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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu> on 2020/11/24 21:57:50 UTC
ctakes 5.0.0 warranted ? Re: Changes to UTS Authentication for
Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS]
I think that trunk has enough new stuff to warrant a major release.
I am sure that I am missing quite a few things, but some clumps of new goodies include:
New Modules (and components):
ctakes-fhir
ctakes-rest
ctakes-dockhand
New (reader, writer, AE) Components:
Case-Sensitive Dictionary Lookup
optional faster Cleartk-Assertion engines
document attribute adjusters
new JDBC writer api
- various sundry
New Facilities, Utilities:
Builders for Annotations, CAS
Accessors for Annotations, CAS
Time normalization
- and more
New Abstractions, "Paradigms"
Semantic Group, Type focus
Patient (grouped document) focus
Simple extendable File Readers, Writers
Stores for cross-document efforts
Other features:
JCas Views usable via piper files
New examples (code, pipers, documents)
... and undoubtedly many updates to models and code that I am forgetting or don't even know about.
I don't know about major incompatibilities. A few classes have been moved, data has changed, maybe a default or two. Anybody using ctakes 4.0.0 as a dependency may have to modify their code on a switch to trunk - as you noticed with the relocation of DotLogger.
Another change for a major release could be removing ytex from the main package and making it a separate build (and deprecated). Anything that people love in ytex can be moved elsewhere in ctakes. There is a lot to discuss here and I might be one of only a few that feel a weaker coupling is useful, but that would be a big change.
Sean
________________________________________
From: Peter Abramowitsch <pa...@gmail.com>
Sent: Tuesday, November 24, 2020 4:19 PM
To: dev@ctakes.apache.org
Subject: Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution *
Sounds reasonable, but just a thought: Are the changes in trunk sufficient to warrant a new major release? Are there major structural or compatibility issues between 4.0 and trunk? - it doesn’t strike me that there are How about 4.0.0 going to 4.0.1 and trunk becoming 4.1.0-SNAPSHOT? I.e. a new feature release... when it comes.
Peter
Sent from my iPad
> On Nov 24, 2020, at 22:10, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Webapp email is killing me ... that email was sent prematurely.
>
>> ctakes-4.0.0-rc3 to ctakes-4.0.1
>
> I think that is certainly one way to do it.
>
> One could checkout the branch
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_branches_ctakes-2D4.0.0_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xeFeUaJNuo194Tf0hhctytlRcvlCCK5kSTbEov9k7fI&s=L-tssYfMezM1lM2e5BDWecnnc0VXLcfLBNju58Nabsc&e=
> and make the changes to that code.
>
> Would the method be:
> 1. Checkout 4.0.0 branch
> 2. Apply the patch
> 3. Continue with the full release process, checkin and tag 4.0.1 ?
> 4. Keep working on trunk for the next release
> 5. Change the version numbers in trunk to ctakes-5.0.0-SNAPSHOT
> ^- this would force all external projects using trunk to update their dependency version.
>
> Let us keep this rolling,
> Sean
> ________________________________________
> From: Finan, Sean <Se...@childrens.harvard.edu>
> Sent: Tuesday, November 24, 2020 4:02 PM
> To: dev@ctakes.apache.org
> Subject: Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
>
> * External Email - Caution *
>
>
>> ctakes-4.0.0-rc3 to ctakes-4.0.1
>
> I think that is certainly one way to do it.
>
> One could checkout the branch
>
> Would the method be:
> 1. Checkout 4.0.0-rc3
> 2. Apply the patch
> 3. Continue with the full release process, checkin and tag?
> 4. Keep working on trunk for the next release
>
>
> ________________________________________
> From: Miller, Timothy <Ti...@childrens.harvard.edu>
> Sent: Tuesday, November 24, 2020 2:22 PM
> To: dev@ctakes.apache.org
> Subject: Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
>
> * External Email - Caution *
>
>
> Specifically, is the way to go to branch from the tag at:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D4.0.0-2Drc3&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=FQFm_YbfeRux_ry1zWBtjd3hgCIPEZvQqmrh1W9UAVE&s=F1goCJ3-zDm3bXn-8Z-aBDBSeOhu6U8vMwtDGnmxTE4&e=
>
> (the latest release candidate before release I believe)
> into
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D4.0.1&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=FQFm_YbfeRux_ry1zWBtjd3hgCIPEZvQqmrh1W9UAVE&s=5acAKSY9--DM3OWA_Kl4H7Uwt7AGhttmPYKUzdnYLEY&e=
>
> ?
>
> Tim
>
>> On Tue, 2020-11-24 at 20:14 +0100, Peter Abramowitsch wrote:
>> * External Email - Caution *
>>
>>
>> Right, then.
>> I'll get that done.
>>
>> Peter
>>
>> On Tue, Nov 24, 2020 at 7:53 PM Finan, Sean <
>> Sean.Finan@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 <pa...@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.Miller@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 <Ti...@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 pabramowitsch@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 <
>>>>>> gms@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 <
>>>>>>> pabramowitsch@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 <
>>>>>>>> gms@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 <
>>>>>>>>> gms@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]
>>>>>>>>>> <pa...@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.mclaughlin@nih.gov
>>>>>>>>>>> *Sent:* Wednesday, September 16, 2020 5:35 PM
>>>>>>>>>>> *To:* dev@ctakes.apache.org
>>>>>>>>>>> *Cc:* Pei Chen <pe...@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.mclaughlin@nih.gov
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> *From:* McLaughlin, Patrick (NIH/NLM) [E] <
>>>>>>> patrick.mclaughlin@nih.gov
>>>>>>>>>>> *Sent:* Friday, August 14, 2020 6:14 PM
>>>>>>>>>>> *To:* dev@ctakes.apache.org
>>>>>>>>>>> *Cc:* Pei Chen <pe...@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.mclaughlin@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
>>>>>>>>>> gms@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
>>>>>>>>> gms@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
>>>>>>> gms@umn.edu
>>>>>>>
Re: ctakes 5.0.0 warranted ? Re: Changes to UTS Authentication for
Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS]
Posted by gandhi rajan <ga...@gmail.com>.
I agree with Sean. Its high time to churn out ctakes 5.0.0 and move forward.
On Wed, Nov 25, 2020 at 3:28 AM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> I think that trunk has enough new stuff to warrant a major release.
>
> I am sure that I am missing quite a few things, but some clumps of new
> goodies include:
>
> New Modules (and components):
> ctakes-fhir
> ctakes-rest
> ctakes-dockhand
>
>
> New (reader, writer, AE) Components:
> Case-Sensitive Dictionary Lookup
> optional faster Cleartk-Assertion engines
> document attribute adjusters
> new JDBC writer api
> - various sundry
>
> New Facilities, Utilities:
> Builders for Annotations, CAS
> Accessors for Annotations, CAS
> Time normalization
> - and more
>
> New Abstractions, "Paradigms"
> Semantic Group, Type focus
> Patient (grouped document) focus
> Simple extendable File Readers, Writers
> Stores for cross-document efforts
>
> Other features:
> JCas Views usable via piper files
> New examples (code, pipers, documents)
>
> ... and undoubtedly many updates to models and code that I am forgetting
> or don't even know about.
>
>
> I don't know about major incompatibilities. A few classes have been
> moved, data has changed, maybe a default or two. Anybody using ctakes
> 4.0.0 as a dependency may have to modify their code on a switch to trunk -
> as you noticed with the relocation of DotLogger.
>
> Another change for a major release could be removing ytex from the main
> package and making it a separate build (and deprecated). Anything that
> people love in ytex can be moved elsewhere in ctakes. There is a lot to
> discuss here and I might be one of only a few that feel a weaker coupling
> is useful, but that would be a big change.
>
>
> Sean
>
>
> ________________________________________
> From: Peter Abramowitsch <pa...@gmail.com>
> Sent: Tuesday, November 24, 2020 4:19 PM
> To: dev@ctakes.apache.org
> Subject: Re: Changes to UTS Authentication for Authorized Content
> Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
>
> * External Email - Caution *
>
>
> Sounds reasonable, but just a thought: Are the changes in trunk
> sufficient to warrant a new major release? Are there major structural or
> compatibility issues between 4.0 and trunk? - it doesn’t strike me that
> there are How about 4.0.0 going to 4.0.1 and trunk becoming
> 4.1.0-SNAPSHOT? I.e. a new feature release... when it comes.
>
> Peter
>
> Sent from my iPad
>
> > On Nov 24, 2020, at 22:10, Finan, Sean <Se...@childrens.harvard.edu>
> wrote:
> >
> > Webapp email is killing me ... that email was sent prematurely.
> >
> >> ctakes-4.0.0-rc3 to ctakes-4.0.1
> >
> > I think that is certainly one way to do it.
> >
> > One could checkout the branch
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_branches_ctakes-2D4.0.0_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xeFeUaJNuo194Tf0hhctytlRcvlCCK5kSTbEov9k7fI&s=L-tssYfMezM1lM2e5BDWecnnc0VXLcfLBNju58Nabsc&e=
> > and make the changes to that code.
> >
> > Would the method be:
> > 1. Checkout 4.0.0 branch
> > 2. Apply the patch
> > 3. Continue with the full release process, checkin and tag 4.0.1 ?
> > 4. Keep working on trunk for the next release
> > 5. Change the version numbers in trunk to ctakes-5.0.0-SNAPSHOT
> > ^- this would force all external projects using trunk to update their
> dependency version.
> >
> > Let us keep this rolling,
> > Sean
> > ________________________________________
> > From: Finan, Sean <Se...@childrens.harvard.edu>
> > Sent: Tuesday, November 24, 2020 4:02 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Changes to UTS Authentication for Authorized Content
> Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
> >
> > * External Email - Caution *
> >
> >
> >> ctakes-4.0.0-rc3 to ctakes-4.0.1
> >
> > I think that is certainly one way to do it.
> >
> > One could checkout the branch
> >
> > Would the method be:
> > 1. Checkout 4.0.0-rc3
> > 2. Apply the patch
> > 3. Continue with the full release process, checkin and tag?
> > 4. Keep working on trunk for the next release
> >
> >
> > ________________________________________
> > From: Miller, Timothy <Ti...@childrens.harvard.edu>
> > Sent: Tuesday, November 24, 2020 2:22 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Changes to UTS Authentication for Authorized Content
> Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
> >
> > * External Email - Caution *
> >
> >
> > Specifically, is the way to go to branch from the tag at:
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D4.0.0-2Drc3&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=FQFm_YbfeRux_ry1zWBtjd3hgCIPEZvQqmrh1W9UAVE&s=F1goCJ3-zDm3bXn-8Z-aBDBSeOhu6U8vMwtDGnmxTE4&e=
> >
> > (the latest release candidate before release I believe)
> > into
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D4.0.1&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=FQFm_YbfeRux_ry1zWBtjd3hgCIPEZvQqmrh1W9UAVE&s=5acAKSY9--DM3OWA_Kl4H7Uwt7AGhttmPYKUzdnYLEY&e=
> >
> > ?
> >
> > Tim
> >
> >> On Tue, 2020-11-24 at 20:14 +0100, Peter Abramowitsch wrote:
> >> * External Email - Caution *
> >>
> >>
> >> Right, then.
> >> I'll get that done.
> >>
> >> Peter
> >>
> >> On Tue, Nov 24, 2020 at 7:53 PM Finan, Sean <
> >> Sean.Finan@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 <pa...@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.Miller@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 <Ti...@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 pabramowitsch@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 <
> >>>>>> gms@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 <
> >>>>>>> pabramowitsch@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 <
> >>>>>>>> gms@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 <
> >>>>>>>>> gms@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]
> >>>>>>>>>> <pa...@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.mclaughlin@nih.gov
> >>>>>>>>>>> *Sent:* Wednesday, September 16, 2020 5:35 PM
> >>>>>>>>>>> *To:* dev@ctakes.apache.org
> >>>>>>>>>>> *Cc:* Pei Chen <pe...@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.mclaughlin@nih.gov
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> *From:* McLaughlin, Patrick (NIH/NLM) [E] <
> >>>>>>> patrick.mclaughlin@nih.gov
> >>>>>>>>>>> *Sent:* Friday, August 14, 2020 6:14 PM
> >>>>>>>>>>> *To:* dev@ctakes.apache.org
> >>>>>>>>>>> *Cc:* Pei Chen <pe...@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.mclaughlin@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
> >>>>>>>>>> gms@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
> >>>>>>>>> gms@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
> >>>>>>> gms@umn.edu
> >>>>>>>
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"