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Release Notes - cTAKES - Version 3.2.1 - HTML format

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Sub-task

[CTAKES-312] - upgrade uimafit
[CTAKES-324] - Deploy 3.2.1 resources from SF to Maven Central/OSSonatype

Bug

[CTAKES-162] - Command line scripts leave the user back one directory
[CTAKES-169] - SectionSegmentAnnotator.java is in core, but the sample SectionSegmentAnnotator.xml descriptor is in ctakes-clinical-pipeline
[CTAKES-241] - NullPointerException in ctakes-assertion
[CTAKES-280] - upgrade to cleartk-2.*
[CTAKES-285] - cleartk-ml-liblinear needs to be added to the dependencies
[CTAKES-307] - URI is not hierarchical when running mvn install
[CTAKES-309] - Add SNOMEDCT_US to ytext db scripts
[CTAKES-310] - Dictionary lookup permutations sort issue
[CTAKES-311] - v_document_cui_sent View returns no results in cTAKES-YTEX
[CTAKES-319] - YTEX Web Semantic Search not starting in Linux
[CTAKES-321] - Verify ctakes-ytex 3rd party dependencies
[CTAKES-327] - Make inner classes import explicit - if not, class names can be ambiguous and depend on compiler order.
[CTAKES-334] - GramMatrixExporterImpl initialization failed
[CTAKES-335] - url typo in ctakessql.xml
[CTAKES-337] - YTEX Class Conflict

New Feature

[CTAKES-329] - Add temporal event-event and event-time relation discovery models
[CTAKES-374] - Scaleout of cTAKES pipeline

Improvement

[CTAKES-94] - refactoring assertion module to use a cleartk-based analysis engine (and include evaluation)
[CTAKES-222] - FirstTokenPermLookupInitializerImpl to suppot arraylist of DictionaryLookupWindows
[CTAKES-225] - Common Type System - Add field to save preferredText in Segment
[CTAKES-325] - Create aggregate pipeline to use dictionary-lookup-fast
[CTAKES-326] - Default Assertion to use new clearTK based models
[CTAKES-336] - Allow constituency parser to allow reading of model from input stream

Task

[CTAKES-315] - Update Default UMLS pipeline to use dictionary-lookup-fast
[CTAKES-323] - Create a 3.2.1 Release

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Release Notes - cTAKES - Version 3.2.1
    
<h2>        Sub-task
</h2>
<ul>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-312'>CTAKES-312</a>] -         upgrade uimafit
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-324'>CTAKES-324</a>] -         Deploy 3.2.1 resources from SF to Maven Central/OSSonatype
</li>
</ul>
            
<h2>        Bug
</h2>
<ul>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-162'>CTAKES-162</a>] -         Command line scripts leave the user back one directory
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-169'>CTAKES-169</a>] -         SectionSegmentAnnotator.java is in core, but the sample SectionSegmentAnnotator.xml descriptor is in ctakes-clinical-pipeline
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-241'>CTAKES-241</a>] -         NullPointerException in ctakes-assertion 
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-280'>CTAKES-280</a>] -         upgrade to cleartk-2.*
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-285'>CTAKES-285</a>] -         cleartk-ml-liblinear needs to be added to the dependencies
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-307'>CTAKES-307</a>] -         URI is not hierarchical when running mvn install
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-309'>CTAKES-309</a>] -         Add SNOMEDCT_US to ytext db scripts
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-310'>CTAKES-310</a>] -         Dictionary lookup permutations sort issue
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-311'>CTAKES-311</a>] -         v_document_cui_sent View returns no results in cTAKES-YTEX
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-319'>CTAKES-319</a>] -         YTEX Web Semantic Search not starting in Linux
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-321'>CTAKES-321</a>] -         Verify ctakes-ytex 3rd party dependencies
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-327'>CTAKES-327</a>] -         Make inner classes import explicit - if not, class names can be ambiguous and depend on compiler order.
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-334'>CTAKES-334</a>] -         GramMatrixExporterImpl initialization failed
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-335'>CTAKES-335</a>] -         url typo in ctakessql.xml
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-337'>CTAKES-337</a>] -         YTEX Class Conflict
</li>
</ul>
            
<h2>        New Feature
</h2>
<ul>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-329'>CTAKES-329</a>] -         Add temporal event-event and event-time relation discovery models
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-374'>CTAKES-374</a>] -         Scaleout of cTAKES pipeline
</li>
</ul>
    
<h2>        Improvement
</h2>
<ul>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-94'>CTAKES-94</a>] -         refactoring assertion module to use a cleartk-based analysis engine (and include evaluation)
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-222'>CTAKES-222</a>] -         FirstTokenPermLookupInitializerImpl to suppot arraylist of DictionaryLookupWindows
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-225'>CTAKES-225</a>] -         Common Type System - Add field to save preferredText in Segment
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-325'>CTAKES-325</a>] -         Create aggregate pipeline to use dictionary-lookup-fast
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-326'>CTAKES-326</a>] -         Default Assertion to use new clearTK based models
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-336'>CTAKES-336</a>] -         Allow constituency parser to allow reading of model from input stream
</li>
</ul>
            
<h2>        Task
</h2>
<ul>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-315'>CTAKES-315</a>] -         Update Default UMLS pipeline to use dictionary-lookup-fast
</li>
<li>[<a href='https://issues.apache.org/jira/browse/CTAKES-323'>CTAKES-323</a>] -         Create a 3.2.1 Release
</li>
</ul>