Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm
Precedence: bulk
Reply-To: user@ctakes.apache.org
Received-SPF: pass (nike.apache.org: domain of kjung@stanford.edu designates
 171.67.219.81 as permitted sender)
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0 (Mac OS X Mail 6.3 \(1503\))
Subject: Re: UMLS connection timeout
From: Kenneth Jung <kjung@stanford.edu>
In-Reply-To: <924DE05C19409B438EB81DE683A942D9105271FD@CHEXMBX1A.CHBOSTON.ORG>
Date: Thu, 30 May 2013 11:35:10 -0700
Content-Transfer-Encoding: quoted-printable
Message-Id: <BA6C1E5B-3026-4054-B5BC-97CE95430AFA@stanford.edu>
References: <C2CECF27-027B-4570-A417-6EABB7053A62@stanford.edu>
 <924DE05C19409B438EB81DE683A942D9105271FD@CHEXMBX1A.CHBOSTON.ORG>
To: user@ctakes.apache.org

Hi Pei,
Thanks for responding! =20

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. =20

Are there any other settings related to the proxy, or some way of =
verifying cTAKES is using the proxy as desired? =20

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/%3CCD84AD3=
5.169BD%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?
>=20
> --Pei
>=20
>> -----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
>>=20
>> 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?
>>=20
>> Thanks,
>> Ken
>>=20
>> (Somewhat compressed) console output is appended below in case that
>> helps:
>>=20
>> 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.initiali=
ze
>> 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
>>=20
>=20