Merge pull request #374 from seattleflu/kp2023-etl

Clinical ETL: assign encounter_status as finished for records missing encounter_status field, and use hashed individual ID to create immunization hash.
seattleflu · Nov 21, 2023 · d8dd52b · d8dd52b
2 parents d9e1b5e + 7c7fc95
commit d8dd52b
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/lib/seattleflu/id3c/cli/command/etl/clinical.py b/lib/seattleflu/id3c/cli/command/etl/clinical.py
@@ -464,7 +464,8 @@ def create_immunization_kp2023(record: dict, patient_reference: dict) -> list:
             vaccine_code = cvx_codes[213] # covid vaccines are not specified in this study, so assign code for unspecified covid-19 vaccine
 
         if vaccine_code:
-            immunization_identifier_hash = generate_hash(f"{record['mrn']}{vaccine_code['code']}{immunization_date}".lower())
+            # create hash from collection_id, which is hashed individual id, plus vaccine code and date administered
+            immunization_identifier_hash = generate_hash(f"{record['collection_id']}{vaccine_code['code']}{immunization_date}".lower())
             immunization_identifier = create_identifier(f"{SFS}/immunization", immunization_identifier_hash)
 
             immunization_resource = create_immunization_resource(

diff --git a/lib/seattleflu/id3c/cli/command/etl/clinical_retrospectives.py b/lib/seattleflu/id3c/cli/command/etl/clinical_retrospectives.py
@@ -138,7 +138,7 @@ def create_encounter_status(record: dict) -> str:
     This attribute is required by FHIR for an Encounter resource.
     (https://www.hl7.org/fhir/encounter-definitions.html#Encounter.status)
     """
-    status = record['encounter_status']
+    status = record.get('encounter_status', None)
     if not status:
         return 'finished'