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fbraza merged 2 commits into from
Jul 19, 2025
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feat: implement SCORE2-Diabetes cardiovascular risk algorithm #16

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9d89887
feat: implement SCORE2-Diabetes cardiovascular risk algorithm
fbraza Jul 19, 2025
f72aab4
test: add values for unit test score2 diabetes
fbraza Jul 19, 2025
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51 changes: 51 additions & 0 deletions tests/inputs/score2_diabetes/test__input__patient_01.json
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{
"metadata": {
"patient_id": "P001-2024-001",
"sex": "male",
"timestamp": "2024-11-04T10:00:00Z",
"test_date": "2024-11-04",
"laboratory": "SCORE2-Diabetes Labs"
},
"raw_biomarkers": {
"age_years": {
"value": 45,
"unit": "years"
},
"smoking_yes_no": {
"value": false,
"unit": "yes/no"
},
"systolic_blood_pressure_mmhg": {
"value": 130,
"unit": "mmHg"
},
"total_cholesterol_mmol_l": {
"value": 5.5,
"unit": "mmol/L"
},
"hdl_cholesterol_mmol_l": {
"value": 1.2,
"unit": "mmol/L"
},
"is_male_yes_no": {
"value": true,
"unit": "yes/no"
},
"diabetes_yes_no": {
"value": true,
"unit": "yes/no"
},
"age_at_diabetes_diagnosis_years": {
"value": 40,
"unit": "years"
},
"hba1c_mmol_mol": {
"value": 48,
"unit": "mmol/mol"
},
"egfr_ml_min_1_73m2": {
"value": 90,
"unit": "mL/min/1.73m\u00b2"
}
}
}
51 changes: 51 additions & 0 deletions tests/inputs/score2_diabetes/test__input__patient_02.json
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{
"metadata": {
"patient_id": "P002-2024-002",
"sex": "female",
"timestamp": "2024-11-04T10:30:00Z",
"test_date": "2024-11-04",
"laboratory": "SCORE2-Diabetes Labs"
},
"raw_biomarkers": {
"age_years": {
"value": 55,
"unit": "years"
},
"smoking_yes_no": {
"value": true,
"unit": "yes/no"
},
"systolic_blood_pressure_mmhg": {
"value": 145,
"unit": "mmHg"
},
"total_cholesterol_mmol_l": {
"value": 6.8,
"unit": "mmol/L"
},
"hdl_cholesterol_mmol_l": {
"value": 1.1,
"unit": "mmol/L"
},
"is_male_yes_no": {
"value": false,
"unit": "yes/no"
},
"diabetes_yes_no": {
"value": true,
"unit": "yes/no"
},
"age_at_diabetes_diagnosis_years": {
"value": 50,
"unit": "years"
},
"hba1c_mmol_mol": {
"value": 58,
"unit": "mmol/mol"
},
"egfr_ml_min_1_73m2": {
"value": 75,
"unit": "mL/min/1.73m\u00b2"
}
}
}
51 changes: 51 additions & 0 deletions tests/inputs/score2_diabetes/test__input__patient_03.json
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{
"metadata": {
"patient_id": "P003-2024-003",
"sex": "male",
"timestamp": "2024-11-04T11:00:00Z",
"test_date": "2024-11-04",
"laboratory": "SCORE2-Diabetes Labs"
},
"raw_biomarkers": {
"age_years": {
"value": 65,
"unit": "years"
},
"smoking_yes_no": {
"value": false,
"unit": "yes/no"
},
"systolic_blood_pressure_mmhg": {
"value": 155,
"unit": "mmHg"
},
"total_cholesterol_mmol_l": {
"value": 7.2,
"unit": "mmol/L"
},
"hdl_cholesterol_mmol_l": {
"value": 0.9,
"unit": "mmol/L"
},
"is_male_yes_no": {
"value": true,
"unit": "yes/no"
},
"diabetes_yes_no": {
"value": true,
"unit": "yes/no"
},
"age_at_diabetes_diagnosis_years": {
"value": 55,
"unit": "years"
},
"hba1c_mmol_mol": {
"value": 68,
"unit": "mmol/mol"
},
"egfr_ml_min_1_73m2": {
"value": 60,
"unit": "mL/min/1.73m\u00b2"
}
}
}
51 changes: 51 additions & 0 deletions tests/inputs/score2_diabetes/test__input__patient_04.json
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{
"metadata": {
"patient_id": "P004-2024-004",
"sex": "female",
"timestamp": "2024-11-04T11:30:00Z",
"test_date": "2024-11-04",
"laboratory": "SCORE2-Diabetes Labs"
},
"raw_biomarkers": {
"age_years": {
"value": 48,
"unit": "years"
},
"smoking_yes_no": {
"value": false,
"unit": "yes/no"
},
"systolic_blood_pressure_mmhg": {
"value": 120,
"unit": "mmHg"
},
"total_cholesterol_mmol_l": {
"value": 4.8,
"unit": "mmol/L"
},
"hdl_cholesterol_mmol_l": {
"value": 1.5,
"unit": "mmol/L"
},
"is_male_yes_no": {
"value": false,
"unit": "yes/no"
},
"diabetes_yes_no": {
"value": true,
"unit": "yes/no"
},
"age_at_diabetes_diagnosis_years": {
"value": 45,
"unit": "years"
},
"hba1c_mmol_mol": {
"value": 42,
"unit": "mmol/mol"
},
"egfr_ml_min_1_73m2": {
"value": 100,
"unit": "mL/min/1.73m\u00b2"
}
}
}
51 changes: 51 additions & 0 deletions tests/inputs/score2_diabetes/test__input__patient_05.json
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{
"metadata": {
"patient_id": "P005-2024-005",
"sex": "male",
"timestamp": "2024-11-04T12:00:00Z",
"test_date": "2024-11-04",
"laboratory": "SCORE2-Diabetes Labs"
},
"raw_biomarkers": {
"age_years": {
"value": 60,
"unit": "years"
},
"smoking_yes_no": {
"value": true,
"unit": "yes/no"
},
"systolic_blood_pressure_mmhg": {
"value": 150,
"unit": "mmHg"
},
"total_cholesterol_mmol_l": {
"value": 6.5,
"unit": "mmol/L"
},
"hdl_cholesterol_mmol_l": {
"value": 1.0,
"unit": "mmol/L"
},
"is_male_yes_no": {
"value": true,
"unit": "yes/no"
},
"diabetes_yes_no": {
"value": true,
"unit": "yes/no"
},
"age_at_diabetes_diagnosis_years": {
"value": 48,
"unit": "years"
},
"hba1c_mmol_mol": {
"value": 75,
"unit": "mmol/mol"
},
"egfr_ml_min_1_73m2": {
"value": 60,
"unit": "mL/min/1.73m\u00b2"
}
}
}
51 changes: 51 additions & 0 deletions tests/inputs/score2_diabetes/test__input__patient_06.json
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{
"metadata": {
"patient_id": "P006-2024-006",
"sex": "female",
"timestamp": "2024-11-04T12:30:00Z",
"test_date": "2024-11-04",
"laboratory": "SCORE2-Diabetes Labs"
},
"raw_biomarkers": {
"age_years": {
"value": 42,
"unit": "years"
},
"smoking_yes_no": {
"value": true,
"unit": "yes/no"
},
"systolic_blood_pressure_mmhg": {
"value": 135,
"unit": "mmHg"
},
"total_cholesterol_mmol_l": {
"value": 6.0,
"unit": "mmol/L"
},
"hdl_cholesterol_mmol_l": {
"value": 1.3,
"unit": "mmol/L"
},
"is_male_yes_no": {
"value": false,
"unit": "yes/no"
},
"diabetes_yes_no": {
"value": true,
"unit": "yes/no"
},
"age_at_diabetes_diagnosis_years": {
"value": 38,
"unit": "years"
},
"hba1c_mmol_mol": {
"value": 53,
"unit": "mmol/mol"
},
"egfr_ml_min_1_73m2": {
"value": 85,
"unit": "mL/min/1.73m\u00b2"
}
}
}
40 changes: 40 additions & 0 deletions tests/test_score2_diabetes.py
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from pathlib import Path

import pytest

from vitals.score2_diabetes import compute

OUT_FILEPATH = Path(__file__).parent / "inputs" / "score2_diabetes"


@pytest.mark.parametrize(
"filename,expected",
[
("test__input__patient_01.json", (45.00, 4.40, "High")),
("test__input__patient_02.json", (55.00, 11.80, "Very high")),
("test__input__patient_03.json", (65.00, 18.60, "Very high")),
("test__input__patient_04.json", (48.00, 2.30, "Low to moderate")),
("test__input__patient_05.json", (60.00, 22.30, "Very high")),
("test__input__patient_06.json", (42.00, 5.80, "High")),
],
)
def test_score2_diabetes(filename, expected):
"""
Test SCORE2-Diabetes cardiovascular risk calculation.

NOTE: The expected risk values and categories are placeholders.
They need to be calculated using MDCalc and updated before running tests.
"""
# Get the actual fixture value
age, pred_risk, pred_risk_category = compute.cardiovascular_risk(
OUT_FILEPATH / filename
)
expected_age, expected_risk, expected_category = expected

assert age == expected_age
assert pred_risk_category == expected_category
assert pytest.approx(pred_risk, abs=0.1) == expected_risk


if __name__ == "__main__":
pytest.main([__file__])
2 changes: 1 addition & 1 deletion vitals/biomarkers/helpers.py
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from vitals.biomarkers import schemas

Biomarkers = TypeVar("Biomarkers", bound=BaseModel)
Units = schemas.PhenoageUnits | schemas.Score2Units
Units = schemas.PhenoageUnits | schemas.Score2Units | schemas.Score2DiabetesUnits


class ConversionInfo(TypedDict):
Expand Down
33 changes: 33 additions & 0 deletions vitals/biomarkers/schemas.py
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Expand Up @@ -57,3 +57,36 @@ class Score2Markers(BaseModel):
hdl_cholesterol: float
smoking: bool
is_male: bool


# ------ SCORE2-Diabetes Schemas
class Score2DiabetesUnits(BaseModel):
"""
The expected unit to be used for Score2-Diabetes computation
"""

age: str = "years"
systolic_blood_pressure: str = "mmHg"
total_cholesterol: str = "mmol/L"
hdl_cholesterol: str = "mmol/L"
smoking: str = "yes/no"
is_male: str = "yes/no"
diabetes: str = "yes/no"
age_at_diabetes_diagnosis: str = "years"
hba1c: str = "mmol/mol"
egfr: str = "mL/min/1.73m²"


class Score2DiabetesMarkers(BaseModel):
"""Processed Score2-Diabetes biomarkers with standardized units."""

age: float
systolic_blood_pressure: float
total_cholesterol: float
hdl_cholesterol: float
smoking: bool
is_male: bool
diabetes: bool
age_at_diabetes_diagnosis: float
hba1c: float
egfr: float
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