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Posted to dev@ctakes.apache.org by Dewful <de...@gmail.com> on 2014/01/04 19:23:18 UTC
UMLS Env variables suggestion
In the documentation, in the .sh files to run ctakes;
# If you plan to use the UMLS Resources, set/export env variables
# export ctakes.umlsuser=[username], ctakes.umlspw=[password]
however, simply trying to
export ctakes.umlsuser=myusername, ctakes.umlspw=mypassword
doesnt work because bash3 doesnt allow dots in the keyname and will throw
an error
bin/runctakesCVD.sh: line 42: export: `ctakes.umlsuser=username,': not a
valid identifier
http://stackoverflow.com/questions/15016403/how-to-export-dot-separated-environment-variablesexplains
some solutions
it may be helpful to show how the user can set these easily if they want to
set the env variables this way, possibly using one of the suggestions in SO.
N
RE: UMLS Env variables suggestion
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Sounds good. And I suggest the removal wait until 4.0 or later so we don't break anyone currently using dots during a minor release.
-----Original Message-----
From: dev-return-2363-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2363-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Chen, Pei
Sent: Monday, January 06, 2014 9:55 AM
To: dev@ctakes.apache.org
Subject: RE: UMLS Env variables suggestion
Sounds like a good idea;
we can just update all of the documentation/scripts to use underscore (_), and leave the dot (.) in the code to be deprecated for now?
--Pei
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Saturday, January 04, 2014 10:10 PM
> To: dev@ctakes.apache.org
> Subject: RE: UMLS Env variables suggestion
>
> This went in to 3.1 https://issues.apache.org/jira/browse/CTAKES-164
>
> I agree - the docs need to be updated if there is consensus on the use of this
> method. Personally I think that there should be one supported method, not
> both dot and underscore. I would prefer that we remove the dot
> functionality since it is not operational across all environments, but it isn't up
> to me alone to remove functionality.
>
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Saturday, January 04, 2014 4:08 PM
> To: <de...@ctakes.apache.org>
> Cc: dev@ctakes.apache.org
> Subject: Re: UMLS Env variables suggestion
>
> I believe Sean updated the code to also support underscore (_) as well. But
> the docs just need to be updated...
>
>
> > On Jan 4, 2014, at 4:04 PM, "Dewful" <de...@gmail.com> wrote:
> >
> > In the documentation, in the .sh files to run ctakes;
> >
> > # If you plan to use the UMLS Resources, set/export env variables #
> > export ctakes.umlsuser=[username], ctakes.umlspw=[password]
> >
> > however, simply trying to
> >
> > export ctakes.umlsuser=myusername, ctakes.umlspw=mypassword
> >
> > doesnt work because bash3 doesnt allow dots in the keyname and will
> > throw an error
> >
> > bin/runctakesCVD.sh: line 42: export: `ctakes.umlsuser=username,': not
> > a valid identifier
> >
> > http://stackoverflow.com/questions/15016403/how-to-export-dot-
> separate
> > d-environment-variablesexplains
> > some solutions
> >
> > it may be helpful to show how the user can set these easily if they
> > want to set the env variables this way, possibly using one of the
> suggestions in SO.
> >
> > N
RE: UMLS Env variables suggestion
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
+1
-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Monday, January 06, 2014 10:57 AM
To: dev@ctakes.apache.org
Subject: RE: UMLS Env variables suggestion
Sounds like a good idea;
we can just update all of the documentation/scripts to use underscore (_), and leave the dot (.) in the code to be deprecated for now?
--Pei
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Saturday, January 04, 2014 10:10 PM
> To: dev@ctakes.apache.org
> Subject: RE: UMLS Env variables suggestion
>
> This went in to 3.1 https://issues.apache.org/jira/browse/CTAKES-164
>
> I agree - the docs need to be updated if there is consensus on the use
> of this method. Personally I think that there should be one supported
> method, not both dot and underscore. I would prefer that we remove
> the dot functionality since it is not operational across all
> environments, but it isn't up to me alone to remove functionality.
>
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Saturday, January 04, 2014 4:08 PM
> To: <de...@ctakes.apache.org>
> Cc: dev@ctakes.apache.org
> Subject: Re: UMLS Env variables suggestion
>
> I believe Sean updated the code to also support underscore (_) as
> well. But the docs just need to be updated...
>
>
> > On Jan 4, 2014, at 4:04 PM, "Dewful" <de...@gmail.com> wrote:
> >
> > In the documentation, in the .sh files to run ctakes;
> >
> > # If you plan to use the UMLS Resources, set/export env variables #
> > export ctakes.umlsuser=[username], ctakes.umlspw=[password]
> >
> > however, simply trying to
> >
> > export ctakes.umlsuser=myusername, ctakes.umlspw=mypassword
> >
> > doesnt work because bash3 doesnt allow dots in the keyname and will
> > throw an error
> >
> > bin/runctakesCVD.sh: line 42: export: `ctakes.umlsuser=username,':
> > not a valid identifier
> >
> > http://stackoverflow.com/questions/15016403/how-to-export-dot-
> separate
> > d-environment-variablesexplains
> > some solutions
> >
> > it may be helpful to show how the user can set these easily if they
> > want to set the env variables this way, possibly using one of the
> suggestions in SO.
> >
> > N
RE: UMLS Env variables suggestion
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Sounds like a good idea;
we can just update all of the documentation/scripts to use underscore (_), and leave the dot (.) in the code to be deprecated for now?
--Pei
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Saturday, January 04, 2014 10:10 PM
> To: dev@ctakes.apache.org
> Subject: RE: UMLS Env variables suggestion
>
> This went in to 3.1 https://issues.apache.org/jira/browse/CTAKES-164
>
> I agree - the docs need to be updated if there is consensus on the use of this
> method. Personally I think that there should be one supported method, not
> both dot and underscore. I would prefer that we remove the dot
> functionality since it is not operational across all environments, but it isn't up
> to me alone to remove functionality.
>
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Saturday, January 04, 2014 4:08 PM
> To: <de...@ctakes.apache.org>
> Cc: dev@ctakes.apache.org
> Subject: Re: UMLS Env variables suggestion
>
> I believe Sean updated the code to also support underscore (_) as well. But
> the docs just need to be updated...
>
>
> > On Jan 4, 2014, at 4:04 PM, "Dewful" <de...@gmail.com> wrote:
> >
> > In the documentation, in the .sh files to run ctakes;
> >
> > # If you plan to use the UMLS Resources, set/export env variables #
> > export ctakes.umlsuser=[username], ctakes.umlspw=[password]
> >
> > however, simply trying to
> >
> > export ctakes.umlsuser=myusername, ctakes.umlspw=mypassword
> >
> > doesnt work because bash3 doesnt allow dots in the keyname and will
> > throw an error
> >
> > bin/runctakesCVD.sh: line 42: export: `ctakes.umlsuser=username,': not
> > a valid identifier
> >
> > http://stackoverflow.com/questions/15016403/how-to-export-dot-
> separate
> > d-environment-variablesexplains
> > some solutions
> >
> > it may be helpful to show how the user can set these easily if they
> > want to set the env variables this way, possibly using one of the
> suggestions in SO.
> >
> > N
RE: UMLS Env variables suggestion
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
This went in to 3.1 https://issues.apache.org/jira/browse/CTAKES-164
I agree - the docs need to be updated if there is consensus on the use of this method. Personally I think that there should be one supported method, not both dot and underscore. I would prefer that we remove the dot functionality since it is not operational across all environments, but it isn't up to me alone to remove functionality.
-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Saturday, January 04, 2014 4:08 PM
To: <de...@ctakes.apache.org>
Cc: dev@ctakes.apache.org
Subject: Re: UMLS Env variables suggestion
I believe Sean updated the code to also support underscore (_) as well. But the docs just need to be updated...
> On Jan 4, 2014, at 4:04 PM, "Dewful" <de...@gmail.com> wrote:
>
> In the documentation, in the .sh files to run ctakes;
>
> # If you plan to use the UMLS Resources, set/export env variables #
> export ctakes.umlsuser=[username], ctakes.umlspw=[password]
>
> however, simply trying to
>
> export ctakes.umlsuser=myusername, ctakes.umlspw=mypassword
>
> doesnt work because bash3 doesnt allow dots in the keyname and will
> throw an error
>
> bin/runctakesCVD.sh: line 42: export: `ctakes.umlsuser=username,': not
> a valid identifier
>
> http://stackoverflow.com/questions/15016403/how-to-export-dot-separate
> d-environment-variablesexplains
> some solutions
>
> it may be helpful to show how the user can set these easily if they
> want to set the env variables this way, possibly using one of the suggestions in SO.
>
> N
Re: UMLS Env variables suggestion
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I believe Sean updated the code to also support underscore (_) as well. But the docs just need to be updated...
> On Jan 4, 2014, at 4:04 PM, "Dewful" <de...@gmail.com> wrote:
>
> In the documentation, in the .sh files to run ctakes;
>
> # If you plan to use the UMLS Resources, set/export env variables
> # export ctakes.umlsuser=[username], ctakes.umlspw=[password]
>
> however, simply trying to
>
> export ctakes.umlsuser=myusername, ctakes.umlspw=mypassword
>
> doesnt work because bash3 doesnt allow dots in the keyname and will throw
> an error
>
> bin/runctakesCVD.sh: line 42: export: `ctakes.umlsuser=username,': not a
> valid identifier
>
> http://stackoverflow.com/questions/15016403/how-to-export-dot-separated-environment-variablesexplains
> some solutions
>
> it may be helpful to show how the user can set these easily if they want to
> set the env variables this way, possibly using one of the suggestions in SO.
>
> N