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From "Alex Zbarcea (JIRA)" <j...@apache.org>
Subject [jira] [Resolved] (CTAKES-479) RegressionPipelineTest.testCPE fails because of unavailable UMLS credentials
Date Sat, 18 Nov 2017 01:25:00 GMT

     [ https://issues.apache.org/jira/browse/CTAKES-479?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Alex Zbarcea resolved CTAKES-479.
---------------------------------
       Resolution: Fixed
    Fix Version/s: 4.0.1

> RegressionPipelineTest.testCPE fails because of unavailable UMLS credentials
> ----------------------------------------------------------------------------
>
>                 Key: CTAKES-479
>                 URL: https://issues.apache.org/jira/browse/CTAKES-479
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-regression-test
>    Affects Versions: 4.0.0
>            Reporter: Alex Zbarcea
>            Assignee: Alex Zbarcea
>             Fix For: 4.0.1
>
>         Attachments: testCPE.CTAKES-479.svn.patch
>
>
> stacktrace:
> https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/lastBuild/org.apache.ctakes$ctakes-regression-test/testReport/org.apache.ctakes.regression.test/RegressionPipelineTest/testCPE/
> {code}
> org.apache.uima.resource.ResourceInitializationException: Initialization of CAS Processor
with name "RegressionPipelineAggregateTest" failed.  
> 	at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:81)
> 	at org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
> 	at org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:918)
> 	at org.apache.ctakes.regression.test.RegressionPipelineTest.testCPE(RegressionPipelineTest.java:101)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:498)
> 	at junit.framework.TestCase.runTest(TestCase.java:176)
> 	at junit.framework.TestCase.runBare(TestCase.java:141)
> 	at junit.framework.TestResult$1.protect(TestResult.java:122)
> 	at junit.framework.TestResult.runProtected(TestResult.java:142)
> 	at junit.framework.TestResult.run(TestResult.java:125)
> 	at junit.framework.TestCase.run(TestCase.java:129)
> 	at junit.framework.TestSuite.runTest(TestSuite.java:255)
> 	at junit.framework.TestSuite.run(TestSuite.java:250)
> 	at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:84)
> 	at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249)
> 	at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142)
> 	at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:498)
> 	at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
> 	at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
> 	at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
> 	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104)
> 	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
> Caused by: org.apache.uima.resource.ResourceConfigurationException: Initialization of
CAS Processor with name "RegressionPipelineAggregateTest" failed.  
> 	at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1101)
> 	at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:547)
> 	at org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
> 	at org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
> 	at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:73)
> 	... 28 more
> Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
 (Descriptor: file:/home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
> 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
> 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
> 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
> 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)
> 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448)
> 	at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1085)
> 	... 32 more
> Caused by: org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION
FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
> 	at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:140)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
> 	... 47 more
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: MESSAGE
LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key
Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
> 	at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:198)
> 	at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155)
> 	at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127)
> 	at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138)
> 	... 48 more
> Caused by: java.lang.reflect.InvocationTargetException
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> 	at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195)
> 	... 51 more
> Caused by: java.sql.SQLException: Invalid User for UMLS dictionary sno_rx_16abTerms
> 	at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:29)
> 	... 56 more
> {code}



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