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
