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
