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From "Patawari, Arihant" <apataw...@coh.org>
Subject Error while running AggregatePlainTextFastUMLS processor.
Date Thu, 05 May 2016 23:18:27 GMT
Hi all,

I am running a cTAKES version 3.2.3-Snapshot built from the source. Every other pipeline works
fine except AggregatePlainTextUMLSProcessor and it gives me error as

5/5/16 3:18:11 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
failed.  (Descriptor: file:/Users/Arihant/Downloads/apache-ctakes-3.2.3-SNAPSHOT/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: file:/Users/Arihant/Downloads/apache-ctakes-3.2.3-SNAPSHOT/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
              at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
              at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
              at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
              at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
              at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
              at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
              at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
              at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
              at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
              at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
              at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
              at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
              at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
              at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
              at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
              at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
              at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
              at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
              at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
              at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
              at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
              at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
              at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
              at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
              at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
              at java.awt.Component.processMouseEvent(Component.java:6535)
              at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
              at java.awt.Component.processEvent(Component.java:6300)
              at java.awt.Container.processEvent(Container.java:2236)
              at java.awt.Component.dispatchEventImpl(Component.java:4891)
              at java.awt.Container.dispatchEventImpl(Container.java:2294)
              at java.awt.Component.dispatchEvent(Component.java:4713)
              at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
              at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
              at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
              at java.awt.Container.dispatchEventImpl(Container.java:2280)
              at java.awt.Window.dispatchEventImpl(Window.java:2750)
              at java.awt.Component.dispatchEvent(Component.java:4713)
              at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
              at java.awt.EventQueue.access$500(EventQueue.java:97)
              at java.awt.EventQueue$3.run(EventQueue.java:709)
              at java.awt.EventQueue$3.run(EventQueue.java:703)
              at java.security.AccessController.doPrivileged(Native Method)
              at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
              at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
              at java.awt.EventQueue$4.run(EventQueue.java:731)
              at java.awt.EventQueue$4.run(EventQueue.java:729)
              at java.security.AccessController.doPrivileged(Native Method)
              at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
              at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
              at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
              at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
              at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
              at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
              at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
              at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.NullPointerException
              at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
              at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
              ... 55 more
Any help will be great.

I saw various posts saying that this problem has been resolved in earlier versions. Is it
still not resolved or what's the way around?

Thanks

Best,
Arihant


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