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onconova.interoperability.fhir.schemas.lifestyle

LifestyleProfile

Bases: OnconovaFhirBaseSchema, OnconovaLifestyle

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/lifestyle.py 
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@classmethod
def fhir_to_onconova(cls, obj: fhir.OnconovaLifestyle) -> schemas.LifestyleCreate:
    return schemas.LifestyleCreate(
        externalSource=None,
        externalSourceId=None,
        caseId=obj.fhirpath_single(
            "Observation.subject.reference.getValue()"
        ).replace("Patient/", ""),
        date=obj.fhirpath_single("Observation.effectiveDateTime.getValue()"),
        smokingStatus=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='72166-2').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        smokingPackyears=obj.fhirpath_single(
            "Observation.component.where(code.coding.code='8664-5').valueQuantity.value.getValue()"
        ),
        smokingQuited=(
            Measure(
                value=obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='107339-4').valueQuantity.value.getValue()"
                ),
                unit=obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='107339-4').valueQuantity.code.getValue()"
                ),
            )
            if (
                quantity := obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='107339-4').valueQuantity"
                )
            )
            else None
        ),
        alcoholConsumption=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='1106630-7').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        recreationalDrugs=(
            [CodedConcept.model_validate(drug.model_dump()) for drug in drugs]
            if (
                drugs := obj.fhirpath_values(
                    "Observation.component.where(code.coding.code='C84368').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        exposures=(
            [
                CodedConcept.model_validate(exposure.model_dump())
                for exposure in exposures
            ]
            if (
                exposures := obj.fhirpath_values(
                    "Observation.component.where(code.coding.code='C16552').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        nightSleep=(
            Measure(
                value=obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='93832-4').valueQuantity.value.getValue()"
                ),
                unit=obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='93832-4').valueQuantity.code.getValue()"
                ),
            )
            if (
                quantity := obj.fhirpath_single(
                    "Observation.component.where(code.coding.code='93832-4').valueQuantity"
                )
            )
            else None
        ),
    )

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/lifestyle.py 
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@classmethod
def onconova_to_fhir(cls, obj: schemas.Lifestyle) -> fhir.OnconovaLifestyle:
    resource = fhir.OnconovaLifestyle.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.component = resource.component or []
    if obj.smokingStatus:
        resource.component.append(
            fhir.OnconovaLifestyleSmokingStatus(
                valueCodeableConcept=construct_fhir_codeable_concept(
                    obj.smokingStatus
                )
            )
        )
    if obj.smokingPackyears is not None:
        resource.component.append(
            fhir.OnconovaLifestyleSmokingPackyears(
                valueQuantity=fhir.OnconovaLifestyleValueQuantity(
                    value=obj.smokingPackyears,
                    code="{pack-year}",
                    system="http://unitsofmeasure.org",
                )
            )
        )
    if obj.smokingQuited is not None:
        resource.component.append(
            fhir.OnconovaLifestyleSmokingQuited(
                valueQuantity=Quantity(
                    value=obj.smokingQuited.value,
                    code=obj.smokingQuited.unit,
                    system="http://unitsofmeasure.org",
                )
            )
        )
    if obj.alcoholConsumption:
        resource.component.append(
            fhir.OnconovaLifestyleAlcoholConsumption(
                valueCodeableConcept=construct_fhir_codeable_concept(
                    obj.alcoholConsumption
                )
            )
        )
    if obj.nightSleep is not None:
        resource.component.append(
            fhir.OnconovaLifestyleNightSleep(
                valueQuantity=Quantity(
                    value=obj.nightSleep.value,
                    code=obj.nightSleep.unit,
                    system="http://unitsofmeasure.org",
                )
            )
        )
    for drug in obj.recreationalDrugs or []:
        resource.component.append(
            fhir.OnconovaLifestyleRecreationalDrug(
                valueCodeableConcept=construct_fhir_codeable_concept(drug)
            )
        )
    for exposure in obj.exposures or []:
        resource.component.append(
            fhir.OnconovaLifestyleExposures(
                valueCodeableConcept=construct_fhir_codeable_concept(exposure)
            )
        )
    return resource
runner