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From John Green <john.travis.gr...@gmail.com>
Subject Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Date Tue, 22 Jul 2014 18:36:01 GMT
What exactly needs updated? I have not had the time (unfortunately) to help
with this project very much because of the steep learning curve on the
technology. I'm currently on some protected research time working with
cTakes as of this week and would be happy to help with some grunt work.

JG


On Tue, Jul 22, 2014 at 11:39 AM, Bleeker, Troy C. <Bleeker.Troy@mayo.edu>
wrote:

> One page at a time. At least there's that.
>
> Thanks
> Troy
> -----Original Message-----
> From: Masanz, James J.
> Sent: Tuesday, July 22, 2014 10:38 AM
> To: 'dev@ctakes.apache.org'
> Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
>
> When I asked Troy that question for 3.1.1, he didn't know of a way, and I
> don't either, which is why I had the 3.1.1 page mostly just reference the
> 3.2 documentation.
>
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Tuesday, July 22, 2014 10:00 AM
> To: dev@ctakes.apache.org
> Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
>
> Thanks James.
> I was planning on closing the vote today.
> In the meantime, does anyone a quick way to clone/rename the wiki
> documentation for 3.2?
> --Pei
>
> > -----Original Message-----
> > From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> > Sent: Monday, July 21, 2014 4:25 PM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> >
> > Here's the additional I've done
> >
> > I ran "mvn test" with 0 Failures and 0 Errors.
> > Ran the AggregateTemplateFiller.xml and received same output (except
> > for internal UIMA identifiers) with rc2 as I did with 3.1.1.
> >
> > +1 to release
> >
> > -----Original Message-----
> > From: Masanz, James J.
> > Sent: Wednesday, July 16, 2014 3:59 PM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> >
> > FYI, so far I have done the following steps:
> >
> > downloaded the source archive
> > compiled it using: maven compile
> > downloaded the separately available resources set up classpath to
> > include e.g. jars (from the bin distribution) set ctakes.umlsuser and
> > ctakes.umlspw env vars run  runctakesCVD.bat loaded
> > AggregatePlaintextUMLSProcessor.xml
> > ran against some simple text.
> > verified did not through an exception.
> > verified some EventMention and EntityMention annotations were produced.
> >
> > I will do more testing tomorrow. Just giving a status update.
> >
> > --James
> >
> > -----Original Message-----
> > From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
> > Sent: Saturday, July 12, 2014 6:24 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> >
> > Agreed on that.
> >
> > I downloaded the new resources binary and was able to run my tests on
> > the - bin version of the RC.
> >
> > +1 for making this the release.
> >
> > Tim
> >
> >
> > ________________________________________
> > From: Masanz, James J. [Masanz.James@mayo.edu]
> > Sent: Friday, July 11, 2014 7:27 PM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> >
> > I agree about keeping the thread open.
> >
> > -- James
> >
> > -----Original Message-----
> > From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> > Sent: Friday, July 11, 2014 4:28 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> >
> > Updated the lvg.properties file within ctakes-resources on sourceforge
> [1].
> > Since the Apache cTAKES artifacts didn't change, I would like to keep
> > this VOTE thread open.
> >
> > Also renamed it to 3.2.0 (even though they technically do not have to
> > follow each other, but probably nice to keep it consistent for users
> > as James
> > suggested.) [1]
> > http://sourceforge.net/projects/ctakesresources/files/ctakes-resources
> > -
> > 3.2.0.zip/download
> >
> > > -----Original Message-----
> > > From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> > > Sent: Thursday, July 10, 2014 5:53 PM
> > > To: 'dev@ctakes.apache.org'
> > > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> > >
> > > Can you also give ctakesresources the number 3.2 or 3.2.0 instead of
> > > 3.1.3
> > >
> > > -----Original Message-----
> > > From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> > > Sent: Thursday, July 10, 2014 2:12 PM
> > > To: dev@ctakes.apache.org
> > > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> > >
> > > I think this is due to the fact that the default lvg.properties also
> > > exits in the ctakes-resources project, so if you download and
> > > replace, it will override the ctakes configured one.
> > > I think it's a bug, but probably always been there...
> > > I'll fix up ctakes-resources on sourceforge nethertheless but it
> > > shouldn't require any changes to the release candidates.
> > >
> > > > -----Original Message-----
> > > > From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> > > > Sent: Thursday, July 10, 2014 11:59 AM
> > > > To: 'dev@ctakes.apache.org'
> > > > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> > > >
> > > > Hi Tim,
> > > >
> > > > When you say that it didn't seem to affect the run, where you
> > > > comparing output to last release or just checking if data seemed
> > > > OK at a
> > > glance?
> > > >
> > > > -----Original Message-----
> > > > From: Miller, Timothy
> > > > [mailto:Timothy.Miller@childrens.harvard.edu]
> > > > Sent: Thursday, July 10, 2014 7:29 AM
> > > > To: dev@ctakes.apache.org
> > > > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> > > >
> > > > I was able to run the binary without issues this time.
> > > > I also downloaded the resources from sourceforge and integrated
> > > > into the bin release and ran with the ctakes dictionary.
> > > >
> > > > I did get some weird exceptions thrown that didn't seem to affect
> > > > the run -- looks like some hardcoded file paths in LVG? (See
> > > > below)
> > > >
> > > > Tim
> > > >
> > > >
> > > > Exception: java.io.FileNotFoundException:
> > > > /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data
> > > > (No such file or directory)
> > > > ** Error: problem of opening/reading stop words file:
> > > >
> > '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data
> > > > (No such file or directory)
> > > > ** Error: problem of opening/reading non-Info words file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.dat
> > > > a'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.d
> > > > ata (No such file or directory)
> > > > ** Error: problem of opening/reading conjunction words file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.
> > > > data'.
> > > > ** ERR: problem of opening/reading diacritics file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da
> > > > ta'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da
> > > > ta (No such file or directory)
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da
> > > > ta (No such file or directory)
> > > > ** Error: problem of opening/reading ligature file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da
> > > > ta'.
> > > > ** Error: problem of opening/reading symbol synonym file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.
> > > > data'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.d
> > > > ata (No such file or directory)
> > > > **Error: problem of opening/reading file
> > > > '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'.
> > > > Exception: java.io.FileNotFoundException:
> > > > /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data
> > > (No
> > > > such file or directory)
> > > > ** Error: problem of opening/reading Unicode symbol file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.da
> > > > ta'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.dat
> > > > a (No such file or directory)
> > > > ** Error: problem of opening/reading Unicode file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.d
> > > > ata'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.da
> > > > ta (No such file or directory)
> > > > ** Error: problem of opening/reading nonStripMap file:
> > > >
> > >
> > '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d
> > > > ata'.
> > > > Exception: java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d
> > > > ata (No such file or directory)
> > > > java.sql.SQLException: File input/output error
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properti
> > > > es java.io.FileNotFoundException:
> > > >
> > >
> > /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properti
> > > > es.new (No such file or directory)
> > > >
> > > > ________________________________________
> > > > From: Masanz, James J. [Masanz.James@mayo.edu]
> > > > Sent: Wednesday, July 09, 2014 2:26 PM
> > > > To: 'dev@ctakes.apache.org'
> > > > Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> > > >
> > > > So far for rc2, I've
> > > >
> > > > Verified MD5  and signatures of .zip archives Verified that source
> > > > at tag matches source in.zip Imported source from archive into
> > > > eclipse as maven
> > > > project(s) and compiled without any Errors.
> > > >
> > > > --  James
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Pei Chen [mailto:chenpei@apache.org]
> > > > Sent: Tuesday, July 08, 2014 5:11 PM
> > > > To: dev@ctakes.apache.org
> > > > Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
> > > >
> > > > Hi all,
> > > >
> > > > The main difference between rc1 and rc2 is that we removed the
> > > > lvg-res and assertion-res.jar from the distro.  They still need to
> > > > be
> > unpacked.
> > > >
> > > > This is a call for a vote on releasing the following candidate
> > > > (rc2) as Apache cTAKES 3.2.0.
> > > > The major changes include:
> > > > - New optional YTEX component(s) (Yale Extensions to cTAKES)
> > > > - New optional improved/faster dictionary lookup
> > > > (dictionary-lookup-fast)
> > > > - New optional Temporal component (Time + Event extraction.
> > > > Relations will be including in a future release.)
> > > > - Other bug fixes/enhancements from Jira
> > > >
> > > > [TODO: Online documentation still needs to be updated on wiki]
> > > >
> > > > For more detailed information on the changes/release notes, please
> visit:
> > > > https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=1
> > > > 23
> > > > 13
> > > > 621
> > > > &version=12324066
> > > >
> > > > The release was made using the cTAKES release process documented
> > here:
> > > > http://ctakes.apache.org/ctakes-release-guide.html
> > > >
> > > > The candidate is available at:
> > > > http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctak
> > > > es
> > > > -
> > > > 3.2.0-src.tar.gz
> > > > /.zip
> > > >
> > > > The tag to be voted on:
> > > > http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2
> > > >
> > > > The MD5 checksum of the tarball can be found at:
> > > > http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctak
> > > > es
> > > > -
> > > > 3.2.0-src.tar.gz.md5
> > > > /.zip.md5
> > > >
> > > > The signature of the tarball can be found at:
> > > > http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctak
> > > > es
> > > > -
> > > > 3.2.0-src.tar.gz.asc
> > > > /.zip.asc
> > > >
> > > > Apache cTAKES' KEYS file, containing the PGP keys used to sign the
> > release:
> > > > https://dist.apache.org/repos/dist/release/ctakes/KEYS
> > > >
> > > > Please vote on releasing these packages as Apache cTAKES 3.2.0.
> > > > The vote is open for at least the next 72 hours.
> > > > Only votes from the cTAKES PMC are binding, but folks are welcome
> > > > to check the release candidate and voice their approval or
> disapproval.
> > > > The vote passes if at least three binding +1 votes are cast.
> > > >
> > > > [ ] +1 Release the packages as Apache cTAKES 3.2.0 [ ] -1 Do not
> > > > release the packages because...
> > > >
> > > > Also, the convenience binary can be found at:
> > > > http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctak
> > > > es
> > > > -
> > > > 3.2.0-bin.tar.gz
> > > > /.zip
> > > >
> > > > Note: It's temporarily on people.a.o because the artifacts were
> > > > too large for https://dist.apache.org/repos/dist/dev/ctakes
> > > > (Working with infra on increasing the limit).
> > > >
> > > >
> > > > Thanks!
>

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