refs/refs/fhir-x-omop/fhir_x_omop/to_omop/visit_occurrence.py

 1from fhir.resources.encounter import Encounter
 2from omop_pydantic import VisitOccurrence
 3
 4from chidian import DataMapping, Mapper
 5import chidian.partials as p
 6
 7def get_attending_provider_id(participants):
 8    if not participants:
 9        return None
10    for participant in participants:
11        if (participant.type and 
12            participant.type[0].coding and 
13            participant.type[0].coding[0].code == 'ATND' and
14            participant.individual and
15            participant.individual.reference):
16            return int(participant.individual.reference.split('/')[1])
17    return None
18
19visit_occurrence_mapper = Mapper(
20    lambda src: {
21        "visit_occurrence_id": (p.get("id") | p.int())(src),
22        "person_id": p.get("subject.reference", getter=lambda x: int(x.split('/')[1]) if x else None)(src),
23        "visit_concept_id": p.case(p.get("class.code")(src), {
24            "IMP": 9201,      # Inpatient Visit
25            "AMB": 9202,      # Outpatient Visit  
26            "EMER": 9203,     # Emergency Room Visit
27            "HH": 581379,     # Home Health
28            "VR": 32036,      # Virtual
29        }, default=9202),   # Default to Outpatient
30        "visit_start_date": p.get("period.start", getter=lambda x: x.split('T')[0] if x else None)(src),
31        "visit_start_datetime": p.get("period.start")(src),
32        "visit_end_date": p.get("period.end", getter=lambda x: x.split('T')[0] if x else None)(src),
33        "visit_end_datetime": p.get("period.end")(src),
34        "visit_type_concept_id": 44818518,  # Visit derived from EHR
35        "provider_id": p.get("participant", getter=get_attending_provider_id)(src),
36        "care_site_id": p.get("serviceProvider.reference", getter=lambda x: int(x.split('/')[1]) if x else None)(src),
37        "visit_source_value": p.get("type[0].coding[0].code")(src),
38        "visit_source_concept_id": 0,
39        "admitted_from_concept_id": 0,
40        "admitted_from_source_value": p.get("hospitalization.admitSource.coding[0].code")(src),
41        "discharge_to_concept_id": p.case(p.get("hospitalization.dischargeDisposition.coding[0].code")(src), {
42            "home": 8536,
43            "snf": 8676,
44            "rehab": 8615,
45            "exp": 4216643,
46        }, default=0),
47        "discharge_to_source_value": p.get("hospitalization.dischargeDisposition.coding[0].display")(src),
48        "preceding_visit_occurrence_id": None,
49    }
50)
51
52to_omop_visit_occurrence = DataMapping(
53    mapper=visit_occurrence_mapper,
54    input_schema=Encounter,
55    output_schema=VisitOccurrence,
56)