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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: [VOTE] Release Apache cTAKES 3.1 (rc3)
Date Sun, 01 Sep 2013 18:53:22 GMT
Thanks James, I went and tried to fix 1) and 3) myself. I can try to do
5) a bit later unless someone else really wants to do it!

For 4), are other people able to run the umls pipeline with the current
memory settings (1024m)? I've never been able to run full cTAKES with
that setting.
Tim

On 09/01/2013 02:28 PM, Masanz, James J. wrote:
> 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
> ctakes-coreference-3.1.0-sources.jar.asc
> ctakes-coreference-3.1.0.pom
> ctakes-ne-contexts-res-3.1.0.pom.asc
> ctakes-ne-contexts-res-3.1.0-sources.jar.asc
> 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
> ctakes-context-tokenizer-3.1.0-javadoc.jar.asc
> 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
> ctakes-assertion-zoner-res-3.1.0.pom.asc
> 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
> ctakes-pad-term-spotter-res-3.1.0.pom.asc
> ctakes-relation-extractor-res-3.1.0-sources.jar
> ctakes-relation-extractor-res-3.1.0.jar.asc
> 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
> ctakes-assertion-3.1.0.pom
> ctakes-assertion-3.1.0-sources.jar
> ctakes-assertion-3.1.0-javadoc.jar
> ctakes-constituency-parser-res-3.1.0.jar
> 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
> ctakes-constituency-parser-res-3.1.0-sources.jar
> ctakes-coreference-res-3.1.0-sources.jar.asc
> ctakes-coreference-res-3.1.0-sources.jar
> ctakes-coreference-res-3.1.0.pom.asc
> ctakes-coreference-res-3.1.0.jar
> ctakes-coreference-res-3.1.0.pom
> ctakes-coreference-res-3.1.0.jar.asc
> ctakes-pos-tagger-3.1.0.pom.asc
> ctakes-pos-tagger-3.1.0-sources.jar.asc
> ctakes-pos-tagger-3.1.0.jar.asc
> ctakes-pos-tagger-3.1.0.jar
> ctakes-pos-tagger-3.1.0-javadoc.jar.asc
> ctakes-pos-tagger-3.1.0-javadoc.jar
> ctakes-pos-tagger-3.1.0.pom
> ctakes-pos-tagger-3.1.0-sources.jar
> ctakes-side-effect-3.1.0-javadoc.jar
> ctakes-side-effect-3.1.0-javadoc.jar.asc
> ctakes-side-effect-3.1.0-sources.jar
> ctakes-side-effect-3.1.0.jar
> ctakes-side-effect-3.1.0.jar.asc
> ctakes-side-effect-3.1.0.pom.asc
> ctakes-side-effect-3.1.0.pom
> ctakes-side-effect-3.1.0-sources.jar.asc
> ctakes-ne-contexts-3.1.0-javadoc.jar
> ctakes-ne-contexts-3.1.0-javadoc.jar.asc
> ctakes-ne-contexts-3.1.0.jar.asc
> ctakes-ne-contexts-3.1.0.jar
> ctakes-ne-contexts-3.1.0-sources.jar.asc
> ctakes-ne-contexts-3.1.0-sources.jar
> ctakes-ne-contexts-3.1.0.pom.asc
> ctakes-ne-contexts-3.1.0.pom
> ctakes-utils-3.1.0.jar.asc
> ctakes-utils-3.1.0-sources.jar.asc
> ctakes-utils-3.1.0.pom.asc
> ctakes-utils-3.1.0-sources.jar
> ctakes-utils-3.1.0.pom
> ctakes-utils-3.1.0-javadoc.jar
> ctakes-utils-3.1.0.jar
> ctakes-utils-3.1.0-javadoc.jar.asc
> ctakes-chunker-res-3.1.0-sources.jar
> ctakes-chunker-res-3.1.0.jar
> ctakes-chunker-res-3.1.0-sources.jar.asc
> ctakes-chunker-res-3.1.0.pom
> ctakes-chunker-res-3.1.0.pom.asc
> ctakes-chunker-res-3.1.0.jar.asc
> ctakes-lvg-3.1.0-javadoc.jar
> ctakes-lvg-3.1.0-javadoc.jar.asc
> ctakes-lvg-3.1.0.jar.asc
> ctakes-lvg-3.1.0.pom
> ctakes-lvg-3.1.0-sources.jar.asc
> ctakes-lvg-3.1.0-sources.jar
> ctakes-lvg-3.1.0.pom.asc
> ctakes-lvg-3.1.0.jar
> ctakes-dictionary-lookup-3.1.0-javadoc.jar
> ctakes-dictionary-lookup-3.1.0.jar.asc
> ctakes-dictionary-lookup-3.1.0.jar
> ctakes-dictionary-lookup-3.1.0.pom.asc
> ctakes-dictionary-lookup-3.1.0-sources.jar.asc
> ctakes-dictionary-lookup-3.1.0-javadoc.jar.asc
> ctakes-dictionary-lookup-3.1.0.pom
> ctakes-dictionary-lookup-3.1.0-sources.jar
> ctakes-drug-ner-res-3.1.0.pom.asc
> ctakes-drug-ner-res-3.1.0-sources.jar
> ctakes-drug-ner-res-3.1.0.pom
> ctakes-drug-ner-res-3.1.0-sources.jar.asc
> ctakes-drug-ner-res-3.1.0.jar
> ctakes-drug-ner-res-3.1.0.jar.asc
> ctakes-assertion-zoner-3.1.0-sources.jar.asc
> ctakes-assertion-zoner-3.1.0-sources.jar
> ctakes-assertion-zoner-3.1.0.pom
> ctakes-assertion-zoner-3.1.0-javadoc.jar
> ctakes-assertion-zoner-3.1.0-javadoc.jar.asc
> ctakes-assertion-zoner-3.1.0.jar.asc
> ctakes-assertion-zoner-3.1.0.jar
> ctakes-assertion-zoner-3.1.0.pom.asc
> ctakes-smoking-status-res-3.1.0.pom
> ctakes-smoking-status-res-3.1.0.pom.asc
> ctakes-smoking-status-res-3.1.0.jar
> ctakes-smoking-status-res-3.1.0.jar.asc
> ctakes-smoking-status-res-3.1.0-sources.jar
> ctakes-smoking-status-res-3.1.0-sources.jar.asc
> ctakes-dependency-parser-res-3.1.0.pom
> ctakes-dependency-parser-res-3.1.0-sources.jar.asc
> ctakes-dependency-parser-res-3.1.0-sources.jar
> ctakes-dependency-parser-res-3.1.0.pom.asc
> ctakes-dependency-parser-res-3.1.0.jar
> ctakes-dependency-parser-res-3.1.0.jar.asc
> ctakes-template-filler-3.1.0-javadoc.jar
> ctakes-template-filler-3.1.0-sources.jar
> ctakes-template-filler-3.1.0-sources.jar.asc
> ctakes-template-filler-3.1.0.jar
> ctakes-template-filler-3.1.0.pom.asc
> ctakes-template-filler-3.1.0-javadoc.jar.asc
> ctakes-template-filler-3.1.0.jar.asc
> ctakes-template-filler-3.1.0.pom
> ctakes-pad-term-spotter-3.1.0-sources.jar
> ctakes-pad-term-spotter-3.1.0-sources.jar.asc
> ctakes-pad-term-spotter-3.1.0.jar.asc
> ctakes-pad-term-spotter-3.1.0-javadoc.jar
> ctakes-pad-term-spotter-3.1.0-javadoc.jar.asc
> ctakes-pad-term-spotter-3.1.0.jar
> ctakes-pad-term-spotter-3.1.0.pom.asc
> ctakes-pad-term-spotter-3.1.0.pom
> ctakes-type-system-3.1.0.pom
> ctakes-type-system-3.1.0.jar.asc
> ctakes-type-system-3.1.0.jar
> ctakes-type-system-3.1.0-javadoc.jar.asc
> ctakes-type-system-3.1.0-sources.jar.asc
> ctakes-type-system-3.1.0.pom.asc
> ctakes-type-system-3.1.0-sources.jar
> ctakes-type-system-3.1.0-javadoc.jar
> ctakes-core-3.1.0-javadoc.jar
> ctakes-core-3.1.0-sources.jar.asc
> ctakes-core-3.1.0.jar
> ctakes-core-3.1.0-sources.jar
> ctakes-core-3.1.0-javadoc.jar.asc
> ctakes-core-3.1.0.pom.asc
> ctakes-core-3.1.0.jar.asc
> ctakes-core-3.1.0.pom
> ctakes-core-res-3.1.0.pom
> ctakes-core-res-3.1.0.pom.asc
> ctakes-core-res-3.1.0-sources.jar.asc
> ctakes-core-res-3.1.0.jar
> ctakes-core-res-3.1.0-sources.jar
> ctakes-core-res-3.1.0.jar.asc
> ctakes-regression-test-3.1.0.pom.asc
> ctakes-regression-test-3.1.0-sources.jar
> ctakes-regression-test-3.1.0.pom
> ctakes-regression-test-3.1.0-sources.jar.asc
> ctakes-regression-test-3.1.0.jar
> ctakes-regression-test-3.1.0.jar.asc
> ctakes-dictionary-lookup-res-3.1.0.jar
> ctakes-dictionary-lookup-res-3.1.0-sources.jar.asc
> ctakes-dictionary-lookup-res-3.1.0.jar.asc
> ctakes-dictionary-lookup-res-3.1.0-sources.jar
> ctakes-dictionary-lookup-res-3.1.0.pom
> ctakes-dictionary-lookup-res-3.1.0.pom.asc
> ctakes-relation-extractor-3.1.0-sources.jar
> ctakes-relation-extractor-3.1.0-javadoc.jar.asc
> ctakes-relation-extractor-3.1.0-javadoc.jar
> ctakes-relation-extractor-3.1.0.pom.asc
> ctakes-relation-extractor-3.1.0.pom
> ctakes-relation-extractor-3.1.0.jar
> ctakes-relation-extractor-3.1.0.jar.asc
> ctakes-relation-extractor-3.1.0-sources.jar.asc
> ctakes-lvg-res-3.1.0-sources.jar
> ctakes-lvg-res-3.1.0.jar
> ctakes-lvg-res-3.1.0-sources.jar.asc
> ctakes-lvg-res-3.1.0.pom
> ctakes-lvg-res-3.1.0.jar.asc
> ctakes-lvg-res-3.1.0.pom.asc
> ctakes-pos-tagger-res-3.1.0.pom.asc
> ctakes-pos-tagger-res-3.1.0.jar.asc
> ctakes-pos-tagger-res-3.1.0-sources.jar.asc
> ctakes-pos-tagger-res-3.1.0.pom
> ctakes-pos-tagger-res-3.1.0.jar
> ctakes-pos-tagger-res-3.1.0-sources.jar
> ctakes-preprocessor-3.1.0-sources.jar.asc
> ctakes-preprocessor-3.1.0-javadoc.jar.asc
> ctakes-preprocessor-3.1.0-sources.jar
> ctakes-preprocessor-3.1.0.jar
> ctakes-preprocessor-3.1.0.pom
> ctakes-preprocessor-3.1.0.pom.asc
> ctakes-preprocessor-3.1.0.jar.asc
> ctakes-preprocessor-3.1.0-javadoc.jar
> ctakes-chunker-3.1.0-sources.jar
> ctakes-chunker-3.1.0.pom.asc
> ctakes-chunker-3.1.0.jar
> ctakes-chunker-3.1.0-javadoc.jar
> ctakes-chunker-3.1.0-sources.jar.asc
> ctakes-chunker-3.1.0.jar.asc
> ctakes-chunker-3.1.0.pom
> ctakes-chunker-3.1.0-javadoc.jar.asc
> ctakes-smoking-status-3.1.0-javadoc.jar
> ctakes-smoking-status-3.1.0.pom.asc
> ctakes-smoking-status-3.1.0.pom
> ctakes-smoking-status-3.1.0-sources.jar.asc
> ctakes-smoking-status-3.1.0-javadoc.jar.asc
> ctakes-smoking-status-3.1.0-sources.jar
> ctakes-smoking-status-3.1.0.jar.asc
> ctakes-smoking-status-3.1.0.jar
> ctakes-side-effect-res-3.1.0.jar.asc
> ctakes-side-effect-res-3.1.0.pom
> ctakes-side-effect-res-3.1.0-sources.jar
> ctakes-side-effect-res-3.1.0.pom.asc
> ctakes-side-effect-res-3.1.0-sources.jar.asc
> ctakes-side-effect-res-3.1.0.jar
> ctakes-drug-ner-3.1.0-javadoc.jar
> ctakes-drug-ner-3.1.0.pom.asc
> ctakes-drug-ner-3.1.0.pom
> ctakes-drug-ner-3.1.0.jar
> ctakes-drug-ner-3.1.0.jar.asc
> ctakes-drug-ner-3.1.0-sources.jar
> ctakes-drug-ner-3.1.0-sources.jar.asc
> ctakes-drug-ner-3.1.0-javadoc.jar.asc
> ctakes-assertion-res-3.1.0.jar.asc
> ctakes-assertion-res-3.1.0-sources.jar
> ctakes-assertion-res-3.1.0-sources.jar.asc
> ctakes-assertion-res-3.1.0.jar
> ctakes-assertion-res-3.1.0.pom.asc
> ctakes-assertion-res-3.1.0.pom
> ctakes-dependency-parser-3.1.0.jar
> ctakes-dependency-parser-3.1.0-javadoc.jar
> ctakes-dependency-parser-3.1.0.pom
> ctakes-dependency-parser-3.1.0-javadoc.jar.asc
> ctakes-dependency-parser-3.1.0.pom.asc
> ctakes-dependency-parser-3.1.0-sources.jar.asc
> ctakes-dependency-parser-3.1.0.jar.asc
> ctakes-dependency-parser-3.1.0-sources.jar


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