Hi Tim, Peter, Just in case Peter can't get back to you right away,
>I'm actually setting this via my VM options as: -Dctakes_umlspw=<my umls api key> I think that you want to use -Dctakes.umls_apikey On some systems/shells the dot doesn't work. ctakes will also accept (dot to underscore) -Dctakes_umls_apikey I think that is what I used ... ________________________________________ From: Miller, Timothy <timothy.mil...@childrens.harvard.edu> Sent: Tuesday, December 8, 2020 11:52 AM To: dev@ctakes.apache.org Subject: Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Hi Peter, Sorry to leave you in the lurch so long, I've been trying it this morning and running into some issues (I don't think patch-related issues but just trouble getting to where I can test it). So far: 1) Had to add dictionary-fast to the dictionary pom to get it to compile 2) had to remove all ytex modules from main pom to get it to compile 3) org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java looks to have some old code and doesn't compile (bypassed by changing to "no error check" Then I had to remember what classes in 4.0.0 I could try to check it, and settled on org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java with no credentials, I get a UMLS authentication error (as expected). with my old credentials, I get these errors: 08 Dec 2020 11:43:21 ERROR UmlsUserApprover - The user property must now be set to 'umls_api_key' 08 Dec 2020 11:43:21 ERROR UmlsUserApprover - Verify that you are setting command-line option --user, or ctakes property umlsUser, or environment variable umlsUser properly. 08 Dec 2020 11:43:21 ERROR UmlsDictionaryLookupAnnotator - Error: Invalid UMLS License. A UMLS License is required to use the UMLS dictionary lookup. (also seems about right). If i set ctakes_umlsuser=umls_api_key and ctakes_umlspw=<my umls api key>, I'm still getting an error: 08 Dec 2020 11:49:05 ERROR UmlsUserApprover - UMLS Account at https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1zoXt5XWcztipmIoZwSHyBw0N4u9aig3s4i2cVZ6EM4&s=IyrSaDgcbPb4YT4a_k99DLUDNJtuXQVMg1sDAUsUcyw&e= is not valid. 08 Dec 2020 11:49:05 ERROR UmlsUserApprover - Verify that you are setting command-line option --user, or ctakes property umlsUser, or environment variable umlsUser properly. 08 Dec 2020 11:49:05 ERROR UmlsUserApprover - Verify that you are setting command-line option --pass, or ctakes property umlsPass, or environment variable umlsPass properly. I'm actually setting this via my VM options as: -Dctakes_umlspw=<my umls api key> should I be doing something else? Thanks Tim On Tue, 2020-12-08 at 12:21 +0100, Peter Abramowitsch wrote: > * External Email - Caution * > > > Attn Tim Miller > ============= > Hi Tim, > > Were you able to test out the 4.0.0 umls authentication patch? It > would > be good to know if it and its instructions can be dropped in without > much > further work. > > Peter > > On Tue, Dec 1, 2020 at 3:34 PM Miller, Timothy < > timothy.mil...@childrens.harvard.edu> wrote: > > > Peter, I saw the readme attachment, but it sounded from your email > > like > > there was a patch attachment too that I didn't see. Did that not > > come > > through? > > Tim > > > > On Fri, 2020-11-27 at 18:19 +0000, Finan, Sean wrote: > > > * External Email - Caution * > > > > > > > > > ?Thanks Peter, > > > > > > > > > Happy Thanksgiving all > > > > > > > > > ________________________________ > > > From: Peter Abramowitsch <pabramowit...@gmail.com> > > > Sent: Friday, November 27, 2020 11:47 AM > > > To: dev@ctakes.apache.org > > > Subject: 4.0.0 UMLS Authentication Patch - for Developers - Not a > > > release [EXTERNAL] > > > > > > * External Email - Caution * > > > > > > > > > Hi Sean > > > > > > Given that you're still deciding about the tagging or branching > > > for > > > the 4.0.0 back-patch, I won't check the changes in, but they are > > > attached here. They need to be unloaded at the top of the > > > source > > > tree. > > > > > > Gandhi: I've attached a slightly modified version of the > > > instructions for your Wiki updates. > > > If anyone wants the two unofficial 4.0.0 jars for testing, I > > > would be > > > happy to put them in dropbox > > > > > > Regards & Happy Thanksgiving > > > Peter > > >
