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fix(mimic-iv): do not treat CANCELLED cultures as positive#2120

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fix(mimic-iv): do not treat CANCELLED cultures as positive#2120
acnimma wants to merge 1 commit into
MIT-LCP:mainfrom
acnimma:fix/soi-cancelled-not-positive

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@acnimma acnimma commented Jul 20, 2026

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Summary

  • Exclude org_itemid 90760 (CANCELLED) from positiveculture in suspicion_of_infection.sql
  • Also exclude org_name = 'CANCELLED'
  • Update postgres and duckdb dialect copies

Test plan

  • Source + dialect copies exclude 90760 / CANCELLED
  • Specimen with only CANCELLED → positive_culture = 0
  • Specimen with a real organism → positive_culture = 1

positiveculture treated any non-NULL, non-empty org_name as positive except NEGATIVE (90856). CANCELLED cultures (org_itemid 90760) are not microbial growth, but were counted as positive and could inflate positive_culture on the suspicion-of-infection table. Exclude CANCELLED the same way NEGATIVE is excluded.

Fixes #1677

suspicion_of_infection marked any non-empty org_name as positiveculture
except NEGATIVE (90856). CANCELLED (90760) is not organism growth; exclude
it (and the CANCELLED label) so positive_culture stays accurate.

Fixes MIT-LCP#1677
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identify negative culture

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