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From "Liu, Ying" <L...@advisory.com>
Subject errors when run BagOfCUIsGenerator.java
Date Wed, 16 Apr 2014 17:12:06 GMT
It failed when run BagOfCUIsGenerator.java. The followings are the error information. Thanks
for your help.
Ying



Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization
of annotator class "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
failed.  (Descriptor: file:/C:/Users/Ying/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:354)
    at org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath(AnalysisEngineFactory.java:147)
    at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:42)
    at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:36)
    at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:16)
    at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:49)
Caused by: org.apache.uima.resource.ResourceInitializationException
    at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:79)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
    ... 18 more
Caused by: java.net.ConnectException: Connection timed out: connect
    at java.net.DualStackPlainSocketImpl.connect0(Native Method)
    at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
    at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
    at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
    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:93)
    at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:70)
    ... 19 more





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