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fix: respect SimpleTerm.excluded in gyn_phenopacket's narrative feature - #115

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VarenyaJ merged 1 commit into
vj/developfrom
vj/fix-gyn-narrative-negation
Jul 21, 2026
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VarenyaJ merged 1 commit into
vj/developfrom
vj/fix-gyn-narrative-negation

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Same bug already fixed in observer_phenopacket.py and viewpoint_phenopacket.py (PR6/#111), present here too since gyn_phenopacket.py was copied from the same original code before that fix existed. _narrative_feature() never read term.excluded, so fenominal's negation detection was silently dropped.

Real fixture (Gwen_Sally_pretty.json) already has a negated finding ("No evidence of hydronephrosis"), so no new fixture needed. Verified the new regression test fails without the fix and passes with it.

Same bug already fixed in observer_phenopacket.py and
viewpoint_phenopacket.py (PR6/#111), present here too since
gyn_phenopacket.py was copied from the same original code before that
fix existed. _narrative_feature() never read term.excluded, so
fenominal's negation detection was silently dropped.

Real fixture (Gwen_Sally_pretty.json) already has a negated finding
("No evidence of hydronephrosis"), so no new fixture needed. Verified
the new regression test fails without the fix and passes with it.
@VarenyaJ VarenyaJ added this to the prenatalseq refinements milestone Jul 21, 2026
@VarenyaJ VarenyaJ self-assigned this Jul 21, 2026
@VarenyaJ VarenyaJ added the enhancement New feature or request label Jul 21, 2026
@VarenyaJ
VarenyaJ merged commit 39ce310 into vj/develop Jul 21, 2026
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@VarenyaJ
VarenyaJ deleted the vj/fix-gyn-narrative-negation branch September 16, 2026 15:26
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