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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: cTAKES-trunk » Apache cTAKES YTEX #3
Date Thu, 28 Sep 2017 23:01:23 GMT
See <https://builds.apache.org/job/cTAKES-trunk/org.apache.ctakes$ctakes-ytex/3/display/redirect>

------------------------------------------
[...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

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