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onconova.interoperability.fhir.schemas.tumor_neoantigen_burden

TumorNeoantigenBurdenProfile

Bases: OnconovaFhirBaseSchema, OnconovaTumorNeoantigenBurden

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/tumor_neoantigen_burden.py 
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@classmethod
def fhir_to_onconova(
    cls, obj: fhir.OnconovaTumorNeoantigenBurden
) -> schemas.TumorNeoantigenBurdenCreate:
    return schemas.TumorNeoantigenBurdenCreate(
        externalSource=None,
        externalSourceId=None,
        caseId=obj.fhirpath_single(
            "Observation.subject.reference.getValue()"
        ).replace("Patient/", ""),
        date=obj.fhirpath_single("Observation.effectiveDateTime.getValue()"),
        value=obj.fhirpath_single("Observation.valueQuantity.value.getValue()"),
    )

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/tumor_neoantigen_burden.py 
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@classmethod
def onconova_to_fhir(
    cls, obj: schemas.TumorNeoantigenBurden
) -> fhir.OnconovaTumorNeoantigenBurden:
    resource = fhir.OnconovaTumorNeoantigenBurden.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.effectiveDateTime = obj.date.isoformat()
    resource.subject = Reference(
        reference=f"Patient/{obj.caseId}",
    )
    resource.valueQuantity = fhir.OnconovaTumorNeoantigenBurdenValueQuantity(
        value=obj.value,
    )
    return resource
runner