ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Kenneth Jung <kj...@stanford.edu>
Subject Re: UMLS connection timeout
Date Thu, 30 May 2013 18:35:10 GMT
Hi Pei,
Thanks for responding!  

I added the proxy and proxy port settings as described that thread but to no avail; the proxy
does not require credentials.  If I set HTTP_PROXY and run 'curl https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser'
from the command line, I get a response (empty of course), while running the same command
without HTTP_PROXY set hangs like cTAKES.  So I know the proxy is up and functional, at least.
 

Are there any other settings related to the proxy, or some way of verifying cTAKES is using
the proxy as desired?  

Thanks,
Ken

On May 29, 2013, at 2:21 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:

> 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
>> 
> 


Mime
View raw message