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From Deepal Dhariwal <deepaldhari...@gmail.com>
Subject Re: Invoking UMLS lookup annotator from Eclipse
Date Wed, 06 Feb 2013 13:15:13 GMT
Further when I try to load UMLS Dictionary Look up Annotator from
lookup/analysis engine/DictionaryLookupAnnotatorUMLS.xml I get the
following exceptions:
I want to basicially access annotation results in Eclipse and process them
further. Hence I am trying to invoke annotators from Eclipse. If there is a
better solution for accessing ctakes annotation results in Eclipse kindly
let me know.
2/6/13 8:06:17 AM - 14:
org.apache.uima.tools.cvd.MainFrame.internalRunAE(1528): INFO: Process
trace of AE run:
Component Name: HeartfaidOntologyMappingDescriptor
Event Type: Analysis
Duration: 1114ms (100%)

2/6/13 8:10:59 AM - 14:
org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Error
initializing "org.apache.uima.resource.impl.DataResource_impl" from
descriptor
file:/C:/cTAKES-2.5.0/cTAKESdesc/lookupdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
org.apache.uima.resource.ResourceInitializationException: Error
initializing "org.apache.uima.resource.impl.DataResource_impl" from
descriptor
file:/C:/cTAKES-2.5.0/cTAKESdesc/lookupdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
at
org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:144)
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.produceResource(UIMAFramework.java:243)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:565)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
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:477)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: org.apache.uima.resource.ResourceInitializationException: Could
not access the resource data at
file:lookupresources/lookup/LookupDesc_Db.xml.
at
org.apache.uima.resource.impl.DataResource_impl.initialize(DataResource_impl.java:127)
at
org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:123)
... 53 more

Thanks
Deepal Dhariwal

On Wed, Feb 6, 2013 at 7:35 AM, Deepal Dhariwal <deepaldhariwal@gmail.com>wrote:

> Hello all,
>
> I have an UIMA project developed in Eclipse and I run the Configuration
> using UIMA CVD. However when I try to load AggregatePlainTextUMLSProcessor
> Analysis Engine I am getting the following error:
> 2/6/13 7:29:14 AM - 14:
> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Annotator
> class "edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE" was not
> found. (Descriptor:
> file:/C:/cTAKES-2.5.0/cTAKESdesc/dpdesc/analysis_engine/ClearParserDependencyParserAE.xml)
> org.apache.uima.resource.ResourceInitializationException: Annotator class
> "edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE" was not found.
> (Descriptor:
> file:/C:/cTAKES-2.5.0/cTAKESdesc/dpdesc/analysis_engine/ClearParserDependencyParserAE.xml)
>  at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:207)
> 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:477)
>  at
> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
> at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>  at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>  at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> at javax.swing.AbstractButton.doClick(Unknown Source)
>  at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
> Source)
>  at java.awt.Component.processMouseEvent(Unknown Source)
> at javax.swing.JComponent.processMouseEvent(Unknown Source)
>  at java.awt.Component.processEvent(Unknown Source)
> at java.awt.Container.processEvent(Unknown Source)
>  at java.awt.Component.dispatchEventImpl(Unknown Source)
> at java.awt.Container.dispatchEventImpl(Unknown Source)
>  at java.awt.Component.dispatchEvent(Unknown Source)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>  at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>  at java.awt.Container.dispatchEventImpl(Unknown Source)
> at java.awt.Window.dispatchEventImpl(Unknown Source)
>  at java.awt.Component.dispatchEvent(Unknown Source)
> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>  at java.awt.EventQueue.access$200(Unknown Source)
> at java.awt.EventQueue$3.run(Unknown Source)
>  at java.awt.EventQueue$3.run(Unknown Source)
> at java.security.AccessController.doPrivileged(Native Method)
>  at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
>  at java.awt.EventQueue$4.run(Unknown Source)
> at java.awt.EventQueue$4.run(Unknown Source)
>  at java.security.AccessController.doPrivileged(Native Method)
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
>  at java.awt.EventQueue.dispatchEvent(Unknown Source)
> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>  at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>  at java.awt.EventDispatchThread.run(Unknown Source)
> Caused by: java.lang.ClassNotFoundException:
> edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE
>  at java.net.URLClassLoader$1.run(Unknown Source)
> at java.net.URLClassLoader$1.run(Unknown Source)
>  at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(Unknown Source)
>  at java.lang.ClassLoader.loadClass(Unknown Source)
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
>  at java.lang.ClassLoader.loadClass(Unknown Source)
> at java.lang.Class.forName0(Native Method)
>  at java.lang.Class.forName(Unknown Source)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:204)
>  ... 54 more
>
> Could some throw some light on whether am I missing some dependency? I
> checked the
> /C:/cTAKES-2.5.0/cTAKESdesc/dpdesc/analysis_engine/ClearParserDependencyParserAE.xml.
> The ClearParser...xml file is present in the folder.
>
> Thanks in advance.
>
> Regards
> Deepal Dhariwal
>

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