Thanks Sean, that's just what I replied too. But if Tim is trying to run 4.0.0, the following is important: the URL is also buried in code in ctakes_dictionary_lookup (the old one). So he would need both new jars. or to make sure he compiled with my sources in both of those projects. The old lookup now uses the fast lookup's new auth mechanism. Sorry if that sounded contorted
Peter On Tue, Dec 8, 2020 at 6:39 PM Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > In your dictionary configuration xml file? That would be > resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml - > depending upon what dictionary you are using. > > You will find two sections that look like this: > > <property key="umlsUrl" value=" > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/> > <property key="umlsVendor" value="NLM-6515182895"/> > <property key="umlsUser" value="CHANGE_ME"/> > <property key="umlsPass" value="CHANGE_ME"/> > > > > ________________________________________ > From: Miller, Timothy <timothy.mil...@childrens.harvard.edu> > Sent: Tuesday, December 8, 2020 12:18 PM > To: dev@ctakes.apache.org > Subject: Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a > release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] > > * External Email - Caution * > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=7jjWEe7tIQEjuL1bxNuOtUY3RXS1He-CqwN-1jMluqo&s=5v4infTOKs_DKS1MU9guMdb9vBk3jRrvQixooV2M8ZY&e= > : > > > 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 > > > > > >
