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

49 lines · jq
 1#
 2# Converts FHIR AllergyIntolerance resources to OMOPCDM condition_occurrence DB table records.
 3#
 4# REPO="https://github.com/barabo/fhir-to-omop-demo"
 5# FILE="demo/translate/map/AllergyIntolerance.jq"
 6#
 7
 8include "fhir";
 9include "fhir/common";
10
11
12# TODO: inject concepts for .clinicalStatus and .verificationStatus
13def condition:
14  .code.coding[] // {}
15;
16
17def clinical_status:
18  .clinicalStatus.coding[] // {}
19;
20
21def verification_status:
22  .verificationStatus.coding[].code.concept // {}
23;
24
25
26# FHIR AllergyIntolerance -> OMOPCDM condition_occurrence
27AllergyIntolerance |
28[
29  "condition_occurrence",                # TABLE COLUMNS
30    .id,                                 # condition_occurrence_id
31    .patient.id,                         # person_id
32    condition.concept.concept_id,        # condition_concept_id
33    .recordedDate,                       # condition_start_date
34    .recordedDate,                       # condition_start_datetime
35    null,  # condition_end_date
36    null,  # condition_end_datetime
37    32817,                               # condition_type_concept_id  # provenance: EHR
38    clinical_status.concept.concept_id,  # condition_status_concept_id
39    null,  # stop_reason
40    null,  # provider_id
41    null,  # visit_occurrence_id
42    null,  # visit_detail_id
43    condition.code,                       # condition_source_value
44    condition.vocabulary.concept_id,      # condition_source_concept_id
45    clinical_status.code                  # condition_status_source_value
46]
47|
48@tsv
49