I also forgot to follow some of the instructions for setting umls url and other fields in the descriptor to empty string. But now I get:
08 Dec 2020 12:15:15 WARN UmlsUserApprover - Using alternate umlsURL found via: properties 08 Dec 2020 12:15:15 INFO UmlsUserApprover - Checking UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser: where is it finding this other umlsURL??? Tim On Tue, 2020-12-08 at 17:06 +0000, Finan, Sean wrote: > * External Email - Caution * > > > 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 > > > >
