"""
Profile: http://hl7.org/fhir/StructureDefinition/Specimen
Release: R5
Version: 5.0.0
Build ID: 2aecd53
Last updated: 2023-03-26T15:21:02.749+11:00
"""

from __future__ import annotations as _annotations

import typing

from pydantic import Field

from . import backboneelement, domainresource, fhirtypes


class Specimen(domainresource.DomainResource):
    """Disclaimer: Any field name ends with ``__ext`` doesn't part of
    Resource StructureDefinition, instead used to enable Extensibility feature
    for FHIR Primitive Data Types.

    Sample for analysis.
    A sample to be used for analysis.
    """

    __resource_type__ = "Specimen"

    accessionIdentifier: fhirtypes.IdentifierType | None = Field(
        default=None,
        alias="accessionIdentifier",
        title="Identifier assigned by the lab",
        description=(
            "The identifier assigned by the lab when accessioning specimen(s). This"
            " is not necessarily the same as the specimen identifier, depending on "
            "local lab procedures."
        ),
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
        },
    )

    collection: fhirtypes.SpecimenCollectionType | None = Field(
        default=None,
        alias="collection",
        title="Collection details",
        description="Details concerning the specimen collection.",
        json_schema_extra={
            "element_property": True,
        },
    )

    combined: fhirtypes.CodeType | None = Field(
        default=None,
        alias="combined",
        title="grouped | pooled",
        description="This element signifies if the specimen is part of a group or pooled.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # note: Enum values can be used in validation,
            # but use in your own responsibilities, read official FHIR documentation.
            "enum_values": ["grouped", "pooled"],
        },
    )
    combined__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None, alias="_combined", title="Extension field for ``combined``."
    )

    condition: typing.List[fhirtypes.CodeableConceptType] | None = Field(
        default=None,
        alias="condition",
        title="State of the specimen",
        description="A mode or state of being that describes the nature of the specimen.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
        },
    )

    container: typing.List[fhirtypes.SpecimenContainerType] | None = Field(
        default=None,
        alias="container",
        title="Direct container of specimen (tube/slide, etc.)",
        description=(
            "The container holding the specimen.  The recursive nature of "
            "containers; i.e. blood in tube in tray in rack is not addressed here."
        ),
        json_schema_extra={
            "element_property": True,
        },
    )

    feature: typing.List[fhirtypes.SpecimenFeatureType] | None = Field(
        default=None,
        alias="feature",
        title="The physical feature of a specimen",
        description=(
            "A physical feature or landmark on a specimen, highlighted for context "
            "by the collector of the specimen (e.g. surgeon), that identifies the "
            "type of feature as well as its meaning (e.g. the red ink indicating "
            "the resection margin of the right lobe of the excised prostate tissue "
            "or wire loop at radiologically suspected tumor location)."
        ),
        json_schema_extra={
            "element_property": True,
        },
    )

    identifier: typing.List[fhirtypes.IdentifierType] | None = Field(
        default=None,
        alias="identifier",
        title="External Identifier",
        description="Id for specimen.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
        },
    )

    note: typing.List[fhirtypes.AnnotationType] | None = Field(
        default=None,
        alias="note",
        title="Comments",
        description=(
            "To communicate any details or issues about the specimen or during the "
            "specimen collection. (for example: broken vial, sent with patient, "
            "frozen)."
        ),
        json_schema_extra={
            "element_property": True,
        },
    )

    parent: typing.List[fhirtypes.ReferenceType] | None = Field(
        default=None,
        alias="parent",
        title="Specimen from which this specimen originated",
        description=(
            "Reference to the parent (source) specimen which is used when the "
            "specimen was either derived from or a component of another specimen."
        ),
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["Specimen"],
        },
    )

    processing: typing.List[fhirtypes.SpecimenProcessingType] | None = Field(
        default=None,
        alias="processing",
        title="Processing and processing step details",
        description="Details concerning processing and processing steps for the specimen.",
        json_schema_extra={
            "element_property": True,
        },
    )

    receivedTime: fhirtypes.DateTimeType | None = Field(
        default=None,
        alias="receivedTime",
        title="The time when specimen is received by the testing laboratory",
        description=(
            "Time when specimen is received by the testing laboratory for "
            "processing or testing."
        ),
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
        },
    )
    receivedTime__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None,
        alias="_receivedTime",
        title="Extension field for ``receivedTime``.",
    )

    request: typing.List[fhirtypes.ReferenceType] | None = Field(
        default=None,
        alias="request",
        title="Why the specimen was collected",
        description=(
            "Details concerning a service request that required a specimen to be "
            "collected."
        ),
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["ServiceRequest"],
        },
    )

    role: typing.List[fhirtypes.CodeableConceptType] | None = Field(
        default=None,
        alias="role",
        title="The role the specimen serves",
        description="The role or reason for the specimen in the testing workflow.",
        json_schema_extra={
            "element_property": True,
        },
    )

    status: fhirtypes.CodeType | None = Field(
        default=None,
        alias="status",
        title="available | unavailable | unsatisfactory | entered-in-error",
        description="The availability of the specimen.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # note: Enum values can be used in validation,
            # but use in your own responsibilities, read official FHIR documentation.
            "enum_values": [
                "available",
                "unavailable",
                "unsatisfactory",
                "entered-in-error",
            ],
        },
    )
    status__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None, alias="_status", title="Extension field for ``status``."
    )

    subject: fhirtypes.ReferenceType | None = Field(
        default=None,
        alias="subject",
        title=(
            "Where the specimen came from. This may be from patient(s), from a "
            "location (e.g., the source of an environmental sample), or a sampling "
            "of a substance, a biologically-derived product, or a device"
        ),
        description=None,
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": [
                "Patient",
                "Group",
                "Device",
                "BiologicallyDerivedProduct",
                "Substance",
                "Location",
            ],
        },
    )

    type: fhirtypes.CodeableConceptType | None = Field(
        default=None,
        alias="type",
        title="Kind of material that forms the specimen",
        description="The kind of material that forms the specimen.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
        },
    )

    @classmethod
    def elements_sequence(cls) -> typing.List[str]:
        """returning all element names from
        ``Specimen`` according to specification,
        with preserving the original sequence order.
        """
        return [
            "id",
            "meta",
            "implicitRules",
            "language",
            "text",
            "contained",
            "extension",
            "modifierExtension",
            "identifier",
            "accessionIdentifier",
            "status",
            "type",
            "subject",
            "receivedTime",
            "parent",
            "request",
            "combined",
            "role",
            "feature",
            "collection",
            "processing",
            "container",
            "condition",
            "note",
        ]

    @classmethod
    def summary_elements_sequence(cls) -> typing.List[str]:
        """returning all element names (those have summary mode are enabled) from ``Specimen`` according to specification,
        with preserving the original sequence order.
        """
        return [
            "id",
            "meta",
            "implicitRules",
            "modifierExtension",
            "identifier",
            "accessionIdentifier",
            "status",
            "type",
            "subject",
            "receivedTime",
            "combined",
            "condition",
        ]


class SpecimenCollection(backboneelement.BackboneElement):
    """Disclaimer: Any field name ends with ``__ext`` doesn't part of
    Resource StructureDefinition, instead used to enable Extensibility feature
    for FHIR Primitive Data Types.

    Collection details.
    Details concerning the specimen collection.
    """

    __resource_type__ = "SpecimenCollection"

    bodySite: fhirtypes.CodeableReferenceType | None = Field(
        default=None,
        alias="bodySite",
        title="Anatomical collection site",
        description=(
            "Anatomical location from which the specimen was collected (if subject "
            "is a patient). This is the target site.  This element is not used for "
            "environmental specimens."
        ),
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["BodyStructure"],
        },
    )

    collectedDateTime: fhirtypes.DateTimeType | None = Field(
        default=None,
        alias="collectedDateTime",
        title="Collection time",
        description=(
            "Time when specimen was collected from subject - the physiologically "
            "relevant time."
        ),
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # Choice of Data Types. i.e collected[x]
            "one_of_many": "collected",
            "one_of_many_required": False,
        },
    )
    collectedDateTime__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None,
        alias="_collectedDateTime",
        title="Extension field for ``collectedDateTime``.",
    )

    collectedPeriod: fhirtypes.PeriodType | None = Field(
        default=None,
        alias="collectedPeriod",
        title="Collection time",
        description=(
            "Time when specimen was collected from subject - the physiologically "
            "relevant time."
        ),
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # Choice of Data Types. i.e collected[x]
            "one_of_many": "collected",
            "one_of_many_required": False,
        },
    )

    collector: fhirtypes.ReferenceType | None = Field(
        default=None,
        alias="collector",
        title="Who collected the specimen",
        description="Person who collected the specimen.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": [
                "Practitioner",
                "PractitionerRole",
                "Patient",
                "RelatedPerson",
            ],
        },
    )

    device: fhirtypes.CodeableReferenceType | None = Field(
        default=None,
        alias="device",
        title="Device used to perform collection",
        description=(
            "A coded value specifying the technique that is used to perform the "
            "procedure."
        ),
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["Device"],
        },
    )

    duration: fhirtypes.DurationType | None = Field(
        default=None,
        alias="duration",
        title="How long it took to collect specimen",
        description="The span of time over which the collection of a specimen occurred.",
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
        },
    )

    fastingStatusCodeableConcept: fhirtypes.CodeableConceptType | None = Field(
        default=None,
        alias="fastingStatusCodeableConcept",
        title="Whether or how long patient abstained from food and/or drink",
        description=(
            "Abstinence or reduction from some or all food, drink, or both, for a "
            "period of time prior to sample collection."
        ),
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # Choice of Data Types. i.e fastingStatus[x]
            "one_of_many": "fastingStatus",
            "one_of_many_required": False,
        },
    )

    fastingStatusDuration: fhirtypes.DurationType | None = Field(
        default=None,
        alias="fastingStatusDuration",
        title="Whether or how long patient abstained from food and/or drink",
        description=(
            "Abstinence or reduction from some or all food, drink, or both, for a "
            "period of time prior to sample collection."
        ),
        json_schema_extra={
            "element_property": True,
            "summary_element_property": True,
            # Choice of Data Types. i.e fastingStatus[x]
            "one_of_many": "fastingStatus",
            "one_of_many_required": False,
        },
    )

    method: fhirtypes.CodeableConceptType | None = Field(
        default=None,
        alias="method",
        title="Technique used to perform collection",
        description=(
            "A coded value specifying the technique that is used to perform the "
            "procedure."
        ),
        json_schema_extra={
            "element_property": True,
        },
    )

    procedure: fhirtypes.ReferenceType | None = Field(
        default=None,
        alias="procedure",
        title="The procedure that collects the specimen",
        description=(
            "The procedure event during which the specimen was collected (e.g. the "
            "surgery leading to the collection of a pathology sample)."
        ),
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["Procedure"],
        },
    )

    quantity: fhirtypes.QuantityType | None = Field(
        default=None,
        alias="quantity",
        title="The quantity of specimen collected",
        description=(
            "The quantity of specimen collected; for instance the volume of a blood"
            " sample, or the physical measurement of an anatomic pathology sample."
        ),
        json_schema_extra={
            "element_property": True,
        },
    )

    @classmethod
    def elements_sequence(cls) -> typing.List[str]:
        """returning all element names from
        ``SpecimenCollection`` according to specification,
        with preserving the original sequence order.
        """
        return [
            "id",
            "extension",
            "modifierExtension",
            "collector",
            "collectedDateTime",
            "collectedPeriod",
            "duration",
            "quantity",
            "method",
            "device",
            "procedure",
            "bodySite",
            "fastingStatusCodeableConcept",
            "fastingStatusDuration",
        ]

    @classmethod
    def summary_elements_sequence(cls) -> typing.List[str]:
        """returning all element names (those have summary mode are enabled) from ``SpecimenCollection`` according to specification,
        with preserving the original sequence order.
        """
        return [
            "modifierExtension",
            "collector",
            "collectedDateTime",
            "collectedPeriod",
            "duration",
            "fastingStatusCodeableConcept",
            "fastingStatusDuration",
        ]

    def get_one_of_many_fields(self) -> typing.Dict[str, typing.List[str]]:
        """https://www.hl7.org/fhir/formats.html#choice
        A few elements have a choice of more than one data type for their content.
        All such elements have a name that takes the form nnn[x].
        The "nnn" part of the name is constant, and the "[x]" is replaced with
        the title-cased name of the type that is actually used.
        The table view shows each of these names explicitly.

        Elements that have a choice of data type cannot repeat - they must have a
        maximum cardinality of 1. When constructing an instance of an element with a
        choice of types, the authoring system must create a single element with a
        data type chosen from among the list of permitted data types.
        """
        one_of_many_fields = {
            "collected": ["collectedDateTime", "collectedPeriod"],
            "fastingStatus": ["fastingStatusCodeableConcept", "fastingStatusDuration"],
        }
        return one_of_many_fields


class SpecimenContainer(backboneelement.BackboneElement):
    """Disclaimer: Any field name ends with ``__ext`` doesn't part of
    Resource StructureDefinition, instead used to enable Extensibility feature
    for FHIR Primitive Data Types.

    Direct container of specimen (tube/slide, etc.).
    The container holding the specimen.  The recursive nature of containers;
    i.e. blood in tube in tray in rack is not addressed here.
    """

    __resource_type__ = "SpecimenContainer"

    device: fhirtypes.ReferenceType = Field(
        default=...,
        alias="device",
        title="Device resource for the container",
        description=(
            "The device resource for the the container holding the specimen. If the"
            " container is in a holder then the referenced device will point to a "
            "parent device."
        ),
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["Device"],
        },
    )

    location: fhirtypes.ReferenceType | None = Field(
        default=None,
        alias="location",
        title="Where the container is",
        description="The location of the container holding the specimen.",
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["Location"],
        },
    )

    specimenQuantity: fhirtypes.QuantityType | None = Field(
        default=None,
        alias="specimenQuantity",
        title="Quantity of specimen within container",
        description=(
            "The quantity of specimen in the container; may be volume, dimensions, "
            "or other appropriate measurements, depending on the specimen type."
        ),
        json_schema_extra={
            "element_property": True,
        },
    )

    @classmethod
    def elements_sequence(cls) -> typing.List[str]:
        """returning all element names from
        ``SpecimenContainer`` according to specification,
        with preserving the original sequence order.
        """
        return [
            "id",
            "extension",
            "modifierExtension",
            "device",
            "location",
            "specimenQuantity",
        ]

    @classmethod
    def summary_elements_sequence(cls) -> typing.List[str]:
        """returning all element names (those have summary mode are enabled) from ``SpecimenContainer`` according to specification,
        with preserving the original sequence order.
        """
        return ["modifierExtension"]


class SpecimenFeature(backboneelement.BackboneElement):
    """Disclaimer: Any field name ends with ``__ext`` doesn't part of
    Resource StructureDefinition, instead used to enable Extensibility feature
    for FHIR Primitive Data Types.

    The physical feature of a specimen.
    A physical feature or landmark on a specimen, highlighted for context by
    the collector of the specimen (e.g. surgeon), that identifies the type of
    feature as well as its meaning (e.g. the red ink indicating the resection
    margin of the right lobe of the excised prostate tissue or wire loop at
    radiologically suspected tumor location).
    """

    __resource_type__ = "SpecimenFeature"

    description: fhirtypes.StringType | None = Field(
        default=None,
        alias="description",
        title="Information about the feature",
        description="Description of the feature of the specimen.",
        json_schema_extra={
            "element_property": True,
            "element_required": True,
        },
    )
    description__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None, alias="_description", title="Extension field for ``description``."
    )

    type: fhirtypes.CodeableConceptType = Field(
        default=...,
        alias="type",
        title="Highlighted feature",
        description="The landmark or feature being highlighted.",
        json_schema_extra={
            "element_property": True,
        },
    )

    @classmethod
    def elements_sequence(cls) -> typing.List[str]:
        """returning all element names from
        ``SpecimenFeature`` according to specification,
        with preserving the original sequence order.
        """
        return ["id", "extension", "modifierExtension", "type", "description"]

    @classmethod
    def summary_elements_sequence(cls) -> typing.List[str]:
        """returning all element names (those have summary mode are enabled) from ``SpecimenFeature`` according to specification,
        with preserving the original sequence order.
        """
        return ["modifierExtension"]

    def get_required_fields(self) -> typing.List[typing.Tuple[str, str]]:
        """https://www.hl7.org/fhir/extensibility.html#Special-Case
        In some cases, implementers might find that they do not have appropriate data for
        an element with minimum cardinality = 1. In this case, the element must be present,
        but unless the resource or a profile on it has made the actual value of the primitive
        data type mandatory, it is possible to provide an extension that explains why
        the primitive value is not present.
        """
        required_fields = [("description", "description__ext")]
        return required_fields


class SpecimenProcessing(backboneelement.BackboneElement):
    """Disclaimer: Any field name ends with ``__ext`` doesn't part of
    Resource StructureDefinition, instead used to enable Extensibility feature
    for FHIR Primitive Data Types.

    Processing and processing step details.
    Details concerning processing and processing steps for the specimen.
    """

    __resource_type__ = "SpecimenProcessing"

    additive: typing.List[fhirtypes.ReferenceType] | None = Field(
        default=None,
        alias="additive",
        title="Material used in the processing step",
        description=None,
        json_schema_extra={
            "element_property": True,
            # note: Listed Resource Type(s) should be allowed as Reference.
            "enum_reference_types": ["Substance"],
        },
    )

    description: fhirtypes.StringType | None = Field(
        default=None,
        alias="description",
        title="Textual description of procedure",
        description=None,
        json_schema_extra={
            "element_property": True,
        },
    )
    description__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None, alias="_description", title="Extension field for ``description``."
    )

    method: fhirtypes.CodeableConceptType | None = Field(
        default=None,
        alias="method",
        title="Indicates the treatment step  applied to the specimen",
        description="A coded value specifying the method used to process the specimen.",
        json_schema_extra={
            "element_property": True,
        },
    )

    timeDateTime: fhirtypes.DateTimeType | None = Field(
        default=None,
        alias="timeDateTime",
        title="Date and time of specimen processing",
        description=(
            "A record of the time or period when the specimen processing occurred."
            "  For example the time of sample fixation or the period of time the "
            "sample was in formalin."
        ),
        json_schema_extra={
            "element_property": True,
            # Choice of Data Types. i.e time[x]
            "one_of_many": "time",
            "one_of_many_required": False,
        },
    )
    timeDateTime__ext: fhirtypes.FHIRPrimitiveExtensionType | None = Field(
        default=None,
        alias="_timeDateTime",
        title="Extension field for ``timeDateTime``.",
    )

    timePeriod: fhirtypes.PeriodType | None = Field(
        default=None,
        alias="timePeriod",
        title="Date and time of specimen processing",
        description=(
            "A record of the time or period when the specimen processing occurred."
            "  For example the time of sample fixation or the period of time the "
            "sample was in formalin."
        ),
        json_schema_extra={
            "element_property": True,
            # Choice of Data Types. i.e time[x]
            "one_of_many": "time",
            "one_of_many_required": False,
        },
    )

    @classmethod
    def elements_sequence(cls) -> typing.List[str]:
        """returning all element names from
        ``SpecimenProcessing`` according to specification,
        with preserving the original sequence order.
        """
        return [
            "id",
            "extension",
            "modifierExtension",
            "description",
            "method",
            "additive",
            "timeDateTime",
            "timePeriod",
        ]

    @classmethod
    def summary_elements_sequence(cls) -> typing.List[str]:
        """returning all element names (those have summary mode are enabled) from ``SpecimenProcessing`` according to specification,
        with preserving the original sequence order.
        """
        return ["modifierExtension"]

    def get_one_of_many_fields(self) -> typing.Dict[str, typing.List[str]]:
        """https://www.hl7.org/fhir/formats.html#choice
        A few elements have a choice of more than one data type for their content.
        All such elements have a name that takes the form nnn[x].
        The "nnn" part of the name is constant, and the "[x]" is replaced with
        the title-cased name of the type that is actually used.
        The table view shows each of these names explicitly.

        Elements that have a choice of data type cannot repeat - they must have a
        maximum cardinality of 1. When constructing an instance of an element with a
        choice of types, the authoring system must create a single element with a
        data type chosen from among the list of permitted data types.
        """
        one_of_many_fields = {"time": ["timeDateTime", "timePeriod"]}
        return one_of_many_fields
