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From vijay garla <vnga...@gmail.com>
Subject Re: YTEX cTAKES 3.1.1 ready
Date Tue, 07 Jan 2014 16:00:29 GMT
see answers inline


On Tue, Jan 7, 2014 at 10:35 AM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

> > * How can I distribute the ctakes binary distribution to ytex users
> before the
> > merge? Can we make the branch build available somewhere?  The binary
> > distribution is too large to host on the ytex google code site (max 200
> MB)
> Is this for testing purposes?  Or official release? If it's just for
> testing, there will be more options...
> Are you referring to the convenience binary/zip file?  Or maven artifacts
> that could be deployed to the SNAPSHOTS repo [1]?
> If it's for testing, you can always have users build from source via mvn
> package (assuming you added the ytex* to the ctakes-distribution module)?
> Again if it's for testing, you can always try the svn or home dir.  But
> it's not the recommended channel for actual distribution to users because
> that normally has to go through the normal release process (Voting, etc.).
>

This is for testing.  Ytex has been added to the ctakes distro


>
> > * Non-ASF libraries - I have segregated these out into their own zip
> file that
> > can be distributed via sourceforge.  As a stopgap, I can upload this to
> the ytex
> > google code site, but would prefer to upload to sourceforge.
> Are these optional 3rd party libs available via maven central?
>

Most of them are.  The only exception is the MS SQL Driver, which is freely
redistributable (see http://msdn.microsoft.com/en-us/sqlserver/aa937725).
 I did not find anything similar for the oracle jdbc driver so I left that
out (users will have to download that separately).

The zip is here:
https://ytex.googlecode.com/files/ctakes-ytex-lib-3.1.2-SNAPSHOT.zip


>
> > * UMLS Derivatives - Ditto for these - would like to move to sourceforge.
> Are you planning to distribute them via maven central?  I think it would
> be nice to make these available as maven artifacts.
> If so, what is your sourceforge id? We can grant you access to the
> existing ctakes resourcse project [2]:
> The pom.xml is already setup to upload to OSS Sonatype (request a login
> for oss sonatype to perform a mvn deploy for the actual upload later on)...
>

I have placed the umls resources behind a server that requires UTS
authentication (note that this obviates the need for supplying umls
username and password in ctakes config files/scripts).

The umls resources are here:
http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip

This is a plain old apache http server with the module for CAS (the other
CAS) authentication.  If ctakes has an apache server somewhere, we could do
the same.


>
> > * Documentation - How can I update the confluence docs?  I would migrate
> > the documentation from the google code website.
> This would be great; You've been added to the cTAKES confluence space [3].
>
> Downloading the code now... To be continued...
>
> [1]
> https://repository.apache.org/content/groups/snapshots/org/apache/ctakes/
> [2] http://sourceforge.net/p/ctakesresources/code/HEAD/tree/trunk/
> [3] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES
>
> > -----Original Message-----
> > From: vijay garla [mailto:vngarla@gmail.com]
> > Sent: Friday, January 03, 2014 10:23 PM
> > To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org
> > Subject: YTEX cTAKES 3.1.1 ready
> >
> > Hello All,
> >
> > I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
>  Most of the
> > YTEX functionality has been ported and integrated with cTAKES, and I've
> > tested with MySQL and MS SQL Server (oracle tests pending).
> >
> > Most of the changes were made in new projects - very little existing
> cTAKES
> > code has been modified.  The only non-trivial changes are in /ctakes-
> > assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api
> > - here I modified CharacterOffsetToLineTokenConverterCtakesImpl &
> > SingleDocumentProcessorCtakes to deal with newlines within sentences
> > correctly.  Can somebody take a look at the changes in the ytex branch?
> >
> > I believe that the branch
> > https://svn.apache.org/repos/asf/ctakes/branches/ytex is ready to be
> > merged into ctakes trunk, but would like other users to test it as well.
> >  Questions:
> >
> > * How can I distribute the ctakes binary distribution to ytex users
> before the
> > merge? Can we make the branch build available somewhere?  The binary
> > distribution is too large to host on the ytex google code site (max 200
> MB)
> > * Non-ASF libraries - I have segregated these out into their own zip
> file that
> > can be distributed via sourceforge.  As a stopgap, I can upload this to
> the ytex
> > google code site, but would prefer to upload to sourceforge.
> > * UMLS Derivatives - Ditto for these - would like to move to sourceforge.
> > * Documentation - How can I update the confluence docs?  I would migrate
> > the documentation from the google code website.
> >
> > Here the installation instructions (putting the wagon in front of the
> horse
> > ...)
> >
> > https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?ts=13887939
> > 98&updated=Installation_cTAKES_3_1
> >
> > Best,
> >
> > VJ
>

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