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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: YTEX cTAKES 3.1.1 ready
Date Thu, 06 Feb 2014 04:18:31 GMT
Hi Vijay,
I gave you write access to the cTAKES space on the confluence site

-- James

-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com] 
Sent: Wednesday, February 05, 2014 8:29 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 which most probably is outdated, talks about installing cTakes 3.1.1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.zip
>>>
>>> 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/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=1388793998&updated=Installation_cTAKES_3_1
>>>>>
>>>>> Best,
>>>>>
>>>>> VJ
>>>>>
>>>>>
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>
>

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