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From Rajen Aldis <rajendra.al...@gmail.com>
Subject Analysis engine process exception cTAKES 3.1.1
Date Tue, 18 Mar 2014 00:34:06 GMT
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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