omnipy.components.isa.models.source_schema

ISA model representing a source in an investigation.

ISA denotes Investigation/Study/Assay metadata represented as ISA-JSON JSON-LD in these generated models.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaProcessOrProtocolApplicationSchema  inputs
    •  IsaSampleSchema  derivesFrom
  • isa models
    •  process_schema  IsaProcessOrProtocolApplicationSchema  inputs
    •  sample_schema  IsaSampleSchema  derivesFrom

CLASS	DESCRIPTION
FieldType	JSON-LD type labels used for ISA source entities.
IsaSourceModel	Omnipy model wrapper for ISA source records.
IsaSourceSchema	Schema for source materials in ISA study definitions.

FieldType

Bases: Enum

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

              

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

JSON-LD type labels used for ISA source entities.

ATTRIBUTE	DESCRIPTION
Source	Marks a JSON object as an ISA source.

Returned by:

• Reference Code reference omnipy components
  •  isa  IsaSourceSchema  field_type
  • isa models  source_schema  IsaSourceSchema  field_type

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

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

    Attributes:
        Source: Marks a JSON object as an ISA source.
    """

    Source = 'Source'

Source class-attribute instance-attribute

Source = 'Source'

IsaSourceModel

Bases: Model[IsaSourceSchema]

              flowchart BT
              omnipy.components.isa.models.source_schema.IsaSourceModel[IsaSourceModel]
              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.source_schema.IsaSourceModel
                                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.source_schema.IsaSourceModel href "" "omnipy.components.isa.models.source_schema.IsaSourceModel"
              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 source records.

Provides Omnipy model behavior on top of :class:IsaSourceSchema validation.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaProcessOrProtocolApplicationSchema  inputs
    •  IsaSampleSchema  derivesFrom
  • isa models
    •  process_schema  IsaProcessOrProtocolApplicationSchema  inputs
    •  sample_schema  IsaSampleSchema  derivesFrom

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

class IsaSourceModel(Model[IsaSourceSchema]):
    """Omnipy model wrapper for ISA source records.

    Provides Omnipy model behavior on top of
    :class:`IsaSourceSchema` validation.
    """

    ...

IsaSourceSchema

Bases: pyd.BaseModel

              flowchart BT
              omnipy.components.isa.models.source_schema.IsaSourceSchema[IsaSourceSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.models.source_schema.IsaSourceSchema
                


              click omnipy.components.isa.models.source_schema.IsaSourceSchema href "" "omnipy.components.isa.models.source_schema.IsaSourceSchema"
            

Schema for source materials in ISA study definitions.

ATTRIBUTE	DESCRIPTION
name	Source name or identifier. TYPE: str | None
characteristics	Material attribute values describing the source. TYPE: list[material_attribute_value_schema.IsaMaterialAttributeValueModel] | None
comments	Optional comments attached to the source entry. TYPE: list[comment_schema.IsaCommentModel] | None

Subclassed by:

• Reference Code reference
  •  omnipy  IsaSourceModel
  • omnipy components isa models  source_schema  IsaSourceModel

CLASS	DESCRIPTION
Config	Validation settings for ISA source schema parsing.

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

class IsaSourceSchema(pyd.BaseModel):
    """Schema for source materials in ISA study definitions.

    Attributes:
        name: Source name or identifier.
        characteristics: Material attribute values describing the source.
        comments: Optional comments attached to the source entry.
    """
    class Config:
        """Validation settings for ISA source schema parsing.

        Attributes:
            extra: Rejects undeclared keys in payloads.
            use_enum_values: Serializes enum members to value strings.
        """

        extra = pyd.Extra.forbid
        use_enum_values = True
        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
    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

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 source schema parsing.

ATTRIBUTE	DESCRIPTION
extra	Rejects undeclared keys in payloads.
use_enum_values	Serializes enum members to value strings.

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

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

    Attributes:
        extra: Rejects undeclared keys in payloads.
        use_enum_values: Serializes enum members to value strings.
    """

    extra = pyd.Extra.forbid
    use_enum_values = True
    use_enum_values = True

extra class-attribute instance-attribute

extra = pyd.Extra.forbid

use_enum_values class-attribute instance-attribute

use_enum_values = True