ctakes-notifications mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #4
Date Fri, 29 Sep 2017 18:12:24 GMT
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

Mime
View raw message