 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 18:10:51,528 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 18:10:51,531 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 18:10:51,667 INFO hsqldb.db..ENGINE - open start - state not modified
2017-09-29 18:10:51,734 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-09-29 18:10:51,735 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-09-29 18:10:51,782 INFO org.hibernate.dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-09-29 18:10:51,904 INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-09-29 18:10:51,909 INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
2017-09-29 18:10:52,107 INFO org.hibernate.cache.spi.UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-09-29 18:10:52,113 INFO org.hibernate.cache.internal.StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-09-29 18:10:52,898 INFO org.springframework.orm.hibernate4.HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager
2017-09-29 18:10:53,200 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
2017-09-29 18:10:53,223 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-09-29 18:10:53,224 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-09-29 18:10:53,228 INFO hsqldb.db..ENGINE - Database closed
2017-09-29 18:10:53,329 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: 5.048 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.69 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.571 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.459 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.767 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.621 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.769 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-09-29 18:11:01,914 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
2017-09-29 18:11:01,941 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.739 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 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: 0.116 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.621 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.635 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