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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