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From "douglas song (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-48) negation annotator - Sentence type used in code not in descr
Date Fri, 14 Jun 2013 21:49:20 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-48?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13683831#comment-13683831
] 

douglas song commented on CTAKES-48:
------------------------------------

I also got this error with Drug-ner in cTakes3.0, is there any workaround? Thanks.

: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Annotator processing failed.
   
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator processing failed.
   
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
	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(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$200(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.typesystem.type.textspan.Segment"
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.drugner.ae.CopyDrugAnnotator.process(CopyDrugAnnotator.java:130)
	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)
	... 43 more
                
> negation annotator - Sentence type used in code not in descr
> ------------------------------------------------------------
>
>                 Key: CTAKES-48
>                 URL: https://issues.apache.org/jira/browse/CTAKES-48
>             Project: cTAKES
>          Issue Type: Improvement
>            Reporter: Pei Chen
>            Priority: Minor
>
> Found at the SHARPn summit/f2f:
> tried to run the negation annotator by itself and this error was thrown:
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "edu.mayo.bmi.uima.core.type.textspan.Sentence"
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.JCasImpl.getAnnotationIndex(JCasImpl.java:1531)
> at edu.mayo.bmi.uima.context.ContextAnnotator.process(ContextAnnotator.java:2

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