Mailing-List: contact dev-help@ctakes.apache.org; run by ezmlm
Precedence: bulk
Reply-To: dev@ctakes.apache.org
MIME-Version: 1.0
In-Reply-To: <393252F14C42F946952F1ED75D316CAD65C35BBA@CHEXMBX4A.CHBOSTON.ORG>
References: 
 <CAMVhMeCN7Grt2hLzmTwwJRoQojxzSRNXrtrpA75ucod7UwXLLw@mail.gmail.com>
	<393252F14C42F946952F1ED75D316CAD65C35A38@CHEXMBX4A.CHBOSTON.ORG>
	<393252F14C42F946952F1ED75D316CAD65C35A4D@CHEXMBX4A.CHBOSTON.ORG>
	<AFF41593707152499F0B47DCF0E0D183A31D052C@VMPROEXP02.uqo.local>
	<393252F14C42F946952F1ED75D316CAD65C35BBA@CHEXMBX4A.CHBOSTON.ORG>
Date: Tue, 12 May 2015 09:47:33 -0600
Message-ID: 
 <CAOVrvua-DFvF5nBe+CBoi-22Zq=LdiXT5ftgY5x5MgWEghJeXw@mail.gmail.com>
Subject: Re: UMLS Authentication failing despite correct username and password
From: Bruce Tietjen <bruce.tietjen@perfectsearchcorp.com>
To: dev@ctakes.apache.org
Content-Type: multipart/alternative; boundary=f46d04426730ad6e110515e4697b

--f46d04426730ad6e110515e4697b
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Would it be possible to loosen up the checking a little to avoid this kind
of problem in the future, such as pass if the the result contain
"<Result>true</Result>"?


 [image: IMAT Solutions] <http://imatsolutions.com>
 Bruce Tietjen
Senior Software Engineer
[image: Mobile:] 801.634.1547
bruce.tietjen@imatsolutions.com

On Tue, May 12, 2015 at 7:27 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Michal,
>
> Thank you very much for pinpointing the problem.  Pei created Jira
> CTAKES-359.  I checked in a fix for both the -old- and -fast- dictionary
> lookups.  I also reported the problem to the UMLS people and forwarded yo=
ur
> discovery to their mailing list.
>
> Unfortunately, all ctakes users need to upgrade to today's trunk version =
-
> or at least incorporate the required changes.  Pei is making sure that it
> gets moved into the release candidate.
>
> Cheers,
> Sean
>
> -----Original Message-----
> From: Michal.Iglewski@uqo.ca [mailto:Michal.Iglewski@uqo.ca]
> Sent: Monday, May 11, 2015 11:27 PM
> To: dev@ctakes.apache.org
> Subject: RE: UMLS Authentication failing despite correct username and
> password
>
> Hi Pedro and Sean,
>
>
>
> It seems to me that the service
> https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__uts-2Dws.nlm.nih.g=
ov_restful_isValidUMLSUser&d=3DBQIGaQ&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMSd=
ioCoppxeFU&r=3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3DjZe4a0OF4b0U=
ehhgbKoEMUfkTADm8RVRexPavSKlqCE&s=3DE62_dTnV7yCr1SUBnSbsSxcmyckz4y-PQkFQGoB=
3WQU&e=3D
> returns now "<?xml version=3D'1.0' encoding=3D'UTF-8'?><Result>true</Resu=
lt>"
> instead of "<Result>true</Result>". It means that the line
>
>
>
> result =3D line.trim().equalsIgnoreCase("<Result>true</Result>");
>
>
>
> in isValidUMLSUser()  should be replaced with
>
>
>
> result =3D line.trim().equalsIgnoreCase("<?xml version=3D'1.0'
> encoding=3D'UTF-8'?><Result>true</Result>");
>
>
>
> Michal
>
>
>
> -----Message d'origine-----
>
> De : Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
>
> Envoy=C3=A9 : May-11-15 5:41 PM
>
> =C3=80 : dev@ctakes.apache.org
>
> Objet : RE: UMLS Authentication failing despite correct username and
> password
>
>
>
> 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=3D"umlsUrl" value=3D" 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=3D"umlsUrl" value=3D"
> https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__uts-2Dws.nlm.nih.g=
ov_restful_isValidUMLSUser&d=3DBQIGaQ&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMSd=
ioCoppxeFU&r=3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3DbSJDuEveKkCQ=
oYKfh2CwhxDx8I92siVZvxm45BoxGtE&s=3DA5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UD=
h-S8&e=3D
> "/>
>
>
>
>
>
>
>
> In an older version of cTAKES with an output message as you have:
>
>
>
> >>11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Default - Loadin=
g
> 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 passwor=
d
>
>
>
>
>
>
>
> 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 so=
me
> 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 follow=
s
> (with the username/password blocked out).
>
>
>
>
>
>
>
> 11 May 2015 15:59:26  INFO LvgCmdApiResourceImpl - cwd =3D
>
>
>
> /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 dictionar=
y
>
>
>
> specifications:
>
>
>
>
> /home/PT/cTAKES/apache-ctakes-3.2.1/resources/org/apache/ctakes/dictionar=
y/lookup/fast/cTakesHsql.xml
>
>
>
> 11 May 2015 15:59:48 ERROR UmlsUserApprover - UMLS Account at
> https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__uts-2Dws.nlm.nih.g=
ov_restful_isValidUMLSUser&d=3DBQIBaQ&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMSd=
ioCoppxeFU&r=3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3DoVzYGAl69NhM=
u6lQpKeatJrIGk2o_z2AZvjq7Z5J69g&s=3D_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551ho=
u2dM&e=3D
> 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 wit=
h
> cTAKES has previously experienced and resolved the issue.
>
>
>
>
>
>
>
> Thanks!
>
>
>
>

--f46d04426730ad6e110515e4697b--