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fix molecConseq FHIR mapping #90

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merged 2 commits into from
Jun 14, 2024
Merged

fix molecConseq FHIR mapping #90

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0eff356
fix molecConseq FHIR mapping
rhdolin Jun 14, 2024
4ece890
update molConseq test cases
rhdolin Jun 14, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@
.pytest_cache
__pycache__
.venv
utilities/FASTA
14 changes: 10 additions & 4 deletions app/common.py
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Expand Up @@ -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

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17 changes: 4 additions & 13 deletions tests/expected_outputs/find_subject_molecular_consequences/1.json
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Expand Up @@ -104,20 +104,11 @@
}
]
}
},
}
],
"interpretation": [
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "functional-effect",
"display": "Functional Effect"
}
]
},
"valueCodeableConcept": {
"text": "MODERATE"
}
"text": "MODERATE"
}
]
}
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13 changes: 12 additions & 1 deletion tests/expected_outputs/find_subject_molecular_consequences/2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -116,9 +116,20 @@
]
},
"valueCodeableConcept": {
"text": "HIGH"
"coding": [
{
"system": "http://sequenceontology.org",
"code": "SO:0002054",
"display": "loss_of_function_variant"
}
]
}
}
],
"interpretation": [
{
"text": "HIGH"
}
]
}
},
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