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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: UMLS connection timeout
Date Wed, 29 May 2013 21:21:32 GMT
Ken,
If it works with a machine w/o a proxy, it sounds like it's most likely a proxy setting issue:
Have you seen this thread: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201304.mbox/%3CCD84AD35.169BD%25mcoarr%40mitre.org%3E
- Adding both the http and https proxy settings as arguments?
- Does the proxy require credentials? If so, http.proxyUser/Password set?

--Pei

> -----Original Message-----
> From: Kenneth Jung [mailto:kjung@stanford.edu]
> Sent: Wednesday, May 29, 2013 4:01 PM
> To: user@ctakes.apache.org
> Subject: UMLS connection timeout
> 
> 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.initi
> alize(UmlsDictionaryLookupAnnotator.java:79)
> 	at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
> AnalysisComponent(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:3
> 27)
> 	at
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImp
> l.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.getNew
> HttpClient(AbstractDelegateHttpsURLConnection.java:191)
> 	at
> sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConn
> ection.java:876)
> 	at
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(
> AbstractDelegateHttpsURLConnection.java:177)
> 	at
> sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLC
> onnection.java:979)
> 	at
> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Htt
> psURLConnectionImpl.java:250)
> 	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)
> 	... 25 more
> 


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