Re: Authentication fails for uts.nlm.nih.gov

2015-05-13 Thread britt fitch 
Hi Sangram this was discussed on the list yesterday: 
https://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3c393252f14c42f946952f1ed75d316cad65c35...@chexmbx4a.chboston.org%3e
 



Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com

> On May 13, 2015, at 1:13 AM, Sangram Patil  wrote:
> 
> Hi,
> 
> For https://uts.nlm.nih.gov/ I have got license approval. So I am able to
> login to https://uts.nlm.nih.gov/with no problem.
> 
> When I try to access through cTakes utility, it ends up with an ERROR
> "UmlsUserApprover - UMLS Account at
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user
> Sangram". For couple of days after receiving license, I have used cTakes
> accessing https://uts-ws.nlm.nih.gov with no issues.
> 
> I had communication with UMLS support team, in response they said -"User is
> valid and active".
> 
> Please suggest!
> 
> Sincerely,
> Sangram Patil



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[VOTE] Release Apache cTAKES 3.2.2 (rc2)

2015-05-13 Thread Pei Chen 
This is a call for a vote on releasing the following candidate (rc2) as
Apache cTAKES 3.2.2.

The major change since rc1 was to include the fix for CTAKES-359 - UMLS
Authentication failing despite correct username and password.

For more detailed information on the changes/release notes, please visit:
https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621&version=12328717

The release was made using the cTAKES release process documented here:
http://svn.apache.org/repos/asf/ctakes/site/backup/content/ctakes-release-guide.mdtext

The candidate is available at:
https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/apache-ctakes-3.2.2-src.tar.gz
/.zip

The tag to be voted on:
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.2-rc2
The MD5 checksum of the tarball can be found at:
https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/apache-ctakes-3.2.2-src.tar.gz.md5
/.zip.md5

The signature of the tarball can be found at:
https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/apache-ctakes-3.2.2-src.tar.gz.asc
/.zip.asc

Apache cTAKES' KEYS file, containing the PGP keys used to sign the release:
https://dist.apache.org/repos/dist/release/ctakes/KEYS

Please vote on releasing these packages as Apache cTAKES 3.2.2. The vote is
open for at least the next 72 hours.

The vote passes if at least three binding +1 votes are cast.
[ ] +1 Release the packages as Apache cTAKES 3.2.2
[ ] -1 Do not release the packages because...

Also, the convenience binary can be found at:
https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/apache-ctakes-3.2.2-bin.tar.gz.md5
/.zip

Re: Authentication fails for uts.nlm.nih.gov

2015-05-13 Thread Pei Chen 
A release candidate that includes the UMLS Authentication fix is ready
(ctakes-3.2.2-rc2) now.
Please feel free to test and cast your VOTE to release it by replying to
the email thread[2]

[1] https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/
[2] Subject: [VOTE] Release Apache cTAKES 3.2.2 (rc2)

Thanks,
Pei

On Wed, May 13, 2015 at 7:37 AM, britt fitch <
britt.fi...@wiredinformatics.com> wrote:

> Hi Sangram this was discussed on the list yesterday:
> https://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3c393252f14c42f946952f1ed75d316cad65c35...@chexmbx4a.chboston.org%3e
> 
>
>
> Britt Fitch
> Wired Informatics
> 265 Franklin St Ste 1702
> Boston, MA 02110
> http://wiredinformatics.com
> britt.fi...@wiredinformatics.com
>
> On May 13, 2015, at 1:13 AM, Sangram Patil  wrote:
>
> Hi,
>
> For https://uts.nlm.nih.gov/ I have got license approval. So I am able to
> login to https://uts.nlm.nih.gov/with no problem.
>
> When I try to access through cTakes utility, it ends up with an ERROR
> "UmlsUserApprover - UMLS Account at
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user
> Sangram". For couple of days after receiving license, I have used cTakes
> accessing https://uts-ws.nlm.nih.gov with no issues.
>
> I had communication with UMLS support team, in response they said -"User is
> valid and active".
>
> Please suggest!
>
> Sincerely,
> Sangram Patil
>
>
>

Re: UMLS Authentication failing despite correct username and password

2015-05-13 Thread samir chabou 
I got the same error.Please verify your UMLS license settings in the 
DictionaryLookupAnnotatorUMLS.xml configuration.
Although I'm able to connect to UMLS via the  website using my user name and 
password. Any idea ? 
Thanks  


 On Monday, May 11, 2015 5:44 PM, "Finan, Sean" 
 wrote:
   

 Hi Pedro,

Check the cTakesHsql.xml and make sure that the line matches:

https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>

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:teixeir...@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!

RE: UMLS Authentication failing despite correct username and password

2015-05-13 Thread Oranit Dror 
Dear Samir,

Take a look at: 
https://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3c393252f14c42f946952f1ed75d316cad65c35...@chexmbx4a.chboston.org%3e
Also, the cTAKES developers have released a version that includes their UMLS 
authentication fix:
https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/

Best,
Oranit.



-Original Message-
From: samir chabou [mailto:samir...@yahoo.com.INVALID] 
Sent: Thursday, May 14, 2015 5:46 AM
To: dev@ctakes.apache.org
Subject: Re: UMLS Authentication failing despite correct username and password

I got the same error.Please verify your UMLS license settings in the 
DictionaryLookupAnnotatorUMLS.xml configuration.
Although I'm able to connect to UMLS via the  website using my user name and 
password. Any idea ? 
Thanks  


 On Monday, May 11, 2015 5:44 PM, "Finan, Sean" 
 wrote:
   

 Hi Pedro,

Check the cTakesHsql.xml and make sure that the line matches:

https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>

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:teixeir...@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!