refs/refs/fhir-to-omop-demo/demo/translate/map/MedicationAdministration.jq

59 lines · jq 
 1#
 2# Transforms FHIR MedicationAdministrations into OMOP table records.
 3#
 4
 5include "fhir";
 6include "fhir/common";
 7
 8
 9def drug:
10  if (.medicationCodeableConcept.coding | length) > 1 then
11    error("Multiple medicationCodeableConcept.codings in MedicationAdministration/\(.id)")
12  end
13  | .medicationCodeableConcept.coding[0].concept
14;
15
16
17# See: https://ohdsi.github.io/CommonDataModel/drug_dose.html
18# TODO: include the 'has dose form' value in concept
19# TODO: include numerator in concept
20def quantity:
21  if (drug | has("drug") and drug.has_dose_form) then
22    drug.drug.numerator
23  else
24    null
25  end
26;
27
28MedicationAdministration |
29[
30  "drug_exposure",              # TABLE COLUMNS
31    .id,                          # drug_exposure_id
32    .subject.id,                  # person_id
33    drug.concept_id,              # drug_concept_id
34    .effectiveDateTime,           # drug_exposure_start_date
35    .effectiveDateTime,           # drug_exposure_start_datetime
36    .effectiveDateTime,           # drug_exposure_end_date
37    .effectiveDateTime,           # drug_exposure_end_datetime
38    null,                         # verbatim_end_date
39    32818,                        # drug_type_concept_id - EHR administration record
40    null,                         # stop_reason
41    null,                         # refills
42    quantity,                     # quantity
43    null,                         # days_supply
44    .note,                        # sig
45    null,                         # route_concept_id
46    null,                         # lot_number
47    null,                         # provider_id
48    .context.id,                  # visit_occurrence_id
49    null,                         # visit_detail_id
50    drug.concept_code,            # drug_source_value
51    drug.source_concept_id,       # drug_source_concept_id
52    null,                         # route_source_value
53    null                          # dose_unit_source_value
54]
55| select(
56  ((.[0] == "drug_exposure") and length == 24)
57)
58|
59@tsv