From 2c59b2c03bafbf634cd03fec2fb862630ca047a0 Mon Sep 17 00:00:00 2001 From: Sally Grindstaff Date: Tue, 31 Oct 2023 08:42:31 -0700 Subject: [PATCH] KP2023 ETL: Assign ambiguous flu vaccines as unspecified in FHIR bundle --- lib/seattleflu/id3c/cli/command/etl/clinical.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/lib/seattleflu/id3c/cli/command/etl/clinical.py b/lib/seattleflu/id3c/cli/command/etl/clinical.py index 1f52b764..e6641f90 100644 --- a/lib/seattleflu/id3c/cli/command/etl/clinical.py +++ b/lib/seattleflu/id3c/cli/command/etl/clinical.py @@ -425,11 +425,11 @@ def create_immunization_kp2023(record: dict, patient_reference: dict) -> list: "fluad quadrivalent": 205, "fluarix quadrivalent": 150, "flublok quadrivalent": 185, - # "flucelvax quadrivalent" - not known whether with or without preservative - # "flulaval quadrivalent" - not known whether with or without preservative + "flucelvax quadrivalent": 88, # mark as unspecified because not known whether with or without preservative + "flulaval quadrivalent": 88, # mark as unspecified not known whether with or without preservative "flumist quadrivalent": 149, - "fluzone high-dose quadrivlanet": 197, #assuming not the southern hemisphere? - # "fluzone quadrivalent" - not known whether with or without preservative, or whether pediatric + "fluzone high-dose quadrivalent": 88, # probably 197, but marking as unspecified because don't want to assume not southern hemisphere version + "fluzone quadrivalent": 88 # mark as unspecified because not known whether with or without preservative, or whether pediatric } for column_map in immunization_columns: @@ -455,7 +455,7 @@ def create_immunization_kp2023(record: dict, patient_reference: dict) -> list: if vaccine_name in flu_vaccine_mapper: vaccine_code = cvx_codes[flu_vaccine_mapper[vaccine_name]] if flu_vaccine_mapper[vaccine_name] else None else: - raise UnknownVaccine (f"Unknown vaccine «{vaccine_name}».") # we already standardize vaccine names in parse-kp2023, so this is just for extra safety + raise UnknownVaccine (f"Unknown vaccine «{vaccine_name}».") # assign name and code for covid vaccines elif 'covid' in column_map['date']: @@ -514,7 +514,6 @@ def create_icd10_conditions_kp2023(record:dict, patient_reference: dict) -> list Create a condition resource for each ICD-10 code, following the FHIR format (http://www.hl7.org/implement/standards/fhir/condition.html) """ - # todo: raise unknown icd10 error if icd10 code not in mapper condition_entries = []