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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: sectionSegmentAnnotator
Date Wed, 02 Jul 2014 01:51:14 GMT
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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