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. <[email protected]> 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:[email protected]] > Sent: Tuesday, July 01, 2014 6:04 PM > To: [email protected] > 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 >
