Rajen,
Try adding the below to your descriptor?
<typeSystemDescription>
<imports>
<import name="org.apache.ctakes.drugner.types.TypeSystem"/>
</imports>
</typeSystemDescription>
James,
Not sure if it was a custom pipeline xml, but once we find out which
Aggregate this is coming from, we could add in the import by default drug
ner?
--Pei
On Tue, Mar 18, 2014 at 10:58 AM, Masanz, James J. <[email protected]>wrote:
> 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:[email protected]]
> *Sent:* Monday, March 17, 2014 7:34 PM
> *To:* [email protected]
> *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
>
