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Date: Mon, 11 May 2015 18:09:52 -0500
Message-ID: 
 <CANiJ+gwhJh=WhhhMtEPz+6hddnPN0KiEtGpVZ9SXx7tz=2su0w@mail.gmail.com>
Subject: Re: UMLS Authentication failing despite correct username and password
From: Tom Devel <develxy@gmail.com>
To: dev@ctakes.apache.org
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Sean,

No, I do not get
INFO AbstractJCasTermAnnotator - Default - Loading dictionary into memory.
Initial run may take few mins to load. Please be patient...

I am just getting the ERROR UmlsUserApprover - UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid....

Of course, I can log in successfully on the UMLS page with my credentials.

I am using cTAKES 3.2.1.

Pei:

The machine I am using does not have any ports blocked or restricted as far
that I know, but sadly I do not know if there is some proxy/firewall going
on.

On Mon, May 11, 2015 at 6:03 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> I have logged the issue with the nlm.
>
> If you wish to write a test for the umls validation, check
> https://uts.nlm.nih.gov//help/license/validateumlsuserhelp.html
>
> Sean
>
> -----Original Message-----
> From: Tom Devel [mailto:develxy@gmail.com]
> Sent: Monday, May 11, 2015 6:17 PM
> To: dev@ctakes.apache.org
> Subject: Re: UMLS Authentication failing despite correct username and
> password
>
> I have the same ERROR, even when running the CVD and loading the clinical
> pipeline.
>
> The file cTakesHsql.xml contains the lines:
>
>
> <property key=3D"umlsUrl" value=3D"
>
> https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__uts-2Dws.nlm.nih.g=
ov_restful_isValidUMLSUser&d=3DBQIFaQ&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMSd=
ioCoppxeFU&r=3Dfs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3DSqM8_gfeGar3=
NDMMF1sUsVsBlj7SfS3EGm8784A3EpA&s=3D308nXLFCjLbwHAKgN7tnemjemuQwGZU-VMBoTBK=
nChM&e=3D
> "/>
>
> 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=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 -
> 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 =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 - Loadin=
g
> > 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 V=
BN
> > VBP VBZ WDT WP WPS WRB
> >
> > 11 May 2015 15:59:47  INFO AbstractJCasTermAnnotator - Using minimum te=
rm
> > 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/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 issu=
e
> > but I haven't heard back from them yet and was hoping perhaps someone
> with
> > cTAKES has previously experienced and resolved the issue.
> >
> >
> >
> > Thanks!
> >
> >
>

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