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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: YTEX cTAKES 3.1.1 ready
Date Thu, 06 Feb 2014 15:19:39 GMT
VJ,
Aside from the changes to the existing cTAKES code (sentence detector, etc.) [which we could
leave out if it's still being debated], 
Do you think it's worth migrating the ytex code to trunk at this point?  As you mentioned
earlier, it's largely complementary.
[I was just thinking of saving effort to maintain the separate branch and for simplicity for
dev...]

--Pei

> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Wednesday, February 05, 2014 9:30 PM
> To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> vlad.valtchinov@gmail.com
> Subject: Re: YTEX cTAKES 3.1.1 ready
> 
> Hi Vlad,
> 
> I Updated the umls install guide; see
> https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
> 
> I would prefer to add the docs in the ctakes confluence, but as far as I can
> tell, I don't have write access there - can somebody give me write privileges
> on the ctakes confluence site?
> 
> There was a bug in the umls install; copy
> https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> ytex/scripts/data/build.xmlover
> the corresponding file in your ctakes-3.1.2 install
> (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set.  The
> import is currently running on the UMLS 2013AA (I assume this will complete
> without issues as long as the umls schema hasn't changed from 2012).
> 
> what trial and error did you have to go through to build the distro?
> 
> -vj
> 
> 
> On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vngarla@gmail.com> wrote:
> 
> > Hi Vlad,
> >
> > sorry that the instructions aren't clear.
> >
> > re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot
> > as usual (this is unchanged from 3.1.1).  After that you still have to
> > apply the lib and resources (these are things that cannot be
> > distributed via apache).
> >
> > re 2) Yes, I need to update those docs.  Hopefully will get to that at
> > some point.  However, I assume you already have a UMLS DB (also assume
> > SQL Server).  If you can't/don't want to use your existing umls DB,
> > please tell me.  The I'll priortize upgrading the doc on importing the
> > umls tables (the scripts are there).
> >
> > best,
> >
> > VJ
> >
> >
> > On Wed, Feb 5, 2014 at 4:44 PM, <vlad.valtchinov@gmail.com> wrote:
> >
> >> Hi VJ-
> >>
> >> so, with trial and error were able to make the distribution and now
> >> have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> >>
> >> Here's what's unclear.
> >>
> >> 1. Is now this the only (combined) thing that you need for ctakes
> >> 3.1.1 + Ytex?
> >> the current documentation (https://code.google.com/p/yte
> >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> >> lation_cTAKES_3_1)
> >> which most probably is outdated, talks about installing cTakes 3.1.1
> >> first and then applying 2 SNAPSHOT archives (downloadable) , lib and
> >> resources.
> >> This is a confusion point.
> >>
> >> 2. The directions to import UMLS subset are then outdated as well.
> >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8) to
> >> import the RRF files for the UMLS subset and then just use the
> >> resulting db. Thoughts?
> >>
> >> Thanks,
> >> Vlad Valtchinov
> >> Brigham Rad
> >>
> >>
> >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> >>
> >>> Hi Vlad,
> >>>
> >>>
> >> All of ytex has been moved into ctakes, it is currently in a branch (
> >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex).  You don't
> >>> have to install ytex-0.8 - instead you will have to build and
> >>> install from the ytex branch to create your own distribution.  Steps 2 &
3
> are correct.
> >>>
> >>> Although it is a pain, if you have the jdk, maven, and svn, you can
> >>> easily build your own distro:
> >>> * open a command prompt
> >>> * make sure jdk, maven, and svn are in your path
> >>> * cd to some directory where you want to check stuff out (I like
> >>> c:\temp)
> >>> * run the following commands
> >>> rmdir /s /q ctakes
> >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
> >>> cd ctakes mvn clean install -DskipTests
> >>>
> >>> And you will have the ctakes (with ytex) distro in
> >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.z
> >>> ip
> >>>
> >>> What is the process for getting the ytex branch merged into trunk?
> >>> As I mentioned, there are very few changes to other ctakes
> >>> classes/types - this should be completely complementary and not
> >>> affect any existing ctakes functionality.
> >>>
> >>> -vj
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, Jan 30, 2014 at 4:56 PM, <vlad.va...@gmail.com> wrote:
> >>>
> >>>> Hi VJ--
> >>>>
> >>>> this is great!! Thanks for all the hard work on it!
> >>>>
> >>>> We're starting to look into the new install. For now we're trying
> >>>> the binaries out.
> >>>>
> >>>> There were these questions about the proper install steps:
> >>>>
> >>>> 1. Do we first install ytex-0.8
> >>>> 2. Then install the new cTakes 3.1.1 instance and also apply the
> >>>> SNAPSHOT lib and resources zips 3. Work our way to install the UMLS
> >>>> ontologies in the db
> >>>>
> >>>> Its is not entirely clear from the new document (
> >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> >>>> if there's still need to install ytex-0.8, or YTEX has been
> >>>> entirely merged into cTakes?
> >>>>
> >>>> If the last statement is correct, there are missing parts in i.e
> >>>> the UMLS install steps that are linked from the new ctakes 3.1.1
> document.
> >>>>
> >>>> Thanks,
> >>>> vlad
> >>>>
> >>>>
> >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> >>>>>
> >>>>> 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/medfac
> >>>>> ts/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=1388793998&updated=Installation_cTAKES_3_1
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> VJ
> >>>>>
> >>>>>
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