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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 22:23:53 GMT
Ill play with it tonight or tomorrow night.


JG
—
Sent from Mailbox for iPhone

On Tue, Jul 22, 2014 at 4:27 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

> There is currently no guides on the confluence wiki for cTAKES 3.2.0...
> I was thinking of just cloning 3.1.1
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.1
> And just add the YTEX and/or any new changes to it...
> Would be grateful for any help here...
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Tuesday, July 22, 2014 2:37 PM
>> To: dev@ctakes.apache.org
>> Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
>> 
>> 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-resourc
>> > > es
>> > > -
>> > > 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.d
>> > > a
>> > > > > 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-ct
>> > > > > ak
>> > > > > 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-ct
>> > > > > ak
>> > > > > 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-ct
>> > > > > ak
>> > > > > 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-ct
>> > > > > ak
>> > > > > 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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