From 0eff35636faccf588210cf4c87cd6b243df0f844 Mon Sep 17 00:00:00 2001 From: bdolin Date: Fri, 14 Jun 2024 12:04:53 -0700 Subject: [PATCH] fix molecConseq FHIR mapping --- .gitignore | 1 + app/common.py | 14 ++++++++++---- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 119aa245..5022eda4 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ .pytest_cache __pycache__ .venv +utilities/FASTA \ No newline at end of file diff --git a/app/common.py b/app/common.py index 057aabb4..70303e92 100644 --- a/app/common.py +++ b/app/common.py @@ -730,11 +730,17 @@ def create_molecular_consequence_profile(molecular_consequence, subject, vids): "code": f"{feature_consequence['code']}", "display": f"{feature_consequence['display']}"}]}}) + if 'functionalEffect' in molecular_consequence: + for functionalEffect in molecular_consequence["functionalEffect"]: + resource["component"].append({"code": {"coding": [{"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "functional-effect", + "display": "Functional Effect"}]}, + "valueCodeableConcept": {"coding": [{"system": f"{functionalEffect['system']}", + "code": f"{functionalEffect['code']}", + "display": f"{functionalEffect['display']}"}]}}) + if 'impact' in molecular_consequence: - resource["component"].append({"code": {"coding": [{"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "functional-effect", - "display": "Functional Effect"}]}, - "valueCodeableConcept": {"text": f"{molecular_consequence['impact']}"}}) + resource["interpretation"] = [{"text": molecular_consequence['impact']}] return resource