See
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/16/display/redirect>
------------------------------------------
[...truncated 52.85 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] 2017-10-25 17:18:26,807 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-25 17:18:26,814 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo
(site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-25 17:18:27,488 INFO hsqldb.db..ENGINE - open start -
state not modified
[java] 2017-10-25 17:18:27,593 INFO hsqldb.db..ENGINE - dataFileCache
open start
[java] 2017-10-25 17:18:27,624 INFO hsqldb.db..ENGINE - dataFileCache
open end
[java] 2017-10-25 17:18:27,683 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,685 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,686 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,687 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,688 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,689 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,690 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,692 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,693 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,693 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,695 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,697 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,699 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,700 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,701 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-25 17:18:27,721 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-25 17:18:27,758 INFO hsqldb.db..ENGINE - dataFileCache
commit start
[java] 2017-10-25 17:18:27,766 INFO hsqldb.db..ENGINE - dataFileCache
commit end
[java] 2017-10-25 17:18:27,769 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/ytex388609511.sql
25 Oct 2017 17:18:28 INFO ENGINE - open start - state not modified
25 Oct 2017 17:18:28 INFO ENGINE - dataFileCache open start
25 Oct 2017 17:18:28 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex388609511.sql
25 Oct 2017 17:18:28 INFO ENGINE - dataFileCache commit start
25 Oct 2017 17:18:28 INFO ENGINE - dataFileCache commit end
25 Oct 2017 17:18:28 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex388609511.sql
[delete] Deleting: /tmp/ytex1962777733use.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] 2017-10-25 17:18:32,773 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-25 17:18:32,783 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword
(stopword) values (?)
[java] 2017-10-25 17:18:33,447 INFO hsqldb.db..ENGINE - open start -
state not modified
[java] 2017-10-25 17:18:33,521 INFO hsqldb.db..ENGINE - dataFileCache
open start
[java] 2017-10-25 17:18:33,545 INFO hsqldb.db..ENGINE - dataFileCache
open end
[java] 2017-10-25 17:18:33,639 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-25 17:18:33,651 INFO hsqldb.db..ENGINE - dataFileCache
commit start
[java] 2017-10-25 17:18:33,661 INFO hsqldb.db..ENGINE - dataFileCache
commit end
[java] 2017-10-25 17:18:33,664 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/ytex1378878255.sql
25 Oct 2017 17:18:34 INFO ENGINE - open start - state not modified
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache open start
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1378878255.sql
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache commit start
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache commit end
25 Oct 2017 17:18:34 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1378878255.sql
[delete] Deleting: /tmp/ytex349576933use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex932595007.sql
25 Oct 2017 17:18:34 INFO ENGINE - open start - state not modified
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache open start
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex932595007.sql
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache commit start
25 Oct 2017 17:18:34 INFO ENGINE - dataFileCache commit end
25 Oct 2017 17:18:34 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex932595007.sql
[delete] Deleting: /tmp/ytex2105463793use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory:
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-25 17:18:35,754 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@2669b199:
startup date [Wed Oct 25 17:18:35 UTC 2017]; root of context hierarchy
2017-10-25 17:18:35,816 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-25 17:18:35,989 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-25 17:18:35,999 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]]>
2017-10-25 17:18:36,021 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
2017-10-25 17:18:36,084 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@670002:
startup date [Wed Oct 25 17:18:36 UTC 2017]; root of context hierarchy
2017-10-25 17:18:36,086 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-25 17:18:36,302 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-25 17:18:36,327 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-25 17:18:36,500 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2017-10-25 17:18:36,501 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-25 17:18:36,501 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-25 17:18:36,540 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
2017-10-25 17:18:36,582 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-25 17:18:37,357 INFO org.hibernate.annotations.common.Version -
HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-25 17:18:37,362 INFO org.hibernate.Version - HHH000412: Hibernate
Core {4.2.6.Final}
2017-10-25 17:18:37,364 INFO org.hibernate.cfg.Environment - HHH000206:
hibernate.properties not found
2017-10-25 17:18:37,366 INFO org.hibernate.cfg.Environment - HHH000021:
Bytecode provider name : javassist
2017-10-25 17:18:38,173 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-25 17:18:38,259 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-25 17:18:38,284 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-25 17:18:38,355 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-25 17:18:38,356 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-25 17:18:38,360 INFO hsqldb.db..ENGINE - Database closed
2017-10-25 17:18:38,503 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-25 17:18:38,551 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-25 17:18:38,551 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-25 17:18:38,590 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2017-10-25 17:18:38,709 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-25 17:18:38,715 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2017-10-25 17:18:38,899 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-25 17:18:38,905 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2017-10-25 17:18:39,793 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate
SessionFactory for HibernateTransactionManager
2017-10-25 17:18:40,048 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
2017-10-25 17:18:40,069 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-25 17:18:40,070 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-25 17:18:40,072 INFO hsqldb.db..ENGINE - Database closed
2017-10-25 17:18:40,174 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: 4.677 sec <<<
FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-25 17:18:40,850 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@2669b199:
startup date [Wed Oct 25 17:18:40 UTC 2017]; root of context hierarchy
2017-10-25 17:18:40,914 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-25 17:18:41,114 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-25 17:18:41,125 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]]>
2017-10-25 17:18:41,143 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
2017-10-25 17:18:41,214 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@670002:
startup date [Wed Oct 25 17:18:41 UTC 2017]; root of context hierarchy
2017-10-25 17:18:41,217 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-25 17:18:41,422 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-25 17:18:41,454 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-25 17:18:41,638 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2017-10-25 17:18:41,639 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-25 17:18:41,640 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-25 17:18:41,677 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
2017-10-25 17:18:41,724 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-25 17:18:42,500 INFO org.hibernate.annotations.common.Version -
HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-25 17:18:42,506 INFO org.hibernate.Version - HHH000412: Hibernate
Core {4.2.6.Final}
2017-10-25 17:18:42,508 INFO org.hibernate.cfg.Environment - HHH000206:
hibernate.properties not found
2017-10-25 17:18:42,510 INFO org.hibernate.cfg.Environment - HHH000021:
Bytecode provider name : javassist
2017-10-25 17:18:43,344 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-25 17:18:43,448 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-25 17:18:43,466 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-25 17:18:43,568 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-25 17:18:43,569 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-25 17:18:43,572 INFO hsqldb.db..ENGINE - Database closed
2017-10-25 17:18:43,735 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-25 17:18:43,779 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-25 17:18:43,780 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-25 17:18:43,847 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2017-10-25 17:18:43,980 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-25 17:18:43,985 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2017-10-25 17:18:44,160 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-25 17:18:44,165 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2017-10-25 17:18:45,051 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate
SessionFactory for HibernateTransactionManager
2017-10-25 17:18:45,368 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
2017-10-25 17:18:45,399 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-25 17:18:45,401 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-25 17:18:45,405 INFO hsqldb.db..ENGINE - Database closed
2017-10-25 17:18:45,506 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: 4.941 sec <<<
FAILURE!
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.197 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.548 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.679 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-25 17:18:50,671 INFO org.apache.ctakes.jdl.data.loader.CsvLoader -
delimiter 44 encapsulator 65534
2017-10-25 17:18:50,701 INFO org.apache.ctakes.jdl.data.loader.CsvLoader -
delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.722 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.702 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.748 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.698 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.727 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.463 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.281 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.535 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
