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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: [VOTE] Release Apache cTAKES 3.1 (rc3)
Date Sun, 01 Sep 2013 18:28:15 GMT
Thanks for the review and the comments Tim.

I totally agree about #6 - Concept is not a good choice

I can take a look at #2 later. it sounds like the ctakesresources zip doesn't contain the
log4j.xml but I'm not sure why it's required there offhand.

To request a user ID on the wiki, go to this page
https://cwiki.apache.org/confluence/signup.action

________________________________________
From: dev-return-1926-Masanz.James=mayo.edu@ctakes.apache.org [dev-return-1926-Masanz.James=mayo.edu@ctakes.apache.org]
on behalf of Miller, Timothy [Timothy.Miller@childrens.harvard.edu]
Sent: Sunday, September 01, 2013 1:01 PM
To: dev@ctakes.apache.org
Subject: Re: [VOTE] Release Apache cTAKES 3.1 (rc3)

Going through the user install instructions (here: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide)
have a few questions (not all relating to the RC, but probably should be fixed concurrently
with the release so people can use it.

1) Step 4 under install is a little confusing: The first sentence is "Download [cTAKES 3.1
Dictionaries and Models]," where the brackets are a link, but not a link to the download site.
The download link is lower on the instruction.

2) Running the regular aggregate processor (no UMLS), I get an exception at the command line:
log4j:ERROR Could not parse url [file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.1.0/config/log4j.xml].
java.io.FileNotFoundException: /home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.1.0/config/log4j.xml
(No such file or directory)

3) Under Add UMLS Access Rights, step 3 is not necessary.

4) Trying to run the umls pipeline I get an out of heap space exception during load-time:
Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space
I changed the -Xmx1024M option to -Xmx2g in the runctakesCVD.sh script and it fixed it.

5) Under CVD, step 6, where the user is instructed to look through a few annotations, I think
the example we use there -- Concept -- is probably not the greatest. I believe that is an
internal type to the assertion tool, but it might sound to a newcomer like the main entity
type. Since this type doesn't contain much additional info it may mislead about the capabilities
of cTAKES. (It would be best to rename or remove that type going forward but for now at least
our tutorial should avoid mentioning it.

Some of these issues I could change myself, what credentials do I use to log into the wiki
-- apache, jira, or something new?

Tim



On 08/31/2013 12:36 AM, Masanz, James J. wrote:


Hello all,

This is a call for a vote on releasing the following candidate as Apache cTAKES 3.1.0. This
will be our first release as a TLP.

For more detailed information on the changes/release notes, please visit:
https://issues.apache.org/jira/secure/ReleaseNote.jspa?version=12323276&projectId=12313621

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/~james-masanz/RCs/ctakes-3.1.0/rc3/apache-ctakes-3.1.0-src.tar.gz
/.zip

The tag to be voted on:
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.0-rc3/

The MD5 checksum of the tarball can be found at:
http://people.apache.org/~james-masanz/RCs/ctakes-3.1.0/rc3/apache-ctakes-3.1.0-src.tar.gz.md5
/ .zip.md5

The signature of the tarball can be found at:
http://people.apache.org/~james-masanz/RCs/ctakes-3.1.0/rc3/apache-ctakes-3.1.0-src.tar.gz.asc
/.zip.asc

Apache cTAKES' KEYS file, containing the PGP keys used to sign the release:
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.0-rc3/KEYS

Please vote on releasing these packages as Apache cTAKES 3.1.0. 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 3.1.0
[ ] -1 Do not release the packages because...

Also, the convenience binary is:
http://people.apache.org/~james-masanz/RCs/ctakes-3.1.0/rc3/apache-ctakes-3.1.0-bin.tar.gz
/.zip

The nexus staging repository:
https://repository.apache.org/content/repositories/orgapachectakes-125/

Thanks!
James Masanz


Sent: Friday, August 30, 2013 11:23 PM
To: James Joseph Masanz
Subject: Nexus: Staging Completed.


Description:

apache ctakes-3.1.0-rc3

Details:

The following artifacts have been staged to the org.apache.ctakes-125 (u:james-masanz, a:71.82.125.95)
repository.

archetype-catalog.xml
ctakes-coreference-3.1.0.jar
ctakes-coreference-3.1.0-javadoc.jar.asc
ctakes-coreference-3.1.0.pom.asc
ctakes-coreference-3.1.0.jar.asc
ctakes-coreference-3.1.0-javadoc.jar
ctakes-coreference-3.1.0-sources.jar
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ctakes-coreference-3.1.0.pom
ctakes-ne-contexts-res-3.1.0.pom.asc
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ctakes-ne-contexts-res-3.1.0.pom
ctakes-ne-contexts-res-3.1.0.jar.asc
ctakes-ne-contexts-res-3.1.0.jar
ctakes-ne-contexts-res-3.1.0-sources.jar
ctakes-constituency-parser-3.1.0-javadoc.jar
ctakes-constituency-parser-3.1.0-sources.jar.asc
ctakes-constituency-parser-3.1.0-sources.jar
ctakes-constituency-parser-3.1.0.pom.asc
ctakes-constituency-parser-3.1.0.pom
ctakes-constituency-parser-3.1.0-javadoc.jar.asc
ctakes-constituency-parser-3.1.0.jar.asc
ctakes-constituency-parser-3.1.0.jar
ctakes-context-tokenizer-3.1.0-sources.jar
ctakes-context-tokenizer-3.1.0.jar
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ctakes-context-tokenizer-3.1.0.jar.asc
ctakes-context-tokenizer-3.1.0-sources.jar.asc
ctakes-context-tokenizer-3.1.0.pom.asc
ctakes-context-tokenizer-3.1.0.pom
ctakes-context-tokenizer-3.1.0-javadoc.jar
ctakes-assertion-zoner-res-3.1.0-sources.jar.asc
ctakes-assertion-zoner-res-3.1.0.jar.asc
ctakes-assertion-zoner-res-3.1.0-sources.jar
ctakes-assertion-zoner-res-3.1.0.pom
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ctakes-assertion-zoner-res-3.1.0.jar
ctakes-clinical-pipeline-3.1.0-javadoc.jar.asc
ctakes-clinical-pipeline-3.1.0.pom
ctakes-clinical-pipeline-3.1.0-sources.jar
ctakes-clinical-pipeline-3.1.0-sources.jar.asc
ctakes-clinical-pipeline-3.1.0.jar.asc
ctakes-clinical-pipeline-3.1.0-javadoc.jar
ctakes-clinical-pipeline-3.1.0.pom.asc
ctakes-clinical-pipeline-3.1.0.jar
ctakes-3.1.0.pom.asc
ctakes-3.1.0-source-release.zip.asc
ctakes-3.1.0-source-release.zip
ctakes-3.1.0.pom
ctakes-pad-term-spotter-res-3.1.0-sources.jar
ctakes-pad-term-spotter-res-3.1.0-sources.jar.asc
ctakes-pad-term-spotter-res-3.1.0.jar.asc
ctakes-pad-term-spotter-res-3.1.0.pom
ctakes-pad-term-spotter-res-3.1.0.jar
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ctakes-relation-extractor-res-3.1.0.pom.asc
ctakes-relation-extractor-res-3.1.0-sources.jar.asc
ctakes-relation-extractor-res-3.1.0.jar
ctakes-relation-extractor-res-3.1.0.pom
ctakes-assertion-3.1.0-sources.jar.asc
ctakes-assertion-3.1.0.pom.asc
ctakes-assertion-3.1.0.jar.asc
ctakes-assertion-3.1.0-javadoc.jar.asc
ctakes-assertion-3.1.0.jar
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ctakes-assertion-3.1.0-sources.jar
ctakes-assertion-3.1.0-javadoc.jar
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ctakes-constituency-parser-res-3.1.0.pom
ctakes-constituency-parser-res-3.1.0.pom.asc
ctakes-constituency-parser-res-3.1.0.jar.asc
ctakes-constituency-parser-res-3.1.0-sources.jar.asc
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ctakes-coreference-res-3.1.0-sources.jar
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ctakes-coreference-res-3.1.0.jar
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ctakes-pos-tagger-3.1.0-sources.jar
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ctakes-side-effect-3.1.0-sources.jar
ctakes-side-effect-3.1.0.jar
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ctakes-side-effect-3.1.0.pom.asc
ctakes-side-effect-3.1.0.pom
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ctakes-ne-contexts-3.1.0-javadoc.jar
ctakes-ne-contexts-3.1.0-javadoc.jar.asc
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ctakes-smoking-status-res-3.1.0-sources.jar.asc
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ctakes-relation-extractor-3.1.0.pom
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ctakes-lvg-res-3.1.0-sources.jar
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ctakes-pos-tagger-res-3.1.0.jar
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ctakes-preprocessor-3.1.0-sources.jar.asc
ctakes-preprocessor-3.1.0-javadoc.jar.asc
ctakes-preprocessor-3.1.0-sources.jar
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ctakes-smoking-status-3.1.0.pom
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ctakes-smoking-status-3.1.0-javadoc.jar.asc
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ctakes-assertion-res-3.1.0.jar.asc
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ctakes-assertion-res-3.1.0.pom.asc
ctakes-assertion-res-3.1.0.pom
ctakes-dependency-parser-3.1.0.jar
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ctakes-dependency-parser-3.1.0.pom.asc
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ctakes-dependency-parser-3.1.0-sources.jar
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