[jira] [Created] (CTAKES-450) CDASegmentAnnotator misses all headings after empty segment

["Kean Kaufmann (JIRA)" <ji...@apache.org>]

Kean Kaufmann created CTAKES-450:
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             Summary: CDASegmentAnnotator misses all headings after empty segment
                 Key: CTAKES-450
                 URL: https://issues.apache.org/jira/browse/CTAKES-450
             Project: cTAKES
          Issue Type: Bug
          Components: ctakes-core
            Reporter: Kean Kaufmann
         Attachments: CDASegmentAnnotator.diff

If the CDASegmentAnnotator encounters an empty segment, it throws away everything after that in the document.  You can see this in the test document provided for TestCDASegmentAnnotator. The heading "CURRENT HEALTH STATUS" is followed immediately by the heading "Medications"; the test case misses the "Medications" heading, and "FAMILY HISTORY" after that. The sorted_segments loop is only incrementing the index variable for non-empty segments.

Patch attached.

TestCDASegmentAnnotator output before fix (with getPreferredText()):

Segment:2.16.840.1.113883.10.20.22.1.1 Begin:92 End:159: Header
Segment:1.3.6.1.4.1.19376.1.5.3.1.1.13.2.1 Begin:176 End:1612: CHIEF COMPLAINT
Segment:2.16.840.1.113883.10.20.22.2.20 Begin:1634 End:1696: HISTORY OF PAST ILLNESS
Segment:2.16.840.1.113883.10.20.22.2.2.1 Begin:1711 End:2271: History of immunizations

After fix:

Segment:2.16.840.1.113883.10.20.22.1.1 Begin:92 End:159: Header
Segment:1.3.6.1.4.1.19376.1.5.3.1.1.13.2.1 Begin:176 End:1612: CHIEF COMPLAINT
Segment:2.16.840.1.113883.10.20.22.2.20 Begin:1634 End:1696: HISTORY OF PAST ILLNESS
Segment:2.16.840.1.113883.10.20.22.2.2.1 Begin:1711 End:2271: History of immunizations
Segment:2.16.840.1.113883.10.20.22.2.1.1 Begin:2307 End:3506: HISTORY OF MEDICATION USE
Segment:2.16.840.1.113883.10.20.22.2.15 Begin:3522 End:5608: Family History




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