Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS]
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 +, Finan, Sean wrote: > * External Email - Caution * > > > ?Thanks Peter, > > > Happy Thanksgiving all > > > > From: Peter Abramowitsch > 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 >
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS]
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 +, Finan, Sean wrote: > > * External Email - Caution * > > > > > > ?Thanks Peter, > > > > > > Happy Thanksgiving all > > > > > > > > From: Peter Abramowitsch > > 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 > > >
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS]
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=, I'm still getting an error: 08 Dec 2020 11:49:05 ERROR UmlsUserApprover - UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser 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= 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 +, Finan, Sean wrote: > > > * External Email - Caution * > > > > > > > > > ?Thanks Peter, > > > > > > > > > Happy Thanksgiving all > > > > > > > > > > > > From: Peter Abramowitsch > > > 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 > > >
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
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= 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 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=, 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= 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 +, Finan, Sean wrote: > > > * External Email - Caution * > > > > > > > > > ?Thanks Peter, > > > > > > > > > Happy Thanksgiving all > > > > > > > > > > > > From: Peter Abramowitsch > > > 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 > > >
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
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 +, 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= > > 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 > 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= 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= > > 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 +, Finan, Sean wrote: > > > > * External Email - Caution * > > > > > > > > > > > > ?Thanks Peter, > > > > > > > > > > > > Happy Thanksgiving all > > > > > > > > > &g
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Hi Tim I had some compile problems with the rest of the code 4.0.0 too, but you could just try the jar I sent in a pure 4.0.0 binary release. About alternate URL, you need to look through ALL your desc/xml files for the old validator url and set the value of url, user, password and content provider to an empty string. Also in resources, you will find them in the dictionary.xml e.g. resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml There too, you need to set them to an empty string. And yes to Sean, for Windows you can set the sysprop -Dctakes.umls_apikey=xyz to be -Dctakes_umls_apikey=xyz Peter On Tue, Dec 8, 2020 at 6:18 PM Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > 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 +, 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= > > > > 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 > > 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= > 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= > > > > should I be doing something else? > > > > Thanks > > Tim > > > > > >
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
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: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/> From: Miller, Timothy 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 +, 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= > > 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 > 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= 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= > > 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 i
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
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 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: > > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/> > > > > > > > > From: Miller, Timothy > 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 +, 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= > > > > 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 > > 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= > 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=1zoXt5XWcztipmIoZwSHyBw0N4u9aig
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Sounds good, thanks! From: Peter Abramowitsch Sent: Tuesday, December 8, 2020 12:59 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 * 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 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: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser-2522_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l--krqXh9H5lDKksNr8naGjmqSoXJMeeoB7wUe0ORzU&s=kg7MUqD3VRSKcRi0ft0m9LEBgBPWG3P_Fqn_rtGU_mQ&e= > > > > > > > > > > From: Miller, Timothy > 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 +, 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= > > > > 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 > > 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
Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
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 +, 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: > > 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= > > > > > > > > > > From: Miller, Timothy > 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 +, 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= > > > > 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 > > 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= > 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.ni
