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onconova.interoperability.fhir.schemas.medication_administration

MedicationAdministrationProfile

Bases: OnconovaFhirBaseSchema, OnconovaMedicationAdministration

__model__ class-attribute instance-attribute

__schema__ class-attribute instance-attribute

construct_medication_administration(obj, medication) classmethod

Source code in onconova/interoperability/fhir/schemas/medication_administration.py 
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@classmethod
def construct_medication_administration(
    cls, obj, medication
) -> fhir.OnconovaMedicationAdministration:
    resource = fhir.OnconovaMedicationAdministration.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.effectivePeriod = fhir.Period(
        start=obj.period.start.isoformat() if obj.period.start else None,
        end=obj.period.end.isoformat() if obj.period.end else None,
    )
    resource.reasonReference = (
        [
            Reference(reference=f"Condition/{conditionId}")
            for conditionId in obj.targetedEntitiesIds
        ]
        if obj.targetedEntitiesIds
        else None
    )

    if obj.terminationReason:
        resource.statusReason = construct_fhir_codeable_concept(
            obj.terminationReason
        )

    resource.extension = [
        fhir.MedicationAdministrationIsPrimaryTherapy(
            valueBoolean=obj.isAdjunctive is not None,
        ),
        fhir.ProcedureIntent(
            valueCodeableConcept=construct_fhir_codeable_concept(
                cls.map_to_fhir("treatmentIntents", obj.intent)
            )
        ),
    ]
    if obj.cycles:
        resource.extension.append(
            fhir.MedicationAdministrationCycles(valueInteger=obj.cycles)
        )
    if obj.adjunctiveRole:
        resource.extension.append(
            fhir.MedicationAdministrationAdjunctiveRole(
                valueCodeableConcept=construct_fhir_codeable_concept(
                    obj.adjunctiveRole
                )
            )
        )
    if obj.therapyLineId:
        resource.extension.append(
            fhir.TherapyLineReference(
                valueReference=Reference(reference=f"List/{obj.therapyLineId}")
            )
        )
    # Process first medication
    resource.medicationCodeableConcept = construct_fhir_codeable_concept(
        medication.drug
    )
    if (
        medication.dosageMassConcentration
        or medication.dosageMass
        or medication.dosageVolume
        or medication.dosageMassSurface
    ) or (
        medication.dosageRateMassConcentration
        or medication.dosageRateMass
        or medication.dosageRateVolume
        or medication.dosageRateMassSurface
    ):
        resource.dosage = fhir.MedicationAdministrationDosage(
            route=(
                construct_fhir_codeable_concept(medication.route)
                if medication.route
                else None
            ),
            dose=(
                Quantity(
                    value=dose.value,
                    code=internal_to_ucum(dose.unit),
                    system="http://unitsofmeasure.org",
                )
                if (
                    dose := (
                        medication.dosageMassConcentration
                        or medication.dosageMass
                        or medication.dosageVolume
                        or medication.dosageMassSurface
                    )
                )
                else None
            ),
            rateQuantity=(
                Quantity(
                    value=rate.value,
                    code=internal_to_ucum(rate.unit),
                    system="http://unitsofmeasure.org",
                )
                if (
                    rate := (
                        medication.dosageRateMassConcentration
                        or medication.dosageRateMass
                        or medication.dosageRateVolume
                        or medication.dosageRateMassSurface
                    )
                )
                else None
            ),
        )
    return resource

fhir_to_onconova(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/medication_administration.py 
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@classmethod
def fhir_to_onconova(
    cls, obj: fhir.OnconovaMedicationAdministration
) -> schemas.SystemicTherapyCreate:
    return schemas.SystemicTherapyCreate(
        caseId=obj.fhirpath_single(
            "MedicationAdministration.subject.reference.getValue()"
        ).replace("Patient/", ""),
        period=Period.model_validate(
            obj.fhirpath_single(
                "MedicationAdministration.effectivePeriod"
            ).model_dump()
        ),
        intent=cls.map_to_internal(
            "TreatmentIntents",
            obj.fhirpath_single(
                "MedicationAdministration.extension('http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-procedure-intent').valueCodeableConcept.coding"
            ),
        ),
        targetedEntitiesIds=obj.fhirpath_values(
            "MedicationAdministration.reasonReference.reference.getValue().replace('Condition/','')"
        ),
        therapyLineId=obj.fhirpath_single(
            "MedicationAdministration.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-therapy-line-reference').valueReference.reference.getValue().replace('List/','')"
        ),
        cycles=obj.fhirpath_single(
            "MedicationAdministration.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-medication-administration-cycles').valueInteger.getValue()"
        ),
        adjunctiveRole=(
            CodedConcept.model_validate(role.model_dump())
            if (
                role := obj.fhirpath_single(
                    "MedicationAdministration.extension('http://onconova.github.io/fhir/StructureDefinition/onconova-ext-medication-administration-adjunctive-role').valueCodeableConcept.coding"
                )
            )
            else None
        ),
        terminationReason=(
            CodedConcept.model_validate(reason.model_dump())
            if (
                reason := obj.fhirpath_single(
                    "MedicationAdministration.statusReason.coding"
                )
            )
            else None
        ),
    )
Source code in onconova/interoperability/fhir/schemas/medication_administration.py 
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@classmethod
def fhir_to_onconova_related(
    cls, obj: fhir.OnconovaMedicationAdministration
) -> list[
    tuple[models.SystemicTherapyMedication, schemas.SystemicTherapyMedicationCreate]
]:
    data = []
    medications = [obj, *obj.fhirpath_values("contained")]
    for medication in medications:
        payload = schemas.SystemicTherapyMedicationCreate(
            drug=CodedConcept.model_validate(
                medication.fhirpath_single(
                    "medicationCodeableConcept.coding"
                ).model_dump()
            ),
            route=CodedConcept.model_validate(
                medication.fhirpath_single("dosage.route.coding").model_dump()
            ),
            dosageMassConcentration=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(dose.code.matches({get_units_collection_fhirpath(MassConcentration)})).dose"
                    )
                )
                else None
            ),
            dosageMass=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(dose.code.matches({get_units_collection_fhirpath(Mass)})).dose"
                    )
                )
                else None
            ),
            dosageVolume=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(dose.code.matches({get_units_collection_fhirpath(Volume)})).dose"
                    )
                )
                else None
            ),
            dosageMassSurface=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(dose.code.matches({get_units_collection_fhirpath(MassPerArea)})).dose"
                    )
                )
                else None
            ),
            dosageRateMassConcentration=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(rateQuantity.code.matches({get_units_collection_fhirpath(MassConcentrationPerTime)})).rateQuantity"
                    )
                )
                else None
            ),
            dosageRateMass=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(rateQuantity.code.matches({get_units_collection_fhirpath(MassPerTime)})).rateQuantity"
                    )
                )
                else None
            ),
            dosageRateVolume=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(rateQuantity.code.matches({get_units_collection_fhirpath(VolumePerTime)})).rateQuantity"
                    )
                )
                else None
            ),
            dosageRateMassSurface=(
                Measure(
                    value=str(quantity.value),
                    unit=ucum_to_internal(str(quantity.code)),
                )
                if (
                    quantity := medication.fhirpath_single(
                        f"dosage.where(rateQuantity.code.matches({get_units_collection_fhirpath(MassPerAreaPerTime)})).rateQuantity"
                    )
                )
                else None
            ),
        )
        data.append(
            (
                models.SystemicTherapyMedication.objects.filter(
                    systemic_therapy__id=obj.id,
                    drug__code=medication.fhirpath_single(
                        "medicationCodeableConcept.coding.code.getValue()"
                    ),
                ).first()
                or models.SystemicTherapyMedication(
                    systemic_therapy=get_object_or_404(
                        models.SystemicTherapy, id=obj.id
                    )
                ),
                payload,
            )
        )
    return data

onconova_to_fhir(obj) classmethod

Source code in onconova/interoperability/fhir/schemas/medication_administration.py 
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@classmethod
def onconova_to_fhir(
    cls, obj: schemas.SystemicTherapy
) -> fhir.OnconovaMedicationAdministration:

    resource = cls.construct_medication_administration(obj, obj.medications[0])
    resource.contained = []
    for n, medication in enumerate(obj.medications[1:]):
        contained_resource = cls.construct_medication_administration(
            obj, medication
        )
        # Insert dummy local id to reference contained resource
        contained_resource.id = f"combined-administration-{n+1}"
        resource.contained.append(contained_resource)
        resource.extension.append(
            fhir.MedicationAdministrationCombinedWith(
                valueReference=Reference(reference=f"")
            )
        )
        resource.extension[-1].valueReference.reference = (
            f"#{contained_resource.id}"
        )

    return resource

get_units_collection_fhirpath(measure)

Source code in onconova/interoperability/fhir/schemas/medication_administration.py 
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def get_units_collection_fhirpath(measure):
    return (
        "'^("
        + "|".join([f"{internal_to_ucum(unit)}" for unit in measure.get_units()])
        + ")$'"
    )
runner