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
