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
