Hello, Thank you so much for getting back, it works but I am trying to access the features (like segmentid, preferredText, begin and end ) of a segment object but I am not able to access these.
I am using AnnotationFS curAnnot = (AnnotationFS) aIterator.get(); which is inside a method the method is recursive. and aIteraor is object of FSIterator. Thank you so much. Harpreet On Wed, Jul 2, 2014 at 11:10 AM, Chen, Pei <pei.c...@childrens.harvard.edu> wrote: > 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" <hsk5...@rit.edu> > 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. <masanz.ja...@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:hsk5...@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 > >> >
