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:[email protected]] > Sent: Wednesday, April 16, 2014 1:13 PM > To: [email protected] > 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 > > >
