Hello. I installed ctakes 3.1.1 and have been trying to annotate a sample text using UmlsDictionaryLookupAnnotator.xml analysis engine. It loads fine in the CVD, but when I try to run it after loading I get an error saying
org.apache.uima.analysis_engine.AnalysisEngineProcessException: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" used in Java code, but was not declared in the XML type descriptor. Many other analysis engine give similar error when running. I've attached the log file for reference. Any help will be greatly appreciated. Thanks!
12/6/14 5:37:21 PM - 12: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(407): SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" 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.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:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3311) 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:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" 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) ... 45 more Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" 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) ... 46 more 12/6/14 5:37:21 PM - 12: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" 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.LookupWindowAnnotation" 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.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:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java: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(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3311) 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:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" 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) ... 45 more Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation" 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) ... 46 more
