One can try the CDASegmentAnnotator. Both are rules/regex based but it's much simpler and doesn't require the find struct 3rd party lib.
Sent from my iPhone > On Jul 1, 2014, at 10:19 PM, "Harpreet Khanduja" <[email protected]> wrote: > > Hello,p > 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 >>
