See
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/9/display/redirect>
------------------------------------------
[...truncated 51.76 KB...]
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-02 21:38:08,028 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-10-02 21:38:08,038 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo
(site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2017-10-02 21:38:08,614 INFO hsqldb.db..ENGINE - open start -
state not modified
[java] 2017-10-02 21:38:08,717 INFO hsqldb.db..ENGINE - dataFileCache
open start
[java] 2017-10-02 21:38:08,741 INFO hsqldb.db..ENGINE - dataFileCache
open end
[java] 2017-10-02 21:38:08,796 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,797 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,798 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,799 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,800 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,801 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,803 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,804 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,805 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,806 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,808 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,809 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,810 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,811 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,812 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2017-10-02 21:38:08,813 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
[java] 2017-10-02 21:38:08,821 INFO hsqldb.db..ENGINE - dataFileCache
commit start
[java] 2017-10-02 21:38:08,826 INFO hsqldb.db..ENGINE - dataFileCache
commit end
[java] 2017-10-02 21:38:08,829 INFO hsqldb.db..ENGINE - Database closed
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex265782330.sql
02 Oct 2017 21:38:09 INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex265782330.sql
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:09 INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:09 INFO ENGINE - Database closed
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex265782330.sql
[delete] Deleting: /tmp/ytex1427625299use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-10-02 21:38:13,573 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-10-02 21:38:13,589 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword
(stopword) values (?)
[java] 2017-10-02 21:38:14,181 INFO hsqldb.db..ENGINE - open start -
state not modified
[java] 2017-10-02 21:38:14,262 INFO hsqldb.db..ENGINE - dataFileCache
open start
[java] 2017-10-02 21:38:14,288 INFO hsqldb.db..ENGINE - dataFileCache
open end
[java] 2017-10-02 21:38:14,385 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-10-02 21:38:14,400 INFO hsqldb.db..ENGINE - dataFileCache
commit start
[java] 2017-10-02 21:38:14,410 INFO hsqldb.db..ENGINE - dataFileCache
commit end
[java] 2017-10-02 21:38:14,413 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex824337993.sql
02 Oct 2017 21:38:14 INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex824337993.sql
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:15 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex824337993.sql
[delete] Deleting: /tmp/ytex1487798293use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex177981942.sql
02 Oct 2017 21:38:15 INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex177981942.sql
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:15 INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:15 INFO ENGINE - Database closed
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex177981942.sql
[delete] Deleting: /tmp/ytex621876601use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory:
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-10-02 21:38:16,266 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@2669b199:
startup date [Mon Oct 02 21:38:16 UTC 2017]; root of context hierarchy
2017-10-02 21:38:16,328 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:16,546 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:16,555 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Overriding bean definition for bean 'kernelApplicationContext': replacing
[Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-02 21:38:16,576 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-02 21:38:16,649 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@670002:
startup date [Mon Oct 02 21:38:16 UTC 2017]; root of context hierarchy
2017-10-02 21:38:16,651 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 21:38:16,884 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 21:38:16,916 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 21:38:17,118 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 21:38:17,119 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:17,119 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 21:38:17,162 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-10-02 21:38:17,206 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:18,134 INFO org.hibernate.annotations.common.Version -
HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 21:38:18,141 INFO org.hibernate.Version - HHH000412: Hibernate
Core {4.2.6.Final}
2017-10-02 21:38:18,144 INFO org.hibernate.cfg.Environment - HHH000206:
hibernate.properties not found
2017-10-02 21:38:18,146 INFO org.hibernate.cfg.Environment - HHH000021:
Bytecode provider name : javassist
2017-10-02 21:38:18,986 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-02 21:38:19,095 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:19,104 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:19,165 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:19,166 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:19,169 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:19,330 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-02 21:38:19,368 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:19,369 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:19,403 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 21:38:19,543 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 21:38:19,550 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2017-10-02 21:38:19,719 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 21:38:19,726 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2017-10-02 21:38:20,539 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate
SessionFactory for HibernateTransactionManager
2017-10-02 21:38:20,784 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-10-02 21:38:20,815 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:20,816 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:20,819 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:20,920 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.945 sec <<<
FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-02 21:38:21,720 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@2669b199:
startup date [Mon Oct 02 21:38:21 UTC 2017]; root of context hierarchy
2017-10-02 21:38:21,789 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:21,985 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:21,994 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Overriding bean definition for bean 'kernelApplicationContext': replacing
[Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-10-02 21:38:22,025 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-02 21:38:22,102 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@670002:
startup date [Mon Oct 02 21:38:22 UTC 2017]; root of context hierarchy
2017-10-02 21:38:22,105 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 21:38:22,332 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 21:38:22,368 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 21:38:22,583 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 21:38:22,584 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:22,584 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 21:38:22,647 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-10-02 21:38:22,705 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:23,557 INFO org.hibernate.annotations.common.Version -
HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2017-10-02 21:38:23,565 INFO org.hibernate.Version - HHH000412: Hibernate
Core {4.2.6.Final}
2017-10-02 21:38:23,568 INFO org.hibernate.cfg.Environment - HHH000206:
hibernate.properties not found
2017-10-02 21:38:23,574 INFO org.hibernate.cfg.Environment - HHH000021:
Bytecode provider name : javassist
2017-10-02 21:38:24,406 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-02 21:38:24,502 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:24,514 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:24,630 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:24,632 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:24,641 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:24,803 INFO hsqldb.db..ENGINE - open start - state not
modified
2017-10-02 21:38:24,852 INFO hsqldb.db..ENGINE - dataFileCache open start
2017-10-02 21:38:24,853 INFO hsqldb.db..ENGINE - dataFileCache open end
2017-10-02 21:38:24,903 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 21:38:25,017 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 21:38:25,023 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2017-10-02 21:38:25,196 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 21:38:25,200 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2017-10-02 21:38:25,928 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate
SessionFactory for HibernateTransactionManager
2017-10-02 21:38:26,231 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-10-02 21:38:26,243 INFO hsqldb.db..ENGINE - dataFileCache commit start
2017-10-02 21:38:26,245 INFO hsqldb.db..ENGINE - dataFileCache commit end
2017-10-02 21:38:26,248 INFO hsqldb.db..ENGINE - Database closed
2017-10-02 21:38:26,350 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.918 sec <<<
FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.754 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.713 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.388 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.607 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.573 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-02 21:38:34,320 INFO org.apache.ctakes.jdl.data.loader.CsvLoader -
delimiter 44 encapsulator 65534
2017-10-02 21:38:34,348 INFO org.apache.ctakes.jdl.data.loader.CsvLoader -
delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.547 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.594 sec
Results :
Tests in error:
testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to
initialize group definition. Group resource name
[classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key
[kernelApplicationContext]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating bean
with name 'kernelApplicationContext' defined in URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>:
Instantiation of bean failed; nested exception is
org.springframework.beans.BeanInstantiationException: Could not instantiate
bean class
[org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating bean
with name 'gramMatrixExporter' defined in class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
nested exception is org.springframework.beans.FatalBeanException: Failed to
obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between
read and write methods
testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to
initialize group definition. Group resource name
[classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key
[kernelApplicationContext]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating bean
with name 'kernelApplicationContext' defined in URL
[file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>:
Instantiation of bean failed; nested exception is
org.springframework.beans.BeanInstantiationException: Could not instantiate
bean class
[org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating bean
with name 'gramMatrixExporter' defined in class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
nested exception is org.springframework.beans.FatalBeanException: Failed to
obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between
read and write methods
Tests run: 36, Failures: 0, Errors: 2, Skipped: 4
[JENKINS] Recording test results
[JENKINS] Archiving disabled
