Those are the ones that I set to the empty string, I don't know how it's still finding something. I'll poke around. Tim
On Tue, 2020-12-08 at 17:39 +0000, Finan, Sean wrote: > * External Email - Caution * > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser-2522_&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=uRA81eRtCuJYVkMEzd47jQTacPEI0XTrHeDpgKY_Ma0&s=9SE2vJimnmdqHHlSYjb0EtK6QJ0DDzB7O7PBZQ6ayJI&e= > > > <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 > > > > >
