KP2023 ETL: Map KP2023 to site KaiserPermanente in id3c

lib/seattleflu/id3c/cli/command/etl/clinical.py

@@ -112,7 +112,9 @@ def etl_clinical(*, db: DatabaseSession):
             # PHSKC and KP2023 will be handled differently than other clinical records, converted
             # to FHIR format and inserted into receiving.fhir table to be processed
             # by the FHIR ETL. When time allows, SCH and KP should follow suit.
-            if site.identifier in ('RetrospectivePHSKC', 'KaiserPermanente2023'):
+            # Since KP2023 and KP samples both have KaiserPermanente as their site in id3c,
+            # use the ndjson document's site to distinguish KP vs KP2023 samples
+            if site.identifier == 'RetrospectivePHSKC' or record.document["site"].upper() == 'KP2023':
                 fhir_bundle = generate_fhir_bundle(db, record.document, site.identifier)
                 insert_fhir_bundle(db, fhir_bundle)
 
@@ -248,7 +250,7 @@ def generate_fhir_bundle(db: DatabaseSession, record: dict, site_id: str) -> Opt
     # ideally would not require site id for this, since it makes it more difficult to incorporate future projects
     if site_id == 'RetrospectivePHSKC':
         location_entries, location_references = create_resident_locations(record)
-    elif site_id == 'KaiserPermanente2023':
+    elif record["site"].upper() == 'KP2023':
         location_entries, location_references = create_location_tract_only(record)
     else:
         LOG.warning(f'Function generate_fhir_bundle does not currently create location resource entries for site {site_id}')
@@ -298,7 +300,7 @@ def generate_fhir_bundle(db: DatabaseSession, record: dict, site_id: str) -> Opt
     if diagnostic_report_resource_entry:
         resource_entries.append(diagnostic_report_resource_entry)
 
-    if site_id == 'KaiserPermanente2023':
+    if record["site"].upper() == 'KP2023':
         # KP2023 includes some types of metadata that PHSKC does not
         icd10_condition_entries = create_icd10_conditions_kp2023(record, patient_reference)
         symptom_condition_entries = create_symptom_conditions(record, patient_reference, encounter_reference)
@@ -1093,7 +1095,7 @@ def site_identifier(site_name: str) -> str:
         "SCH": "RetrospectiveChildrensHospitalSeattle",
         "KP": "KaiserPermanente",
         "PHSKC": "RetrospectivePHSKC",
-        "KP2023": "KaiserPermanente2023"
+        "KP2023": "KaiserPermanente" # kp2023 samples should be mapped to kp site in id3c; they are marked as kp2023 in manifest document because they will be processed into fhir bundles, unlike earlier kp samples
     }
     if site_name not in site_map:
         raise UnknownSiteError(f"Unknown site name «{site_name}»")