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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: sectionSegmentAnnotator
Date Wed, 02 Jul 2014 02:19:21 GMT
Hello,
Thanks for getting back.
I tried again and this is the error.

Exception in thread "main" java.lang.NoSuchMethodError:
org.jdom.Element.addContent(Lorg/jdom/Element;)Lorg/jdom/Element;
at findstruct.StructModel$SM.process(StructModel.java:234)
at findstruct.StructModel.process(StructModel.java:43)
at findstruct.StructFinder.execute(StructFinder.java:53)
at
org.apache.ctakes.core.ae.SectionSegmentAnnotator.process(SectionSegmentAnnotator.java:90)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$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.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:80)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)

Thank you so much,

Harpreet


On Tue, Jul 1, 2014 at 9:51 PM, Masanz, James J. <Masanz.James@mayo.edu>
wrote:

> Was the system you were trying to run cTAKES on connected to the  internet
> at the time?
>
> In among all those messages is this line:
>
> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
>
> Or perhaps it was just a temporary glitch in your connection?
>
> -- James
>
> -----Original Message-----
> From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
> Sent: Tuesday, July 01, 2014 6:04 PM
> To: dev@ctakes.apache.org
> Subject: sectionSegmentAnnotator
>
> Hello,
>
> I would really appreciate if anyone could help me on this.
>
>  I am trying to use SectionSegmentAnnotator in developer version of ctakes
> inside eclipse.
>
> I have included
>  <delegateAnalysisEngine key="SectionSegmentAnnotator">
>     <import location="SectionSegmentAnnotator.xml"/>
>     </delegateAnalysisEngine>
>
> and
>
>   <node>SectionSegmentAnnotator</node>
>
>  in the file aggregateplaintextMLSprocessor.xml.
>
> I am getting the following error.
>
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> annotator class
> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
> failed.  (Descriptor:
>
> file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.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: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.produceResource(UIMAFramework.java:314)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> at
>
> org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
> at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
> at
>
> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
> Caused by: org.apache.uima.resource.ResourceInitializationException
> at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 25 more
> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
> at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
> at java.net.PlainSocketImpl.connect(Unknown Source)
> at java.net.SocksSocketImpl.connect(Unknown Source)
> at java.net.Socket.connect(Unknown Source)
> at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
> at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
> at sun.net.NetworkClient.doConnect(Unknown Source)
> at sun.net.www.http.HttpClient.openServer(Unknown Source)
> at sun.net.www.http.HttpClient.openServer(Unknown Source)
> at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
> at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
> at
>
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
> Source)
> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
> at
>
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
> Source)
> at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
> Source)
> at
> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
> Source)
> at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99)
> at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:76)
> ... 26 more
>
>
> Thank you so much!
>
> Harpreet
>

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