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  1. cTAKES
  2. CTAKES-527

getting exception w/ AggregatePlaintextFastUMLSProcessor: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Resolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: file:/Users/kjacoby/openNLPprojects/practice/target/scala-2.12/classes/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
      at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:274)
      at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:172)
      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:435)
      at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379)
      at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192)
      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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:109)
      at ctakes.jdbc.TestAE$.delayedEndpoint$ctakes$jdbc$TestAE$1(ScalaJdbcConnectSelect.scala:90)
      at ctakes.jdbc.TestAE$delayedInit$body.apply(ScalaJdbcConnectSelect.scala:85)
      at scala.Function0.apply$mcV$sp(Function0.scala:34)
      at scala.Function0.apply$mcV$sp$(Function0.scala:34)
      at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
      at scala.App.$anonfun$main$1$adapted(App.scala:76)
      at scala.collection.immutable.List.foreach(List.scala:389)
      at scala.App.main(App.scala:76)
      at scala.App.main$(App.scala:74)
      at ctakes.jdbc.TestAE$.main(ScalaJdbcConnectSelect.scala:85)
      at ctakes.jdbc.TestAE.main(ScalaJdbcConnectSelect.scala)
      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:131)
      at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267)
      ... 26 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:199)
      at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156)
      at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128)
      at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
      ... 27 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:196)
      ... 30 more
      Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -7
      at java.lang.String.substring(String.java:1967)
      at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
      at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
      at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
      at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
      at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
      ... 35 more

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            • Assignee:
              Unassigned
              Reporter:
              freygirrl Kim Jacoby
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              • Created:
                Updated:
                Resolved: