Hi James, Thank you for your feedback. I got it working.
Indeed, there is no need to specify the umlsvendor. In this case, the hardcoded NLM-6515182895 <(651)%20518-2895> is used, but with my credentials. Using my own umlsvendor (which translates to licensecode key in the payload), will trigger the exception above. On Mon, Sep 4, 2017 at 3:26 PM, James Masanz <masanz.ja...@gmail.com> wrote: > > I ran a test on Windows using cTAKES 4.0 (from the binary download) and my > UMLS user ID validates OK: > > 04 Sep 2017 15:15:32 INFO UmlsUserApprover - Checking UMLS Account at > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user jamesmasanz: > ..04 Sep 2017 15:15:33 INFO UmlsUserApprover - UMLS Account at > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user jamesmasanz > has been validated > > When I get a UMLS user validation error, things I check are > - is the site/service up? > - can I login to the interactive site with my credentials? Look for "Sign > In" on the upper right of https://uts.nlm.nih.gov/ > - are there special characters in my password (or user ID) that could > cause a problem for the shell/script > > Also, there's no need to specify ctakes.umlsvendor or ctakes.umlsaddr in > the script, so it's better not to, for clarity. > localhost isn't what you'd want there, but it looks like, from the log > you posted, that -Dctakes.umlsaddr is not having an effect anyway. > > > > On Mon, Sep 4, 2017 at 9:37 AM, Alexandru Zbarcea <al...@apache.org> > wrote: > >> Hi, >> >> I'm trying to run cTAKES following the documentation [1], and even after >> getting an UMLS Account, the runctakesCVD loads with exception: >> "org.apache.uima.resource.ResourceInitializationException: >> Initialization of annotator class "org.apache.ctakes.dictionary. >> lookup2.ae.DefaultCasTermAnnotator" failed", but the only error in the >> log is: >> >> ./bin/runctakesCVD.sh -desc desc/ctakes-clinical-pipeline/ >> desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml >> (...) >> 03 Sep 2017 22:00:37 INFO Chunker - Chunker model file: >> org/apache/ctakes/chunker/models/chunker-model.zip >> 03 Sep 2017 22:00:38 INFO TokenizerAnnotatorPTB - Initializing >> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB >> 03 Sep 2017 22:00:38 INFO ContextDependentTokenizerAnnotator - Finite >> state machines loaded. >> 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Using dictionary >> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence >> 03 Sep 2017 22:00:38 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 >> 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Using minimum term >> text span: 3 >> 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Using Dictionary >> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml >> 03 Sep 2017 22:00:38 INFO DictionaryDescriptorParser - Parsing >> dictionary specifications: >> 03 Sep 2017 22:00:38 INFO UmlsUserApprover - Checking UMLS Account at >> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user <username>: >> .03 Sep 2017 22:00:39 ERROR UmlsUserApprover - UMLS Account at >> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user >> <username> with <password> >> >> Tunneling the connection I can see: >> >> POST /restful/isValidUMLSUser HTTP/1.1 >> User-Agent: Java/1.8.0_144 >> Host: uts-ws.nlm.nih.gov:80 >> Accept: text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2 >> Connection: keep-alive >> Content-type: application/x-www-form-urlencoded >> Content-Length: 76 >> >> licenseCode=<license>&user=<username>&password=<password> >> >> HTTP/1.0 301 Moved Permanently >> Location: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser >> Strict-Transport-Security: max-age=31536000; includeSubDomains; preload >> Server: BigIP >> Connection: Keep-Alive >> Content-Length: 0 >> >> Where instead of <licensecode>, <username> and <password> are used the >> valid entries from the https://uts.nlm.nih.gov/ account. >> >> and the runtakesCVD.sh is changed as: >> >> java -Dctakes.umlsuser=<username> \ >> -Dctakes.umlspw="<password>" \ >> -Dctakes.umlsvendor="<licensecode>" \ >> -Dctakes.umlsaddr="http://localhost:8080/restful/isValidUMLSUser"; \ >> -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* \ >> -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml \ >> -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel \ >> -Dawt.useSystemAAFontSettings=on \ >> -Dsun.java2d.dpiaware=true \ >> -Xms512M \ >> -Xmx3g \ >> org.apache.uima.tools.cvd.CVD "$@" >> >> Going to: https://uts.nlm.nih.gov/services/nwsSemanticNetwork, I see >> that the wsdl [2] (all WSDLs [3]) is no longer available. For this reason I >> wonder if the API is still supported. >> >> OS: archlinux >> Java: openjdk version "1.8.0_144" >> OpenJDK Runtime Environment (build 1.8.0_144-b01) >> OpenJDK 64-Bit Server VM (build 25.144-b01, mixed mode) >> Network: no-proxy >> UMLS Account: <licensecode>, <username>, <password> >> >> Regards, >> Alexandru Zbarcea >> >> [1] - https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4. >> 0+Developer+Install+Guide guide >> [2] - https://uts.nlm.nih.gov:443/restful/isValidUMLSUser?wsdl >> [3] - https://uts.nlm.nih.gov/services/nwsSemanticNetwork >> > >
