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From "Kline, Larry D" <Larry.Kl...@USONCOLOGY.COM>
Subject ConceptMapper TokenAnnotation
Date Fri, 03 Aug 2012 19:47:47 GMT
I am trying to change the parameter TokenAnnotation to something other
than uima.tt.TokenAnnotation.  Specifically I wanted to use
uima.tt.NPAnnotation.  When I make this change and run my AE in CAS
Visual Debugger I get the stack trace below.  I added the file that
contains NPAnnotation to the types and I added NPAnnotation as input in
the Capabilities.  I also tried an override from the aggregate AE that
calls ConceptMapper.  Nothing helps.  Any suggestion would be
appreciated.  Thanks.

 

 

TokenFilter.initTypes(), Could not find type: uima.tt.NPAnnotation

TokenFilter.initTypes(), Could not find type: uima.tt.NPAnnotation

org.ohnlp.medkat.conceptMapper.support.tokens.UnknownTypeException:
TokenFilter.initTypes(), Could not find type: uima.tt.NPAnnotation

       at
org.ohnlp.medkat.conceptMapper.support.tokens.TokenFilter.initTypes(Toke
nFilter.java:336)

       at
org.ohnlp.medkat.conceptMapper.support.dictionaryResource.annotatorAdapt
or.AnnotatorAdaptor.processCAS(AnnotatorAdaptor.java:119)

       at
org.ohnlp.medkat.conceptMapper.support.dictionaryResource.annotatorAdapt
or.AnnotatorAdaptor.runCPM(AnnotatorAdaptor.java:107)

       at
org.ohnlp.medkat.conceptMapper.support.dictionaryResource.DictionaryReso
urce_impl$DictLoader.startElement(DictionaryResource_impl.java:743)

       at
org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)

       at
org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown
Source)

       at
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown
Source)

       at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDis
patcher.dispatch(Unknown Source)

       at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unkno
wn Source)

       at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
Source)

       at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
Source)

       at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)

       at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
Source)

       at
org.ohnlp.medkat.conceptMapper.support.dictionaryResource.DictionaryReso
urce_impl$DictLoader.setDictionary(DictionaryResource_impl.java:942)

       at
org.ohnlp.medkat.conceptMapper.support.dictionaryResource.DictionaryReso
urce_impl.loadDictionaryContents(DictionaryResource_impl.java:263)

       at
org.ohnlp.medkat.conceptMapper.ConceptMapper.initialize(ConceptMapper.ja
va:340)

       at
org.apache.uima.analysis_engine.impl.compatibility.AnnotatorAdapter.init
ialize(AnnotatorAdapter.java:109)

       at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initia
lizeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)

       at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initia
lize(PrimitiveAnalysisEngine_impl.java:155)

       at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis
EngineFactory_impl.java:94)

       at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo
siteResourceFactory_impl.java:62)

       at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:267)

       at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3
61)

       at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:25
4)

       at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS
B(AggregateAnalysisEngine_impl.java:431)

       at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia
lizeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)

       at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initia
lize(AggregateAnalysisEngine_impl.java:185)

       at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysis
EngineFactory_impl.java:94)

       at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Compo
siteResourceFactory_impl.java:62)

       at
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:267)

       at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3
35)

       at
org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1464)

       at
org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)

       at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerfor
med(AnnotatorOpenEventHandler.java:52)

       at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)

       at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2
341)

       at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.ja
va:402)

       at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

       at javax.swing.AbstractButton.doClick(AbstractButton.java:376)

       at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)

       at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuIt
emUI.java:877)

       at java.awt.Component.processMouseEvent(Component.java:6505)

       at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)

       at java.awt.Component.processEvent(Component.java:6270)

       at java.awt.Container.processEvent(Container.java:2229)

       at java.awt.Component.dispatchEventImpl(Component.java:4861)

       at java.awt.Container.dispatchEventImpl(Container.java:2287)

       at java.awt.Component.dispatchEvent(Component.java:4687)

       at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)

       at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)

       at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)

       at java.awt.Container.dispatchEventImpl(Container.java:2273)

       at java.awt.Window.dispatchEventImpl(Window.java:2713)

       at java.awt.Component.dispatchEvent(Component.java:4687)

       at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:707)

       at java.awt.EventQueue.access$000(EventQueue.java:101)

       at java.awt.EventQueue$3.run(EventQueue.java:666)

       at java.awt.EventQueue$3.run(EventQueue.java:664)

       at java.security.AccessController.doPrivileged(Native Method)

       at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomai
n.java:76)

       at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomai
n.java:87)

       at java.awt.EventQueue$4.run(EventQueue.java:680)

       at java.awt.EventQueue$4.run(EventQueue.java:678)

       at java.security.AccessController.doPrivileged(Native Method)

       at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomai
n.java:76)

       at java.awt.EventQueue.dispatchEvent(EventQueue.java:677)

       at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.
java:211)

       at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.jav
a:128)

       at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.
java:117)

       at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:113)

       at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:105)

       at java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

 

 

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