Apache cTAKES 3.2.1 (rc1)

["Chen, Pei" <Pe...@childrens.harvard.edu>]

RC1 ready for testing:
Binary Artifacts: https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.1/
Tag: https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.1-rc1/

Would be great if folks have time to test/verify especially if you opened any of the Jira's below to ensure the bugs have been fixed/integrated.

Changes:
Sub-task
·         [CTAKES-312<https://issues.apache.org/jira/browse/CTAKES-312>] - upgrade uimafit
·         [CTAKES-324<https://issues.apache.org/jira/browse/CTAKES-324>] - Deploy 3.2.1 resources from SF to Maven Central/OSSonatype
Bug
·         [CTAKES-162<https://issues.apache.org/jira/browse/CTAKES-162>] - Command line scripts leave the user back one directory
·         [CTAKES-169<https://issues.apache.org/jira/browse/CTAKES-169>] - SectionSegmentAnnotator.java is in core, but the sample SectionSegmentAnnotator.xml descriptor is in ctakes-clinical-pipeline
·         [CTAKES-241<https://issues.apache.org/jira/browse/CTAKES-241>] - NullPointerException in ctakes-assertion
·         [CTAKES-280<https://issues.apache.org/jira/browse/CTAKES-280>] - upgrade to cleartk-2.*
·         [CTAKES-285<https://issues.apache.org/jira/browse/CTAKES-285>] - cleartk-ml-liblinear needs to be added to the dependencies
·         [CTAKES-307<https://issues.apache.org/jira/browse/CTAKES-307>] - URI is not hierarchical when running mvn install
·         [CTAKES-309<https://issues.apache.org/jira/browse/CTAKES-309>] - Add SNOMEDCT_US to ytext db scripts
·         [CTAKES-310<https://issues.apache.org/jira/browse/CTAKES-310>] - Dictionary lookup permutations sort issue
·         [CTAKES-311<https://issues.apache.org/jira/browse/CTAKES-311>] - v_document_cui_sent View returns no results in cTAKES-YTEX
·         [CTAKES-319<https://issues.apache.org/jira/browse/CTAKES-319>] - YTEX Web Semantic Search not starting in Linux
·         [CTAKES-321<https://issues.apache.org/jira/browse/CTAKES-321>] - Verify ctakes-ytex 3rd party dependencies
·         [CTAKES-327<https://issues.apache.org/jira/browse/CTAKES-327>] - Make inner classes import explicit - if not, class names can be ambiguous and depend on compiler order.
Improvement
·         [CTAKES-94<https://issues.apache.org/jira/browse/CTAKES-94>] - refactoring assertion module to use a cleartk-based analysis engine (and include evaluation)
·         [CTAKES-222<https://issues.apache.org/jira/browse/CTAKES-222>] - FirstTokenPermLookupInitializerImpl to suppot arraylist of DictionaryLookupWindows
·         [CTAKES-225<https://issues.apache.org/jira/browse/CTAKES-225>] - Common Type System - Add field to save preferredText in Segment
·         [CTAKES-325<https://issues.apache.org/jira/browse/CTAKES-325>] - Create aggregate pipeline to use dictionary-lookup-fast
·         [CTAKES-326<https://issues.apache.org/jira/browse/CTAKES-326>] - Default Assertion to use new clearTK based models
New Feature
·         [CTAKES-329<https://issues.apache.org/jira/browse/CTAKES-329>] - Add temporal event-event and event-time relation discovery models
Task
·         [CTAKES-315<https://issues.apache.org/jira/browse/CTAKES-315>] - Update Default UMLS pipeline to use dictionary-lookup-fast
·         [CTAKES-323<https://issues.apache.org/jira/browse/CTAKES-323>] - Create a 3.2.1 Release