omnipy.components.isa.models

MODULE	DESCRIPTION
assay_schema	ISA model representing an assay in an investigation.
comment_schema	ISA model representing a comment in an investigation.
data_schema	ISA model representing a data file in an investigation.
factor_schema	ISA model representing an experimental factor in an investigation.
factor_value_schema	ISA model representing a factor value in an investigation.
investigation_schema	ISA model representing an investigation.
material_attribute_schema	ISA model representing a material attribute category.
material_attribute_value_schema	ISA model representing a material attribute value in an investigation.
material_schema	ISA model representing a material in an investigation.
ontology_annotation_schema	ISA model representing an ontology annotation in an investigation.
ontology_source_reference_schema	ISA model representing an ontology source reference.
organization_schema	ISA model representing an organization in an investigation.
person_schema	ISA model representing a person in an investigation.
process_parameter_value_schema	ISA model representing a process parameter value in an investigation.
process_schema
protocol_parameter_schema	ISA model representing a protocol parameter in an investigation.
protocol_schema	ISA model representing a protocol in an investigation.
publication_schema	ISA model representing a publication in an investigation.
sample_schema	ISA model representing a sample in an investigation.
source_schema	ISA model representing a source in an investigation.
study_group	ISA model representing a study group in an investigation.
study_schema	ISA model representing a study in an investigation.
validators	Validation helpers shared by ISA schema models.

CLASS	DESCRIPTION
FlattenedIsaJsonModel
IsaJsonModel	Union model that accepts both common ISA investigation shapes.
IsaTopLevelModel	Omnipy model wrapper for :class:IsaTopLevelSchema.
IsaTopLevelSchema	Schema for top-level ISA-JSON documents.

ATTRIBUTE	DESCRIPTION
ISA_JSON_MODEL_TOP_LEVEL_KEY	TYPE: str

ISA_JSON_MODEL_TOP_LEVEL_KEY module-attribute

ISA_JSON_MODEL_TOP_LEVEL_KEY: str = 'investigation'

FlattenedIsaJsonModel

Bases: Model[JsonScalarColumnWiseTableWithColNamesModel], PrintableTable

              flowchart BT
              omnipy.components.isa.models.FlattenedIsaJsonModel[FlattenedIsaJsonModel]
              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.components.tables.models.PrintableTable[PrintableTable]

                              omnipy.data.model.Model --> omnipy.components.isa.models.FlattenedIsaJsonModel
                                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
                

                omnipy.components.tables.models.PrintableTable --> omnipy.components.isa.models.FlattenedIsaJsonModel
                


              click omnipy.components.isa.models.FlattenedIsaJsonModel href "" "omnipy.components.isa.models.FlattenedIsaJsonModel"
              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"
              click omnipy.components.tables.models.PrintableTable href "" "omnipy.components.tables.models.PrintableTable"
            

Subclassed by:

• Reference Code reference
  •  omnipy  FlattenedIsaJsonDataset
  • omnipy components
    •  isa  FlattenedIsaJsonDataset
    • isa  datasets  FlattenedIsaJsonDataset

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

class FlattenedIsaJsonModel(Model[JsonScalarColumnWiseTableWithColNamesModel], PrintableTable):
    ...

IsaJsonModel

Bases: Model[IsaInvestigationSchema | IsaTopLevelModel]

              flowchart BT
              omnipy.components.isa.models.IsaJsonModel[IsaJsonModel]
              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.IsaJsonModel
                                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.IsaJsonModel href "" "omnipy.components.isa.models.IsaJsonModel"
              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"
            

Union model that accepts both common ISA investigation shapes.

Input can be either a raw :class:IsaInvestigationSchema object or a top-level wrapper containing the investigation field.

Subclassed by:

• Reference Code reference
  •  omnipy  IsaJsonDataset
  • omnipy components
    •  isa  IsaJsonDataset
    • isa  datasets  IsaJsonDataset

CLASS	DESCRIPTION
Config	Pydantic settings for ISA union parsing behavior.

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

class IsaJsonModel(Model[IsaInvestigationSchema | IsaTopLevelModel]):
    """Union model that accepts both common ISA investigation shapes.

    Input can be either a raw :class:`IsaInvestigationSchema` object or a
    top-level wrapper containing the ``investigation`` field.
    """
    class Config:
        """Pydantic settings for ISA union parsing behavior.

        Attributes:
            smart_union: Keeps explicit branch resolution for union parsing.
        """

        smart_union = False

    @classmethod
    def _parse_data(cls, data: IsaInvestigationSchema | IsaTopLevelModel) -> IsaTopLevelModel:
        if isinstance(data, IsaTopLevelModel):
            return data
        else:
            return IsaTopLevelModel(investigation=data)

Config

Pydantic settings for ISA union parsing behavior.

ATTRIBUTE	DESCRIPTION
smart_union	Keeps explicit branch resolution for union parsing.

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

class Config:
    """Pydantic settings for ISA union parsing behavior.

    Attributes:
        smart_union: Keeps explicit branch resolution for union parsing.
    """

    smart_union = False

smart_union class-attribute instance-attribute

smart_union = False

IsaTopLevelModel

Bases: Model[IsaTopLevelSchema]

              flowchart BT
              omnipy.components.isa.models.IsaTopLevelModel[IsaTopLevelModel]
              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.IsaTopLevelModel
                                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.IsaTopLevelModel href "" "omnipy.components.isa.models.IsaTopLevelModel"
              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 :class:IsaTopLevelSchema.

The wrapper provides Omnipy Model behavior while preserving the top-level ISA-JSON document shape.

Subclassed by:

• Reference Code reference
  •  omnipy  IsaJsonModel
  • omnipy components
    •  isa  IsaJsonModel
    • isa  models  IsaJsonModel

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

class IsaTopLevelModel(Model[IsaTopLevelSchema]):
    """Omnipy model wrapper for :class:`IsaTopLevelSchema`.

    The wrapper provides Omnipy ``Model`` behavior while preserving the
    top-level ISA-JSON document shape.
    """

    ...

IsaTopLevelSchema

Bases: pyd.BaseModel

              flowchart BT
              omnipy.components.isa.models.IsaTopLevelSchema[IsaTopLevelSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.models.IsaTopLevelSchema
                


              click omnipy.components.isa.models.IsaTopLevelSchema href "" "omnipy.components.isa.models.IsaTopLevelSchema"
            

Schema for top-level ISA-JSON documents.

This schema reflects the common envelope where an ISA investigation is stored below the investigation key.

ATTRIBUTE	DESCRIPTION
investigation	Wrapped investigation payload when present. TYPE: IsaInvestigationModel | None

Subclassed by:

• Reference Code reference
  •  omnipy  IsaTopLevelModel
  • omnipy components isa  models  IsaTopLevelModel

CLASS	DESCRIPTION
Config	Pydantic settings for top-level ISA validation.

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

class IsaTopLevelSchema(pyd.BaseModel):
    """Schema for top-level ISA-JSON documents.

    This schema reflects the common envelope where an ISA investigation is
    stored below the ``investigation`` key.

    Attributes:
        investigation: Wrapped investigation payload when present.
    """
    class Config:
        """Pydantic settings for top-level ISA validation.

        Attributes:
            extra: Forbids keys that are not part of the schema.
            use_enum_values: Serializes enum instances as their value strings.
        """

        extra = pyd.Extra.forbid
        use_enum_values = True

    investigation: IsaInvestigationModel | None = None

investigation class-attribute instance-attribute

investigation: IsaInvestigationModel | None = None

Config

Pydantic settings for top-level ISA validation.

ATTRIBUTE	DESCRIPTION
extra	Forbids keys that are not part of the schema.
use_enum_values	Serializes enum instances as their value strings.

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

class Config:
    """Pydantic settings for top-level ISA validation.

    Attributes:
        extra: Forbids keys that are not part of the schema.
        use_enum_values: Serializes enum instances 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