omnipy.components.isa.models.sample_schema

ISA model representing a sample in an investigation.

ISA stands for Investigation/Study/Assay, and this schema mirrors ISA-JSON JSON-LD sample metadata.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs
    •  IsaStudyGroupSchema  members
  • isa models
    •  process_schema  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs
    •  study_group  IsaStudyGroupSchema  members

CLASS	DESCRIPTION
FieldType	JSON-LD type labels used for ISA sample entities.
IsaSampleModel	Omnipy model wrapper for ISA sample records.
IsaSampleSchema	Schema for sample entities in ISA study materials.

FieldType

Bases: Enum

              flowchart BT
              omnipy.components.isa.models.sample_schema.FieldType[FieldType]

              

              click omnipy.components.isa.models.sample_schema.FieldType href "" "omnipy.components.isa.models.sample_schema.FieldType"
            

JSON-LD type labels used for ISA sample entities.

ATTRIBUTE	DESCRIPTION
Sample	Marks a JSON object as an ISA sample.

Returned by:

• Reference Code reference omnipy components
  •  isa  IsaSampleSchema  field_type
  • isa models  sample_schema  IsaSampleSchema  field_type

Source code in src/omnipy/components/isa/models/sample_schema.py

class FieldType(Enum):
    """JSON-LD type labels used for ISA sample entities.

    Attributes:
        Sample: Marks a JSON object as an ISA sample.
    """

    Sample = 'Sample'

Sample class-attribute instance-attribute

Sample = 'Sample'

IsaSampleModel

Bases: Model[IsaSampleSchema]

              flowchart BT
              omnipy.components.isa.models.sample_schema.IsaSampleModel[IsaSampleModel]
              omnipy.data.model.Model[Model]
              omnipy.data._mixins.display.ModelDisplayMixin[ModelDisplayMixin]
              omnipy.data._mixins.display.BaseDisplayMixin[BaseDisplayMixin]
              omnipy.data._data_class_creator.DataClassBase[DataClassBase]

                              omnipy.data.model.Model --> omnipy.components.isa.models.sample_schema.IsaSampleModel
                                omnipy.data._mixins.display.ModelDisplayMixin --> omnipy.data.model.Model
                                omnipy.data._mixins.display.BaseDisplayMixin --> omnipy.data._mixins.display.ModelDisplayMixin
                

                omnipy.data._data_class_creator.DataClassBase --> omnipy.data.model.Model
                
                omnipy.util.pydantic.GenericModel --> omnipy.data.model.Model
                



              click omnipy.components.isa.models.sample_schema.IsaSampleModel href "" "omnipy.components.isa.models.sample_schema.IsaSampleModel"
              click omnipy.data.model.Model href "" "omnipy.data.model.Model"
              click omnipy.data._mixins.display.ModelDisplayMixin href "" "omnipy.data._mixins.display.ModelDisplayMixin"
              click omnipy.data._mixins.display.BaseDisplayMixin href "" "omnipy.data._mixins.display.BaseDisplayMixin"
              click omnipy.data._data_class_creator.DataClassBase href "" "omnipy.data._data_class_creator.DataClassBase"
            

Omnipy model wrapper for ISA sample records.

Wraps :class:IsaSampleSchema so sample entries can be validated and handled consistently across ISA workflows.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs
    •  IsaStudyGroupSchema  members
  • isa models
    •  process_schema  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs
    •  study_group  IsaStudyGroupSchema  members

Source code in src/omnipy/components/isa/models/sample_schema.py

class IsaSampleModel(Model[IsaSampleSchema]):
    """Omnipy model wrapper for ISA sample records.

    Wraps :class:`IsaSampleSchema` so sample entries can be validated and
    handled consistently across ISA workflows.
    """

    ...

IsaSampleSchema

Bases: pyd.BaseModel

              flowchart BT
              omnipy.components.isa.models.sample_schema.IsaSampleSchema[IsaSampleSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.models.sample_schema.IsaSampleSchema
                


              click omnipy.components.isa.models.sample_schema.IsaSampleSchema href "" "omnipy.components.isa.models.sample_schema.IsaSampleSchema"
            

Schema for sample entities in ISA study materials.

ATTRIBUTE	DESCRIPTION
name	Sample name or identifier. TYPE: str | None
characteristics	Material attribute values describing the sample. TYPE: list[material_attribute_value_schema.IsaMaterialAttributeValueModel] | None
factorValues	Factor assignments associated with the sample. TYPE: list[factor_value_schema.IsaFactorValueModel] | None
derivesFrom	Source materials from which the sample originates. TYPE: list[source_schema.IsaSourceModel] | None
comments	Optional comments attached to the sample. TYPE: list[comment_schema.IsaCommentModel] | None

Subclassed by:

• Reference Code reference
  •  omnipy  IsaSampleModel
  • omnipy components isa models  sample_schema  IsaSampleModel

CLASS	DESCRIPTION
Config	Validation settings for ISA sample schema parsing.

Source code in src/omnipy/components/isa/models/sample_schema.py

class IsaSampleSchema(pyd.BaseModel):
    """Schema for sample entities in ISA study materials.

    Attributes:
        name: Sample name or identifier.
        characteristics: Material attribute values describing the sample.
        factorValues: Factor assignments associated with the sample.
        derivesFrom: Source materials from which the sample originates.
        comments: Optional comments attached to the sample.
    """
    class Config:
        """Validation settings for ISA sample schema parsing.

        Attributes:
            extra: Rejects unknown keys in input payloads.
            use_enum_values: Serializes enums to their raw values.
        """

        extra = pyd.Extra.forbid
        use_enum_values = True

    field_id: Optional[str] = pyd.Field(None, alias='@id')
    field_context: Optional[str] = pyd.Field(None, alias='@context')
    field_type: Optional[FieldType] = pyd.Field(None, alias='@type')
    name: Optional[str] = None
    characteristics: Optional[List[
        material_attribute_value_schema.IsaMaterialAttributeValueModel]] = None
    factorValues: Optional[List[factor_value_schema.IsaFactorValueModel]] = None
    derivesFrom: Optional[List[source_schema.IsaSourceModel]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

characteristics class-attribute instance-attribute

characteristics: list[material_attribute_value_schema.IsaMaterialAttributeValueModel] | None = None

comments class-attribute instance-attribute

comments: list[comment_schema.IsaCommentModel] | None = None

derivesFrom class-attribute instance-attribute

derivesFrom: list[source_schema.IsaSourceModel] | None = None

factorValues class-attribute instance-attribute

factorValues: list[factor_value_schema.IsaFactorValueModel] | None = None

field_context class-attribute instance-attribute

field_context: str | None = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: str | None = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: FieldType | None = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: str | None = None

Config

Validation settings for ISA sample schema parsing.

ATTRIBUTE	DESCRIPTION
extra	Rejects unknown keys in input payloads.
use_enum_values	Serializes enums to their raw values.

Source code in src/omnipy/components/isa/models/sample_schema.py

class Config:
    """Validation settings for ISA sample schema parsing.

    Attributes:
        extra: Rejects unknown keys in input payloads.
        use_enum_values: Serializes enums to their raw values.
    """

    extra = pyd.Extra.forbid
    use_enum_values = True

extra class-attribute instance-attribute

extra = pyd.Extra.forbid

use_enum_values class-attribute instance-attribute

use_enum_values = True