You are viewing a plain text version of this content. The canonical link for it is here.
Posted to user@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2020/12/16 11:37:06 UTC
Re: How to add the UMLS credential [EXTERNAL]
Hi Roberto,
The existing mechanism should be functional until January 15. After
that point changes to the cTAKES code are required to use the new UMLS authentication mechanism. We are working on this and will release patches and/or new releases.
Tim
On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> * External Email - Caution *
>
>
> Dear All,
>
> I'm new to cTAKES and I'd like to analyze some texts by using
> AggregatePlaintextUMLSProcessor that requires the UMLS resource.
>
> According to the runctakesCVD file, to enable the use of the UMLS
> resources you have to set your UMLS credential, i.e.,
> Dctakes.umlsuser, Dctakes.umlspw
>
> Since, UMLS Terminology Services accounts have been migrated to a
> service that allows you to sign in to UTS using Google, Microsoft,
> ... I don't have any username and password with which to set the
> variables above. Do you have any suggestions?
>
> Thanks in advance
> Roberto
>
>
>
>
> --
> Le informazioni contenute nella presente comunicazione sono di
> natura privata e come tali sono da considerarsi riservate ed
> indirizzate esclusivamente ai destinatari indicati e per le finalità
> strettamente legate al relativo contenuto. Se avete ricevuto questo
> messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> comunicazione all’indirizzo e-mail del mittente.
> --
> The information transmitted is intended only for the person or entity
> to which it is addressed and may contain confidential and/or
> privileged material. If you received this in error, please contact
> the sender and delete the material.
Re: How to add the UMLS credential [EXTERNAL]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Thanks very much Alain for helping Roberto out! Great to see the ctakes
user community working together.
Tim
On Thu, 2020-12-17 at 14:53 +0100, Roberto Zanoli wrote:
> * External Email - Caution *
>
>
> Great!
> I've followed your instructions step by step and I succeeded in
> installing cTAKES. Everything was exactly as you said it would be!
>
> Thank you very much for your help
> Best
> Roberto
>
> On Thu, Dec 17, 2020 at 1:04 PM Alain Leblanc <aa...@gmail.com>
> wrote:
> > OK then.
> >
> >
> >
> > You mentioned Microsoft in your original post so I thought you were
> > doing everything with windows. Anyway first step is to check out
> > the code: I would create a new directory, go into it then type:
> >
> >
> >
> > svn co https://svn.apache.org/repos/asf/ctakes/trunk/
> >
> >
> >
> > This will create a ‘trunk’ directory. Go into it, type
> >
> >
> >
> > mvn compile
> >
> >
> >
> > This will compile and test the code. You may want to grab a coffee
> > or a beer while it’s running. At the end it will tell you if
> > there’s any error. If there’s no error type
> >
> >
> >
> > mvn install
> >
> >
> >
> > When this is done you will have a file ./org/apache/ctakes/ctakes-
> > distribution/4.0.1-SNAPSHOT/ctakes-distribution-4.0.1-SNAPSHOT-
> > bin.zip.
> >
> >
> >
> > From there you follow the instructions on
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
> > , including the addition of ctakes-resources, modifying the
> > file/path names based on your new package name.
> >
> >
> >
> > The only step not included in the instructions is how to add your
> > key. If you’re the only one using your computer you can just add
> > the lines
> >
> >
> >
> > set ctakes.umls_apikey=<your key>
> >
> > set ctakes.umlsaddr=https://utslogin.nlm.nih.gov/cas/v1/api-key
> >
> >
> >
> > (or export ctakes.umls_apikey … if on Linux)
> >
> >
> >
> > on top of the runctakesCVD.bat file (or .sh, on Linux), or add the
> > options to the command line as explained in the instructions (-
> > Dctakes.umls_...). I suspect that setting ctakes.umlsaddr won’t be
> > necessary in the final version, but when I tested last week the old
> > URL was being used if this option was not set.
> >
> >
> >
> > Let us know how it works for you.
> >
> >
> >
> > A
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > From: Roberto Zanoli
> > Sent: Thursday, December 17, 2020 5:36 AM
> > To: user@ctakes.apache.org
> > Subject: Re: How to add the UMLS credential [EXTERNAL]
> >
> >
> >
> >
> >
> > Thanks Alain. I'm used to linux but I've created the installation
> > for windows to be aligned with you.
> >
> > I think I'm ready to follow the next steps.
> >
> >
> >
> > On Wed, Dec 16, 2020 at 5:22 PM Alain Leblanc <aa...@gmail.com>
> > wrote:
> >
> > > Sure Roberto.
> > >
> > >
> > >
> > > I don't know how much of a programmer you are and how comfortable
> > > you are with using the command line (on windows using the
> > > powershell or the old Command Prompt program) and installing
> > > software. You may need a bit of time to learn the basic commands,
> > > but it may come handy later. I assume you're on Windows. Let me
> > > know if you're using something else.
> > >
> > >
> > >
> > > The first step would be to install java 8, subversion and maven.
> > >
> > >
> > >
> > > You have many options for subversion. I would suggest SilkSVN
> > > since it doesn't try to take over your machine. Download link is
> > > https://sliksvn.com/download/
> > >
> > >
> > >
> > > You need to install java 8 before Maven. Link is
> > > https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html
> > > . You may have to register with Oracle. You need the file jdk-
> > > 8u271-windows-x64.exe (as of today). The 8u271 part may change
> > > if a new version is released.
> > >
> > >
> > >
> > > Then for maven there are good instructions here:
> > > https://www.baeldung.com/install-maven-on-windows-linux-mac
> > >
> > >
> > >
> > >
> > >
> > > Let me know when they are installed.
> > >
> > >
> > >
> > > a
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Le mer. 16 déc. 2020 à 10:18, Roberto Zanoli <za...@fbk.eu> a
> > > écrit :
> > >
> > > >
> > > >
> > > >
> > > >
> > > > On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy <
> > > > Timothy.Miller@childrens.harvard.edu> wrote:
> > > >
> > > > > That's unfortunate but great to know, and good to know about
> > > > > the
> > > > > changes you needed as well.
> > > > > Thanks
> > > > > Tim
> > > > >
> > > > > On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
> > > > > > * External Email - Caution *
> > > > > >
> > > > > > The old user/password method stopped working for me a week
> > > > > or so ago.
> > > > > > However I was able to use the api key method after checking
> > > > > out the
> > > > > > latest (as of last week) source code from subversion and
> > > > > building
> > > > > > locally. The only changes I had to make was to set the
> > > > > environment
> > > > > > variables ctakes.umlsaddr to
> > > > > > https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the
> > > > > old url
> > > > > > was used) and ctakes.umls_apikey to my api key.
> > > > > >
> > > > > > Roberto if you need more detailed instructions I can post
> > > > > them.
> > > > >
> > > >
> > > >
> > > >
> > > > It would be very useful if you could provide some more
> > > > information
> > > >
> > > > Thanks a lot
> > > >
> > > > Roberto
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > >
> > > > > > a
> > > > > >
> > > > > >
> > > > > > Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
> > > > > > Timothy.Miller@childrens.harvard.edu> a écrit :
> > > > > > > Hi Roberto,
> > > > > > > The existing mechanism should be functional until January
> > > > > 15. After
> > > > > > > that point changes to the cTAKES code are required to use
> > > > > the new
> > > > > > > UMLS authentication mechanism. We are working on this and
> > > > > will
> > > > > > > release patches and/or new releases.
> > > > > > >
> > > > > > > Tim
> > > > > > >
> > > > > > >
> > > > > > > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> > > > > > > > * External Email - Caution *
> > > > > > > >
> > > > > > > >
> > > > > > > > Dear All,
> > > > > > > >
> > > > > > > > I'm new to cTAKES and I'd like to analyze some texts by
> > > > > using
> > > > > > > > AggregatePlaintextUMLSProcessor that requires the UMLS
> > > > > resource.
> > > > > > > >
> > > > > > > > According to the runctakesCVD file, to enable the use
> > > > > of the UMLS
> > > > > > > > resources you have to set your UMLS credential, i.e.,
> > > > > > > > Dctakes.umlsuser, Dctakes.umlspw
> > > > > > > >
> > > > > > > > Since, UMLS Terminology Services accounts have been
> > > > > migrated to a
> > > > > > > > service that allows you to sign in to UTS using
> > > > > Google,
> > > > > > > Microsoft,
> > > > > > > > ... I don't have any username and password with which
> > > > > to set the
> > > > > > > > variables above. Do you have any suggestions?
> > > > > > > >
> > > > > > > > Thanks in advance
> > > > > > > > Roberto
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > Le informazioni contenute nella presente comunicazione
> > > > > sono di
> > > > > > > > natura privata e come tali sono da considerarsi
> > > > > riservate ed
> > > > > > > > indirizzate esclusivamente ai destinatari indicati e
> > > > > per le
> > > > > > > finalità
> > > > > > > > strettamente legate al relativo contenuto. Se avete
> > > > > ricevuto
> > > > > > > questo
> > > > > > > > messaggio per errore, vi preghiamo di eliminarlo e di
> > > > > inviare una
> > > > > > > > comunicazione all’indirizzo e-mail del mittente.
> > > > > > > > --
> > > > > > > > The information transmitted is intended only for the
> > > > > person or
> > > > > > > entity
> > > > > > > > to which it is addressed and may contain confidential
> > > > > and/or
> > > > > > > > privileged material. If you received this in error,
> > > > > please
> > > > > > > contact
> > > > > > > > the sender and delete the material.
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
> > > > Le informazioni contenute nella presente comunicazione sono di
> > > > natura privata e come tali sono da considerarsi riservate ed
> > > > indirizzate esclusivamente ai destinatari indicati e per le
> > > > finalità strettamente legate al relativo contenuto. Se avete
> > > > ricevuto questo messaggio per errore, vi preghiamo di
> > > > eliminarlo e di inviare una comunicazione all’indirizzo e-mail
> > > > del mittente.
> > > >
> > > > --
> > > >
> > > > The information transmitted is intended only for the person or
> > > > entity to which it is addressed and may contain confidential
> > > > and/or privileged material. If you received this in error,
> > > > please contact the sender and delete the material.
> > > >
> >
> >
> >
> >
> >
> >
> > --
> >
> > Le informazioni contenute nella presente comunicazione sono di
> > natura privata e come tali sono da considerarsi riservate ed
> > indirizzate esclusivamente ai destinatari indicati e per le
> > finalità strettamente legate al relativo contenuto. Se avete
> > ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e
> > di inviare una comunicazione all’indirizzo e-mail del mittente.
> >
> > --
> >
> > The information transmitted is intended only for the person or
> > entity to which it is addressed and may contain confidential and/or
> > privileged material. If you received this in error, please contact
> > the sender and delete the material.
> >
> >
> >
> >
> > Virus-free. www.avg.com
>
>
>
> --
> Le informazioni contenute nella presente comunicazione sono di
> natura privata e come tali sono da considerarsi riservate ed
> indirizzate esclusivamente ai destinatari indicati e per le finalità
> strettamente legate al relativo contenuto. Se avete ricevuto questo
> messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> comunicazione all’indirizzo e-mail del mittente.
> --
> The information transmitted is intended only for the person or entity
> to which it is addressed and may contain confidential and/or
> privileged material. If you received this in error, please contact
> the sender and delete the material.
Re: How to add the UMLS credential [EXTERNAL]
Posted by Roberto Zanoli <za...@fbk.eu>.
Great!
I've followed your instructions step by step and I succeeded in installing
cTAKES. Everything was exactly as you said it would be!
Thank you very much for your help
Best
Roberto
On Thu, Dec 17, 2020 at 1:04 PM Alain Leblanc <aa...@gmail.com> wrote:
> OK then.
>
>
>
> You mentioned Microsoft in your original post so I thought you were doing
> everything with windows. Anyway first step is to check out the code: I
> would create a new directory, go into it then type:
>
>
>
> svn co https://svn.apache.org/repos/asf/ctakes/trunk/
>
>
>
> This will create a ‘trunk’ directory. Go into it, type
>
>
>
> mvn compile
>
>
>
> This will compile and test the code. You may want to grab a coffee or a
> beer while it’s running. At the end it will tell you if there’s any error.
> If there’s no error type
>
>
>
> mvn install
>
>
>
> When this is done you will have a file
> ./org/apache/ctakes/ctakes-distribution/4.0.1-SNAPSHOT/ctakes-distribution-4.0.1-SNAPSHOT-bin.zip.
>
>
>
>
> From there you follow the instructions on
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide,
> including the addition of ctakes-resources, modifying the file/path names
> based on your new package name.
>
>
>
> The only step not included in the instructions is how to add your key. If
> you’re the only one using your computer you can just add the lines
>
>
>
> set ctakes.umls_apikey=<your key>
>
> set ctakes.umlsaddr=https://utslogin.nlm.nih.gov/cas/v1/api-key
>
>
>
> (or export ctakes.umls_apikey … if on Linux)
>
>
>
> on top of the runctakesCVD.bat file (or .sh, on Linux), or add the options
> to the command line as explained in the instructions (-Dctakes.umls_...). I
> suspect that setting ctakes.umlsaddr won’t be necessary in the final
> version, but when I tested last week the old URL was being used if this
> option was not set.
>
>
>
> Let us know how it works for you.
>
>
>
> A
>
>
>
>
>
>
>
>
>
>
>
>
>
> *From: *Roberto Zanoli <za...@fbk.eu>
> *Sent: *Thursday, December 17, 2020 5:36 AM
> *To: *user@ctakes.apache.org
> *Subject: *Re: How to add the UMLS credential [EXTERNAL]
>
>
>
>
>
> Thanks Alain. I'm used to linux but I've created the installation for
> windows to be aligned with you.
>
> I think I'm ready to follow the next steps.
>
>
>
> On Wed, Dec 16, 2020 at 5:22 PM Alain Leblanc <aa...@gmail.com> wrote:
>
> Sure Roberto.
>
>
>
> I don't know how much of a programmer you are and how comfortable you are
> with using the command line (on windows using the powershell or the old
> Command Prompt program) and installing software. You may need a bit of time
> to learn the basic commands, but it may come handy later. I assume you're
> on Windows. Let me know if you're using something else.
>
>
>
> The first step would be to install java 8, subversion and maven.
>
>
>
> You have many options for subversion. I would suggest SilkSVN since it
> doesn't try to take over your machine. Download link is
> https://sliksvn.com/download/
>
>
>
> You need to install java 8 before Maven. Link is
> https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html.
> You may have to register with Oracle. You need the
> file jdk-8u271-windows-x64.exe (as of today). The 8u271 part may change if
> a new version is released.
>
>
>
> Then for maven there are good instructions here:
> https://www.baeldung.com/install-maven-on-windows-linux-mac
>
>
>
>
>
> Let me know when they are installed.
>
>
>
> a
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Le mer. 16 déc. 2020 à 10:18, Roberto Zanoli <za...@fbk.eu> a écrit :
>
>
>
>
>
> On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
> That's unfortunate but great to know, and good to know about the
> changes you needed as well.
> Thanks
> Tim
>
> On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
> > * External Email - Caution *
> >
> > The old user/password method stopped working for me a week or so ago.
> > However I was able to use the api key method after checking out the
> > latest (as of last week) source code from subversion and building
> > locally. The only changes I had to make was to set the environment
> > variables ctakes.umlsaddr to
> > https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the old url
> > was used) and ctakes.umls_apikey to my api key.
> >
> > Roberto if you need more detailed instructions I can post them.
>
>
>
> It would be very useful if you could provide some more information
>
> Thanks a lot
>
> Roberto
>
>
>
>
>
> >
> > a
> >
> >
> > Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
> > Timothy.Miller@childrens.harvard.edu> a écrit :
> > > Hi Roberto,
> > > The existing mechanism should be functional until January 15. After
> > > that point changes to the cTAKES code are required to use the new
> > > UMLS authentication mechanism. We are working on this and will
> > > release patches and/or new releases.
> > >
> > > Tim
> > >
> > >
> > > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> > > > * External Email - Caution *
> > > >
> > > >
> > > > Dear All,
> > > >
> > > > I'm new to cTAKES and I'd like to analyze some texts by using
> > > > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
> > > >
> > > > According to the runctakesCVD file, to enable the use of the UMLS
> > > > resources you have to set your UMLS credential, i.e.,
> > > > Dctakes.umlsuser, Dctakes.umlspw
> > > >
> > > > Since, UMLS Terminology Services accounts have been migrated to a
> > > > service that allows you to sign in to UTS using Google,
> > > Microsoft,
> > > > ... I don't have any username and password with which to set the
> > > > variables above. Do you have any suggestions?
> > > >
> > > > Thanks in advance
> > > > Roberto
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Le informazioni contenute nella presente comunicazione sono di
> > > > natura privata e come tali sono da considerarsi riservate ed
> > > > indirizzate esclusivamente ai destinatari indicati e per le
> > > finalità
> > > > strettamente legate al relativo contenuto. Se avete ricevuto
> > > questo
> > > > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> > > > comunicazione all’indirizzo e-mail del mittente.
> > > > --
> > > > The information transmitted is intended only for the person or
> > > entity
> > > > to which it is addressed and may contain confidential and/or
> > > > privileged material. If you received this in error, please
> > > contact
> > > > the sender and delete the material.
>
>
>
>
>
>
> --
>
> Le informazioni contenute nella presente comunicazione sono di
> natura privata e come tali sono da considerarsi riservate ed
> indirizzate esclusivamente ai destinatari indicati e per le finalità
> strettamente legate al relativo contenuto. Se avete ricevuto questo
> messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> comunicazione all’indirizzo e-mail del mittente.
>
> --
>
> The information transmitted is intended only for the person or entity to
> which it is addressed and may contain confidential and/or privileged
> material. If you received this in error, please contact the sender and
> delete the material.
>
>
>
>
>
>
> --
>
> Le informazioni contenute nella presente comunicazione sono di
> natura privata e come tali sono da considerarsi riservate ed
> indirizzate esclusivamente ai destinatari indicati e per le finalità
> strettamente legate al relativo contenuto. Se avete ricevuto questo
> messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> comunicazione all’indirizzo e-mail del mittente.
>
> --
>
> The information transmitted is intended only for the person or entity to
> which it is addressed and may contain confidential and/or privileged
> material. If you received this in error, please contact the sender and
> delete the material.
>
>
>
>
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> Virus-free.
> www.avg.com
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
> <#m_-6204106018491291241_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
--
--
Le informazioni contenute nella presente comunicazione sono di natura
privata e come tali sono da considerarsi riservate ed indirizzate
esclusivamente ai destinatari indicati e per le finalità strettamente
legate al relativo contenuto. Se avete ricevuto questo messaggio per
errore, vi preghiamo di eliminarlo e di inviare una comunicazione
all’indirizzo e-mail del mittente.
--
The information transmitted is
intended only for the person or entity to which it is addressed and may
contain confidential and/or privileged material. If you received this in
error, please contact the sender and delete the material.
RE: How to add the UMLS credential [EXTERNAL]
Posted by Alain Leblanc <aa...@gmail.com>.
OK then.
You mentioned Microsoft in your original post so I thought you were doing everything with windows. Anyway first step is to check out the code: I would create a new directory, go into it then type:
svn co https://svn.apache.org/repos/asf/ctakes/trunk/
This will create a ‘trunk’ directory. Go into it, type
mvn compile
This will compile and test the code. You may want to grab a coffee or a beer while it’s running. At the end it will tell you if there’s any error. If there’s no error type
mvn install
When this is done you will have a file ./org/apache/ctakes/ctakes-distribution/4.0.1-SNAPSHOT/ctakes-distribution-4.0.1-SNAPSHOT-bin.zip.
From there you follow the instructions on https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide, including the addition of ctakes-resources, modifying the file/path names based on your new package name.
The only step not included in the instructions is how to add your key. If you’re the only one using your computer you can just add the lines
set ctakes.umls_apikey=<your key>
set ctakes.umlsaddr=https://utslogin.nlm.nih.gov/cas/v1/api-key
(or export ctakes.umls_apikey … if on Linux)
on top of the runctakesCVD.bat file (or .sh, on Linux), or add the options to the command line as explained in the instructions (-Dctakes.umls_...). I suspect that setting ctakes.umlsaddr won’t be necessary in the final version, but when I tested last week the old URL was being used if this option was not set.
Let us know how it works for you.
A
From: Roberto Zanoli
Sent: Thursday, December 17, 2020 5:36 AM
To: user@ctakes.apache.org
Subject: Re: How to add the UMLS credential [EXTERNAL]
Thanks Alain. I'm used to linux but I've created the installation for windows to be aligned with you.
I think I'm ready to follow the next steps.
On Wed, Dec 16, 2020 at 5:22 PM Alain Leblanc <aa...@gmail.com> wrote:
Sure Roberto.
I don't know how much of a programmer you are and how comfortable you are with using the command line (on windows using the powershell or the old Command Prompt program) and installing software. You may need a bit of time to learn the basic commands, but it may come handy later. I assume you're on Windows. Let me know if you're using something else.
The first step would be to install java 8, subversion and maven.
You have many options for subversion. I would suggest SilkSVN since it doesn't try to take over your machine. Download link is https://sliksvn.com/download/
You need to install java 8 before Maven. Link is https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html. You may have to register with Oracle. You need the file jdk-8u271-windows-x64.exe (as of today). The 8u271 part may change if a new version is released.
Then for maven there are good instructions here: https://www.baeldung.com/install-maven-on-windows-linux-mac
Let me know when they are installed.
a
Le mer. 16 déc. 2020 à 10:18, Roberto Zanoli <za...@fbk.eu> a écrit :
On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy <Ti...@childrens.harvard.edu> wrote:
That's unfortunate but great to know, and good to know about the
changes you needed as well.
Thanks
Tim
On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
> * External Email - Caution *
>
> The old user/password method stopped working for me a week or so ago.
> However I was able to use the api key method after checking out the
> latest (as of last week) source code from subversion and building
> locally. The only changes I had to make was to set the environment
> variables ctakes.umlsaddr to
> https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the old url
> was used) and ctakes.umls_apikey to my api key.
>
> Roberto if you need more detailed instructions I can post them.
It would be very useful if you could provide some more information
Thanks a lot
Roberto
>
> a
>
>
> Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> a écrit :
> > Hi Roberto,
> > The existing mechanism should be functional until January 15. After
> > that point changes to the cTAKES code are required to use the new
> > UMLS authentication mechanism. We are working on this and will
> > release patches and/or new releases.
> >
> > Tim
> >
> >
> > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> > > * External Email - Caution *
> > >
> > >
> > > Dear All,
> > >
> > > I'm new to cTAKES and I'd like to analyze some texts by using
> > > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
> > >
> > > According to the runctakesCVD file, to enable the use of the UMLS
> > > resources you have to set your UMLS credential, i.e.,
> > > Dctakes.umlsuser, Dctakes.umlspw
> > >
> > > Since, UMLS Terminology Services accounts have been migrated to a
> > > service that allows you to sign in to UTS using Google,
> > Microsoft,
> > > ... I don't have any username and password with which to set the
> > > variables above. Do you have any suggestions?
> > >
> > > Thanks in advance
> > > Roberto
> > >
> > >
> > >
> > >
> > > --
> > > Le informazioni contenute nella presente comunicazione sono di
> > > natura privata e come tali sono da considerarsi riservate ed
> > > indirizzate esclusivamente ai destinatari indicati e per le
> > finalità
> > > strettamente legate al relativo contenuto. Se avete ricevuto
> > questo
> > > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> > > comunicazione all’indirizzo e-mail del mittente.
> > > --
> > > The information transmitted is intended only for the person or
> > entity
> > > to which it is addressed and may contain confidential and/or
> > > privileged material. If you received this in error, please
> > contact
> > > the sender and delete the material.
--
Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente.
--
The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.
--
Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente.
--
The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.
--
This email has been checked for viruses by AVG.
https://www.avg.com
Re: How to add the UMLS credential [EXTERNAL]
Posted by Roberto Zanoli <za...@fbk.eu>.
Thanks Alain. I'm used to linux but I've created the installation for
windows to be aligned with you.
I think I'm ready to follow the next steps.
On Wed, Dec 16, 2020 at 5:22 PM Alain Leblanc <aa...@gmail.com> wrote:
> Sure Roberto.
>
> I don't know how much of a programmer you are and how comfortable you are
> with using the command line (on windows using the powershell or the old
> Command Prompt program) and installing software. You may need a bit of time
> to learn the basic commands, but it may come handy later. I assume you're
> on Windows. Let me know if you're using something else.
>
> The first step would be to install java 8, subversion and maven.
>
> You have many options for subversion. I would suggest SilkSVN since it
> doesn't try to take over your machine. Download link is
> https://sliksvn.com/download/
>
> You need to install java 8 before Maven. Link is
> https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html.
> You may have to register with Oracle. You need the
> file jdk-8u271-windows-x64.exe (as of today). The 8u271 part may change if
> a new version is released.
>
> Then for maven there are good instructions here:
> https://www.baeldung.com/install-maven-on-windows-linux-mac
>
>
> Let me know when they are installed.
>
> a
>
>
>
>
>
>
>
> Le mer. 16 déc. 2020 à 10:18, Roberto Zanoli <za...@fbk.eu> a écrit :
>
>>
>>
>> On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy <
>> Timothy.Miller@childrens.harvard.edu> wrote:
>>
>>> That's unfortunate but great to know, and good to know about the
>>> changes you needed as well.
>>> Thanks
>>> Tim
>>>
>>> On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
>>> > * External Email - Caution *
>>> >
>>> > The old user/password method stopped working for me a week or so ago.
>>> > However I was able to use the api key method after checking out the
>>> > latest (as of last week) source code from subversion and building
>>> > locally. The only changes I had to make was to set the environment
>>> > variables ctakes.umlsaddr to
>>> > https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the old url
>>> > was used) and ctakes.umls_apikey to my api key.
>>> >
>>> > Roberto if you need more detailed instructions I can post them.
>>>
>>
>> It would be very useful if you could provide some more information
>> Thanks a lot
>> Roberto
>>
>>
>>
>>> >
>>> > a
>>> >
>>> >
>>> > Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
>>> > Timothy.Miller@childrens.harvard.edu> a écrit :
>>> > > Hi Roberto,
>>> > > The existing mechanism should be functional until January 15. After
>>> > > that point changes to the cTAKES code are required to use the new
>>> > > UMLS authentication mechanism. We are working on this and will
>>> > > release patches and/or new releases.
>>> > >
>>> > > Tim
>>> > >
>>> > >
>>> > > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
>>> > > > * External Email - Caution *
>>> > > >
>>> > > >
>>> > > > Dear All,
>>> > > >
>>> > > > I'm new to cTAKES and I'd like to analyze some texts by using
>>> > > > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
>>> > > >
>>> > > > According to the runctakesCVD file, to enable the use of the UMLS
>>> > > > resources you have to set your UMLS credential, i.e.,
>>> > > > Dctakes.umlsuser, Dctakes.umlspw
>>> > > >
>>> > > > Since, UMLS Terminology Services accounts have been migrated to a
>>> > > > service that allows you to sign in to UTS using Google,
>>> > > Microsoft,
>>> > > > ... I don't have any username and password with which to set the
>>> > > > variables above. Do you have any suggestions?
>>> > > >
>>> > > > Thanks in advance
>>> > > > Roberto
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > > --
>>> > > > Le informazioni contenute nella presente comunicazione sono di
>>> > > > natura privata e come tali sono da considerarsi riservate ed
>>> > > > indirizzate esclusivamente ai destinatari indicati e per le
>>> > > finalità
>>> > > > strettamente legate al relativo contenuto. Se avete ricevuto
>>> > > questo
>>> > > > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
>>> > > > comunicazione all’indirizzo e-mail del mittente.
>>> > > > --
>>> > > > The information transmitted is intended only for the person or
>>> > > entity
>>> > > > to which it is addressed and may contain confidential and/or
>>> > > > privileged material. If you received this in error, please
>>> > > contact
>>> > > > the sender and delete the material.
>>>
>>
>>
>>
>> --
>> Le informazioni contenute nella presente comunicazione sono di natura privata
>> e come tali sono da considerarsi riservate ed indirizzate esclusivamente
>> ai destinatari indicati e per le finalità strettamente legate al
>> relativo contenuto. Se avete ricevuto questo messaggio per errore, vi
>> preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo
>> e-mail del mittente.
>> --
>> The information transmitted is intended only for the person or entity to
>> which it is addressed and may contain confidential and/or privileged
>> material. If you received this in error, please contact the sender and
>> delete the material.
>>
>
--
--
Le informazioni contenute nella presente comunicazione sono di natura
privata e come tali sono da considerarsi riservate ed indirizzate
esclusivamente ai destinatari indicati e per le finalità strettamente
legate al relativo contenuto. Se avete ricevuto questo messaggio per
errore, vi preghiamo di eliminarlo e di inviare una comunicazione
all’indirizzo e-mail del mittente.
--
The information transmitted is
intended only for the person or entity to which it is addressed and may
contain confidential and/or privileged material. If you received this in
error, please contact the sender and delete the material.
Re: How to add the UMLS credential [EXTERNAL]
Posted by Alain Leblanc <aa...@gmail.com>.
Sure Roberto.
I don't know how much of a programmer you are and how comfortable you are
with using the command line (on windows using the powershell or the old
Command Prompt program) and installing software. You may need a bit of time
to learn the basic commands, but it may come handy later. I assume you're
on Windows. Let me know if you're using something else.
The first step would be to install java 8, subversion and maven.
You have many options for subversion. I would suggest SilkSVN since it
doesn't try to take over your machine. Download link is
https://sliksvn.com/download/
You need to install java 8 before Maven. Link is
https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html.
You may have to register with Oracle. You need the
file jdk-8u271-windows-x64.exe (as of today). The 8u271 part may change if
a new version is released.
Then for maven there are good instructions here:
https://www.baeldung.com/install-maven-on-windows-linux-mac
Let me know when they are installed.
a
Le mer. 16 déc. 2020 à 10:18, Roberto Zanoli <za...@fbk.eu> a écrit :
>
>
> On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
>> That's unfortunate but great to know, and good to know about the
>> changes you needed as well.
>> Thanks
>> Tim
>>
>> On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
>> > * External Email - Caution *
>> >
>> > The old user/password method stopped working for me a week or so ago.
>> > However I was able to use the api key method after checking out the
>> > latest (as of last week) source code from subversion and building
>> > locally. The only changes I had to make was to set the environment
>> > variables ctakes.umlsaddr to
>> > https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the old url
>> > was used) and ctakes.umls_apikey to my api key.
>> >
>> > Roberto if you need more detailed instructions I can post them.
>>
>
> It would be very useful if you could provide some more information
> Thanks a lot
> Roberto
>
>
>
>> >
>> > a
>> >
>> >
>> > Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
>> > Timothy.Miller@childrens.harvard.edu> a écrit :
>> > > Hi Roberto,
>> > > The existing mechanism should be functional until January 15. After
>> > > that point changes to the cTAKES code are required to use the new
>> > > UMLS authentication mechanism. We are working on this and will
>> > > release patches and/or new releases.
>> > >
>> > > Tim
>> > >
>> > >
>> > > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
>> > > > * External Email - Caution *
>> > > >
>> > > >
>> > > > Dear All,
>> > > >
>> > > > I'm new to cTAKES and I'd like to analyze some texts by using
>> > > > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
>> > > >
>> > > > According to the runctakesCVD file, to enable the use of the UMLS
>> > > > resources you have to set your UMLS credential, i.e.,
>> > > > Dctakes.umlsuser, Dctakes.umlspw
>> > > >
>> > > > Since, UMLS Terminology Services accounts have been migrated to a
>> > > > service that allows you to sign in to UTS using Google,
>> > > Microsoft,
>> > > > ... I don't have any username and password with which to set the
>> > > > variables above. Do you have any suggestions?
>> > > >
>> > > > Thanks in advance
>> > > > Roberto
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Le informazioni contenute nella presente comunicazione sono di
>> > > > natura privata e come tali sono da considerarsi riservate ed
>> > > > indirizzate esclusivamente ai destinatari indicati e per le
>> > > finalità
>> > > > strettamente legate al relativo contenuto. Se avete ricevuto
>> > > questo
>> > > > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
>> > > > comunicazione all’indirizzo e-mail del mittente.
>> > > > --
>> > > > The information transmitted is intended only for the person or
>> > > entity
>> > > > to which it is addressed and may contain confidential and/or
>> > > > privileged material. If you received this in error, please
>> > > contact
>> > > > the sender and delete the material.
>>
>
>
>
> --
> Le informazioni contenute nella presente comunicazione sono di natura privata
> e come tali sono da considerarsi riservate ed indirizzate esclusivamente
> ai destinatari indicati e per le finalità strettamente legate al relativo
> contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di
> eliminarlo e di inviare una comunicazione all’indirizzo e-mail del
> mittente.
> --
> The information transmitted is intended only for the person or entity to
> which it is addressed and may contain confidential and/or privileged
> material. If you received this in error, please contact the sender and
> delete the material.
>
Re: How to add the UMLS credential [EXTERNAL]
Posted by Roberto Zanoli <za...@fbk.eu>.
On Wed, Dec 16, 2020 at 3:30 PM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> That's unfortunate but great to know, and good to know about the
> changes you needed as well.
> Thanks
> Tim
>
> On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
> > * External Email - Caution *
> >
> > The old user/password method stopped working for me a week or so ago.
> > However I was able to use the api key method after checking out the
> > latest (as of last week) source code from subversion and building
> > locally. The only changes I had to make was to set the environment
> > variables ctakes.umlsaddr to
> > https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the old url
> > was used) and ctakes.umls_apikey to my api key.
> >
> > Roberto if you need more detailed instructions I can post them.
>
It would be very useful if you could provide some more information
Thanks a lot
Roberto
> >
> > a
> >
> >
> > Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
> > Timothy.Miller@childrens.harvard.edu> a écrit :
> > > Hi Roberto,
> > > The existing mechanism should be functional until January 15. After
> > > that point changes to the cTAKES code are required to use the new
> > > UMLS authentication mechanism. We are working on this and will
> > > release patches and/or new releases.
> > >
> > > Tim
> > >
> > >
> > > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> > > > * External Email - Caution *
> > > >
> > > >
> > > > Dear All,
> > > >
> > > > I'm new to cTAKES and I'd like to analyze some texts by using
> > > > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
> > > >
> > > > According to the runctakesCVD file, to enable the use of the UMLS
> > > > resources you have to set your UMLS credential, i.e.,
> > > > Dctakes.umlsuser, Dctakes.umlspw
> > > >
> > > > Since, UMLS Terminology Services accounts have been migrated to a
> > > > service that allows you to sign in to UTS using Google,
> > > Microsoft,
> > > > ... I don't have any username and password with which to set the
> > > > variables above. Do you have any suggestions?
> > > >
> > > > Thanks in advance
> > > > Roberto
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Le informazioni contenute nella presente comunicazione sono di
> > > > natura privata e come tali sono da considerarsi riservate ed
> > > > indirizzate esclusivamente ai destinatari indicati e per le
> > > finalità
> > > > strettamente legate al relativo contenuto. Se avete ricevuto
> > > questo
> > > > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> > > > comunicazione all’indirizzo e-mail del mittente.
> > > > --
> > > > The information transmitted is intended only for the person or
> > > entity
> > > > to which it is addressed and may contain confidential and/or
> > > > privileged material. If you received this in error, please
> > > contact
> > > > the sender and delete the material.
>
--
--
Le informazioni contenute nella presente comunicazione sono di natura
privata e come tali sono da considerarsi riservate ed indirizzate
esclusivamente ai destinatari indicati e per le finalità strettamente
legate al relativo contenuto. Se avete ricevuto questo messaggio per
errore, vi preghiamo di eliminarlo e di inviare una comunicazione
all’indirizzo e-mail del mittente.
--
The information transmitted is
intended only for the person or entity to which it is addressed and may
contain confidential and/or privileged material. If you received this in
error, please contact the sender and delete the material.
Re: How to add the UMLS credential [EXTERNAL]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
That's unfortunate but great to know, and good to know about the
changes you needed as well.
Thanks
Tim
On Wed, 2020-12-16 at 08:31 -0500, Alain Leblanc wrote:
> * External Email - Caution *
>
> The old user/password method stopped working for me a week or so ago.
> However I was able to use the api key method after checking out the
> latest (as of last week) source code from subversion and building
> locally. The only changes I had to make was to set the environment
> variables ctakes.umlsaddr to
> https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise the old url
> was used) and ctakes.umls_apikey to my api key.
>
> Roberto if you need more detailed instructions I can post them.
>
> a
>
>
> Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> a écrit :
> > Hi Roberto,
> > The existing mechanism should be functional until January 15. After
> > that point changes to the cTAKES code are required to use the new
> > UMLS authentication mechanism. We are working on this and will
> > release patches and/or new releases.
> >
> > Tim
> >
> >
> > On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> > > * External Email - Caution *
> > >
> > >
> > > Dear All,
> > >
> > > I'm new to cTAKES and I'd like to analyze some texts by using
> > > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
> > >
> > > According to the runctakesCVD file, to enable the use of the UMLS
> > > resources you have to set your UMLS credential, i.e.,
> > > Dctakes.umlsuser, Dctakes.umlspw
> > >
> > > Since, UMLS Terminology Services accounts have been migrated to a
> > > service that allows you to sign in to UTS using Google,
> > Microsoft,
> > > ... I don't have any username and password with which to set the
> > > variables above. Do you have any suggestions?
> > >
> > > Thanks in advance
> > > Roberto
> > >
> > >
> > >
> > >
> > > --
> > > Le informazioni contenute nella presente comunicazione sono di
> > > natura privata e come tali sono da considerarsi riservate ed
> > > indirizzate esclusivamente ai destinatari indicati e per le
> > finalità
> > > strettamente legate al relativo contenuto. Se avete ricevuto
> > questo
> > > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> > > comunicazione all’indirizzo e-mail del mittente.
> > > --
> > > The information transmitted is intended only for the person or
> > entity
> > > to which it is addressed and may contain confidential and/or
> > > privileged material. If you received this in error, please
> > contact
> > > the sender and delete the material.
Re: How to add the UMLS credential [EXTERNAL]
Posted by Alain Leblanc <aa...@gmail.com>.
The old user/password method stopped working for me a week or so ago.
However I was able to use the api key method after checking out the latest
(as of last week) source code from subversion and building locally. The
only changes I had to make was to set the environment variables
ctakes.umlsaddr to https://utslogin.nlm.nih.gov/cas/v1/api-key (otherwise
the old url was used) and ctakes.umls_apikey to my api key.
Roberto if you need more detailed instructions I can post them.
a
Le mer. 16 déc. 2020 à 06:37, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> a écrit :
> Hi Roberto,
> The existing mechanism should be functional until January 15. After
> that point changes to the cTAKES code are required to use the new UMLS
> authentication mechanism. We are working on this and will release patches
> and/or new releases.
>
> Tim
>
>
> On Wed, 2020-12-16 at 10:12 +0100, Roberto Zanoli wrote:
> > * External Email - Caution *
> >
> >
> > Dear All,
> >
> > I'm new to cTAKES and I'd like to analyze some texts by using
> > AggregatePlaintextUMLSProcessor that requires the UMLS resource.
> >
> > According to the runctakesCVD file, to enable the use of the UMLS
> > resources you have to set your UMLS credential, i.e.,
> > Dctakes.umlsuser, Dctakes.umlspw
> >
> > Since, UMLS Terminology Services accounts have been migrated to a
> > service that allows you to sign in to UTS using Google, Microsoft,
> > ... I don't have any username and password with which to set the
> > variables above. Do you have any suggestions?
> >
> > Thanks in advance
> > Roberto
> >
> >
> >
> >
> > --
> > Le informazioni contenute nella presente comunicazione sono di
> > natura privata e come tali sono da considerarsi riservate ed
> > indirizzate esclusivamente ai destinatari indicati e per le finalità
> > strettamente legate al relativo contenuto. Se avete ricevuto questo
> > messaggio per errore, vi preghiamo di eliminarlo e di inviare una
> > comunicazione all’indirizzo e-mail del mittente.
> > --
> > The information transmitted is intended only for the person or entity
> > to which it is addressed and may contain confidential and/or
> > privileged material. If you received this in error, please contact
> > the sender and delete the material.
>