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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: Analysis engine process exception cTAKES 3.1.1
Date Tue, 18 Mar 2014 14:58:06 GMT
Which project/directory are you getting the  Aggregate Plaintext UMLS Processor from?

This part of the error message makes it look like you are trying to run the Drug NER pipeline,
not the AggregatePlaintextUMLSProcessor that is under ctakes-clinical-pipeline

"org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation" used in Java code,
 but was not declared in the XML type descriptor.

From: Rajen Aldis [mailto:rajendra.aldis@gmail.com]
Sent: Monday, March 17, 2014 7:34 PM
To: user@ctakes.apache.org
Subject: Analysis engine process exception cTAKES 3.1.1

I have just installed cTAKES 3.1.1, and am getting the following exception when trying to
run the Aggregate Plaintext UMLS Processor:

3/17/14 8:23:31 PM - 10: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
JCas type "org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation" used in
Java code,  but was not declared in the XML type descriptor.
org.apache.uima.analysis_engine.AnalysisEngineProcessException: JCas type "org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation"
used in Java code,  but was not declared in the XML type descriptor.
    at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:128)
    at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
    at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
    at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
    at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
    at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
    at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
    at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526)
    at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:430)
    at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
    at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
    at java.awt.Component.processMouseEvent(Component.java:6414)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
    at java.awt.Component.processEvent(Component.java:6179)
    at java.awt.Container.processEvent(Container.java:2084)
    at java.awt.Component.dispatchEventImpl(Component.java:4776)
    at java.awt.Container.dispatchEventImpl(Container.java:2142)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)
    at java.awt.Container.dispatchEventImpl(Container.java:2128)
    at java.awt.Window.dispatchEventImpl(Window.java:2492)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
    at java.awt.EventQueue.access$400(EventQueue.java:82)
    at java.awt.EventQueue$2.run(EventQueue.java:676)
    at java.awt.EventQueue$2.run(EventQueue.java:674)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:690)
    at java.awt.EventQueue$3.run(EventQueue.java:688)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException: JCas
type "org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation" used in Java
code,  but was not declared in the XML type descriptor.
    at org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl.getLookupWindowIterator(FirstTokenPermLookupInitializerImpl.java:183)
    at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:112)
    ... 50 more
Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation"
used in Java code,  but was not declared in the XML type descriptor.
    at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
    at org.apache.uima.jcas.impl.JCasImpl.getCasType(JCasImpl.java:436)
    at org.apache.uima.jcas.impl.JFSIndexRepositoryImpl.getAnnotationIndex(JFSIndexRepositoryImpl.java:80)
    at org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl.getLookupWindowIterator(FirstTokenPermLookupInitializerImpl.java:180)
    ... 51 more


I'm not sure if this is relevant, but I have downloaded the most recent resources folder and
merged it into the existing folder, and I have obtained a UMLS username and password which
have been entered into the shell script that starts cTAKES.
Any guidance would be greatly appreciated.

Thank you,

Rajen

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