See
<https://builds.apache.org/job/ctakes-trunk-package/704/display/redirect?page=changes>
Changes:
[clin] Add section filter for CONTAINS multi-pass model evaluation:
EvaluationOfNeuralJointRelations
Add spaces around a newline character in the token sequence output, in order to
avoid cases like "newlineheight".
Add Classify.sh file
------------------------------------------
[...truncated 401.57 KB...]
A ctakes-drug-ner-res/src/test
A ctakes-drug-ner-res/LICENSE
A ctakes-ne-contexts-res
A ctakes-ne-contexts-res/pom.xml
A ctakes-ne-contexts-res/src
A ctakes-ne-contexts-res/src/main
A ctakes-ne-contexts-res/src/main/resources
A ctakes-ne-contexts-res/src/main/resources/org
A ctakes-ne-contexts-res/src/main/resources/org/apache
A ctakes-ne-contexts-res/src/main/resources/org/apache/ctakes
A ctakes-ne-contexts-res/src/main/resources/org/apache/ctakes/necontexts
A
ctakes-ne-contexts-res/src/main/resources/org/apache/ctakes/necontexts/pipeline
A
ctakes-ne-contexts-res/src/main/resources/org/apache/ctakes/necontexts/pipeline/NeContextsSubPipe.piper
A
ctakes-ne-contexts-res/src/main/resources/org/apache/ctakes/necontexts/desc
A
ctakes-ne-contexts-res/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml
A ctakes-ne-contexts-res/src/test
A ctakes-ne-contexts-res/LICENSE
A ctakes-pos-tagger-res
A ctakes-pos-tagger-res/pom.xml
A ctakes-pos-tagger-res/src
A ctakes-pos-tagger-res/src/main
A ctakes-pos-tagger-res/src/main/resources
A ctakes-pos-tagger-res/src/main/resources/org
A ctakes-pos-tagger-res/src/main/resources/org/apache
A ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes
A ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger
A
ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models
A
ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/clearnlp
AU
ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/clearnlp/mayo-en-pos-1.3.0.jar
AU
ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/mayo-pos.zip
A
ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/README
A ctakes-pos-tagger-res/src/test
A ctakes-pos-tagger-res/LICENSE
A ctakes-side-effect-res
A ctakes-side-effect-res/pom.xml
A ctakes-side-effect-res/src
A ctakes-side-effect-res/src/main
A ctakes-side-effect-res/src/main/resources
A ctakes-side-effect-res/src/main/resources/org
A ctakes-side-effect-res/src/main/resources/org/apache
A ctakes-side-effect-res/src/main/resources/org/apache/ctakes
A ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/lookup
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/classifier
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/classifier/libsvm_model_onWholeSet
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/data
A
ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/data/sentenceLevelMetaKeywords.txt
A ctakes-side-effect-res/src/test
A ctakes-side-effect-res/LICENSE
A ctakes-smoking-status-res
A ctakes-smoking-status-res/pom.xml
A ctakes-smoking-status-res/src
A ctakes-smoking-status-res/src/main
A ctakes-smoking-status-res/src/main/resources
A ctakes-smoking-status-res/src/main/resources/org
A ctakes-smoking-status-res/src/main/resources/org/apache
A ctakes-smoking-status-res/src/main/resources/org/apache/ctakes
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/boundaryData.txt
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/smoker.dictionary
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt
A
ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
A ctakes-smoking-status-res/src/test
A ctakes-smoking-status-res/LICENSE
A ctakes-template-filler
AU ctakes-template-filler/pom.xml
A ctakes-template-filler/desc
A ctakes-template-filler/desc/analysis_engine
AU
ctakes-template-filler/desc/analysis_engine/AggregateTemplateFiller.xml
AU
ctakes-template-filler/desc/analysis_engine/RelationExtractorAggregateWithoutOrangeBook.xml
AU
ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator.xml
A ctakes-template-filler/src
A ctakes-template-filler/src/main
A ctakes-template-filler/src/main/java
A ctakes-template-filler/src/main/java/org
A ctakes-template-filler/src/main/java/org/apache
A ctakes-template-filler/src/main/java/org/apache/ctakes
A ctakes-template-filler/src/main/java/org/apache/ctakes/template
A ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler
A
ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae
AU
ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
A ctakes-template-filler/src/main/resources
A ctakes-template-filler/src/test
A ctakes-template-filler/src/test/java
A ctakes-template-filler/src/test/resources
A README
AU KEYS
A NOTICE
A LICENSE
U .
At revision 1874488
Parsing POMs
ERROR: Failed to parse POMs
java.io.IOException: Remote call on H41 failed
at hudson.remoting.Channel.call(Channel.java:963)
at hudson.FilePath.act(FilePath.java:1072)
at hudson.FilePath.act(FilePath.java:1061)
at
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:987)
at
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:691)
at
hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:504)
at hudson.model.Run.execute(Run.java:1815)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
at hudson.model.ResourceController.execute(ResourceController.java:97)
at hudson.model.Executor.run(Executor.java:429)
Caused by: java.lang.InternalError: java.io.FileNotFoundException:
/usr/local/asfpackages/java/jdk1.8.0_191/jre/lib/jce.jar
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:1052)
at sun.misc.URLClassPath.getResource(URLClassPath.java:249)
at sun.misc.URLClassPath.getResource(URLClassPath.java:302)
at java.lang.ClassLoader.getBootstrapResource(ClassLoader.java:1264)
at java.lang.ClassLoader.getResource(ClassLoader.java:1093)
at java.lang.ClassLoader.getResource(ClassLoader.java:1091)
at java.lang.ClassLoader.getSystemResource(ClassLoader.java:1226)
at
javax.crypto.JceSecurity.setupJurisdictionPolicies(JceSecurity.java:312)
at javax.crypto.JceSecurity.access$000(JceSecurity.java:50)
at javax.crypto.JceSecurity$1.run(JceSecurity.java:85)
at java.security.AccessController.doPrivileged(Native Method)
at javax.crypto.JceSecurity.<clinit>(JceSecurity.java:82)
at javax.crypto.JceSecurityManager.<clinit>(JceSecurityManager.java:65)
at javax.crypto.Cipher.getConfiguredPermission(Cipher.java:2586)
at javax.crypto.Cipher.getMaxAllowedKeyLength(Cipher.java:2610)
at
sun.security.ssl.CipherSuite$BulkCipher.isUnlimited(CipherSuite.java:535)
at sun.security.ssl.CipherSuite$BulkCipher.<init>(CipherSuite.java:507)
at sun.security.ssl.CipherSuite.<clinit>(CipherSuite.java:614)
at
sun.security.ssl.SSLContextImpl.getApplicableCipherSuiteList(SSLContextImpl.java:294)
at sun.security.ssl.SSLContextImpl.access$100(SSLContextImpl.java:42)
at
sun.security.ssl.SSLContextImpl$AbstractTLSContext.<clinit>(SSLContextImpl.java:432)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at java.security.Provider$Service.getImplClass(Provider.java:1634)
at java.security.Provider$Service.newInstance(Provider.java:1592)
at sun.security.jca.GetInstance.getInstance(GetInstance.java:236)
at sun.security.jca.GetInstance.getInstance(GetInstance.java:164)
at javax.net.ssl.SSLContext.getInstance(SSLContext.java:156)
at javax.net.ssl.SSLContext.getDefault(SSLContext.java:96)
at javax.net.ssl.SSLSocketFactory.getDefault(SSLSocketFactory.java:122)
at
javax.net.ssl.HttpsURLConnection.getDefaultSSLSocketFactory(HttpsURLConnection.java:332)
at
org.apache.maven.wagon.shared.http.AbstractHttpClientWagon.createConnManager(AbstractHttpClientWagon.java:362)
at
org.apache.maven.wagon.shared.http.AbstractHttpClientWagon.<clinit>(AbstractHttpClientWagon.java:288)
at
org.apache.maven.wagon.providers.http.HttpWagon$__sisu20$$FastClassByGuice$$aa2b9cf5.newInstance(<generated>)
at
com.google.inject.internal.cglib.reflect.$FastConstructor.newInstance(FastConstructor.java:40)
at
com.google.inject.internal.DefaultConstructionProxyFactory$1.newInstance(DefaultConstructionProxyFactory.java:61)
at
com.google.inject.internal.ConstructorInjector.provision(ConstructorInjector.java:105)
at
com.google.inject.internal.ConstructorInjector.access$000(ConstructorInjector.java:32)
at
com.google.inject.internal.ConstructorInjector$1.call(ConstructorInjector.java:89)
at
com.google.inject.internal.ProvisionListenerStackCallback$Provision.provision(ProvisionListenerStackCallback.java:115)
at
com.google.inject.internal.ProvisionListenerStackCallback$Provision.provision(ProvisionListenerStackCallback.java:133)
at
com.google.inject.internal.ProvisionListenerStackCallback.provision(ProvisionListenerStackCallback.java:68)
at
com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:87)
at
com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:267)
at
com.google.inject.internal.InjectorImpl$2$1.call(InjectorImpl.java:1016)
at
com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1103)
at com.google.inject.internal.InjectorImpl$2.get(InjectorImpl.java:1012)
at
com.google.inject.internal.InjectorImpl.getInstance(InjectorImpl.java:1051)
at
org.eclipse.sisu.space.AbstractDeferredClass.get(AbstractDeferredClass.java:48)
at
com.google.inject.internal.ProviderInternalFactory.provision(ProviderInternalFactory.java:81)
at
com.google.inject.internal.InternalFactoryToInitializableAdapter.provision(InternalFactoryToInitializableAdapter.java:53)
at
com.google.inject.internal.ProviderInternalFactory$1.call(ProviderInternalFactory.java:65)
at
com.google.inject.internal.ProvisionListenerStackCallback$Provision.provision(ProvisionListenerStackCallback.java:115)
at
com.google.inject.internal.ProvisionListenerStackCallback$Provision.provision(ProvisionListenerStackCallback.java:133)
at
com.google.inject.internal.ProvisionListenerStackCallback.provision(ProvisionListenerStackCallback.java:68)
at
com.google.inject.internal.ProviderInternalFactory.circularGet(ProviderInternalFactory.java:63)
at
com.google.inject.internal.InternalFactoryToInitializableAdapter.get(InternalFactoryToInitializableAdapter.java:45)
at
com.google.inject.internal.InjectorImpl$2$1.call(InjectorImpl.java:1016)
at
com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1092)
at com.google.inject.internal.InjectorImpl$2.get(InjectorImpl.java:1012)
at org.eclipse.sisu.inject.Guice4$1.get(Guice4.java:162)
at org.eclipse.sisu.inject.LazyBeanEntry.getValue(LazyBeanEntry.java:81)
at
org.eclipse.sisu.plexus.LazyPlexusBean.getValue(LazyPlexusBean.java:51)
at
org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:263)
at
org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:255)
at
org.eclipse.aether.internal.transport.wagon.PlexusWagonProvider.lookup(PlexusWagonProvider.java:65)
at
org.eclipse.aether.transport.wagon.WagonTransporter.lookupWagon(WagonTransporter.java:279)
at
org.eclipse.aether.transport.wagon.WagonTransporter.<init>(WagonTransporter.java:123)
at
org.eclipse.aether.transport.wagon.WagonTransporterFactory.newInstance(WagonTransporterFactory.java:136)
at
org.eclipse.aether.internal.impl.DefaultTransporterProvider.newTransporter(DefaultTransporterProvider.java:113)
at
org.eclipse.aether.connector.basic.BasicRepositoryConnector.<init>(BasicRepositoryConnector.java:125)
at
org.eclipse.aether.connector.basic.BasicRepositoryConnectorFactory.newInstance(BasicRepositoryConnectorFactory.java:175)
at
org.eclipse.aether.internal.impl.DefaultRepositoryConnectorProvider.newRepositoryConnector(DefaultRepositoryConnectorProvider.java:116)
at
org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads(DefaultArtifactResolver.java:494)
at
org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:399)
at
org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:224)
at
org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:201)
at
org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveArtifact(DefaultRepositorySystem.java:260)
at
org.apache.maven.project.ProjectModelResolver.resolveModel(ProjectModelResolver.java:193)
at
org.apache.maven.project.ProjectModelResolver.resolveModel(ProjectModelResolver.java:243)
at
org.apache.maven.model.building.DefaultModelBuilder.readParentExternally(DefaultModelBuilder.java:1052)
at
org.apache.maven.model.building.DefaultModelBuilder.readParent(DefaultModelBuilder.java:830)
at
org.apache.maven.model.building.DefaultModelBuilder.build(DefaultModelBuilder.java:332)
at
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:432)
at
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:400)
at
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:363)
at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:370)
at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:340)
at
hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1329)
at
hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1126)
at hudson.FilePath$FileCallableWrapper.call(FilePath.java:3052)
at hudson.remoting.UserRequest.perform(UserRequest.java:212)
at hudson.remoting.UserRequest.perform(UserRequest.java:54)
at hudson.remoting.Request$2.run(Request.java:369)
at
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Suppressed: hudson.remoting.Channel$CallSiteStackTrace: Remote call to
H41
at
hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1743)
at
hudson.remoting.UserRequest$ExceptionResponse.retrieve(UserRequest.java:357)
at hudson.remoting.Channel.call(Channel.java:957)
at hudson.FilePath.act(FilePath.java:1072)
at hudson.FilePath.act(FilePath.java:1061)
at
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:987)
at
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:691)
at
hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:504)
at hudson.model.Run.execute(Run.java:1815)
at
hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
at
hudson.model.ResourceController.execute(ResourceController.java:97)
at hudson.model.Executor.run(Executor.java:429)
Caused by: java.io.FileNotFoundException:
/usr/local/asfpackages/java/jdk1.8.0_191/jre/lib/jce.jar
at sun.misc.URLClassPath$JarLoader.getJarFile(URLClassPath.java:938)
at sun.misc.URLClassPath$JarLoader.access$800(URLClassPath.java:801)
at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:886)
at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:879)
at java.security.AccessController.doPrivileged(Native Method)
at sun.misc.URLClassPath$JarLoader.ensureOpen(URLClassPath.java:878)
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:1050)
... 98 more
