ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Pei Chen <chen...@apache.org>
Subject Re: UMLS Authentication failing despite correct username and password
Date Mon, 11 May 2015 22:42:34 GMT
By any chance, are you behind a firewall or proxy server?


On Mon, May 11, 2015 at 6:15 PM, Tom Devel <develxy@gmail.com> wrote:

> I have the same ERROR, even when running the CVD and loading the clinical
> pipeline.
>
> The file cTakesHsql.xml contains the lines:
>
>
> <property key="umlsUrl" value="
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
>
> cTAKES was working fine last week and I did not make any config change
> since then.
>
> Does anyone have an idea how to resolve this?
>
>
> On Mon, May 11, 2015 at 4:40 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Argh.  Our email server may have mucked with the url that I pasted:
> >
> > H t t p s : / / uts - ws . nlm . nih . gov / restful / isValidUMLSUser
> >
> > <property key="umlsUrl" value=" INSERT URL HERE, NO SPACES "/>
> >
> > -----Original Message-----
> > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> > Sent: Monday, May 11, 2015 5:38 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: UMLS Authentication failing despite correct username and
> > password
> >
> > Hi Pedro,
> >
> >
> >
> > Check the cTakesHsql.xml and make sure that the line matches:
> >
> >
> >
> > <property key="umlsUrl" value="
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtE&s=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8&e=
> > "/>
> >
> >
> >
> > In an older version of cTAKES with an output message as you have:
> >
> > >>11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Default -
> Loading
> > dictionary into memory.  Initial run may take few mins to load. Please be
> > patient...
> >
> > That line got corrupted.
> >
> >
> >
> > Sean
> >
> >
> >
> > -----Original Message-----
> >
> > From: Pedro Teixeira [mailto:teixeira09@gmail.com]
> >
> > Sent: Monday, May 11, 2015 5:30 PM
> >
> > To: dev@ctakes.apache.org
> >
> > Subject: UMLS Authentication failing despite correct username and
> password
> >
> >
> >
> > So I've checked the Dictionary lookup XML file and that password works to
> > log in via the website. This was also working last week but stopped at
> some
> > point over the last week. I've got cTAKES running on a linux system so I
> > can index batches of documents via a script. The exact error is as
> follows
> > (with the username/password blocked out).
> >
> >
> >
> > 11 May 2015 15:59:26  INFO LvgCmdApiResourceImpl - cwd =
> >
> > /home/PT/cTAKES/apache-ctakes-3.2.1
> >
> > 11 May 2015 15:59:26  INFO LvgCmdApiResourceImpl - cd
> > /home/PT/cTAKES/apache-ctakes-3.2.1/resources/org/apache/ctakes/lvg/
> >
> > 11 May 2015 15:59:27  INFO LvgCmdApiResourceImpl - cd
> >
> > /home/PT/cTAKES/apache-ctakes-3.2.1
> >
> > 11 May 2015 15:59:27  INFO ClearNLPDependencyParserAE - using Morphy
> > analysis? true Loading configuration.
> >
> > Loading feature templates.
> >
> > Loading lexica.
> >
> > Loading model:
> >
> >
> >
> ........................................................................................
> >
> > 11 May 2015 15:59:42  INFO Chunker - Chunker model file:
> >
> > org/apache/ctakes/chunker/models/chunker-model.zip
> >
> > 11 May 2015 15:59:44  INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> >
> > 11 May 2015 15:59:44  INFO ConstituencyParser - Initializing parser...
> >
> > 11 May 2015 15:59:46  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> >
> > 11 May 2015 15:59:46  INFO NegationContextAnalyzer - initBoundaryData()
> > called for ContextInitializer
> >
> > 11 May 2015 15:59:47  INFO POSTagger - POS tagger model file:
> >
> > org/apache/ctakes/postagger/models/mayo-pos.zip
> >
> > 11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Default - Loading
> > dictionary into memory.  Initial run may take few mins to load. Please be
> > patient...
> >
> > 11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Using dictionary
> > lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
> >
> > 11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Exclusion tagset
> >
> > loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN
> > VBP VBZ WDT WP WPS WRB
> >
> > 11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Using minimum term
> > text span: 3
> >
> > 11 May 2015 15:59:47  INFO DictionaryDescriptorParser - Parsing
> dictionary
> >
> > specifications:
> >
> >
> >
> /home/PT/cTAKES/apache-ctakes-3.2.1/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml
> >
> > 11 May 2015 15:59:48 ERROR UmlsUserApprover - UMLS Account at
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69g&s=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551hou2dM&e=
> > is not valid for user ######### with ###################### Couldn't
> > initialize processing engine.
> >
> >   Initialization of CAS Processor with name
> > "AggregatePlaintextFastUMLSProcessor" failed.
> >
> >
> >
> >
> >
> > I also have a test implementation on a local windows 8 laptop that also
> > fails now due to the same error so it seems like it's UMLS related issue
> > but I haven't heard back from them yet and was hoping perhaps someone
> with
> > cTAKES has previously experienced and resolved the issue.
> >
> >
> >
> > Thanks!
> >
> >
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message