See
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/15/display/redirect?page=changes>
Changes:
[seanfinan] Set document count in patient note store
[seanfinan] patient store, etc. use total doc count instead of previous/next
------------------------------------------
[...truncated 780.80 KB...]
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p
%c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
24 Oct 2017 20:17:37 INFO LvgAnnotator - URL for lvg.properties
=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
24 Oct 2017 20:17:39 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
24 Oct 2017 20:17:39 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:17:39 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
jar: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
24 Oct 2017 20:17:39 INFO LvgCmdApiResourceImpl - config file absolute path
=
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/jar>: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
24 Oct 2017 20:17:39 INFO LvgCmdApiResourceImpl - cwd =
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:17:39 INFO LvgCmdApiResourceImpl - cd
jar: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/
** Configuration Error:
jar: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:
'jar: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.
** Configuration Error:
jar: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:
'jar: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.
24 Oct 2017 20:17:39 INFO LvgCmdApiResourceImpl - cd
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:17:39 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
24 Oct 2017 20:17:39 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
24 Oct 2017 20:17:58 INFO ClearNLPDependencyParserAE - Initializing ClearNLP
dependency parser, using lemmatizer: true
24 Oct 2017 20:18:00 INFO SentenceDetector - Starting processing.
24 Oct 2017 20:18:00 INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:00 INFO LvgAnnotator - process(JCas)
24 Oct 2017 20:18:00 INFO ContextDependentTokenizerAnnotator - process(JCas)
24 Oct 2017 20:18:00 INFO POSTagger - process(JCas)
24 Oct 2017 20:18:00 INFO ClearNLPDependencyParserAE - Dependency parser
starting with thread:main
24 Oct 2017 20:18:00 INFO ClearNLPDependencyParserAE - Dependency parser
ending with thread:main
24 Oct 2017 20:18:01 INFO EventTimeRelationAnnotatorTest - Relation:
RelationArgument
id: 0
argument: TimeMention
sofa: _InitialView
begin: 58
end: 66
id: 0
ontologyConceptArr: <null>
typeID: 0
segmentID: <null>
sentenceID: <null>
discoveryTechnique: 0
confidence: 0.0
polarity: 0
uncertainty: 0
conditional: false
generic: false
subject: <null>
historyOf: 0
originalText: <null>
date: <null>
time: <null>
timeClass: "DATE"
role: "Arg1"
participatesIn: <null>
RelationArgument
id: 0
argument: EventMention
sofa: _InitialView
begin: 67
end: 76
id: 0
ontologyConceptArr: <null>
typeID: 0
segmentID: <null>
sentenceID: <null>
discoveryTechnique: 0
confidence: 1.3807402
polarity: 0
uncertainty: 0
conditional: false
generic: false
subject: <null>
historyOf: 0
originalText: <null>
event: Event
id: 0
ontologyConcept: <null>
mentions: <null>
discoveryTechnique: 0
confidence: 0.0
conditional: false
generic: false
subject: <null>
polarity: 0
uncertainty: 0
historyOf: 0
properties: EventProperties
contextualModality: <null>
contextualAspect: <null>
permanence: <null>
category: <null>
aspect: <null>
docTimeRel: <null>
degree: <null>
polarity: 0
role: "Arg2"
participatesIn: <null>
Category: CONTAINS
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 26.761 sec
Running org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest
24 Oct 2017 20:18:01 INFO LvgAnnotator - URL for lvg.properties
=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
24 Oct 2017 20:18:02 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
24 Oct 2017 20:18:02 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:02 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
jar: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
24 Oct 2017 20:18:02 INFO LvgCmdApiResourceImpl - config file absolute path
=
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/jar>: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
24 Oct 2017 20:18:02 INFO LvgCmdApiResourceImpl - cwd =
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:02 INFO LvgCmdApiResourceImpl - cd
jar: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/
** Configuration Error:
jar: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:
'jar: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.
** Configuration Error:
jar: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:
'jar: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.
24 Oct 2017 20:18:02 INFO LvgCmdApiResourceImpl - cd
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:02 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
24 Oct 2017 20:18:02 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
24 Oct 2017 20:18:16 INFO ClearNLPDependencyParserAE - Initializing ClearNLP
dependency parser, using lemmatizer: true
24 Oct 2017 20:18:19 INFO SentenceDetector - Starting processing.
24 Oct 2017 20:18:19 INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:19 INFO LvgAnnotator - process(JCas)
24 Oct 2017 20:18:19 INFO ContextDependentTokenizerAnnotator - process(JCas)
24 Oct 2017 20:18:19 INFO POSTagger - process(JCas)
24 Oct 2017 20:18:19 INFO ClearNLPDependencyParserAE - Dependency parser
starting with thread:main
24 Oct 2017 20:18:19 INFO ClearNLPDependencyParserAE - Dependency parser
ending with thread:main
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.495 sec
Running org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest
24 Oct 2017 20:18:19 INFO LvgAnnotator - URL for lvg.properties
=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
24 Oct 2017 20:18:21 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
24 Oct 2017 20:18:21 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:21 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
jar: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
24 Oct 2017 20:18:21 INFO LvgCmdApiResourceImpl - config file absolute path
=
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/jar>: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
24 Oct 2017 20:18:21 INFO LvgCmdApiResourceImpl - cwd =
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:21 INFO LvgCmdApiResourceImpl - cd
jar: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/
** Configuration Error:
jar: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:
'jar: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.
** Configuration Error:
jar: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:
'jar: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.
24 Oct 2017 20:18:21 INFO LvgCmdApiResourceImpl - cd
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:21 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
24 Oct 2017 20:18:21 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
24 Oct 2017 20:24:01 INFO ClearNLPDependencyParserAE - Initializing ClearNLP
dependency parser, using lemmatizer: true
Results :
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: Failed to parse POMs
java.io.IOException: Backing channel 'ubuntu-us1' is disconnected.
at
hudson.remoting.RemoteInvocationHandler.channelOrFail(RemoteInvocationHandler.java:192)
at
hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:257)
at com.sun.proxy.$Proxy129.isAlive(Unknown Source)
at hudson.Launcher$RemoteLauncher$ProcImpl.isAlive(Launcher.java:1138)
at hudson.maven.ProcessCache$MavenProcess.call(ProcessCache.java:166)
at
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:879)
at
hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:496)
at hudson.model.Run.execute(Run.java:1737)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
at hudson.model.ResourceController.execute(ResourceController.java:97)
at hudson.model.Executor.run(Executor.java:419)
Caused by: hudson.remoting.Channel$OrderlyShutdown
at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1138)
at hudson.remoting.Channel$1.handle(Channel.java:535)
at
hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:83)
Caused by: Command close created at
at hudson.remoting.Command.<init>(Command.java:60)
at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1132)
at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1130)
at hudson.remoting.Channel.close(Channel.java:1290)
at hudson.remoting.Channel.close(Channel.java:1272)
at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1137)
... 2 more
FATAL: channel is already closed
Command close created at
at hudson.remoting.Command.<init>(Command.java:60)
at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1132)
at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1130)
at hudson.remoting.Channel.close(Channel.java:1290)
at hudson.remoting.Channel.close(Channel.java:1272)
at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1137)
Caused: hudson.remoting.Channel$OrderlyShutdown
at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1138)
at hudson.remoting.Channel$1.handle(Channel.java:535)
at
hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:83)
Caused: hudson.remoting.ChannelClosedException: channel is already closed
at hudson.remoting.Channel.send(Channel.java:613)
at hudson.remoting.Request.call(Request.java:130)
at hudson.remoting.Channel.call(Channel.java:838)
at hudson.Launcher$RemoteLauncher.kill(Launcher.java:1079)
at
hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:502)
at hudson.model.Run.execute(Run.java:1737)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
at hudson.model.ResourceController.execute(ResourceController.java:97)
at hudson.model.Executor.run(Executor.java:419)
