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

 1#
 2# Transforms FHIR MedicationRequests into OMOP table records.
 3#
 4
 5include "fhir";
 6include "fhir/common";
 7
 8
 9# Include the route_concept_id in the drug concept.
10def drug:
11  if has("medicationCodeableConcept") then
12    if (.medicationCodeableConcept.coding | length) > 1 then
13      debug("Multiple medicationCodeableConcept.codings in MedicationRequest/\(.id)")
14    end
15    | .medicationCodeableConcept.coding[0].concept
16  else
17    {
18      "concept_id": null,
19      "concept_code": null,
20      "route_concept_id": null,
21      "source_concept_id": null
22    }
23  end
24;
25
26
27# See: https://ohdsi.github.io/CommonDataModel/drug_dose.html
28# TODO: include the 'has dose form' value in concept
29# TODO: include numerator in concept
30# TODO: if there is a dosageQuantity, use it, too
31def quantity:
32  if (drug | has("drug") and drug.has_dose_form) then
33    drug.drug.numerator
34  else
35    null
36  end
37;
38
39# If this is a MedicationReference, then the contents of this record will be
40# merged with the Medication record contents in the next phase of loading.
41def id:
42  if has("medicationReference") then
43    .medicationReference.id
44  else
45    .id
46  end
47;
48
49
50MedicationRequest |
51[
52  "drug_exposure",              # TABLE COLUMNS
53    id,                           # drug_exposure_id
54    .subject.id,                  # person_id
55    drug.concept_id,              # drug_concept_id
56    .authoredOn,                  # drug_exposure_start_date
57    .authoredOn,                  # drug_exposure_start_datetime
58    null,                  # drug_exposure_end_date
59    null,                  # drug_exposure_end_datetime
60    null,                         # verbatim_end_date
61    32838,                        # drug_type_concept_id - EHR prescription
62    null,                         # stop_reason
63    null,                         # refills
64    quantity,                     # quantity
65    null,                         # days_supply
66    .note,                        # sig
67    drug.route_concept_id,        # route_concept_id
68    null,                         # lot_number
69    .requester.id,                # provider_id
70    .encounter.id,                # visit_occurrence_id
71    null,                         # visit_detail_id
72    drug.concept_code,            # drug_source_value
73    drug.source_concept_id,       # drug_source_concept_id
74    null,                         # route_source_value
75    null                          # dose_unit_source_value
76]
77| select(
78  ((.[0] == "drug_exposure") and length == 24)
79)
80|
81@tsv