UMLS Issue
Hello, I’m having issues both with UMLS authentication, and with downloading cTAKES 4.0.0.1 from the mirror sites. I have an API key set up, but cTAKES 4.0 is not accepting it as an argument. Is there another option available besides downloading cTAKES 4.0.0.1? Thanks, John R Caskey, PhD Senior Data Scientist Department of Medicine University of Wisconsin-Madison
Fw: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch
Hi all, I have been getting your emails and jira items informing me that the download targets on the ctakes website have still not been populated. Thank you for letting me know. ?I apologize for the inconvenience and as soon as I can I will work with the Apache Infra team to see why we are having this problem. As soon as I witness working links I will let you all know. Thank you, Sean From: Finan, Sean Sent: Wednesday, January 20, 2021 10:24 AM To: dev@ctakes.apache.org; u...@ctakes.apache.org Subject: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch ???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] [SUSPICIOUS]
+1 Amazing effort by the community led by Sean and Peter, thank you! --Guergana -Original Message- From: Miller, Timothy [mailto:timothy.mil...@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.fi...@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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZM > > SdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrH > > Eo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=CVA7xXHE > > y4dOSNfEju1Or1cr6KZd3QY7bnY4yIDye3I= > > > > > > 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=DwIBaQ=qS4goWBT7pop > > lM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDR > > RNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhh > > d8GDDdhA=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo= > > > > > > 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_=DwIBaQ=qS4goWBT7poplM69z > > y_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXi > > powRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDD > > dhA=1jNLJHU_4gH08DUNZDjfC4BLGsPSKdiOe63D48Qqekw= > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio > > CoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8u > > Yx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=7ICwdr1JlzQe > > T2skY6TMXmU_u3WAZlxTYKpIZGmGQfs= > > > > > > 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_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=H > > eup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=Ko > > UGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=uM_5s0vlGN8eJc1nK4s9RPxN > > Q2o5KB3vWRC1M0qo2HU= > > > > > > 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=DwIBaQ=qS4goWBT7pop > > lM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDR > > RNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhh > > d8GDDdhA=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo= > > > > > > > > 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 >
Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch [EXTERNAL]
Please unsubscribe me from the mailing list On Thu, Jan 21, 2021 at 5:46 PM Miller, Timothy < timothy.mil...@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.fi...@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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=CVA7xXHEy4dOSNfEju1Or1cr6KZd3QY7bnY4yIDye3I= > > > > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo= > > > > > > > > > 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_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=1jNLJHU_4gH08DUNZDjfC4BLGsPSKdiOe63D48Qqekw= > > > > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=7ICwdr1JlzQeT2skY6TMXmU_u3WAZlxTYKpIZGmGQfs= > > > > > > > > > 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_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=uM_5s0vlGN8eJc1nK4s9RPxNQ2o5KB3vWRC1M0qo2HU= > > > > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo= > > > > > > > > > > > > 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]
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.fi...@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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=CVA7xXHEy4dOSNfEju1Or1cr6KZd3QY7bnY4yIDye3I= > > > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo= > > > > > > > > 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_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=1jNLJHU_4gH08DUNZDjfC4BLGsPSKdiOe63D48Qqekw= > > > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=7ICwdr1JlzQeT2skY6TMXmU_u3WAZlxTYKpIZGmGQfs= > > > > > > > > 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_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=uM_5s0vlGN8eJc1nK4s9RPxNQ2o5KB3vWRC1M0qo2HU= > > > > > > > > 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=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=KoUGdRx91vEVMVc0CokYc1Uhsfa38K34Dhhd8GDDdhA=5Fxduqd71TO5P2AWuZyzAYmaBG1BiOM7G3mWXN-ljqo= > > > > > > > > > > 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 > > > >
