onconova.oncology.models.risk_assessment

RiskAssessment

Bases: BaseModel

Represents a risk assessment for a patient's cancer case.

Attributes:

Name	Type	Description
case	ForeignKey[PatientCase]	Reference to the patient's case being assessed.
date	DateField	Date when the risk assessment was performed and recorded.
assessed_entities	ManyToManyField[NeoplasticEntity]	Neoplastic entities assessed to estimate risk.
methodology	CodedConceptField[CancerRiskAssessmentMethod]	Method or type of risk assessment used.
risk	CodedConceptField[CancerRiskAssessmentClassification]	Assessed risk classification.
score	FloatField	Quantitative score used to classify the risk (optional).

assessed_entities class-attribute instance-attribute

case class-attribute instance-attribute

date class-attribute instance-attribute

description property

methodology class-attribute instance-attribute

risk class-attribute instance-attribute

score class-attribute instance-attribute

save(*args, **kwargs)

Source code in onconova/oncology/models/risk_assessment.py

def save(self, *args, **kwargs):
    try:
        validate_risk_classification(self)
        super().save(*args, **kwargs)
    except AssertionError:
        raise ValueError(
            f'{self.risk} is not a valid choice for risk methodology "{self.methodology}".'
        )

validate_risk_classification(assessment)

Validates that the risk classification code in the given assessment matches the expected codes for the specified risk assessment methodology.

The function checks the assessment.methodology.code and asserts that assessment.risk.code is one of the allowed codes for that methodology.

Parameters:

Name	Type	Description	Default
assessment	RiskAssessment | RiskAssessmentSchema	An object containing methodology.code and risk.code attributes.	required

Raises:

Type	Description
AssertionError	If the risk code does not match the expected codes for the methodology.

Source code in onconova/oncology/models/risk_assessment.py

def validate_risk_classification(assessment):
    """
    Validates that the risk classification code in the given assessment matches the expected codes
    for the specified risk assessment methodology.

    The function checks the `assessment.methodology.code` and asserts that `assessment.risk.code`
    is one of the allowed codes for that methodology.

    Args:
        assessment (RiskAssessment | RiskAssessmentSchema): An object containing `methodology.code` and `risk.code` attributes.

    Raises:
        AssertionError: If the risk code does not match the expected codes for the methodology.
    """
    if (
        assessment.methodology.code == "C136962"
    ):  # Follicular Lymphoma International Prognostic Index (FLIPI)
        assert assessment.risk.code in (
            "C136965",  # FLIPI Score 0-1, Low Risk
            "C136967",  # FLIPI Score 2, Intermediate Risk
            "C136968",  # FLIPI Score Greater than or Equal to 3, High Risk
        )
    elif (
        assessment.methodology.code == "C181086"
    ):  # D'Amico Prostate Cancer Risk Classification
        assert assessment.risk.code in (
            "C102403",  # Low risk
            "C102402",  # Intermediate risk
            "C102401",  # High risk
        )
    elif (
        assessment.methodology.code == "C127872"
    ):  # European Treatment Outcome Study (EUTOS) Score
        assert assessment.risk.code in (
            "C102403",  # Low risk
            "C102401",  # High risk
        )
    elif assessment.methodology.code == "C127873":  # Hasford Score
        assert assessment.risk.code in (
            "C102403",  # Low risk
            "C102402",  # Intermediate risk
            "C102401",  # High risk
        )
    elif assessment.methodology.code == "C127875":  # Sokal Score
        assert assessment.risk.code in (
            "C102403",  # Low risk
            "C102402",  # Intermediate risk
            "C102401",  # High risk
        )
    elif (
        assessment.methodology.code == "C155843"
    ):  # International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) Criteria
        assert assessment.risk.code in (
            "C155844",  # IMDC Favorable risk
            "C155845",  # IMDC Intermediate Risk
            "C155846",  # IMDC Poor risk
        )
    elif (
        assessment.methodology.code == "C161805"
    ):  # International Prognostic Index (IPI) Risk Group
        assert assessment.risk.code in (
            "C161809",  # High Risk
            "C161808",  # High-Intermediate Risk
            "C161806",  # Low Risk
            "C161807",  # Low-Intermediate Risk
        )
    elif (
        assessment.methodology.code == "C177562"
    ):  # European LeukemiaNet Risk Classification
        assert assessment.risk.code in (
            "C188368",  # Adverse-Risk
            "C188369",  # Favorable-Risk
            "C188370",  # Intermediate-Risk
        )
    elif assessment.methodology.code == "C121007":  # Child-Pugh Clinical Classification
        assert assessment.risk.code in (
            "C113691",  # Class A
            "C146790",  # Class A5
            "C146791",  # Class A6
            "C113692",  # Class B
            "C146792",  # Class B7
            "C146793",  # Class B8
            "C146794",  # Class B9
            "C113694",  # Class C
            "C146795",  # Class C10
            "C146796",  # Class C11
            "C146797",  # Class C12
            "C146798",  # Class C13
            "C146799",  # Class C14
            "C146801",  # Class C15
            "C148151",  # Class A-B7 Cirrhosis
        )
    elif (
        assessment.methodology.code == "C181085"
    ):  # USCF Cancer of the Prostate Risk Assessment Score
        assert assessment.risk.code in (
            "C102403",  # Low risk
            "C102402",  # Intermediate risk
            "C102401",  # High risk
        )
    elif (
        assessment.methodology.code == "C162781"
    ):  # Mantle Cell Lymphoma International Prognostic Index (MIPI)
        assert assessment.risk.code in (
            "C102403",  # Low risk
            "C102402",  # Intermediate risk
            "C102401",  # High risk
        )
    elif (
        assessment.methodology.code == "C181084"
    ):  # NCCN Prostate Cancer Risk Stratification for Clinically Localized Disease
        assert assessment.risk.code in (
            "C192873",  # Very Low Risk
            "C192874",  # Low Risk
            "C192877",  # Unfavorable-Intermediate Risk
            "C192876",  # Favorable-Intermediate Risk
            "C192875",  # Intermediate Risk
            "C192878",  # High Risk
            "C192879",  # Very High Risk
        )
    elif assessment.methodology.code == "C177309":  # Seminoma IGCCC Risk Classification
        assert assessment.risk.code in (
            "C177313",  # Good
            "C177314",  # Intermediate
        )
    elif (
        assessment.methodology.code == "C177308"
    ):  # Non-Seminomatous Germ Cell Tumor IGCCC Risk Classification
        assert assessment.risk.code in (
            "C177310",  # Good
            "C177311",  # Intermediate
            "C177312",  # Poor
        )
    elif (
        assessment.methodology.code == "C142346"
    ):  # International Society of Urological Pathology Gleason Grade Group
        assert assessment.risk.code in (
            "C162654",  # Grade Pattern 1
            "C162655",  # Grade Pattern 2
            "C162656",  # Grade Pattern 3
            "C162657",  # Grade Pattern 4
            "C162658",  # Grade Pattern 5
        )

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