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 >
