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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX UIMA #26
Date Wed, 15 Nov 2017 02:05:55 GMT
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/26/display/redirect>

------------------------------------------
[...truncated 209.65 KB...]
2017-11-15 01:56:47,625 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveDocument
2017-11-15 01:56:47,629 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnotationsHib
2017-11-15 01:56:47,629 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoBaseHib
2017-11-15 01:56:47,636 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoBaseHib
2017-11-15 01:56:47,636 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin insertAnnotationContainmentLinks
2017-11-15 01:56:47,639 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end insertAnnotationContainmentLinks
2017-11-15 01:56:47,639 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,639 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,640 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,640 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,640 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,640 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,641 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,641 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,641 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,642 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,642 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoLinks
2017-11-15 01:56:47,642 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoLinks
2017-11-15 01:56:47,643 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnotationsHib
2017-11-15 01:56:47,644 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveDocument
2017-11-15 01:56:47,645 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=27}
2017-11-15 01:56:47,650 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - segmentsAdded: 0
2017-11-15 01:56:47,650 INFO  org.apache.ctakes.ytex.uima.annotators.SentenceDetector  - Starting
processing.
2017-11-15 01:56:47,651 INFO  org.apache.ctakes.core.ae.TokenizerAnnotatorPTB  - process(JCas)
in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
2017-11-15 01:56:47,654 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveDocument
2017-11-15 01:56:47,657 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnotationsHib
2017-11-15 01:56:47,657 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoBaseHib
2017-11-15 01:56:47,662 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoBaseHib
2017-11-15 01:56:47,662 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin insertAnnotationContainmentLinks
2017-11-15 01:56:47,665 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end insertAnnotationContainmentLinks
2017-11-15 01:56:47,665 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,665 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,666 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,666 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,666 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,666 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,666 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,666 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,667 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,669 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,670 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoLinks
2017-11-15 01:56:47,670 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoLinks
2017-11-15 01:56:47,670 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnotationsHib
2017-11-15 01:56:47,697 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveDocument
2017-11-15 01:56:47,697 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=28}
2017-11-15 01:56:47,699 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - segmentsAdded: 0
2017-11-15 01:56:47,699 INFO  org.apache.ctakes.ytex.uima.annotators.SentenceDetector  - Starting
processing.
2017-11-15 01:56:47,700 INFO  org.apache.ctakes.core.ae.TokenizerAnnotatorPTB  - process(JCas)
in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
2017-11-15 01:56:47,706 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveDocument
2017-11-15 01:56:47,710 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnotationsHib
2017-11-15 01:56:47,710 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoBaseHib
2017-11-15 01:56:47,721 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoBaseHib
2017-11-15 01:56:47,722 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin insertAnnotationContainmentLinks
2017-11-15 01:56:47,728 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end insertAnnotationContainmentLinks
2017-11-15 01:56:47,729 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,729 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,729 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,729 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,730 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,730 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,730 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,730 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,730 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,733 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,733 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoLinks
2017-11-15 01:56:47,734 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoLinks
2017-11-15 01:56:47,734 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnotationsHib
2017-11-15 01:56:47,737 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveDocument
2017-11-15 01:56:47,738 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=29}
2017-11-15 01:56:47,739 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - segmentsAdded: 0
2017-11-15 01:56:47,739 INFO  org.apache.ctakes.ytex.uima.annotators.SentenceDetector  - Starting
processing.
2017-11-15 01:56:47,740 INFO  org.apache.ctakes.core.ae.TokenizerAnnotatorPTB  - process(JCas)
in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
2017-11-15 01:56:47,741 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveDocument
2017-11-15 01:56:47,745 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnotationsHib
2017-11-15 01:56:47,745 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoBaseHib
2017-11-15 01:56:47,749 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoBaseHib
2017-11-15 01:56:47,749 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin insertAnnotationContainmentLinks
2017-11-15 01:56:47,751 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end insertAnnotationContainmentLinks
2017-11-15 01:56:47,751 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,751 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,752 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,752 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,752 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,752 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,752 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,754 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,754 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoLinks
2017-11-15 01:56:47,754 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoLinks
2017-11-15 01:56:47,754 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnotationsHib
2017-11-15 01:56:47,756 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveDocument
2017-11-15 01:56:47,757 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=30}
2017-11-15 01:56:47,758 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - segmentsAdded: 0
2017-11-15 01:56:47,758 INFO  org.apache.ctakes.ytex.uima.annotators.SentenceDetector  - Starting
processing.
2017-11-15 01:56:47,760 INFO  org.apache.ctakes.core.ae.TokenizerAnnotatorPTB  - process(JCas)
in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
2017-11-15 01:56:47,764 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveDocument
2017-11-15 01:56:47,769 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnotationsHib
2017-11-15 01:56:47,769 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoBaseHib
2017-11-15 01:56:47,784 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoBaseHib
2017-11-15 01:56:47,784 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin insertAnnotationContainmentLinks
2017-11-15 01:56:47,793 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end insertAnnotationContainmentLinks
2017-11-15 01:56:47,794 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,794 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,794 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,795 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,795 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,795 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,796 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,796 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,796 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoPrimitive
2017-11-15 01:56:47,801 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoPrimitive
2017-11-15 01:56:47,801 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - begin saveAnnoLinks
2017-11-15 01:56:47,802 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnoLinks
2017-11-15 01:56:47,802 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveAnnotationsHib
2017-11-15 01:56:47,805 TRACE org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - end saveDocument
temp dir: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/./target/SparseDataExporterTest-1510710997552/sparsematrix>
temp dir: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/./target/SparseDataExporterTest-1510710997552/weka>
temp dir: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/./target/SparseDataExporterTest-1510710997552/libsvm>
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.624 sec
Running org.apache.ctakes.ytex.uima.annotators.SegmentRegexTest
2017-11-15 01:56:48,766 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - SegmentRegex [regex=(?i)title:\s*(.*)\n, segmentID=TITLE, segmentRegexID=1]
2017-11-15 01:56:48,768 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - SegmentRegex [regex=(?i)history:, segmentID=HISTORY, segmentRegexID=2]
2017-11-15 01:56:49,847 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - applying regex:(?i)title:\s*(.*)\n
2017-11-15 01:56:49,848 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - found match: id=TITLE, begin=7
2017-11-15 01:56:49,848 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - applying regex:(?i)history:
2017-11-15 01:56:49,848 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - found match: id=HISTORY, begin=100
2017-11-15 01:56:49,848 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - segmentsAdded: 2
2017-11-15 01:56:49,849 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - Adding Segment: segment id=TITLE, begin=7, end=29
2017-11-15 01:56:49,849 DEBUG org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
 - Adding Segment: segment id=HISTORY, begin=100, end=125
DEFAULT [Title:]
TITLE [US Left Upper Quadrant]
DEFAULT [
Dr. Doolitle asked patient
to take a deep breath
and exhale slowly.  ]
HISTORY [History: Patient coughed.]
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.281 sec
Running org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexTest
2017-11-15 01:56:50,482 DEBUG org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
 - NamedEntityRegex [code=C00TEST, regex=(?i)COUGH]
[cough]
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.219 sec
Running org.apache.ctakes.ytex.uima.annotators.DBCollectionReaderTest
2017-11-15 01:56:52,857 INFO  org.apache.ctakes.ytex.uima.ApplicationContextHolder  - loading
ytex.properties from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/ytex.properties>
2017-11-15 01:56:52,859 INFO  org.apache.ctakes.ytex.uima.ApplicationContextHolder  - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
2017-11-15 01:56:52,930 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@47af7f3d:
startup date [Wed Nov 15 01:56:52 UTC 2017]; root of context hierarchy
2017-11-15 01:56:53,001 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [jar:file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
2017-11-15 01:56:53,075 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]
2017-11-15 01:56:53,086 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Overriding bean definition for bean 'ytexApplicationContext': 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:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/uima/beanRefContext.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:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
2017-11-15 01:56:53,116 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5f683daf:
defining beans [ytexApplicationContext]; root of factory hierarchy
2017-11-15 01:56:53,189 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@6283d8b8:
startup date [Wed Nov 15 01:56:53 UTC 2017]; root of context hierarchy
2017-11-15 01:56:53,193 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-15 01:56:53,461 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-15 01:56:53,559 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xml]
2017-11-15 01:56:53,587 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
2017-11-15 01:56:53,613 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
2017-11-15 01:56:53,637 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
2017-11-15 01:56:53,668 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Overriding bean definition for bean 'mapperOperation': replacing [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut];
scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true;
primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
with [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true;
primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2017-11-15 01:56:53,803 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-15 01:56:53,803 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-15 01:56:53,804 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-15 01:56:53,847 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5167f57d:
defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,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,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService];
root of factory hierarchy
2017-11-15 01:56:53,893 INFO  org.springframework.beans.factory.config.PropertiesFactoryBean
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-15 01:56:54,653 INFO  org.hibernate.annotations.common.Version  - HCANN000001: Hibernate
Commons Annotations {4.0.2.Final}
2017-11-15 01:56:54,660 INFO  org.hibernate.Version  - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-15 01:56:54,662 INFO  org.hibernate.cfg.Environment  - HHH000206: hibernate.properties
not found
2017-11-15 01:56:54,665 INFO  org.hibernate.cfg.Environment  - HHH000021: Bytecode provider
name : javassist
2017-11-15 01:56:55,534 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache open start
2017-11-15 01:56:55,546 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache open end
2017-11-15 01:56:55,906 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - checkpointClose start
2017-11-15 01:56:55,976 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache commit start
2017-11-15 01:56:56,361 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache commit end
2017-11-15 01:56:56,411 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - checkpointClose end
2017-11-15 01:56:56,564 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache commit start
2017-11-15 01:56:56,597 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache commit end
2017-11-15 01:56:56,666 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - Database closed
2017-11-15 01:56:56,823 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache open start
2017-11-15 01:56:56,824 INFO  hsqldb.db.HSQLDB5FBD635293.ENGINE  - dataFileCache open end
2017-11-15 01:56:56,898 INFO  org.hibernate.dialect.Dialect  - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-15 01:56:57,063 WARN  org.hibernate.mapping.RootClass  - HHH000038: Composite-id class
does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
2017-11-15 01:56:57,063 WARN  org.hibernate.mapping.RootClass  - HHH000039: Composite-id class
does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
2017-11-15 01:56:57,069 INFO  org.hibernate.engine.transaction.internal.TransactionFactoryInitiator
 - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-15 01:56:57,075 INFO  org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory  -
HHH000397: Using ASTQueryTranslatorFactory
2017-11-15 01:56:57,266 INFO  org.hibernate.cache.spi.UpdateTimestampsCache  - HHH000250:
Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-15 01:56:57,272 INFO  org.hibernate.cache.internal.StandardQueryCache  - HHH000248:
Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-15 01:56:57,287 INFO  org.hibernate.id.enhanced.TableGenerator  - HHH000398: Explicit
segment value for id generator [PUBLIC.hibernate_sequences.sequence_name] suggested; using
default [default]
2017-11-15 01:56:57,499 WARN  org.hibernate.cache.ehcache.AbstractEhcacheRegionFactory  -
HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType];
using defaults.
2017-11-15 01:56:57,501 WARN  org.hibernate.cache.ehcache.internal.strategy.EhcacheAccessStrategyFactoryImpl
 - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
2017-11-15 01:56:58,134 INFO  org.springframework.orm.hibernate4.HibernateTransactionManager
 - Using DataSource [org.apache.commons.dbcp.BasicDataSource@6b0615ae] of Hibernate SessionFactory
for HibernateTransactionManager
2017-11-15 01:56:58,544 INFO  org.springframework.cache.ehcache.EhCacheManagerFactoryBean
 - Initializing EHCache CacheManager
2017-11-15 01:56:58,559 WARN  net.sf.ehcache.CacheManager  - Creating a new instance of CacheManager
using the diskStorePath "/tmp" which is already used by an existing CacheManager.
The source of the configuration was net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@129bd55d.
The diskStore path for this CacheManager will be set to /tmp/ehcache_auto_created_1510711018559.
To avoid this warning consider using the CacheManager factory methods to create a singleton
CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager
instance.
2017-11-15 01:56:59,098 INFO  org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
 - begin initialization for concept graph: sct-rxnorm
2017-11-15 01:56:59,190 INFO  org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl  - could not
load conceptGraph from classpath, attempt to load from: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz>
2017-11-15 01:56:59,191 INFO  org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl  - <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz>
not found, cannot load concept graph
2017-11-15 01:56:59,191 INFO  org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl  - could not
load conceptGraph: sct-rxnorm
2017-11-15 01:56:59,243 WARN  org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
 - concept graph null, name: sct-rxnorm
2017-11-15 01:56:59,243 INFO  org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
 - end initialization for concept graph: sct-rxnorm
2017-11-15 01:56:59,624 INFO  org.hibernate.dialect.Dialect  - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-15 01:56:59,845 INFO  org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - document table name = PUBLIC.document
2017-11-15 01:56:59,849 DEBUG org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
 - docTableCols: {}
2017-11-15 01:57:00,333 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=0}
2017-11-15 01:57:00,353 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=1}
2017-11-15 01:57:00,356 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=2}
2017-11-15 01:57:00,357 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=3}
2017-11-15 01:57:00,358 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=4}
2017-11-15 01:57:00,359 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=5}
2017-11-15 01:57:00,361 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=6}
2017-11-15 01:57:00,363 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=7}
2017-11-15 01:57:00,365 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=8}
2017-11-15 01:57:00,367 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=9}
2017-11-15 01:57:00,369 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=10}
2017-11-15 01:57:00,370 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=11}
2017-11-15 01:57:00,372 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=12}
2017-11-15 01:57:00,374 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=13}
2017-11-15 01:57:00,376 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=14}
2017-11-15 01:57:00,378 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=15}
2017-11-15 01:57:00,381 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=16}
2017-11-15 01:57:00,383 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=17}
2017-11-15 01:57:00,385 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=18}
2017-11-15 01:57:00,387 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=19}
2017-11-15 01:57:00,388 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=20}
2017-11-15 01:57:00,401 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=21}
2017-11-15 01:57:00,403 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=22}
2017-11-15 01:57:00,404 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=23}
2017-11-15 01:57:00,405 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=24}
2017-11-15 01:57:00,407 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=25}
2017-11-15 01:57:00,408 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=26}
2017-11-15 01:57:00,410 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=27}
2017-11-15 01:57:00,411 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=28}
2017-11-15 01:57:00,412 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=29}
2017-11-15 01:57:00,414 INFO  org.apache.ctakes.ytex.uima.DBCollectionReader  - loading document
with id = {INSTANCE_ID=30}
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.505 sec
Running org.apache.ctakes.ytex.tools.SetupAuiFirstWordTest
2017-11-15 01:57:01,308 WARN  org.apache.ctakes.ytex.tools.SetupAuiFirstWord  - classpath:ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml
not available, attempting to load from file system
2017-11-15 01:57:01,492 INFO  org.apache.ctakes.ytex.tools.SetupAuiFirstWord  - loading lvg.properties
from:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
** Configuration Error: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/file>:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: '<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex-uima/ws/file>:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg//file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
UmlsAuiFirstWord [aui=1tok, fword=heart]
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.4 sec

Results :

Failed tests:   testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest)

Tests run: 13, Failures: 1, Errors: 0, Skipped: 0

[JENKINS] Recording test results
[JENKINS] Archiving disabled

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