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omnipy.components.isa.models.process_schema

Returned by:
CLASS DESCRIPTION
FieldType

JSON-LD type labels used for ISA process entities.
IsaProcessOrProtocolApplicationModel

Omnipy model wrapper for ISA process-step records.
IsaProcessOrProtocolApplicationSchema

Schema for process or protocol application steps in ISA workflows.

FieldType

Bases: Enum


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

              

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

JSON-LD type labels used for ISA process entities.

ATTRIBUTE DESCRIPTION
Process

Marks a JSON object as an ISA process step.
Returned by:
Source code in src/omnipy/components/isa/models/process_schema.py 
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class FieldType(Enum):
    """JSON-LD type labels used for ISA process entities.

    Attributes:
        Process: Marks a JSON object as an ISA process step.
    """

    Process = 'Process'

Process class-attribute instance-attribute 

Process = 'Process'

IsaProcessOrProtocolApplicationModel

Bases: Model[IsaProcessOrProtocolApplicationSchema]


              flowchart BT
              omnipy.components.isa.models.process_schema.IsaProcessOrProtocolApplicationModel[IsaProcessOrProtocolApplicationModel]
              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.process_schema.IsaProcessOrProtocolApplicationModel
                                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.process_schema.IsaProcessOrProtocolApplicationModel href "" "omnipy.components.isa.models.process_schema.IsaProcessOrProtocolApplicationModel"
              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 process-step records.

Provides Omnipy model behavior for values validated by :class:IsaProcessOrProtocolApplicationSchema.

Returned by:
Source code in src/omnipy/components/isa/models/process_schema.py 
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class IsaProcessOrProtocolApplicationModel(Model[IsaProcessOrProtocolApplicationSchema]):
    """Omnipy model wrapper for ISA process-step records.

    Provides Omnipy model behavior for values validated by
    :class:`IsaProcessOrProtocolApplicationSchema`.
    """

    ...

IsaProcessOrProtocolApplicationSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.models.process_schema.IsaProcessOrProtocolApplicationSchema[IsaProcessOrProtocolApplicationSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.models.process_schema.IsaProcessOrProtocolApplicationSchema
                


              click omnipy.components.isa.models.process_schema.IsaProcessOrProtocolApplicationSchema href "" "omnipy.components.isa.models.process_schema.IsaProcessOrProtocolApplicationSchema"

Schema for process or protocol application steps in ISA workflows.

ATTRIBUTE DESCRIPTION
name

Process step label.

TYPE: str | None

executesProtocol

Protocol executed by this step.

TYPE: protocol_schema.IsaProtocolModel | None

parameterValues

Parameter assignments used for execution.

TYPE: list[process_parameter_value_schema.IsaProcessParameterValueModel] | None

inputs

Materials or data consumed by the process.

TYPE: list[source_schema.IsaSourceModel | sample_schema.IsaSampleModel | data_schema.IsaDataModel | material_schema.IsaMaterialModel] | None

outputs

Materials or data produced by the process.

TYPE: list[sample_schema.IsaSampleModel | data_schema.IsaDataModel | material_schema.IsaMaterialModel] | None

previousProcess

Upstream process in a linked process chain.

TYPE: IsaProcessOrProtocolApplicationModel | None

nextProcess

Downstream process in a linked process chain.

TYPE: IsaProcessOrProtocolApplicationModel | None

Subclassed by:
CLASS DESCRIPTION
Config

Validation settings for ISA process-step schema parsing.
Source code in src/omnipy/components/isa/models/process_schema.py 
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class IsaProcessOrProtocolApplicationSchema(pyd.BaseModel):
    """Schema for process or protocol application steps in ISA workflows.

    Attributes:
        name: Process step label.
        executesProtocol: Protocol executed by this step.
        parameterValues: Parameter assignments used for execution.
        inputs: Materials or data consumed by the process.
        outputs: Materials or data produced by the process.
        previousProcess: Upstream process in a linked process chain.
        nextProcess: Downstream process in a linked process chain.
    """
    class Config:
        """Validation settings for ISA process-step schema parsing.

        Attributes:
            extra: Rejects keys outside the declared schema.
            use_enum_values: Serializes enum fields as 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
    executesProtocol: Optional[protocol_schema.IsaProtocolModel] = None
    parameterValues: Optional[List[
        process_parameter_value_schema.IsaProcessParameterValueModel]] = None
    performer: Optional[str] = None
    date: Optional[Union[datetime.datetime, datetime.date, pyd.constr(max_length=0)]] = None
    previousProcess: Optional['IsaProcessOrProtocolApplicationModel'] = None
    nextProcess: Optional['IsaProcessOrProtocolApplicationModel'] = None
    inputs: Optional[List[Union[
        source_schema.IsaSourceModel,
        sample_schema.IsaSampleModel,
        data_schema.IsaDataModel,
        material_schema.IsaMaterialModel,
    ]]] = None
    outputs: Optional[List[Union[
        sample_schema.IsaSampleModel,
        data_schema.IsaDataModel,
        material_schema.IsaMaterialModel,
    ]]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

    _date_to_iso_format = pyd.validator('date', allow_reuse=True)(date_to_iso_format)

comments class-attribute instance-attribute 

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

date class-attribute instance-attribute 

date: datetime.datetime | datetime.date | pyd.constr(max_length=0) | None = None

executesProtocol class-attribute instance-attribute 

executesProtocol: protocol_schema.IsaProtocolModel | 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')

inputs class-attribute instance-attribute 

inputs: (
    list[
        source_schema.IsaSourceModel
        | sample_schema.IsaSampleModel
        | data_schema.IsaDataModel
        | material_schema.IsaMaterialModel
    ]
    | None
) = None

name class-attribute instance-attribute 

name: str | None = None

nextProcess class-attribute instance-attribute 

nextProcess: IsaProcessOrProtocolApplicationModel | None = None

outputs class-attribute instance-attribute 

outputs: (
    list[sample_schema.IsaSampleModel | data_schema.IsaDataModel | material_schema.IsaMaterialModel]
    | None
) = None

parameterValues class-attribute instance-attribute 

parameterValues: list[process_parameter_value_schema.IsaProcessParameterValueModel] | None = None

performer class-attribute instance-attribute 

performer: str | None = None

previousProcess class-attribute instance-attribute 

previousProcess: IsaProcessOrProtocolApplicationModel | None = None

Config

Validation settings for ISA process-step schema parsing.

ATTRIBUTE DESCRIPTION
extra

Rejects keys outside the declared schema.
use_enum_values

Serializes enum fields as raw values.
Source code in src/omnipy/components/isa/models/process_schema.py 
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class Config:
    """Validation settings for ISA process-step schema parsing.

    Attributes:
        extra: Rejects keys outside the declared schema.
        use_enum_values: Serializes enum fields as 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