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

 1#
 2# Transforms FHIR Medication into OMOP table records.
 3#
 4# This transformation is needed to populate missing medication information
 5# from the MedicationRequest records when a MedicationReference is used.
 6#
 7
 8include "fhir";
 9include "fhir/common";
10
11##
12# Select the drug concept from the Medication record.
13#
14def drug:
15  if has("code") then
16    if (.code.coding | length) > 1 then
17      error("Multiple code.codings in Medication/\(.id)")
18    end
19    | .code.coding[0].concept
20  else
21    {
22      "concept_id": null,
23      "concept_code": null,
24      "route_concept_id": null,
25      "source_concept_id": null
26    }
27  end
28;
29
30# See: https://ohdsi.github.io/CommonDataModel/drug_dose.html
31# TODO: include the 'has dose form' value in concept
32# TODO: include numerator in concept
33# TODO: if there is a dosageQuantity, use it, too
34def quantity:
35  if (drug | has("drug") and drug.has_dose_form) then
36    drug.drug.numerator
37  else
38    null
39  end
40;
41
42
43Medication |
44[
45  "drug_exposure",
46    .id,                          # drug_exposure_id
47    null,                         # person_id
48    drug.concept_id,              # drug_concept_id
49    null,                         # drug_exposure_start_date
50    null,                         # drug_exposure_start_datetime
51    null,                         # drug_exposure_end_date
52    null,                         # drug_exposure_end_datetime
53    null,                         # verbatim_end_date
54    null,                         # drug_type_concept_id - EHR prescription
55    null,                         # stop_reason
56    null,                         # refills
57    quantity,                     # quantity
58    null,                         # days_supply
59    null,                         # sig
60    drug.route_concept_id,        # route_concept_id
61    null,                         # lot_number
62    null,                         # provider_id
63    null,                         # visit_occurrence_id
64    null,                         # visit_detail_id
65    drug.concept_code,            # drug_source_value
66    drug.source_concept_id,       # drug_source_concept_id
67    null,                         # route_source_value
68    null                          # dose_unit_source_value
69]
70|
71@tsv
72