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Merge pull request #73 from mihaitodor/fix-find-subject-tx-implicatio…
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…ns-missing-evidence-level

Fix find-subject-tx-implications bug
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@rhdolin
rhdolin authored Sep 21, 2023
2 parents 2b4e1f1 + fc733e9 commit bf7fb87
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Showing 22 changed files with 579 additions and 28 deletions.
9 changes: 5 additions & 4 deletions app/common.py
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Expand Up @@ -716,10 +716,11 @@ def create_tx_implication_profile_civic(implication, subject, vids):
"code": f"{ptc['code']}",
"display": f"{ptc['display']}"}]}})

resource["component"].append({"code": {"coding": [{"system": "http://loinc.org",
"code": "93044-6",
"display": "Level of evidence"}]},
"valueCodeableConcept": {"text": f"{implication['evidenceLevel']}"}})
if 'evidenceLevel' in implication:
resource["component"].append({"code": {"coding": [{"system": "http://loinc.org",
"code": "93044-6",
"display": "Level of evidence"}]},
"valueCodeableConcept": {"text": f"{implication['evidenceLevel']}"}})

for med in implication['medicationAssessed']:
resource["component"].append({"code": {"coding": [{"system": "http://loinc.org",
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_dx_implications/1.json
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Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_dx_implications/2.json
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Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
}
]
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_dx_implications/3.json
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Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_dx_implications/4.json
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Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_specific_haplotypes/1.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_specific_haplotypes/2.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_specific_haplotypes/3.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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6 changes: 3 additions & 3 deletions tests/expected_outputs/find_population_specific_haplotypes/4.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
Expand All @@ -42,7 +42,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
Expand All @@ -67,7 +67,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_specific_variants/1.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
}
]
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4 changes: 2 additions & 2 deletions tests/expected_outputs/find_population_specific_variants/2.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
Expand Down Expand Up @@ -47,4 +47,4 @@
]
}
]
}
}
2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_structural_intersecting_variants/1.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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4 changes: 2 additions & 2 deletions tests/expected_outputs/find_population_structural_intersecting_variants/2.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
}
]
Expand All @@ -38,7 +38,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_structural_intersecting_variants/3.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_structural_subsuming_variants/1.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
}
]
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4 changes: 2 additions & 2 deletions tests/expected_outputs/find_population_structural_subsuming_variants/2.json
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Expand Up @@ -17,7 +17,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
}
]
Expand All @@ -38,7 +38,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_tx_implications/2.json
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Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_tx_implications/3.json
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_tx_implications/4.json
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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2 changes: 1 addition & 1 deletion tests/expected_outputs/find_population_tx_implications/5.json
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Expand Up @@ -13,7 +13,7 @@
{
"name": "denominator",
"valueQuantity": {
"value": 1112
"value": 1114
}
},
{
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