ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: sectionSegmentAnnotator
Date Wed, 02 Jul 2014 17:46:07 GMT
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.Chen@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" <hsk5004@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.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
> >>
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message