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onconova.interoperability.fhir.schemas.cancer_risk_assessment

CancerRiskAssessmentProfile

Bases: OnconovaFhirBaseSchema, OnconovaCancerRiskAssessment

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/cancer_risk_assessment.py 
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@classmethod
def fhir_to_onconova(
    cls, obj: fhir.OnconovaCancerRiskAssessment
) -> schemas.RiskAssessmentCreate:
    return schemas.RiskAssessmentCreate(
        externalSource=None,
        externalSourceId=None,
        caseId=obj.fhirpath_single(
            "Observation.subject.reference.getValue()"
        ).replace("Patient/", ""),
        date=obj.fhirpath_single("Observation.effectiveDateTime.getValue()"),
        assessedEntitiesIds=[
            ref.replace("Condition/", "")
            for ref in obj.fhirpath_values("Observation.focus.reference.getValue()")
        ],
        methodology=CodedConcept.model_validate(
            obj.fhirpath_single("Observation.code.coding").model_dump()
        ),
        risk=CodedConcept.model_validate(
            obj.fhirpath_single(
                "Observation.valueCodeableConcept.coding"
            ).model_dump()
        ),
        score=obj.fhirpath_single(
            "Observation.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-risk-assessment-score').value.getValue()"
        ),
    )

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/cancer_risk_assessment.py 
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@classmethod
def onconova_to_fhir(
    cls, obj: schemas.RiskAssessment
) -> fhir.OnconovaCancerRiskAssessment:
    resource = fhir.OnconovaCancerRiskAssessment.model_construct()
    resource.id = str(obj.id)
    resource.text = Narrative(
        status="generated",
        div=f'<div xmlns="http://www.w3.org/1999/xhtml">{obj.description}</div>',
    )
    resource.subject = Reference(
        reference=f"Patient/{obj.caseId}",
    )
    resource.effectiveDateTime = obj.date.isoformat()
    resource.focus = [
        Reference(reference=f"Condition/{cond_id}")
        for cond_id in obj.assessedEntitiesIds or []
    ]
    resource.code = construct_fhir_codeable_concept(obj.methodology)
    resource.valueCodeableConcept = construct_fhir_codeable_concept(obj.risk)
    if obj.score:
        resource.extension = [
            fhir.RiskAssessmentScore(
                valueDecimal=obj.score if isinstance(obj.score, float) else None,
                valueInteger=obj.score if isinstance(obj.score, int) else None,
            )
        ]

    return resource
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