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From "Alex Zbarcea (JIRA)" <j...@apache.org>
Subject [jira] [Created] (CTAKES-479) RegressionPipelineTest.testCPE fails because of unavailable UMLS credentials
Date Thu, 16 Nov 2017 02:39:00 GMT
Alex Zbarcea created CTAKES-479:
-----------------------------------

             Summary: 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


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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