[jira] [Resolved] (CTAKES-449) PolarityCleartkAnalysisEngine slow for large documents

["Sean Finan (JIRA)" <ji...@apache.org>]

     [ https://issues.apache.org/jira/browse/CTAKES-449?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Sean Finan resolved CTAKES-449.
-------------------------------
       Resolution: Fixed
    Fix Version/s: 4.0.1

Refactored multiple select and selectCovered methods to instead use a single indexCovered.  No difference noticed with smaller files.  The difference should appear for larger files.

> PolarityCleartkAnalysisEngine slow for large documents
> ------------------------------------------------------
>
>                 Key: CTAKES-449
>                 URL: https://issues.apache.org/jira/browse/CTAKES-449
>             Project: cTAKES
>          Issue Type: Improvement
>          Components: ctakes-assertion
>            Reporter: Dmitriy Dligach
>            Assignee: Sean Finan
>            Priority: Major
>             Fix For: 4.0.1
>
>
> As soon as I add at the end of my pipeline the negation AE:
> aggregateBuilder.add( PolarityCleartkAnalysisEngine.createAnnotatorDescription() );
> The pipeline becomes 50-100 times slower. This likely has to do with the line:
> List<Sentence> sents = new ArrayList<>(JCasUtil.selectCovering(jCas, Sentence.class, entityOrEventMention.getBegin(), entityOrEventMention.getEnd()));
> in AssertionCleartkAnalysisEngine. I am running the pipeline on large files (i.e. having a large number of sentences). The slowdown is caused by the code's obtaining all sentences in a document for each identified annotation.
> The full pipeline is here:
> https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java



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