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

 1from fhir.resources.condition import Condition
 2from omop_pydantic import ConditionOccurrence
 3
 4from chidian import DataMapping, Mapper
 5import chidian.partials as p
 6
 7def get_first_existing(src, paths):
 8    for path in paths:
 9        value = p.get(path)(src)
10        if value:
11            return value
12    return None
13
14condition_occurrence_mapper = Mapper(
15    lambda src: {
16        "condition_occurrence_id": (p.get("id") | p.int())(src),
17        "person_id": p.get("subject.reference", getter=lambda x: int(x.split('/')[1]) if x else None)(src),
18        "condition_concept_id": 0,  # Would need concept mapping in production
19        "condition_start_date": p.get(getter=lambda s: (get_first_existing(s, ['onsetDateTime', 'recordedDate']) or '').split('T')[0] or None)(src),
20        "condition_start_datetime": get_first_existing(src, ['onsetDateTime', 'recordedDate']),
21        "condition_end_date": p.get("abatementDateTime", getter=lambda x: x.split('T')[0] if x else None)(src),
22        "condition_end_datetime": p.get("abatementDateTime")(src),
23        "condition_type_concept_id": p.case(p.get("category[0].coding[0].code")(src), {
24            "encounter-diagnosis": 32817,
25            "problem-list-item": 32818,
26            "health-concern": 32819,
27        }, default=32817),
28        "condition_status_concept_id": p.case(p.get("clinicalStatus.coding[0].code")(src), {
29            "active": 32893,
30            "resolved": 32897,
31            "inactive": 32896,
32        }, default=32893),
33        "stop_reason": p.get("note[0].text")(src),
34        "provider_id": p.get("recorder.reference", getter=lambda x: int(x.split('/')[1]) if x else None)(src),
35        "visit_occurrence_id": p.get("encounter.reference", getter=lambda x: int(x.split('/')[1]) if x else None)(src),
36        "visit_detail_id": p.get("encounter.reference", getter=lambda x: int(x.split('/')[1]) if x else None)(src),
37        "condition_source_value": p.get("code.coding[0].code")(src),
38        "condition_source_concept_id": 0,
39        "condition_status_source_value": p.get("clinicalStatus.coding[0].code")(src),
40    }
41)
42
43to_omop_condition_occurrence = DataMapping(
44    mapper=condition_occurrence_mapper,
45    input_schema=Condition,
46    output_schema=ConditionOccurrence,
47)