omnipy.components.isa.models.protocol_parameter_schema

ISA model representing a protocol parameter in an investigation.

ISA-JSON uses JSON-LD to encode Investigation/Study/Assay metadata, and these classes provide typed Omnipy wrappers.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaProcessParameterValueSchema  category
    •  IsaProtocolSchema  parameters
  • isa models
    •  process_parameter_value_schema  IsaProcessParameterValueSchema  category
    •  protocol_schema  IsaProtocolSchema  parameters

CLASS	DESCRIPTION
FieldType	JSON-LD type labels used for ISA protocol-parameter entities.
IsaProtocolParameterModel	Omnipy model wrapper for ISA protocol parameters.
IsaProtocolParameterSchema	Schema for protocol parameters used by ISA process steps.

FieldType

Bases: Enum

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

              

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

JSON-LD type labels used for ISA protocol-parameter entities.

ATTRIBUTE	DESCRIPTION
ProtocolParameter	Marks a JSON object as a protocol parameter.

Returned by:

• Reference Code reference omnipy components
  •  isa  IsaProtocolParameterSchema  field_type
  • isa models  protocol_parameter_schema  IsaProtocolParameterSchema  field_type

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

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

    Attributes:
        ProtocolParameter: Marks a JSON object as a protocol parameter.
    """

    ProtocolParameter = 'ProtocolParameter'

ProtocolParameter class-attribute instance-attribute

ProtocolParameter = 'ProtocolParameter'

IsaProtocolParameterModel

Bases: Model[IsaProtocolParameterSchema]

              flowchart BT
              omnipy.components.isa.models.protocol_parameter_schema.IsaProtocolParameterModel[IsaProtocolParameterModel]
              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.protocol_parameter_schema.IsaProtocolParameterModel
                                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.protocol_parameter_schema.IsaProtocolParameterModel href "" "omnipy.components.isa.models.protocol_parameter_schema.IsaProtocolParameterModel"
              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 protocol parameters.

Wraps :class:IsaProtocolParameterSchema for typed, validated use in ISA protocol and process structures.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaProcessParameterValueSchema  category
    •  IsaProtocolSchema  parameters
  • isa models
    •  process_parameter_value_schema  IsaProcessParameterValueSchema  category
    •  protocol_schema  IsaProtocolSchema  parameters

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

class IsaProtocolParameterModel(Model[IsaProtocolParameterSchema]):
    """Omnipy model wrapper for ISA protocol parameters.

    Wraps :class:`IsaProtocolParameterSchema` for typed, validated use in ISA
    protocol and process structures.
    """

    ...

IsaProtocolParameterSchema

Bases: pyd.BaseModel

              flowchart BT
              omnipy.components.isa.models.protocol_parameter_schema.IsaProtocolParameterSchema[IsaProtocolParameterSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.models.protocol_parameter_schema.IsaProtocolParameterSchema
                


              click omnipy.components.isa.models.protocol_parameter_schema.IsaProtocolParameterSchema href "" "omnipy.components.isa.models.protocol_parameter_schema.IsaProtocolParameterSchema"
            

Schema for protocol parameters used by ISA process steps.

ATTRIBUTE	DESCRIPTION
parameterName	Ontology-backed name of the protocol parameter. TYPE: ontology_annotation_schema.IsaOntologyReferenceModel | None
comments	Optional comments attached to the parameter definition. TYPE: list[comment_schema.IsaCommentModel] | None

Subclassed by:

• Reference Code reference
  •  omnipy  IsaProtocolParameterModel
  • omnipy components isa models  protocol_parameter_schema  IsaProtocolParameterModel

CLASS	DESCRIPTION
Config	Validation settings for ISA protocol-parameter schema parsing.

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

class IsaProtocolParameterSchema(pyd.BaseModel):
    """Schema for protocol parameters used by ISA process steps.

    Attributes:
        parameterName: Ontology-backed name of the protocol parameter.
        comments: Optional comments attached to the parameter definition.
    """
    class Config:
        """Validation settings for ISA protocol-parameter schema parsing.

        Attributes:
            extra: Rejects undeclared keys from input data.
            use_enum_values: Emits enum fields as their value strings.
        """

        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')
    parameterName: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = (None)
    comments: Optional[List[comment_schema.IsaCommentModel]] = 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')

parameterName class-attribute instance-attribute

parameterName: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

Config

Validation settings for ISA protocol-parameter schema parsing.

ATTRIBUTE	DESCRIPTION
extra	Rejects undeclared keys from input data.
use_enum_values	Emits enum fields as their value strings.

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

class Config:
    """Validation settings for ISA protocol-parameter schema parsing.

    Attributes:
        extra: Rejects undeclared keys from input data.
        use_enum_values: Emits enum fields as their value strings.
    """

    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