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From Kenneth Jung <kj...@stanford.edu>
Subject UMLS connection timeout
Date Wed, 29 May 2013 20:00:32 GMT
Hi - 
I am trying to get cTAKES 3.0.0 running on a machine that is in a secure computing environment
(which we use to access patient data) and am getting a timeout error while trying to verify
my UMLS credentials.  The machine does have the outbound https port open via a proxy, and
I can use the UMLS user/password credentials to run cTAKES on other (non-secure) systems without
any problems…  Does anyone have any suggestions for what to look at next?  

Thanks,
Ken

(Somewhat compressed) console output is appended below in case that helps: 

org.apache.uima.resource.ResourceInitializationException: Initialization of CAS Processor
with name "AggregatePlaintextUMLSProcessor" failed.  
Caused by: org.apache.uima.resource.ResourceConfigurationException: Initialization of CAS
Processor with name "AggregatePlaintextUMLSProcessor" failed.  
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator
class "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed.  (Descriptor:
file:/home/kjung/apache-ctakes-3.0.0-incubating/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
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)
	... 24 more
Caused by: java.net.ConnectException: Connection timed out
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
	at java.net.Socket.connect(Socket.java:546)
	at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:584)
	at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:160)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:178)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:409)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:530)
	at sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:275)
	at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:332)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:876)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
	at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:979)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(HttpsURLConnectionImpl.java:250)
	at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:93)
	at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:70)
	... 25 more



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