omnipy.components.isa.models.data_schema

ISA model representing a data file in an investigation.

ISA is the Investigation/Study/Assay metadata model, represented here in ISA-JSON JSON-LD form.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaAssayJsonSchema  dataFiles
    •  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs
  • isa models
    •  assay_schema  IsaAssayJsonSchema  dataFiles
    •  process_schema  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs

CLASS	DESCRIPTION
FieldType	JSON-LD type labels used for ISA data-file entities.
IsaDataModel	Omnipy model wrapper for ISA data-file records.
IsaDataSchema	Schema for a data file entry in an ISA assay.
Type	Allowed ISA data-file category labels.

FieldType

Bases: Enum

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

              

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

JSON-LD type labels used for ISA data-file entities.

ATTRIBUTE	DESCRIPTION
Data	Marks a JSON object as an ISA data file.

Returned by:

• Reference Code reference omnipy components
  •  isa  IsaDataSchema  field_type
  • isa models  data_schema  IsaDataSchema  field_type

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

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

    Attributes:
        Data: Marks a JSON object as an ISA data file.
    """

    Data = 'Data'

Data class-attribute instance-attribute

Data = 'Data'

IsaDataModel

Bases: Model[IsaDataSchema]

              flowchart BT
              omnipy.components.isa.models.data_schema.IsaDataModel[IsaDataModel]
              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.data_schema.IsaDataModel
                                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.data_schema.IsaDataModel href "" "omnipy.components.isa.models.data_schema.IsaDataModel"
              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 data-file records.

Provides Omnipy model semantics for values validated by :class:IsaDataSchema.

Returned by:

• Reference Code reference omnipy components
  •  isa
    •  IsaAssayJsonSchema  dataFiles
    •  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs
  • isa models
    •  assay_schema  IsaAssayJsonSchema  dataFiles
    •  process_schema  IsaProcessOrProtocolApplicationSchema
      •  inputs
      •  outputs

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

class IsaDataModel(Model[IsaDataSchema]):
    """Omnipy model wrapper for ISA data-file records.

    Provides Omnipy model semantics for values validated by
    :class:`IsaDataSchema`.
    """

    ...

IsaDataSchema

Bases: pyd.BaseModel

              flowchart BT
              omnipy.components.isa.models.data_schema.IsaDataSchema[IsaDataSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.models.data_schema.IsaDataSchema
                


              click omnipy.components.isa.models.data_schema.IsaDataSchema href "" "omnipy.components.isa.models.data_schema.IsaDataSchema"
            

Schema for a data file entry in an ISA assay.

ATTRIBUTE	DESCRIPTION
name	Logical or physical filename for the data object. TYPE: str | None
type	Controlled category describing the data file kind. TYPE: Type | None
comments	Optional free-form metadata attached to the file. TYPE: list[comment_schema.IsaCommentModel] | None

Subclassed by:

• Reference Code reference
  •  omnipy  IsaDataModel
  • omnipy components isa models  data_schema  IsaDataModel

CLASS	DESCRIPTION
Config	Validation settings for ISA data-file schema parsing.

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

class IsaDataSchema(pyd.BaseModel):
    """Schema for a data file entry in an ISA assay.

    Attributes:
        name: Logical or physical filename for the data object.
        type: Controlled category describing the data file kind.
        comments: Optional free-form metadata attached to the file.
    """
    class Config:
        """Validation settings for ISA data-file schema parsing.

        Attributes:
            extra: Rejects keys not declared by the schema.
            use_enum_values: Converts enum members to string 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
    type: Optional[Type] = 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')

name class-attribute instance-attribute

name: str | None = None

type class-attribute instance-attribute

type: Type | None = None

Config

Validation settings for ISA data-file schema parsing.

ATTRIBUTE	DESCRIPTION
extra	Rejects keys not declared by the schema.
use_enum_values	Converts enum members to string values.

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

class Config:
    """Validation settings for ISA data-file schema parsing.

    Attributes:
        extra: Rejects keys not declared by the schema.
        use_enum_values: Converts enum members to string 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

Type

Bases: Enum

              flowchart BT
              omnipy.components.isa.models.data_schema.Type[Type]

              

              click omnipy.components.isa.models.data_schema.Type href "" "omnipy.components.isa.models.data_schema.Type"
            

Allowed ISA data-file category labels.

These values follow ISA-JSON controlled vocabulary entries for different kinds of data files generated through assay workflows.

Returned by:

• Reference Code reference omnipy components
  •  isa  IsaDataSchema  type
  • isa models  data_schema  IsaDataSchema  type

ATTRIBUTE	DESCRIPTION
Acquisition_Parameter_Data_File
Array_Data_File
Array_Data_Matrix_File
Derived_Array_Data_File
Derived_Array_Data_Matrix_File
Derived_Data_File
Derived_Spectral_Data_File
Free_Induction_Decay_Data_File
Image_File
Metabolite_Assignment_File
Peptide_Assignment_File
Post_Translational_Modification_Assignment_File
Protein_Assignment_File
Raw_Data_File
Raw_Spectral_Data_File

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

class Type(Enum):
    """Allowed ISA data-file category labels.

    These values follow ISA-JSON controlled vocabulary entries for different
    kinds of data files generated through assay workflows.
    """

    Raw_Data_File = 'Raw Data File'
    Derived_Data_File = 'Derived Data File'
    Image_File = 'Image File'
    Acquisition_Parameter_Data_File = 'Acquisition Parameter Data File'
    Derived_Spectral_Data_File = 'Derived Spectral Data File'
    Protein_Assignment_File = 'Protein Assignment File'
    Raw_Spectral_Data_File = 'Raw Spectral Data File'
    Peptide_Assignment_File = 'Peptide Assignment File'
    Array_Data_File = 'Array Data File'
    Derived_Array_Data_File = 'Derived Array Data File'
    Post_Translational_Modification_Assignment_File = (
        'Post Translational Modification Assignment File')
    Derived_Array_Data_Matrix_File = 'Derived Array Data Matrix File'
    Free_Induction_Decay_Data_File = 'Free Induction Decay Data File'
    Metabolite_Assignment_File = 'Metabolite Assignment File'
    Array_Data_Matrix_File = 'Array Data Matrix File'

Acquisition_Parameter_Data_File class-attribute instance-attribute

Acquisition_Parameter_Data_File = 'Acquisition Parameter Data File'

Array_Data_File class-attribute instance-attribute

Array_Data_File = 'Array Data File'

Array_Data_Matrix_File class-attribute instance-attribute

Array_Data_Matrix_File = 'Array Data Matrix File'

Derived_Array_Data_File class-attribute instance-attribute

Derived_Array_Data_File = 'Derived Array Data File'

Derived_Array_Data_Matrix_File class-attribute instance-attribute

Derived_Array_Data_Matrix_File = 'Derived Array Data Matrix File'

Derived_Data_File class-attribute instance-attribute

Derived_Data_File = 'Derived Data File'

Derived_Spectral_Data_File class-attribute instance-attribute

Derived_Spectral_Data_File = 'Derived Spectral Data File'

Free_Induction_Decay_Data_File class-attribute instance-attribute

Free_Induction_Decay_Data_File = 'Free Induction Decay Data File'

Image_File class-attribute instance-attribute

Image_File = 'Image File'

Metabolite_Assignment_File class-attribute instance-attribute

Metabolite_Assignment_File = 'Metabolite Assignment File'

Peptide_Assignment_File class-attribute instance-attribute

Peptide_Assignment_File = 'Peptide Assignment File'

Post_Translational_Modification_Assignment_File class-attribute instance-attribute

Post_Translational_Modification_Assignment_File = 'Post Translational Modification Assignment File'

Protein_Assignment_File class-attribute instance-attribute

Protein_Assignment_File = 'Protein Assignment File'

Raw_Data_File class-attribute instance-attribute

Raw_Data_File = 'Raw Data File'

Raw_Spectral_Data_File class-attribute instance-attribute

Raw_Spectral_Data_File = 'Raw Spectral Data File'