Right, then. I'll get that done. Peter
On Tue, Nov 24, 2020 at 7:53 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > 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 > > > > > > > >
