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
