refs/refs/fhir-x-omop/fhir_x_omop/to_fhir/immunization.py

73 lines · py
 1from fhir.resources.immunization import Immunization
 2from omop_pydantic import DrugExposure
 3
 4from chidian import DataMapping, Mapper
 5import chidian.partials as p
 6
 7immunization_mapper = Mapper(
 8    lambda src: {
 9        "resourceType": "Immunization",
10        "id": (p.get("drug_exposure_id") | p.str())(src),
11        "identifier": [{
12            "system": "http://omop.org/drug_exposure",
13            "value": (p.get("drug_exposure_id") | p.str())(src),
14        }],
15        "status": "completed",
16        "vaccineCode": {
17            "coding": [{
18                "system": p.case(p.get("drug_type_concept_id")(src), {
19                    38000179: "http://hl7.org/fhir/sid/cvx",
20                    38000180: "http://www.nlm.nih.gov/research/umls/rxnorm",
21                }, default="http://omop.org/drug"),
22                "code": p.get("drug_source_value")(src),
23                "display": p.get("drug_source_value")(src),
24            }]
25        },
26        "patient": {
27            "reference": (p.get("person_id") | p.format("Patient/{}"))(src)
28        },
29        "encounter": {
30            "reference": (p.get("visit_occurrence_id") | p.format("Encounter/{}"))(src)
31        },
32        "occurrenceDateTime": (p.get("drug_exposure_start_datetime") | p.str())(src),
33        "recorded": (p.get("drug_exposure_start_datetime") | p.str())(src),
34        "primarySource": True,
35        "lotNumber": p.get("lot_number")(src),
36        "route": {
37            "coding": [{
38                "system": "http://terminology.hl7.org/CodeSystem/v3-RouteOfAdministration",
39                "code": p.case(p.get("route_source_value")(src), {
40                    "intramuscular": "IM",
41                    "subcutaneous": "SC",
42                    "oral": "PO",
43                    "intranasal": "NASINHL",
44                }, default="IM"),
45                "display": p.get("route_source_value")(src)
46            }]
47        },
48        "doseQuantity": {
49            "value": (p.get("quantity") | p.float())(src),
50            "unit": p.get("dose_unit_source_value", default='dose')(src),
51            "system": "http://unitsofmeasure.org",
52            "code": p.get("dose_unit_source_value", default='dose')(src)
53        },
54        "performer": [{
55            "function": {
56                "coding": [{
57                    "system": "http://terminology.hl7.org/CodeSystem/v2-0443",
58                    "code": "AP",
59                    "display": "Administering Provider"
60                }]
61            },
62            "actor": {
63                "reference": (p.get("provider_id") | p.format("Practitioner/{}"))(src)
64            }
65        }],
66    }
67)
68
69to_fhir_immunization = DataMapping(
70    mapper=immunization_mapper,
71    input_schema=DrugExposure,
72    output_schema=Immunization,
73)