onconova.interoperability.fhir.schemas.cancer_patient

CancerPatientProfile

Bases: OnconovaFhirBaseSchema, OnconovaCancerPatient

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/cancer_patient.py

@classmethod
def fhir_to_onconova(
    cls, obj: fhir.OnconovaCancerPatient
) -> schemas.PatientCaseCreate:
    return schemas.PatientCaseCreate(
        externalSource=None,
        externalSourceId=None,
        clinicalCenter=obj.fhirpath_single(
            "Patient.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-cancer-patient-clinical-center').valueString.getValue()"
        ),
        clinicalIdentifier=obj.fhirpath_single(
            "Patient.identifier.where(type.coding.code='MR').value.getValue()"
        ),
        consentStatus=cls.map_to_internal(
            "consentStatus",
            obj.fhirpath_single(
                "Patient.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-cancer-patient-consent-status').valueCode.getValue()"
            ),
        ),
        vitalStatus=cls.map_to_internal(
            "vitalStatus",
            obj.fhirpath_single(
                "Patient.deceasedDateTime.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-cancer-patient-vital-status').valueCodeableConcept.coding"
            ),
        ),
        gender=CodedConcept(
            code=obj.fhirpath_single("Patient.gender.getValue()"),
            system=cls._get_gender_codesystem(),
        ),
        race=(
            CodedConcept(**coding)
            if (
                coding := obj.fhirpath_single(
                    "Patient.extension('http://hl7.org/fhir/us/core/StructureDefinition/us-core-race').extension('ombCategory').valueCoding"
                )
            )
            else None
        ),
        sexAtBirth=(
            CodedConcept(
                code=code,
                system=cls._get_birthsex_codesystem(),
            )
            if (
                code := obj.fhirpath_single(
                    "Patient.extension('http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex').valueCode.getValue()"
                )
            )
            else None
        ),
        dateOfBirth=obj.fhirpath_single("Patient.birthDate.getValue()"),
        endOfRecords=obj.fhirpath_single(
            "Patient.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-cancer-patient-end-of-records').valueDate.getValue()"
        ),
        dateOfDeath=obj.fhirpath_single("Patient.deceasedDateTime.getValue()"),
        causeOfDeath=(
            CodedConcept.model_validate(coding.model_dump())
            if (
                coding := obj.fhirpath_single(
                    "Patient.deceasedDateTime.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-cancer-patient-cause-of-death').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        genderIdentity=None,
    )

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/cancer_patient.py

@classmethod
def onconova_to_fhir(cls, obj: schemas.PatientCase) -> fhir.OnconovaCancerPatient:
    resource = fhir.OnconovaCancerPatient.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.identifier = [
        fhir.OnconovaCancerPatientOnconovaIdentifier(value=obj.pseudoidentifier),
        fhir.OnconovaCancerPatientClinicalIdentifier(
            value=obj.clinicalIdentifier,
            system=obj.clinicalCenter.replace(" ", "-"),
        ),
    ]
    resource.gender = obj.gender.code
    resource.birthDate = fhir.OnconovaCancerPatientBirthDate(
        value=obj.dateOfBirth,
        extension=[
            ext
            for ext in [
                (
                    fhir.CancerPatientAge(valueInteger=int(obj.age))
                    if obj.age is not None
                    else None
                ),
                (
                    fhir.CancerPatientAgeAtDiagnosis(
                        valueInteger=int(obj.ageAtDiagnosis)
                    )
                    if obj.ageAtDiagnosis is not None
                    else None
                ),
            ]
            if ext is not None
        ],
    )
    resource.deceasedDateTime = fhir.OnconovaCancerPatientDeceasedDateTime(
        value=obj.dateOfDeath,
        extension=[
            ext
            for ext in [
                fhir.OnconovaCancerPatientVitalStatus(
                    valueCodeableConcept=fhir.CodeableConcept(
                        coding=[cls.map_to_fhir("vitalStatus", obj.vitalStatus)]
                    )
                ),
                (
                    fhir.OnconovaCancerPatientCauseOfDeath(
                        valueCodeableConcept=construct_fhir_codeable_concept(
                            obj.causeOfDeath
                        )
                    )
                    if obj.causeOfDeath
                    else None
                ),
            ]
            if ext is not None
        ],
    )
    resource.extension = [
        fhir.CancerPatientClinicalCenter(valueString=obj.clinicalCenter)
    ]
    if obj.endOfRecords is not None:
        resource.extension.append(
            fhir.CancerPatientEndOfRecords(valueDate=obj.endOfRecords)
        )
    if obj.sexAtBirth is not None:
        resource.extension.append(
            fhir.USCoreBirthSexExtension(valueCode=obj.sexAtBirth.code)
        )
    if obj.genderIdentity is not None:
        resource.extension.append(
            fhir.USCoreGenderIdentityExtension(
                valueCodeableConcept=construct_fhir_codeable_concept(
                    obj.genderIdentity
                )
            )
        )

    if obj.dataCompletionRate is not None:
        resource.extension.append(
            fhir.CancerPatientDataCompletionRate(
                valueDecimal=obj.dataCompletionRate
            )
        )
    if obj.contributors is not None and len(obj.contributors) > 0:
        resource.extension.extend(
            [
                fhir.CancerPatientDataContributors(
                    valueReference=Reference(type="Person", display=contributor)
                )
                for contributor in obj.contributors
            ]
        )
    if obj.consentStatus is not None:
        resource.extension.append(
            fhir.CancerPatientConsentStatus(
                valueCode=cls.map_to_fhir("consentStatus", obj.consentStatus)
            )
        )

    if obj.overallSurvival is not None:
        resource.extension.append(
            fhir.CancerPatientOverallSurvival(
                valueDuration=Duration(
                    value=obj.overallSurvival,
                    unit="months",
                    system="http://unitsofmeasure.org",
                    code="m",
                )
            )
        )
    if obj.race is not None:
        resource.extension.append(
            fhir.USCoreRaceExtension(
                extension=[
                    fhir.USCoreRaceExtensionOmbCategory(
                        valueCodeableConcept=fhir.CodeableConcept(
                            coding=[fhir.Coding(**obj.race.model_dump())]
                        )
                    )
                ]
            )
        )
    return resource

2026-04-262026-04-26runner