I think so. Whether we can 'release' it or not, branching code from the 4.0 release is probably a first step. ________________________________________ From: Peter Abramowitsch <pabramowit...@gmail.com> Sent: Tuesday, November 24, 2020 1:23 PM To: dev@ctakes.apache.org Subject: Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution * Sean In the meantime, I think I have the 4.0.0 source somewhere. I can take my copy which is early 4.0.1 and make whatever small changes are needed (if any) to get it to build in 4.0.0. Would that be useful? Peter On Tue, Nov 24, 2020 at 6:46 PM Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > On Tue, 2020-11-24 at 16:29 +0000, Finan, Sean wrote: > > * External Email - Caution * > > > > > > Hi Tim and all, > > > > Peter kindly checked this into trunk last week. > > I tested that version and it seemed to work. > > > > Another question might be "how do we get this into the/a release? > > > > I haven't looked into whether or not Apache svn servers have a > > locking mechanism on release branches, but if not I think that a > > patch of 4.0 using the version that you and Greg tested should be a > > simple checkin. > > I think it's worth checking -- if we're allowed to just branch off the > 4.0.0 tag we can get a 4.0.1 distribution that just has this one > change, and we could have it built and uploaded quickly so we're ready > for the UMLS change. How would we find out? > > Tim > > > > > I am sure that everybody is tired of hearing me say this, but I would > > like to get out a version 5 asap and disclaim that it is required for > > the new umls authentication. That would make patching v4 a non- > > issue. > > > > Regardless of repository inclusion, the documentation (also written > > by Peter) needs to get to the ctakes wiki - and probably the main > > ctakes web site. On that note, the web site needs to be redone > > asap. > > > > Anyway, cheers to Peter for taking upon himself this update! > > We do still have a few things left to do. > > Volunteers? > > > > Sean > > > > ________________________________________ > > From: Miller, Timothy <timothy.mil...@childrens.harvard.edu> > > Sent: Tuesday, November 24, 2020 11:07 AM > > To: dev@ctakes.apache.org > > Subject: Re: Changes to UTS Authentication for Authorized Content > > Distributors [EXTERNAL] [SUSPICIOUS] > > > > * External Email - Caution * > > > > > > Peter, > > I was able to try your changes and get this new authentication > > mechanism to work in the default pipeline. Peter, Sean, et al, what > > are > > the next steps for getting this in to trunk? If you're not > > comfortable > > checking in directly maybe you can share the patch for review. > > Tim > > > > On Sun, 2020-11-15 at 20:54 +0100, Peter Abramowitsch wrote: > > > * External Email - Caution * > > > > > > > > > Hi Greg > > > > > > I've got the modifications finished for the new UMLS authentication > > > method > > > using API keys. If you're game, I'd like you to be next to test > > > it. > > > Contact me at pabramowit...@gmail.com and I'll get you a new > > > ctakes-dictionary-lookup-fast.4.0,1,x,jar and Readme. > > > > > > If it's smooth for you, I'll talk with Sean about checking it in > > > and > > > what > > > wiki locations need to be updated. > > > > > > To get your key you'll need to log into UMLS, If you've not > > > been > > > there > > > recently you'll need to go through their profile upgrade process > > > where user > > > details will be rerouted through one of the public authentication > > > mechanisms. > > > Once in, go to your profile section and you'll find the API_KEY. > > > > > > All of you will need to do this eventually. > > > > > > Regards > > > Peter > > > > > > Regards, Peter > > > > > > On Wed, Nov 11, 2020 at 10:13 PM Greg Silverman < > > > g...@umn.edu.invalid> > > > wrote: > > > > > > > Hi Peter, > > > > Thanks, that would be great. I like the backwards compatible > > > > method. Our > > > > issue is that we have custom configurations for use in Docker and > > > > Kubernetes with UIMA-AS, so this would be ideal. > > > > > > > > Greg-- > > > > > > > > > > > > On Wed, Nov 11, 2020 at 3:07 PM Peter Abramowitsch < > > > > pabramowit...@gmail.com> > > > > wrote: > > > > > > > > > Hi Greg > > > > > It's actually extremely simple for current UMLS licensees. > > > > > The new API uses an API_KEY instead of user/password. Just > > > > > login to > > > > the > > > > > UTS site, go to your profile area and check on your key > > > > > I or someone else will make changes to the cTAKES validator to > > > > > accept > > > > this > > > > > key in lieu of name and password > > > > > > > > > > For new UMLS users, they will need a couple of extra > > > > > steps. They will > > > > get > > > > > an identity from one of the authentication providers like > > > > > Login.gov as a > > > > > part of the UTS registration process. But having completed > > > > > that, they > > > > > will have a profile page with the API_KEY as above > > > > > > > > > > > > > > > > > > > > On Wed, Nov 11, 2020 at 7:27 PM Greg Silverman < > > > > > g...@umn.edu.invalid> > > > > > wrote: > > > > > > > > > > > For example, the user installation guide has not been updated > > > > > > to > > > > reflect > > > > > > the changes NLM is implementing. The impact for our workflow > > > > > > is > > > > > > pretty > > > > > > significant, so without a clear picture about what we need to > > > > > > do in > > > > order > > > > > > to not have any down time is - to put it mildly - leaving us > > > > > > in the > > > > > dark. > > > > > > Greg-- > > > > > > > > > > > > On Tue, Nov 10, 2020 at 9:18 AM Greg Silverman <g...@umn.edu> > > > > > > wrote: > > > > > > > > > > > > > It's still unclear what this means for me as a user of a > > > > > > > piece of > > > > > > software > > > > > > > that uses UTS for authentication purposes. Could someone > > > > > > > please, in > > > > > plain > > > > > > > language, describe what we as normal users who use software > > > > > > > reliant > > > > on > > > > > > this > > > > > > > authentication mechanism will have to do in order to not > > > > > > > disrupt any > > > > > > > running workflows? > > > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > Greg-- > > > > > > > > > > > > > > > > > > > > > On Mon, Nov 9, 2020 at 7:13 AM McLaughlin, Patrick > > > > > > > (NIH/NLM) > > > > > > > [E] > > > > > > > <patrick.mclaugh...@nih.gov.invalid> wrote: > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The UMLS Terminology Services (UTS) is moving from a > > > > username/password > > > > > > > > login to an NIH-federal identity provider system on > > > > > > > > Monday, > > > > > > > > November > > > > > 9. > > > > > > > > UMLS users will begin migrating their accounts to the new > > > > > > > > system on > > > > > this > > > > > > > > date with a migration deadline of January 15, 2021. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > You will need to update any systems that use the UMLS > > > > > > > > user > > > > validation > > > > > > API > > > > > > > > < > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_help_license_validateumlsuserhelp.html&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=vl8aEPfbmDAK-rTVWtqAu41tQQw1y1GI6MV0Gu6YDNI&e= > > > > > > > > > , > > > > as > > > > > > > > described in my previous emails. We recommend you > > > > > > > > implement > > > > > > > > the new > > > > > > > > workflow as soon as possible after November 9. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Attached are instructions for implementing UMLS user > > > > > > > > validation with > > > > > the > > > > > > > > new system. You MUST supply NLM with the domains (e.g., > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.example.com&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=bPC4J-epBecOGMtT2NSBOI26ksBb5TXMGNKArQt9byg&e= > in the instructions), so that > > > > > > > > we > > > > > > > > can > > > > > whitelist > > > > > > > > the domains first. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The UMLS user validation API > > > > > > > > < > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_help_license_validateumlsuserhelp.html&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=vl8aEPfbmDAK-rTVWtqAu41tQQw1y1GI6MV0Gu6YDNI&e= > > > > will > > > > > > > > remain functional through January 15, 2021; however, UMLS > > > > > > > > users that > > > > > > create > > > > > > > > their UTS accounts after November 9 will not have a > > > > > > > > password, and > > > > you > > > > > > will > > > > > > > > be unable to validate their accounts. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Please let us know if you run into any issues or have any > > > > > > > > questions. > > > > > > > > Thank you! > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -Patrick > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *From:* McLaughlin, Patrick (NIH/NLM) [E] < > > > > patrick.mclaugh...@nih.gov > > > > > > > > *Sent:* Wednesday, September 16, 2020 5:35 PM > > > > > > > > *To:* dev@ctakes.apache.org > > > > > > > > *Cc:* Pei Chen <p...@peistation.com> > > > > > > > > *Subject:* RE: Changes to UTS Authentication for > > > > > > > > Authorized > > > > > > > > Content > > > > > > > > Distributors > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I’m following up on my previous message about changes to > > > > > > > > the NLM > > > > UMLS > > > > > > > > Terminology Services (UTS) authentication. As an > > > > > > > > Authorized > > > > > > > > Content > > > > > > > > Distributor of UTS content, you will need to modify your > > > > > implementation > > > > > > to > > > > > > > > accommodate these changes. Our testing environment is now > > > > > > > > available > > > > > for > > > > > > you > > > > > > > > to test. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *We need some information from you.* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > In order for you to test your implementation, we need two > > > > > > > > things: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 1. A domain name from which you will link your users > > > > > > > > to > > > > > > > > our > > > > > > > > authentication service - We will need to whitelist > > > > > > > > your > > > > > > > > domain > > > > name > > > > > > for use > > > > > > > > in our test system. Example: www.yourwebsite.org. > > > > > > > > 2. A Google email address - We will need to configure > > > > > > > > a > > > > > > > > test > > > > > account > > > > > > > > for you so that you can test user authentication. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If you have questions or concerns, please respond to this > > > > > > > > email. We > > > > > > > > appreciate your patience as we make improvements to UTS. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -Patrick > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Patrick McLaughlin > > > > > > > > > > > > > > > > Head, Terminology QA & User Services > > > > > > > > > > > > > > > > National Library of Medicine > > > > > > > > > > > > > > > > 8600 Rockville Pike, MSC 3831, Bethesda, MD 20894 > > > > > > > > > > > > > > > > patrick.mclaugh...@nih.gov > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *From:* McLaughlin, Patrick (NIH/NLM) [E] < > > > > patrick.mclaugh...@nih.gov > > > > > > > > *Sent:* Friday, August 14, 2020 6:14 PM > > > > > > > > *To:* dev@ctakes.apache.org > > > > > > > > *Cc:* Pei Chen <p...@peistation.com> > > > > > > > > *Subject:* Changes to UTS Authentication for Authorized > > > > > > > > Content > > > > > > > > Distributors > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Dear UMLS Licensee, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I’m contacting you from the U.S. National Library of > > > > > > > > Medicine > > > > because > > > > > > you > > > > > > > > are an Authorized Content Distributor of UMLS Terminology > > > > > > > > Services > > > > > (UTS) > > > > > > > > content ( > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_help_license_validateumlsuserhelp.html&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=vl8aEPfbmDAK-rTVWtqAu41tQQw1y1GI6MV0Gu6YDNI&e= > > > > > > ). > > > > > > > > We are contacting you because we are making changes to > > > > > > > > the > > > > > > > > way in > > > > > which > > > > > > UTS > > > > > > > > users authenticate starting this November. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *What is changing?* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > UTS users will no longer authenticate using a username > > > > > > > > and > > > > > > > > password. > > > > > > > > Instead, users will sign in using external authentication > > > > > > > > services > > > > > like > > > > > > > > Login.gov, Google, Facebook, Microsoft, or one of several > > > > > > > > research > > > > > > > > organizations. We anticipate that users will begin > > > > > > > > migrating to > > > > > external > > > > > > > > authentication services on November 9, 2020. Users who > > > > > > > > migrate to > > > > > these > > > > > > > > services will no longer authenticate with a username and > > > > > > > > password. > > > > We > > > > > > also > > > > > > > > anticipate that passwords will be removed from UTS > > > > > > > > accounts > > > > > > > > on > > > > January > > > > > > 1, > > > > > > > > 2021. After that point, it will no longer be possible for > > > > > > > > Authorized > > > > > > > > Content Distributors to authenticate users with a > > > > > > > > username > > > > > > > > and > > > > > password > > > > > > via > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_help_license_validateumlsuserhelp.html&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=vl8aEPfbmDAK-rTVWtqAu41tQQw1y1GI6MV0Gu6YDNI&e= > > > > > > > > . > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *What does this mean for Authorized Content > > > > > > > > Distributors?* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If you wish to continue to authenticate UTS users, *you > > > > > > > > will need to > > > > > > > > implement a web-based authentication service*. To do > > > > > > > > this, > > > > > > > > you will > > > > > need > > > > > > > > to provide your users with a web interface that links to > > > > > > > > our > > > > > > authentication > > > > > > > > service. The user will navigate to your web interface > > > > > > > > using > > > > > > > > their > > > > web > > > > > > > > browser and click a link to our authentication service. > > > > > > > > Our > > > > > > > > service > > > > > will > > > > > > > > then authenticate the user via an external authentication > > > > > > > > service > > > > (for > > > > > > > > example, Google or Facebook) and redirect the user back > > > > > > > > to > > > > > > > > your web > > > > > > > > interface. We will return true / false to you to let you > > > > > > > > know > > > > whether > > > > > > the > > > > > > > > user has an active UTS account. We are working on a test > > > > > > > > environment > > > > > for > > > > > > > > you to test your implementation, and we anticipate that > > > > > > > > will be > > > > ready > > > > > on > > > > > > > > August 15, 2020. This will allow you to test your > > > > > > > > implementation > > > > ahead > > > > > > of > > > > > > > > our November 9 release date. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *We need some information from you.* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > In order for you to test your implementation, we need two > > > > > > > > things: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 1. A domain name from which you will link your users > > > > > > > > to > > > > > > > > our > > > > > > > > authentication service - We will need to whitelist > > > > > > > > your > > > > > > > > domain > > > > name > > > > > > for use > > > > > > > > in our test system. Example: www.yourwebsite.org. > > > > > > > > 2. An email address - We will need to configure a test > > > > > > > > account > > > > for > > > > > > > > you so that you can test user authentication. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If you have questions or concerns, please respond to this > > > > > > > > email. We > > > > > > > > appreciate your patience as we make improvements to UTS. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > > > > > > > Patrick McLaughlin > > > > > > > > > > > > > > > > Head, Terminology QA & User Services > > > > > > > > > > > > > > > > National Library of Medicine > > > > > > > > > > > > > > > > 8600 Rockville Pike, MSC 3831, Bethesda, MD 20894 > > > > > > > > > > > > > > > > Phone: 301-827-5063 > > > > > > > > > > > > > > > > patrick.mclaugh...@nih.gov > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Greg M. Silverman > > > > > > > Senior Systems Developer > > > > > > > NLP/IE < > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__healthinformatics.umn.edu_research_nlpie-2Dgroup&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=r9vXeJWiO4ojPn5GVtqb6GBkEGd9ZTsIJt0sF2Im9Dk&e= > > > > > > > Department of Surgery > > > > > > > University of Minnesota > > > > > > > g...@umn.edu > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Greg M. Silverman > > > > > > Senior Systems Developer > > > > > > NLP/IE < > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__healthinformatics.umn.edu_research_nlpie-2Dgroup&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=r9vXeJWiO4ojPn5GVtqb6GBkEGd9ZTsIJt0sF2Im9Dk&e= > > > > > > Department of Surgery > > > > > > University of Minnesota > > > > > > g...@umn.edu > > > > > > > > > > > > > > -- > > > > Greg M. Silverman > > > > Senior Systems Developer > > > > NLP/IE < > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__healthinformatics.umn.edu_research_nlpie-2Dgroup&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=mRLdzmP8PH1wOUx_Eh0yspc_HfbCKRpLtcwojZLiy1U&s=r9vXeJWiO4ojPn5GVtqb6GBkEGd9ZTsIJt0sF2Im9Dk&e= > > > > Department of Surgery > > > > University of Minnesota > > > > g...@umn.edu > > > > >
