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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: errors when run BagOfCUIsGenerator.java
Date Wed, 16 Apr 2014 17:23:54 GMT
Ying,
Are you behind a proxy or firewall?
If you're trying to use the umls resources, it attempts to make a call to their umls service
to validate your credentials.
--Pei

> -----Original Message-----
> From: Liu, Ying [mailto:LiuY@advisory.com]
> Sent: Wednesday, April 16, 2014 1:13 PM
> To: dev@ctakes.apache.org
> Subject: errors when run BagOfCUIsGenerator.java
> 
> 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.initialize
> AnalysisComponent(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(Analysi
> sEngineFactory_impl.java:94)
>     at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> ompositeResourceFactory_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:25
> 4)
>     at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS
> B(AggregateAnalysisEngine_impl.java:431)
>     at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ
> eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>     at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ
> e(AggregateAnalysisEngine_impl.java:185)
>     at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi
> sEngineFactory_impl.java:94)
>     at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> ompositeResourceFactory_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(An
> alysisEngineFactory.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>(BagOf
> CUIsGenerator.java:16)
>     at
> org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOf
> CUIsGenerator.java:49)
> Caused by: org.apache.uima.resource.ResourceInitializationException
>     at
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initi
> alize(UmlsDictionaryLookupAnnotator.java:79)
>     at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
> AnalysisComponent(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.getNew
> HttpClient(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(Unknow
> n Source)
>     at
> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Un
> known Source)
>     at
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isV
> alidUMLSUser(UmlsDictionaryLookupAnnotator.java:93)
>     at
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initi
> alize(UmlsDictionaryLookupAnnotator.java:70)
>     ... 19 more
> 
> 
> 


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