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  1. cTAKES
  2. CTAKES-450

CDASegmentAnnotator misses all headings after empty segment

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: ctakes-core
    • Labels:
      None
    • Flags:
      Patch

      Description

      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

        Attachments

        1. CDASegmentAnnotator-empty-segment.CTAKES-450.svn.patch
          10 kB
          Alex Zbarcea
        2. CDASegmentAnnotator.diff
          0.7 kB
          Kean Kaufmann

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              • Assignee:
                Unassigned
                Reporter:
                keanR1 Kean Kaufmann
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                Dates

                • Created:
                  Updated: