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Posted to dev@ctakes.apache.org by Peter Abramowitsch <pa...@gmail.com> on 2021/01/20 22:13:45 UTC

Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch

Thanks Sean!

Peter

On Wed, Jan 20, 2021 at 4:25 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> ???As some have experienced, the U.S.A. National Library of Medicine (NLM)
> has changed the authentication method for using the Unified Medical
> Language System (UMLS).
>
> https://www.nlm.nih.gov/research/umls/index.html
>
>
> Though a bit late in its arrival, Apache cTAKES now has a patch release
> that supports the new UMLS authentication method.
>
>
> The release number is 4.0.0.1, an update of the previous release version
> 4.0.0 with a single change to enable the new UMLS authentication.
>
> No other code or functionality has been modified and there are no
> enhancements to the previous release 4.0.0
>
>
> There are instructions for use on the Apache cTAKES wiki.
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0.0.1
>
>
> The source code is available in the 4.0.0.1 tag Subversion (svn)
> repository.
>
> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0.1/
>
>
> The jar and pom files are available from maven central and any
> Applications utilizing Apache cTAKES as an Apache Maven dependency should
> update their pom files.
>
> https://search.maven.org/search?q=ctakes
>
>
> At this time the Apache infra script that points mirror download servers
> to the pre-built zip/archive files has not run.  I hope that the mirror
> servers are updated in a day or two.
>
> When the mirror servers are updated the buttons on the "Downloads" page of
> ctakes.apache.org should trigger a download of the patch version.  Until
> then you will get a "page not found" error.
>
> Until the pre-built archive downloads are available through the website,
> you can find them in the release repository.
>
>
> https://repository.apache.org/content/repositories/releases/org/apache/ctakes/ctakes-core/4.0.0.1/
>
>
> For more information please visit the wiki page on the Apache cTAKES
> 4.0.0.1 patch release.
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0.0.1
>
>
>
> A very special thanks goes to Peter Abramowitsch for conception and
> original implementation of the authentication code and workflow.
>
>
> Many thanks to those who boldly tested, documented and otherwise made this
> patch and its trunk equivalent possible, including
>
> Kean Kaufmann
>
> Gandhi Rajan
>
> Eugenia Monogyiou
>
> Timothy Miller
>
> and anybody else that I have forgotten (apologies).
>
>
> ?And for those of you gave gave me a bit of prodding to get this wrapped
> up and published ... in the end I am grateful and you have done us all a
> service.
>
>
> Cheers,
>
> Sean
>
>

Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch [EXTERNAL]

Posted by moinuddeen smrk <sm...@gmail.com>.

Please unsubscribe me from the mailing list

On Thu, Jan 21, 2021 at 5:46 PM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> Seconded, thanks a lot Sean and Peter for getting this working and
> turned around so quickly!
> Tim
>
> On Wed, 2021-01-20 at 23:13 +0100, Peter Abramowitsch wrote:
> > * External Email - Caution *
> >
> >
> > Thanks Sean!
> >
> > Peter
> >
> > On Wed, Jan 20, 2021 at 4:25 PM Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> > > ???As some have experienced, the U.S.A. National Library of
> > > Medicine (NLM)
> > > has changed the authentication method for using the Unified Medical
> > > Language System (UMLS).
> > >
> > >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_index.html&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=CVA7xXHEy4dOSNfEju1Or1cr6KZd3QY7bnY4yIDye3I&e=
> > >
> > >
> > > Though a bit late in its arrival, Apache cTAKES now has a patch
> > > release
> > > that supports the new UMLS authentication method.
> > >
> > >
> > > The release number is 4.0.0.1, an update of the previous release
> > > version
> > > 4.0.0 with a single change to enable the new UMLS authentication.
> > >
> > > No other code or functionality has been modified and there are no
> > > enhancements to the previous release 4.0.0
> > >
> > >
> > > There are instructions for use on the Apache cTAKES wiki.
> > >
> > >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0.0.1&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo&e=
> > >
> > >
> > > The source code is available in the 4.0.0.1 tag Subversion (svn)
> > > repository.
> > >
> > >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D4.0.0.1_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=1jNLJHU_4gH08DUNZDjfC4BLGsPSKdiOe63D48Qqekw&e=
> > >
> > >
> > > The jar and pom files are available from maven central and any
> > > Applications utilizing Apache cTAKES as an Apache Maven dependency
> > > should
> > > update their pom files.
> > >
> > >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__search.maven.org_search-3Fq-3Dctakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=7ICwdr1JlzQeT2skY6TMXmU_u3WAZlxTYKpIZGmGQfs&e=
> > >
> > >
> > > At this time the Apache infra script that points mirror download
> > > servers
> > > to the pre-built zip/archive files has not run.  I hope that the
> > > mirror
> > > servers are updated in a day or two.
> > >
> > > When the mirror servers are updated the buttons on the "Downloads"
> > > page of
> > > ctakes.apache.org should trigger a download of the patch
> > > version.  Until
> > > then you will get a "page not found" error.
> > >
> > > Until the pre-built archive downloads are available through the
> > > website,
> > > you can find them in the release repository.
> > >
> > >
> > >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__repository.apache.org_content_repositories_releases_org_apache_ctakes_ctakes-2Dcore_4.0.0.1_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=uM_5s0vlGN8eJc1nK4s9RPxNQ2o5KB3vWRC1M0qo2HU&e=
> > >
> > >
> > > For more information please visit the wiki page on the Apache
> > > cTAKES
> > > 4.0.0.1 patch release.
> > >
> > >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0.0.1&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo&e=
> > >
> > >
> > >
> > > A very special thanks goes to Peter Abramowitsch for conception and
> > > original implementation of the authentication code and workflow.
> > >
> > >
> > > Many thanks to those who boldly tested, documented and otherwise
> > > made this
> > > patch and its trunk equivalent possible, including
> > >
> > > Kean Kaufmann
> > >
> > > Gandhi Rajan
> > >
> > > Eugenia Monogyiou
> > >
> > > Timothy Miller
> > >
> > > and anybody else that I have forgotten (apologies).
> > >
> > >
> > > ?And for those of you gave gave me a bit of prodding to get this
> > > wrapped
> > > up and published ... in the end I am grateful and you have done us
> > > all a
> > > service.
> > >
> > >
> > > Cheers,
> > >
> > > Sean
> > >
> > >
>

RE: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch [EXTERNAL] [SUSPICIOUS]

Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.

+1
Amazing effort by the community led by Sean and Peter, thank you!
--Guergana

-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu] 
Sent: Thursday, January 21, 2021 7:16 AM
To: dev@ctakes.apache.org
Subject: Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch [EXTERNAL] [SUSPICIOUS]

* External Email - Caution *


Seconded, thanks a lot Sean and Peter for getting this working and turned around so quickly! 
Tim

On Wed, 2021-01-20 at 23:13 +0100, Peter Abramowitsch wrote:
> * External Email - Caution *
> 
> 
> Thanks Sean!
> 
> Peter
> 
> On Wed, Jan 20, 2021 at 4:25 PM Finan, Sean < 
> Sean.Finan@childrens.harvard.edu> wrote:
> 
> > ???As some have experienced, the U.S.A. National Library of Medicine 
> > (NLM) has changed the authentication method for using the Unified 
> > Medical Language System (UMLS).
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov
> > _research_umls_index.html&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> > SdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrH
> > Eo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=CVA7xXHE
> > y4dOSNfEju1Or1cr6KZd3QY7bnY4yIDye3I&e=
> > 
> > 
> > Though a bit late in its arrival, Apache cTAKES now has a patch 
> > release that supports the new UMLS authentication method.
> > 
> > 
> > The release number is 4.0.0.1, an update of the previous release 
> > version
> > 4.0.0 with a single change to enable the new UMLS authentication.
> > 
> > No other code or functionality has been modified and there are no 
> > enhancements to the previous release 4.0.0
> > 
> > 
> > There are instructions for use on the Apache cTAKES wiki.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
> > g_confluence_display_CTAKES_cTAKES-2B4.0.0.1&d=DwIBaQ&c=qS4goWBT7pop
> > lM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDR
> > RNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhh
> > d8GDDdhA&s=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo&e=
> > 
> > 
> > The source code is available in the 4.0.0.1 tag Subversion (svn) 
> > repository.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_
> > repos_asf_ctakes_tags_ctakes-2D4.0.0.1_&d=DwIBaQ&c=qS4goWBT7poplM69z
> > y_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXi
> > powRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDD
> > dhA&s=1jNLJHU_4gH08DUNZDjfC4BLGsPSKdiOe63D48Qqekw&e=
> > 
> > 
> > The jar and pom files are available from maven central and any 
> > Applications utilizing Apache cTAKES as an Apache Maven dependency 
> > should update their pom files.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__search.maven.or
> > g_search-3Fq-3Dctakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > CoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8u
> > Yx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=7ICwdr1JlzQe
> > T2skY6TMXmU_u3WAZlxTYKpIZGmGQfs&e=
> > 
> > 
> > At this time the Apache infra script that points mirror download 
> > servers to the pre-built zip/archive files has not run.  I hope that 
> > the mirror servers are updated in a day or two.
> > 
> > When the mirror servers are updated the buttons on the "Downloads"
> > page of
> > ctakes.apache.org should trigger a download of the patch version.  
> > Until then you will get a "page not found" error.
> > 
> > Until the pre-built archive downloads are available through the 
> > website, you can find them in the release repository.
> > 
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repository.apac
> > he.org_content_repositories_releases_org_apache_ctakes_ctakes-2Dcore
> > _4.0.0.1_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=H
> > eup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Ko
> > UGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=uM_5s0vlGN8eJc1nK4s9RPxN
> > Q2o5KB3vWRC1M0qo2HU&e=
> > 
> > 
> > For more information please visit the wiki page on the Apache cTAKES
> > 4.0.0.1 patch release.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
> > g_confluence_display_CTAKES_cTAKES-2B4.0.0.1&d=DwIBaQ&c=qS4goWBT7pop
> > lM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDR
> > RNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhh
> > d8GDDdhA&s=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo&e=
> > 
> > 
> > 
> > A very special thanks goes to Peter Abramowitsch for conception and 
> > original implementation of the authentication code and workflow.
> > 
> > 
> > Many thanks to those who boldly tested, documented and otherwise 
> > made this patch and its trunk equivalent possible, including
> > 
> > Kean Kaufmann
> > 
> > Gandhi Rajan
> > 
> > Eugenia Monogyiou
> > 
> > Timothy Miller
> > 
> > and anybody else that I have forgotten (apologies).
> > 
> > 
> > ?And for those of you gave gave me a bit of prodding to get this 
> > wrapped up and published ... in the end I am grateful and you have 
> > done us all a service.
> > 
> > 
> > Cheers,
> > 
> > Sean
> > 
> >

Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch [EXTERNAL]

Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.

Seconded, thanks a lot Sean and Peter for getting this working and
turned around so quickly! 
Tim

On Wed, 2021-01-20 at 23:13 +0100, Peter Abramowitsch wrote:
> * External Email - Caution *
> 
> 
> Thanks Sean!
> 
> Peter
> 
> On Wed, Jan 20, 2021 at 4:25 PM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
> 
> > ???As some have experienced, the U.S.A. National Library of
> > Medicine (NLM)
> > has changed the authentication method for using the Unified Medical
> > Language System (UMLS).
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_index.html&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=CVA7xXHEy4dOSNfEju1Or1cr6KZd3QY7bnY4yIDye3I&e= 
> > 
> > 
> > Though a bit late in its arrival, Apache cTAKES now has a patch
> > release
> > that supports the new UMLS authentication method.
> > 
> > 
> > The release number is 4.0.0.1, an update of the previous release
> > version
> > 4.0.0 with a single change to enable the new UMLS authentication.
> > 
> > No other code or functionality has been modified and there are no
> > enhancements to the previous release 4.0.0
> > 
> > 
> > There are instructions for use on the Apache cTAKES wiki.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0.0.1&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo&e= 
> > 
> > 
> > The source code is available in the 4.0.0.1 tag Subversion (svn)
> > repository.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D4.0.0.1_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=1jNLJHU_4gH08DUNZDjfC4BLGsPSKdiOe63D48Qqekw&e= 
> > 
> > 
> > The jar and pom files are available from maven central and any
> > Applications utilizing Apache cTAKES as an Apache Maven dependency
> > should
> > update their pom files.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__search.maven.org_search-3Fq-3Dctakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=7ICwdr1JlzQeT2skY6TMXmU_u3WAZlxTYKpIZGmGQfs&e= 
> > 
> > 
> > At this time the Apache infra script that points mirror download
> > servers
> > to the pre-built zip/archive files has not run.  I hope that the
> > mirror
> > servers are updated in a day or two.
> > 
> > When the mirror servers are updated the buttons on the "Downloads"
> > page of
> > ctakes.apache.org should trigger a download of the patch
> > version.  Until
> > then you will get a "page not found" error.
> > 
> > Until the pre-built archive downloads are available through the
> > website,
> > you can find them in the release repository.
> > 
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repository.apache.org_content_repositories_releases_org_apache_ctakes_ctakes-2Dcore_4.0.0.1_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=uM_5s0vlGN8eJc1nK4s9RPxNQ2o5KB3vWRC1M0qo2HU&e= 
> > 
> > 
> > For more information please visit the wiki page on the Apache
> > cTAKES
> > 4.0.0.1 patch release.
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0.0.1&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA&s=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo&e= 
> > 
> > 
> > 
> > A very special thanks goes to Peter Abramowitsch for conception and
> > original implementation of the authentication code and workflow.
> > 
> > 
> > Many thanks to those who boldly tested, documented and otherwise
> > made this
> > patch and its trunk equivalent possible, including
> > 
> > Kean Kaufmann
> > 
> > Gandhi Rajan
> > 
> > Eugenia Monogyiou
> > 
> > Timothy Miller
> > 
> > and anybody else that I have forgotten (apologies).
> > 
> > 
> > ?And for those of you gave gave me a bit of prodding to get this
> > wrapped
> > up and published ... in the end I am grateful and you have done us
> > all a
> > service.
> > 
> > 
> > Cheers,
> > 
> > Sean
> > 
> >