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Posted to dev@ctakes.apache.org by "John David Osborne (Campus)" <oz...@uab.edu> on 2014/02/11 00:25:59 UTC
YTEX LVG Fix
These were the changes I made to get the YTEX pipeline working with LVG (2008). It looks like there were just a couple of spots with some old hard-coded paths in SetupAUIFirstWord.java that were appropriate to the old ytex directory structure.
For now I have just swapped them out to fit with the new directory structure, but I suppose the correct fix may be to extract them out somewhere... In any case I don't have write privileges, some someone else may want to fix this (Vijay?)
I also included the YTEXPipeline.xml descriptor file I fixed as well in case anybody needs it.
-John
RE: YTEX LVG Fix
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
> Don't know how we'd find out if anyone is still using it.
I think we can start with the dev@ and user@ mailing lists to see if they're still using PAD Term spotter.
And let them know the plans of removing it in the future major release.
I can volunteer some time for that...
>
> +1 for upgrading resources.
>
> -----Original Message-----
> From: Pei Chen [mailto:chenpei@apache.org]
> Sent: Wednesday, February 12, 2014 10:38 AM
> To: dev@ctakes.apache.org
> Subject: Re: YTEX LVG Fix
>
> +1 for upgrading the LVG resources...
> Not sure how many people are still using the pad term spotter module-
> perhaps we could think about deprecating it if no one is using it??
> --Pei
>
>
> On Wed, Feb 12, 2014 at 11:24 AM, John David Osborne (Campus) <
> ozborn@uab.edu> wrote:
>
> > Thanks Vijay.
> >
> > I'm going to do the rebuild, but one thing I noticed is that YTEX is
> > using the 2008 version of LVG and the old PAD term spotter looks like
> > it is using the one from 2004!
> >
> > I guess they can both use different versions (each one living in its
> > own directory), but given how dated that LVG is (and the number of
> > improvements) maybe we should upgrade and/or share LVG? What do
> others
> > think?
> >
> > I'm likely going to do the rebuild of the ytex branch with an newer
> > version of LVG and see how it goes. I'm not sure how the PAD term
> > spotter would like that though - it looks like it is using MySQL instead of
> HSQL.
> >
> > --
> > John David Osborne
> >
> > Research Associate
> > University of Alabama at Birmingham
> > Biomedical Informatics
> > Center for Clinical and Translational Science
> > 1720 7th Avenue South
> > Sparks Building, Suite 175
> > Birmingham, AL, 35294
> >
> >
> >
> >
> >
> > On 2/11/14 8:19 PM, "vijay garla" <vn...@gmail.com> wrote:
> >
> > >Hi John,
> > >
> > >Thanks for this. I've updated the YTEXPipeline, fixed the lvg paths
> > >in SetupAUIFirstWord.
> > >
> > >If you want to re-run SetupAUIFirstWord (not necessary unless you are
> > >using the stemmed words for dictionary lookup), just svn update,
> > >rebuild ctakes-ytex-uima, and copy the jar to the lib dir of your
> > >ctakes install.
> > >
> > >Best,
> > >
> > >VJ
> > >
> > >
> > >On Mon, Feb 10, 2014 at 6:25 PM, John David Osborne (Campus)
> > ><ozborn@uab.edu
> > >> wrote:
> > >
> > >> These were the changes I made to get the YTEX pipeline working
> > >>with LVG (2008). It looks like there were just a couple of spots
> > >>with some old hard-coded paths in SetupAUIFirstWord.java that were
> > >>appropriate to the old ytex directory structure.
> > >>
> > >> For now I have just swapped them out to fit with the new directory
> > >>structure, but I suppose the correct fix may be to extract them out
> > >>somewhere... In any case I don't have write privileges, some
> > >>someone else may want to fix this (Vijay?)
> > >>
> > >> I also included the YTEXPipeline.xml descriptor file I fixed as
> > >> well in case anybody needs it.
> > >>
> > >> -John
> > >>
> > >>
> > >>
> >
> >
RE: YTEX LVG Fix
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Don't know how we'd find out if anyone is still using it.
+1 for upgrading resources.
-----Original Message-----
From: Pei Chen [mailto:chenpei@apache.org]
Sent: Wednesday, February 12, 2014 10:38 AM
To: dev@ctakes.apache.org
Subject: Re: YTEX LVG Fix
+1 for upgrading the LVG resources...
Not sure how many people are still using the pad term spotter module-
perhaps we could think about deprecating it if no one is using it??
--Pei
On Wed, Feb 12, 2014 at 11:24 AM, John David Osborne (Campus) <
ozborn@uab.edu> wrote:
> Thanks Vijay.
>
> I'm going to do the rebuild, but one thing I noticed is that YTEX is using
> the 2008 version of LVG and the old PAD term spotter looks like it is
> using the one from 2004!
>
> I guess they can both use different versions (each one living in its own
> directory), but given how dated that LVG is (and the number of
> improvements) maybe we should upgrade and/or share LVG? What do others
> think?
>
> I'm likely going to do the rebuild of the ytex branch with an newer
> version of LVG and see how it goes. I'm not sure how the PAD term spotter
> would like that though - it looks like it is using MySQL instead of HSQL.
>
> --
> John David Osborne
>
> Research Associate
> University of Alabama at Birmingham
> Biomedical Informatics
> Center for Clinical and Translational Science
> 1720 7th Avenue South
> Sparks Building, Suite 175
> Birmingham, AL, 35294
>
>
>
>
>
> On 2/11/14 8:19 PM, "vijay garla" <vn...@gmail.com> wrote:
>
> >Hi John,
> >
> >Thanks for this. I've updated the YTEXPipeline, fixed the lvg paths in
> >SetupAUIFirstWord.
> >
> >If you want to re-run SetupAUIFirstWord (not necessary unless you are
> >using
> >the stemmed words for dictionary lookup), just svn update, rebuild
> >ctakes-ytex-uima, and copy the jar to the lib dir of your ctakes install.
> >
> >Best,
> >
> >VJ
> >
> >
> >On Mon, Feb 10, 2014 at 6:25 PM, John David Osborne (Campus)
> ><ozborn@uab.edu
> >> wrote:
> >
> >> These were the changes I made to get the YTEX pipeline working with LVG
> >> (2008). It looks like there were just a couple of spots with some old
> >> hard-coded paths in SetupAUIFirstWord.java that were appropriate to the
> >>old
> >> ytex directory structure.
> >>
> >> For now I have just swapped them out to fit with the new directory
> >> structure, but I suppose the correct fix may be to extract them out
> >> somewhere... In any case I don't have write privileges, some someone
> >>else
> >> may want to fix this (Vijay?)
> >>
> >> I also included the YTEXPipeline.xml descriptor file I fixed as well in
> >> case anybody needs it.
> >>
> >> -John
> >>
> >>
> >>
>
>
Re: YTEX LVG Fix
Posted by Pei Chen <ch...@apache.org>.
+1 for upgrading the LVG resources...
Not sure how many people are still using the pad term spotter module-
perhaps we could think about deprecating it if no one is using it??
--Pei
On Wed, Feb 12, 2014 at 11:24 AM, John David Osborne (Campus) <
ozborn@uab.edu> wrote:
> Thanks Vijay.
>
> I'm going to do the rebuild, but one thing I noticed is that YTEX is using
> the 2008 version of LVG and the old PAD term spotter looks like it is
> using the one from 2004!
>
> I guess they can both use different versions (each one living in its own
> directory), but given how dated that LVG is (and the number of
> improvements) maybe we should upgrade and/or share LVG? What do others
> think?
>
> I'm likely going to do the rebuild of the ytex branch with an newer
> version of LVG and see how it goes. I'm not sure how the PAD term spotter
> would like that though - it looks like it is using MySQL instead of HSQL.
>
> --
> John David Osborne
>
> Research Associate
> University of Alabama at Birmingham
> Biomedical Informatics
> Center for Clinical and Translational Science
> 1720 7th Avenue South
> Sparks Building, Suite 175
> Birmingham, AL, 35294
>
>
>
>
>
> On 2/11/14 8:19 PM, "vijay garla" <vn...@gmail.com> wrote:
>
> >Hi John,
> >
> >Thanks for this. I've updated the YTEXPipeline, fixed the lvg paths in
> >SetupAUIFirstWord.
> >
> >If you want to re-run SetupAUIFirstWord (not necessary unless you are
> >using
> >the stemmed words for dictionary lookup), just svn update, rebuild
> >ctakes-ytex-uima, and copy the jar to the lib dir of your ctakes install.
> >
> >Best,
> >
> >VJ
> >
> >
> >On Mon, Feb 10, 2014 at 6:25 PM, John David Osborne (Campus)
> ><ozborn@uab.edu
> >> wrote:
> >
> >> These were the changes I made to get the YTEX pipeline working with LVG
> >> (2008). It looks like there were just a couple of spots with some old
> >> hard-coded paths in SetupAUIFirstWord.java that were appropriate to the
> >>old
> >> ytex directory structure.
> >>
> >> For now I have just swapped them out to fit with the new directory
> >> structure, but I suppose the correct fix may be to extract them out
> >> somewhere... In any case I don't have write privileges, some someone
> >>else
> >> may want to fix this (Vijay?)
> >>
> >> I also included the YTEXPipeline.xml descriptor file I fixed as well in
> >> case anybody needs it.
> >>
> >> -John
> >>
> >>
> >>
>
>
Re: YTEX LVG Fix
Posted by "John David Osborne (Campus)" <oz...@uab.edu>.
Thanks Vijay.
I'm going to do the rebuild, but one thing I noticed is that YTEX is using
the 2008 version of LVG and the old PAD term spotter looks like it is
using the one from 2004!
I guess they can both use different versions (each one living in its own
directory), but given how dated that LVG is (and the number of
improvements) maybe we should upgrade and/or share LVG? What do others
think?
I'm likely going to do the rebuild of the ytex branch with an newer
version of LVG and see how it goes. I'm not sure how the PAD term spotter
would like that though - it looks like it is using MySQL instead of HSQL.
--
John David Osborne
Research Associate
University of Alabama at Birmingham
Biomedical Informatics
Center for Clinical and Translational Science
1720 7th Avenue South
Sparks Building, Suite 175
Birmingham, AL, 35294
On 2/11/14 8:19 PM, "vijay garla" <vn...@gmail.com> wrote:
>Hi John,
>
>Thanks for this. I've updated the YTEXPipeline, fixed the lvg paths in
>SetupAUIFirstWord.
>
>If you want to re-run SetupAUIFirstWord (not necessary unless you are
>using
>the stemmed words for dictionary lookup), just svn update, rebuild
>ctakes-ytex-uima, and copy the jar to the lib dir of your ctakes install.
>
>Best,
>
>VJ
>
>
>On Mon, Feb 10, 2014 at 6:25 PM, John David Osborne (Campus)
><ozborn@uab.edu
>> wrote:
>
>> These were the changes I made to get the YTEX pipeline working with LVG
>> (2008). It looks like there were just a couple of spots with some old
>> hard-coded paths in SetupAUIFirstWord.java that were appropriate to the
>>old
>> ytex directory structure.
>>
>> For now I have just swapped them out to fit with the new directory
>> structure, but I suppose the correct fix may be to extract them out
>> somewhere... In any case I don't have write privileges, some someone
>>else
>> may want to fix this (Vijay?)
>>
>> I also included the YTEXPipeline.xml descriptor file I fixed as well in
>> case anybody needs it.
>>
>> -John
>>
>>
>>
Re: YTEX LVG Fix
Posted by vijay garla <vn...@gmail.com>.
Hi John,
Thanks for this. I've updated the YTEXPipeline, fixed the lvg paths in
SetupAUIFirstWord.
If you want to re-run SetupAUIFirstWord (not necessary unless you are using
the stemmed words for dictionary lookup), just svn update, rebuild
ctakes-ytex-uima, and copy the jar to the lib dir of your ctakes install.
Best,
VJ
On Mon, Feb 10, 2014 at 6:25 PM, John David Osborne (Campus) <ozborn@uab.edu
> wrote:
> These were the changes I made to get the YTEX pipeline working with LVG
> (2008). It looks like there were just a couple of spots with some old
> hard-coded paths in SetupAUIFirstWord.java that were appropriate to the old
> ytex directory structure.
>
> For now I have just swapped them out to fit with the new directory
> structure, but I suppose the correct fix may be to extract them out
> somewhere... In any case I don't have write privileges, some someone else
> may want to fix this (Vijay?)
>
> I also included the YTEXPipeline.xml descriptor file I fixed as well in
> case anybody needs it.
>
> -John
>
>
>