care.emr.resources.specimen_definition.spec module¶

class SpecimenDefinitionStatusOptions(*values)¶

Bases: str, Enum

Status options for specimen definition

draft = 'draft'¶

active = 'active'¶

retired = 'retired'¶

class PreferenceOptions(*values)¶

Bases: str, Enum

Preference options for specimen type testing

preferred = 'preferred'¶

alternate = 'alternate'¶

class HandlingConditionOptions(*values)¶

Bases: str, Enum

Handling condition options for specimen testing

room = 'room'¶

refrigerated = 'refrigerated'¶

frozen = 'frozen'¶

class QuantitySpec(*, value: float, unit: Coding)¶

Bases: BaseModel

Represents a quantity with value and unit

value: float¶

unit: Coding¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'unit': FieldInfo(annotation=Coding, required=True), 'value': FieldInfo(annotation=float, required=True)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class MinimumVolumeSpec(*, quantity: QuantitySpec | None = None, string: str | None = None)¶

Bases: BaseModel

Specification for minimum volume with support for quantity or string representation

quantity: QuantitySpec | None¶

string: str | None¶

validate_minimum_volume()¶: Validates that only one minimum volume field is provided

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'quantity': FieldInfo(annotation=Union[QuantitySpec, NoneType], required=False, default=None), 'string': FieldInfo(annotation=Union[str, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class ContainerSpec(*, description: str | None = None, capacity: ~care.emr.resources.specimen_definition.spec.QuantitySpec | None = None, minimum_volume: ~care.emr.resources.specimen_definition.spec.MinimumVolumeSpec | None = None, cap: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding | None = None, preparation: str | None = None)¶

Bases: BaseModel

Container specification for specimen collection

description: str | None¶

capacity: QuantitySpec | None¶

minimum_volume: MinimumVolumeSpec | None¶

cap: BoundCoding | None¶

preparation: str | None¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'cap': FieldInfo(annotation=Union[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, NoneType], required=False, default=None), 'capacity': FieldInfo(annotation=Union[QuantitySpec, NoneType], required=False, default=None), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'minimum_volume': FieldInfo(annotation=Union[MinimumVolumeSpec, NoneType], required=False, default=None), 'preparation': FieldInfo(annotation=Union[str, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class DurationSpec(*, value: int, unit: Coding)¶

Bases: BaseModel

Duration specification using value and unit

value: int¶

unit: Coding¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'unit': FieldInfo(annotation=Coding, required=True), 'value': FieldInfo(annotation=int, required=True)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class RangeSpec(*, low: QuantitySpec | None = None, high: QuantitySpec | None = None)¶

Bases: BaseModel

Specification for a range with low and high values

low: QuantitySpec | None¶

high: QuantitySpec | None¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'high': FieldInfo(annotation=Union[QuantitySpec, NoneType], required=False, default=None), 'low': FieldInfo(annotation=Union[QuantitySpec, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class HandlingSpec(*, temperature_qualifier: HandlingConditionOptions | None = None, temperature_range: RangeSpec | None = None, max_duration: DurationSpec | None = None, instruction: str | None = None)¶

Bases: BaseModel

Specification for specimen handling

temperature_qualifier: HandlingConditionOptions | None¶

temperature_range: RangeSpec | None¶

max_duration: DurationSpec | None¶

instruction: str | None¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'instruction': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'max_duration': FieldInfo(annotation=Union[DurationSpec, NoneType], required=False, default=None), 'temperature_qualifier': FieldInfo(annotation=Union[HandlingConditionOptions, NoneType], required=False, default=None), 'temperature_range': FieldInfo(annotation=Union[RangeSpec, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class TypeTestedSpec(*, is_derived: bool, preference: PreferenceOptions, container: ContainerSpec | None = None, requirement: str | None = None, retention_time: DurationSpec | None = None, single_use: bool | None = None, handling: HandlingSpec | None = None)¶

Bases: BaseModel

Specification for tested specimen types

is_derived: bool¶

preference: PreferenceOptions¶

container: ContainerSpec | None¶

requirement: str | None¶

retention_time: DurationSpec | None¶

single_use: bool | None¶

handling: HandlingSpec | None¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'container': FieldInfo(annotation=Union[ContainerSpec, NoneType], required=False, default=None), 'handling': FieldInfo(annotation=Union[HandlingSpec, NoneType], required=False, default=None), 'is_derived': FieldInfo(annotation=bool, required=True), 'preference': FieldInfo(annotation=PreferenceOptions, required=True), 'requirement': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'retention_time': FieldInfo(annotation=Union[DurationSpec, NoneType], required=False, default=None), 'single_use': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class BaseSpecimenDefinitionSpec(*, meta: dict = {}, id: ~typing.Annotated[~uuid.UUID, ~pydantic.types.UuidVersion(uuid_version=4)] | None = None, title: str, derived_from_uri: str | None = None, status: ~care.emr.resources.specimen_definition.spec.SpecimenDefinitionStatusOptions, description: str, type_collected: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, patient_preparation: list[~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding] = [], collection: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding | None = None, type_tested: ~care.emr.resources.specimen_definition.spec.TypeTestedSpec | None = None)¶

Bases: EMRResource

Base model for specimen definition

id: Annotated[UUID, UuidVersion(uuid_version=4)] | None¶

title: str¶

derived_from_uri: str | None¶

status: SpecimenDefinitionStatusOptions¶

description: str¶

type_collected: BoundCoding¶

patient_preparation: list[~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding]¶

collection: BoundCoding | None¶

type_tested: TypeTestedSpec | None¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'collection': FieldInfo(annotation=Union[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, NoneType], required=False, default=None), 'derived_from_uri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'description': FieldInfo(annotation=str, required=True), 'id': FieldInfo(annotation=Union[Annotated[UUID, UuidVersion], NoneType], required=False, default=None), 'meta': FieldInfo(annotation=dict, required=False, default={}), 'patient_preparation': FieldInfo(annotation=list[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding], required=False, default=[]), 'status': FieldInfo(annotation=SpecimenDefinitionStatusOptions, required=True), 'title': FieldInfo(annotation=str, required=True), 'type_collected': FieldInfo(annotation=ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, required=True), 'type_tested': FieldInfo(annotation=Union[TypeTestedSpec, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class SpecimenDefinitionWriteSpec(*, meta: dict = {}, id: ~typing.Annotated[~uuid.UUID, ~pydantic.types.UuidVersion(uuid_version=4)] | None = None, title: str, derived_from_uri: str | None = None, status: ~care.emr.resources.specimen_definition.spec.SpecimenDefinitionStatusOptions, description: str, type_collected: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, patient_preparation: list[~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding] = [], collection: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding | None = None, type_tested: ~care.emr.resources.specimen_definition.spec.TypeTestedSpec | None = None, slug_value: ~typing.Annotated[str, ~annotated_types.MinLen(min_length=5), ~annotated_types.MaxLen(max_length=25), ~pydantic.functional_validators.AfterValidator(func=~care.emr.utils.slug_type.slug_validator)])¶

Bases: BaseSpecimenDefinitionSpec

slug_value: Annotated[str, FieldInfo(annotation=NoneType, required=True, metadata=[MinLen(min_length=5), MaxLen(max_length=25)]), AfterValidator(func=slug_validator)]¶

perform_extra_deserialization(is_update, obj)¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'collection': FieldInfo(annotation=Union[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, NoneType], required=False, default=None), 'derived_from_uri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'description': FieldInfo(annotation=str, required=True), 'id': FieldInfo(annotation=Union[Annotated[UUID, UuidVersion], NoneType], required=False, default=None), 'meta': FieldInfo(annotation=dict, required=False, default={}), 'patient_preparation': FieldInfo(annotation=list[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding], required=False, default=[]), 'slug_value': FieldInfo(annotation=str, required=True, metadata=[MinLen(min_length=5), MaxLen(max_length=25), AfterValidator(func=<function slug_validator>)]), 'status': FieldInfo(annotation=SpecimenDefinitionStatusOptions, required=True), 'title': FieldInfo(annotation=str, required=True), 'type_collected': FieldInfo(annotation=ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, required=True), 'type_tested': FieldInfo(annotation=Union[TypeTestedSpec, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

class SpecimenDefinitionReadSpec(*, meta: dict = {}, id: ~typing.Annotated[~uuid.UUID, ~pydantic.types.UuidVersion(uuid_version=4)] | None = None, title: str, derived_from_uri: str | None = None, status: ~care.emr.resources.specimen_definition.spec.SpecimenDefinitionStatusOptions, description: str, type_collected: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, patient_preparation: list[~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding] = [], collection: ~care.emr.utils.valueset_coding_type.ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding | None = None, type_tested: ~care.emr.resources.specimen_definition.spec.TypeTestedSpec | None = None, version: int | None = None, slug_config: dict, slug: str)¶

Bases: BaseSpecimenDefinitionSpec

Specimen definition read specification

version: int | None¶

slug_config: dict¶

slug: str¶

classmethod perform_extra_serialization(mapping, obj)¶

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'collection': FieldInfo(annotation=Union[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, NoneType], required=False, default=None), 'derived_from_uri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'description': FieldInfo(annotation=str, required=True), 'id': FieldInfo(annotation=Union[Annotated[UUID, UuidVersion], NoneType], required=False, default=None), 'meta': FieldInfo(annotation=dict, required=False, default={}), 'patient_preparation': FieldInfo(annotation=list[ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding], required=False, default=[]), 'slug': FieldInfo(annotation=str, required=True), 'slug_config': FieldInfo(annotation=dict, required=True), 'status': FieldInfo(annotation=SpecimenDefinitionStatusOptions, required=True), 'title': FieldInfo(annotation=str, required=True), 'type_collected': FieldInfo(annotation=ValueSetBoundCoding.__class_getitem__.<locals>.BoundCoding, required=True), 'type_tested': FieldInfo(annotation=Union[TypeTestedSpec, NoneType], required=False, default=None), 'version': FieldInfo(annotation=Union[int, NoneType], required=False, default=None)}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.