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'?><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! > >
