fhirflat.resources

fhirflat.resources

The fhirflat.resources submodule contains FHIR resource classes that are equipped with the capability to read from and write to FHIRflat files. These classes are derived from the fhir.resources package, with additional ISARIC specific FHIR extensions.

class fhirflat.resources.Condition(*, resource_type: str = 'Condition', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[presenceAbsenceType | prespecifiedQueryType | timingPhaseType | timingPhaseDetailType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, abatementAge: AgeType = None, abatementDateTime: DateTime = None, _abatementDateTime: FHIRPrimitiveExtensionType = None, abatementPeriod: PeriodType = None, abatementRange: RangeType = None, abatementString: String = None, _abatementString: FHIRPrimitiveExtensionType = None, bodySite: List[CodeableConceptType] = None, category: List[CodeableConceptType] = None, clinicalStatus: CodeableConceptType, code: CodeableConceptType = None, encounter: ReferenceType = None, evidence: List[CodeableReferenceType] = None, identifier: List[IdentifierType] = None, note: List[AnnotationType] = None, onsetAge: AgeType = None, onsetDateTime: DateTime = None, _onsetDateTime: FHIRPrimitiveExtensionType = None, onsetPeriod: PeriodType = None, onsetRange: RangeType = None, onsetString: String = None, _onsetString: FHIRPrimitiveExtensionType = None, participant: List[ConditionParticipantType] = None, recordedDate: DateTime = None, _recordedDate: FHIRPrimitiveExtensionType = None, severity: CodeableConceptType = None, stage: List[ConditionStageType] = None, subject: ReferenceType, verificationStatus: CodeableConceptType = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.DiagnosticReport(*, resource_type: str = 'DiagnosticReport', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[timingPhaseType | timingPhaseDetailType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, basedOn: List[ReferenceType] = None, category: List[CodeableConceptType] = None, code: CodeableConceptType, composition: ReferenceType = None, conclusion: Markdown = None, _conclusion: FHIRPrimitiveExtensionType = None, conclusionCode: List[CodeableConceptType] = None, effectiveDateTime: DateTime = None, _effectiveDateTime: FHIRPrimitiveExtensionType = None, effectivePeriod: PeriodType = None, encounter: ReferenceType = None, identifier: List[IdentifierType] = None, issued: Instant = None, _issued: FHIRPrimitiveExtensionType = None, media: List[DiagnosticReportMediaType] = None, note: List[AnnotationType] = None, performer: List[ReferenceType] = None, presentedForm: List[AttachmentType] = None, result: List[ReferenceType] = None, resultsInterpreter: List[ReferenceType] = None, specimen: List[ReferenceType] = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, study: List[ReferenceType] = None, subject: ReferenceType = None, supportingInfo: List[DiagnosticReportSupportingInfoType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Encounter(*, resource_type: str = 'Encounter', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[relativePeriodType | timingPhaseType | timingPhaseDetailType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, account: List[ReferenceType] = None, actualPeriod: PeriodType = None, admission: EncounterAdmissionType = None, appointment: List[ReferenceType] = None, basedOn: List[ReferenceType] = None, careTeam: List[ReferenceType] = None, class_fhir: List[CodeableConceptType] = None, diagnosis: List[EncounterDiagnosisType] = None, dietPreference: List[CodeableConceptType] = None, episodeOfCare: List[ReferenceType] = None, identifier: List[IdentifierType] = None, length: DurationType = None, location: List[EncounterLocationType] = None, partOf: ReferenceType = None, participant: List[EncounterParticipantType] = None, plannedEndDate: DateTime = None, _plannedEndDate: FHIRPrimitiveExtensionType = None, plannedStartDate: DateTime = None, _plannedStartDate: FHIRPrimitiveExtensionType = None, priority: CodeableConceptType = None, reason: List[EncounterReasonType] = None, serviceProvider: ReferenceType = None, serviceType: List[CodeableReferenceType] = None, specialArrangement: List[CodeableConceptType] = None, specialCourtesy: List[CodeableConceptType] = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, subject: ReferenceType = None, subjectStatus: CodeableConceptType = None, type: List[CodeableConceptType] = None, virtualService: List[VirtualServiceDetailType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Immunization(*, resource_type: str = 'Immunization', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[timingPhaseType | timingPhaseDetailType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, administeredProduct: CodeableReferenceType = None, basedOn: List[ReferenceType] = None, doseQuantity: QuantityType = None, encounter: ReferenceType = None, expirationDate: Date = None, _expirationDate: FHIRPrimitiveExtensionType = None, fundingSource: CodeableConceptType = None, identifier: List[IdentifierType] = None, informationSource: CodeableReferenceType = None, isSubpotent: bool = None, _isSubpotent: FHIRPrimitiveExtensionType = None, location: ReferenceType = None, lotNumber: String = None, _lotNumber: FHIRPrimitiveExtensionType = None, manufacturer: CodeableReferenceType = None, note: List[AnnotationType] = None, occurrenceDateTime: DateTime = None, _occurrenceDateTime: dateTimeExtensionType = None, occurrenceString: String = None, _occurrenceString: FHIRPrimitiveExtensionType = None, patient: ReferenceType, performer: List[ImmunizationPerformerType] = None, primarySource: bool = None, _primarySource: FHIRPrimitiveExtensionType = None, programEligibility: List[ImmunizationProgramEligibilityType] = None, protocolApplied: List[ImmunizationProtocolAppliedType] = None, reaction: List[ImmunizationReactionType] = None, reason: List[CodeableReferenceType] = None, route: CodeableConceptType = None, site: CodeableConceptType = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, statusReason: CodeableConceptType = None, subpotentReason: List[CodeableConceptType] = None, supportingInformation: List[ReferenceType] = None, vaccineCode: CodeableConceptType)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Location(*, resource_type: str = 'Location', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: List[ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, address: AddressType = None, alias: List[String | None] = None, _alias: List[FHIRPrimitiveExtensionType | None] = None, characteristic: List[CodeableConceptType] = None, contact: List[ExtendedContactDetailType] = None, description: Markdown = None, _description: FHIRPrimitiveExtensionType = None, endpoint: List[ReferenceType] = None, form: CodeableConceptType = None, hoursOfOperation: List[AvailabilityType] = None, identifier: List[IdentifierType] = None, managingOrganization: ReferenceType = None, mode: Code = None, _mode: FHIRPrimitiveExtensionType = None, name: String = None, _name: FHIRPrimitiveExtensionType = None, operationalStatus: CodingType = None, partOf: ReferenceType = None, position: LocationPositionType = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, type: List[CodeableConceptType] = None, virtualService: List[VirtualServiceDetailType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.MedicationAdministration(*, resource_type: str = 'MedicationAdministration', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: List[ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, basedOn: List[ReferenceType] = None, category: List[CodeableConceptType] = None, device: List[CodeableReferenceType] = None, dosage: MedicationAdministrationDosageType = None, encounter: ReferenceType = None, eventHistory: List[ReferenceType] = None, identifier: List[IdentifierType] = None, isSubPotent: bool = None, _isSubPotent: FHIRPrimitiveExtensionType = None, medication: CodeableReferenceType, note: List[AnnotationType] = None, occurenceDateTime: DateTime = None, _occurenceDateTime: FHIRPrimitiveExtensionType = None, occurencePeriod: PeriodType = None, occurenceTiming: TimingType = None, partOf: List[ReferenceType] = None, performer: List[MedicationAdministrationPerformerType] = None, reason: List[CodeableReferenceType] = None, recorded: DateTime = None, _recorded: FHIRPrimitiveExtensionType = None, request: ReferenceType = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, statusReason: List[CodeableConceptType] = None, subPotentReason: List[CodeableConceptType] = None, subject: ReferenceType, supportingInformation: List[ReferenceType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.MedicationStatement(*, resource_type: str = 'MedicationStatement', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: List[ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, adherence: MedicationStatementAdherenceType = None, category: List[CodeableConceptType] = None, dateAsserted: DateTime = None, _dateAsserted: FHIRPrimitiveExtensionType = None, derivedFrom: List[ReferenceType] = None, dosage: List[DosageType] = None, effectiveDateTime: DateTime = None, _effectiveDateTime: FHIRPrimitiveExtensionType = None, effectivePeriod: PeriodType = None, effectiveTiming: TimingType = None, encounter: ReferenceType = None, identifier: List[IdentifierType] = None, informationSource: List[ReferenceType] = None, medication: CodeableReferenceType, note: List[AnnotationType] = None, partOf: List[ReferenceType] = None, reason: List[CodeableReferenceType] = None, relatedClinicalInformation: List[ReferenceType] = None, renderedDosageInstruction: Markdown = None, _renderedDosageInstruction: FHIRPrimitiveExtensionType = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, subject: ReferenceType)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Observation(*, resource_type: str = 'Observation', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[timingPhaseType | timingPhaseDetailType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, basedOn: List[ReferenceType] = None, bodySite: CodeableConceptType = None, bodyStructure: ReferenceType = None, category: List[CodeableConceptType] = None, code: CodeableConceptType, component: list[ObservationComponent] = None, dataAbsentReason: CodeableConceptType = None, derivedFrom: List[ReferenceType] = None, device: ReferenceType = None, effectiveDateTime: DateTime = None, _effectiveDateTime: dateTimeExtensionType = None, effectiveInstant: Instant = None, _effectiveInstant: FHIRPrimitiveExtensionType = None, effectivePeriod: PeriodType = None, effectiveTiming: TimingType = None, encounter: ReferenceType = None, focus: List[ReferenceType] = None, hasMember: List[ReferenceType] = None, identifier: List[IdentifierType] = None, instantiatesCanonical: Canonical = None, _instantiatesCanonical: FHIRPrimitiveExtensionType = None, instantiatesReference: ReferenceType = None, interpretation: List[CodeableConceptType] = None, issued: Instant = None, _issued: FHIRPrimitiveExtensionType = None, method: CodeableConceptType = None, note: List[AnnotationType] = None, partOf: List[ReferenceType] = None, performer: List[ReferenceType] = None, referenceRange: List[ObservationReferenceRangeType] = None, specimen: ReferenceType = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, subject: ReferenceType = None, triggeredBy: List[ObservationTriggeredByType] = None, valueAttachment: AttachmentType = None, valueBoolean: bool = None, _valueBoolean: FHIRPrimitiveExtensionType = None, valueCodeableConcept: CodeableConceptType = None, valueDateTime: DateTime = None, _valueDateTime: FHIRPrimitiveExtensionType = None, valueInteger: Integer = None, _valueInteger: FHIRPrimitiveExtensionType = None, valuePeriod: PeriodType = None, valueQuantity: QuantityType = None, valueRange: RangeType = None, valueRatio: RatioType = None, valueReference: ReferenceType = None, valueSampledData: SampledDataType = None, valueString: String = None, _valueString: FHIRPrimitiveExtensionType = None, valueTime: Time = None, _valueTime: FHIRPrimitiveExtensionType = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Organization(*, resource_type: str = 'Organization', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: List[ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, active: bool = None, _active: FHIRPrimitiveExtensionType = None, alias: List[String | None] = None, _alias: List[FHIRPrimitiveExtensionType | None] = None, contact: List[ExtendedContactDetailType] = None, description: Markdown = None, _description: FHIRPrimitiveExtensionType = None, endpoint: List[ReferenceType] = None, identifier: List[IdentifierType] = None, name: String = None, _name: FHIRPrimitiveExtensionType = None, partOf: ReferenceType = None, qualification: List[OrganizationQualificationType] = None, type: List[CodeableConceptType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Patient(*, resource_type: str = 'Patient', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[ageType | birthSexType | raceType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, active: bool = None, _active: FHIRPrimitiveExtensionType = None, address: List[AddressType] = None, birthDate: Date = None, _birthDate: FHIRPrimitiveExtensionType = None, communication: List[PatientCommunicationType] = None, contact: List[PatientContactType] = None, deceasedBoolean: bool = None, _deceasedBoolean: FHIRPrimitiveExtensionType = None, deceasedDateTime: DateTime = None, _deceasedDateTime: FHIRPrimitiveExtensionType = None, gender: Code = None, _gender: FHIRPrimitiveExtensionType = None, generalPractitioner: List[ReferenceType] = None, identifier: List[IdentifierType] = None, link: List[PatientLinkType] = None, managingOrganization: ReferenceType = None, maritalStatus: CodeableConceptType = None, multipleBirthBoolean: bool = None, _multipleBirthBoolean: FHIRPrimitiveExtensionType = None, multipleBirthInteger: Integer = None, _multipleBirthInteger: FHIRPrimitiveExtensionType = None, name: List[HumanNameType] = None, photo: List[AttachmentType] = None, telecom: List[ContactPointType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Procedure(*, resource_type: str = 'Procedure', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: list[durationType | timingPhaseType | timingPhaseDetailType | relativePeriodType | ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, basedOn: List[ReferenceType] = None, bodySite: List[CodeableConceptType] = None, category: List[CodeableConceptType] = None, code: CodeableConceptType = None, complication: List[CodeableReferenceType] = None, encounter: ReferenceType = None, focalDevice: List[ProcedureFocalDeviceType] = None, focus: ReferenceType = None, followUp: List[CodeableConceptType] = None, identifier: List[IdentifierType] = None, instantiatesCanonical: List[Canonical | None] = None, _instantiatesCanonical: List[FHIRPrimitiveExtensionType | None] = None, instantiatesUri: List[Uri | None] = None, _instantiatesUri: List[FHIRPrimitiveExtensionType | None] = None, location: ReferenceType = None, note: List[AnnotationType] = None, occurrenceAge: AgeType = None, occurrenceDateTime: DateTime = None, _occurrenceDateTime: dateTimeExtensionType = None, occurrencePeriod: PeriodType = None, occurrenceRange: RangeType = None, occurrenceString: String = None, _occurrenceString: FHIRPrimitiveExtensionType = None, occurrenceTiming: TimingType = None, outcome: CodeableConceptType = None, partOf: List[ReferenceType] = None, performer: List[ProcedurePerformerType] = None, reason: List[CodeableReferenceType] = None, recorded: DateTime = None, _recorded: FHIRPrimitiveExtensionType = None, recorder: ReferenceType = None, report: List[ReferenceType] = None, reportedBoolean: bool = None, _reportedBoolean: FHIRPrimitiveExtensionType = None, reportedReference: ReferenceType = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, statusReason: CodeableConceptType = None, subject: ReferenceType, supportingInfo: List[ReferenceType] = None, used: List[CodeableReferenceType] = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.ResearchSubject(*, resource_type: str = 'ResearchSubject', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: List[ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, actualComparisonGroup: Id = None, _actualComparisonGroup: FHIRPrimitiveExtensionType = None, assignedComparisonGroup: Id = None, _assignedComparisonGroup: FHIRPrimitiveExtensionType = None, consent: List[ReferenceType] = None, identifier: List[IdentifierType] = None, period: PeriodType = None, progress: List[ResearchSubjectProgressType] = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, study: ReferenceType, subject: ReferenceType)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values

class fhirflat.resources.Specimen(*, resource_type: str = 'Specimen', fhir_comments: str | List[str] = None, id: Id = None, implicitRules: Uri = None, _implicitRules: FHIRPrimitiveExtensionType = None, language: Code = None, _language: FHIRPrimitiveExtensionType = None, meta: MetaType = None, contained: List[ResourceType] = None, extension: List[ExtensionType] = None, modifierExtension: List[ExtensionType] = None, text: NarrativeType = None, accessionIdentifier: IdentifierType = None, collection: SpecimenCollectionType = None, combined: Code = None, _combined: FHIRPrimitiveExtensionType = None, condition: List[CodeableConceptType] = None, container: List[SpecimenContainerType] = None, feature: List[SpecimenFeatureType] = None, identifier: List[IdentifierType] = None, note: List[AnnotationType] = None, parent: List[ReferenceType] = None, processing: List[SpecimenProcessingType] = None, receivedTime: DateTime = None, _receivedTime: FHIRPrimitiveExtensionType = None, request: List[ReferenceType] = None, role: List[CodeableConceptType] = None, status: Code = None, _status: FHIRPrimitiveExtensionType = None, subject: ReferenceType = None, type: CodeableConceptType = None)

classmethod cleanup(data: dict) → dict

Apply resource-specific changes to references and default values