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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject Re: sectionSegmentAnnotator
Date Wed, 02 Jul 2014 15:10:32 GMT
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
>> 

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