RE: UMLS Authentication failing despite correct username and password
Hi Pedro, B). If the user has already downloaded the UMLS isn't that already indicative that they had a valid account? As I understand it (I wasn't around at the time) this per-user licensing with a jit check was the deal that was worked out with the NLM. I think that repackaging and redistributing any form of the UMLS was not (legally) done before ctakes worked out the current arrangement. I think have heard ytex had an initial check upon installation, and we have talked about (would like to) use this model. The only drawback is a single download, multiple install site distribution possibility - which NLM didn't like. My information could be woefully outdated or just plain wrong. If anybody out there knows better then please chip in. Sean P.S. If anybody would like to try to advocate a different arrangement with the NLM then that would be great. -Original Message- From: Pedro [mailto:teixeir...@gmail.com] Sent: Thursday, May 14, 2015 9:43 AM To: dev@ctakes.apache.org Subject: Re: UMLS Authentication failing despite correct username and password Agreed. Doing a direct string comparison seems like it will just break at the very next update. A). A check to parse the XML result looking for a result tag and that the contents are True seems better B). I'm not familiar with the history of that particular check but it seems overly restrictive to require a valid UMLS account check for every single run. If the user has already downloaded the UMLS isn't that already indicative that they had a valid account? I realize there are more ways around it in that case but requiring an internet connection just to run one of the UMLS analysis engines seems... suboptimal. Thanks for all the help sorting this out!
Re: UMLS Authentication failing despite correct username and password
Agreed. Doing a direct string comparison seems like it will just break at the very next update. A). A check to parse the XML result looking for a result tag and that the contents are True seems better B). I'm not familiar with the history of that particular check but it seems overly restrictive to require a valid UMLS account check for every single run. If the user has already downloaded the UMLS isn't that already indicative that they had a valid account? I realize there are more ways around it in that case but requiring an internet connection just to run one of the UMLS analysis engines seems... suboptimal. Thanks for all the help sorting this out!
RE: UMLS Authentication failing despite correct username and password
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 sean.fi...@childrens.harvard.edu wrote: Hi Pedro, Check the cTakesHsql.xml and make sure that the line matches: property key=umlsUrl value=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_isValidUMLSUserd=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69gs=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551hou2dMe= 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
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 your 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.iglew...@uqo.ca [mailto:michal.iglew...@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=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=jZe4a0OF4b0UehhgbKoEMUfkTADm8RVRexPavSKlqCEs=E62_dTnV7yCr1SUBnSbsSxcmyckz4y-PQkFQGoB3WQUe= returns now ?xml version='1.0' encoding='UTF-8'?Resulttrue/Result instead of Resulttrue/Result. It means that the line result = line.trim().equalsIgnoreCase(Resulttrue/Result); in isValidUMLSUser() should be replaced with result = line.trim().equalsIgnoreCase(?xml version='1.0' encoding='UTF-8'?Resulttrue/Result); Michal -Message d'origine- De : Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Envoyé : May-11-15 5:41 PM À : 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=umlsUrl value= INSERT URL HERE, NO SPACES / -Original Message- From: Finan, Sean [mailto:sean.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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
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://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_isValidUMLSUserd=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69gs=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551hou2dMe= 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
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.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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_isValidUMLSUserd=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69gs=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551hou2dMe= 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
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.fi...@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.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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_isValidUMLSUserd=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69gs=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551hou2dMe= 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
Hi Pedro and Sean, It seems to me that the service https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser returns now ?xml version='1.0' encoding='UTF-8'?Resulttrue/Result instead of Resulttrue/Result. It means that the line result = line.trim().equalsIgnoreCase(Resulttrue/Result); in isValidUMLSUser() should be replaced with result = line.trim().equalsIgnoreCase(?xml version='1.0' encoding='UTF-8'?Resulttrue/Result); Michal -Message d'origine- De : Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Envoyé : May-11-15 5:41 PM À : 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=umlsUrl value= INSERT URL HERE, NO SPACES / -Original Message- From: Finan, Sean [mailto:sean.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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_isValidUMLSUserd=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69gs=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J-n5V551hou2dMe= 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
Re: UMLS Authentication failing despite correct username and password
Michal, Thanks for pointing that out (It would have been nice if they sent out a notice about the change in the API call). Would be great if someone could open a Jira and verify this fix solves the issue... I think we should push out this critical patch asap- I can include it in 3.2.2 and create another RC2. On Mon, May 11, 2015 at 11:25 PM, michal.iglew...@uqo.ca wrote: Hi Pedro and Sean, It seems to me that the service https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser returns now ?xml version='1.0' encoding='UTF-8'?Resulttrue/Result instead of Resulttrue/Result. It means that the line result = line.trim().equalsIgnoreCase(Resulttrue/Result); in isValidUMLSUser() should be replaced with result = line.trim().equalsIgnoreCase(?xml version='1.0' encoding='UTF-8'?Resulttrue/Result); Michal -Message d'origine- De : Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Envoyé : May-11-15 5:41 PM À : 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=umlsUrl value= INSERT URL HERE, NO SPACES / -Original Message- From: Finan, Sean [mailto:sean.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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_isValidUMLSUserd=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=oVzYGAl69NhMu6lQpKeatJrIGk2o_z2AZvjq7Z5J69gs=_JNevHgYhyKm5PjIyFlYxIS1UWuR7J
Re: UMLS Authentication failing despite correct username and password
You can verify the NIH site is working properly and that your userid and password are valid by POSTing the following: *** NOTE: you must POST the request. GET requests will not work. * https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser?user= useridpassword=passwordlicenseCode=NLM-6515182895 Replace userid with your NIH userID Replace password with your password You should get a response that looks like: ?xml version='1.0' encoding='UTF-8'?Resulttrue/Result [image: IMAT Solutions] http://imatsolutions.com Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Mon, May 11, 2015 at 5:09 PM, Tom Devel deve...@gmail.com wrote: 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.fi...@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:deve...@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=umlsUrl value= https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUserd=BQIFaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=SqM8_gfeGar3NDMMF1sUsVsBlj7SfS3EGm8784A3EpAs=308nXLFCjLbwHAKgN7tnemjemuQwGZU-VMBoTBKnChMe= / 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.fi...@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.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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
Re: UMLS Authentication failing despite correct username and password
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.fi...@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:deve...@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=umlsUrl value= https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUserd=BQIFaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=SqM8_gfeGar3NDMMF1sUsVsBlj7SfS3EGm8784A3EpAs=308nXLFCjLbwHAKgN7tnemjemuQwGZU-VMBoTBKnChMe= / 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.fi...@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.fi...@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_isValidUMLSUserd=BQIGaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=bSJDuEveKkCQoYKfh2CwhxDx8I92siVZvxm45BoxGtEs=A5wwcyQgQrPQ_dWwnaF-QHqZb0ttus_rzS-A6UDh-S8e= / 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
