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_isValidUMLSUser&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=jZe4a0OF4b0UehhgbKoEMUfkTADm8RVRexPavSKlqCE&s=E62_dTnV7yCr1SUBnSbsSxcmyckz4y-PQkFQGoB3WQU&e= returns now "<?xml version='1.0' encoding='UTF-8'?><Result>true</Result>" instead of "<Result>true</Result>". It means that the line result = line.trim().equalsIgnoreCase("<Result>true</Result>"); in isValidUMLSUser() should be replaced with result = line.trim().equalsIgnoreCase("<?xml version='1.0' encoding='UTF-8'?><Result>true</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_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: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!
