omnipy.components.isa

ISA-Tab component package providing Investigation, Study, and Assay

models and datasets for working with ISA-Tab structured metadata.

MODULE	DESCRIPTION
`datasets`	Datasets for ISA-JSON documents and flattened ISA-JSON records.
`flows`	Flows for transforming ISA-JSON datasets into flattened tabular-like structures.
`models`

CLASS	DESCRIPTION
`FlattenedIsaJsonDataset`	Dataset containing flattened ISA-JSON records.
`FlattenedIsaJsonModel`
`IsaAssayJsonSchema`	Schema describing an assay block in ISA-JSON.
`IsaCommentSchema`	Schema for comments attached to ISA objects.
`IsaDataSchema`	Schema for a data file entry in an ISA assay.
`IsaFactorSchema`	Schema for an experimental factor defined in a study.
`IsaFactorValueSchema`	Schema for values assigned to study factors.
`IsaInvestigationSchema`	Schema for an ISA investigation document.
`IsaJsonDataset`	Dataset containing validated ISA-JSON documents.
`IsaJsonModel`	Union model that accepts both common ISA investigation shapes.
`IsaMaterialAttributeSchema`	Schema for material attribute categories in ISA.
`IsaMaterialAttributeValueSchema`	Schema for assigned material attribute values.
`IsaMaterialSchema`	Schema for non-sample materials in ISA studies.
`IsaOntologyReferenceSchema`	Schema for ontology terms referenced in ISA metadata.
`IsaOntologySourceReferenceSchema`	Schema for ontology source references in ISA metadata.
`IsaOrganizationSchema`	Schema for organization entries referenced in ISA metadata.
`IsaPersonSchema`	Schema for people associated with ISA investigations.
`IsaProcessOrProtocolApplicationSchema`	Schema for process or protocol application steps in ISA workflows.
`IsaProcessParameterValueSchema`	Schema for protocol parameter values applied in process steps.
`IsaProtocolParameterSchema`	Schema for protocol parameters used by ISA process steps.
`IsaProtocolSchema`	Schema for protocols referenced by ISA process workflows.
`IsaPublicationSchema`	Schema for publication metadata linked to ISA investigations.
`IsaSampleSchema`	Schema for sample entities in ISA study materials.
`IsaSourceSchema`	Schema for source materials in ISA study definitions.
`IsaStudyGroupSchema`	Schema for study groups used to organize related samples.
`IsaStudySchema`	Schema for study entries inside an ISA investigation.

FUNCTION	DESCRIPTION
`flatten_isa_json`	Flatten ISA-JSON documents into tabular-like records.

FlattenedIsaJsonDataset

Bases: Dataset[FlattenedIsaJsonModel]


              flowchart BT
              omnipy.components.isa.FlattenedIsaJsonDataset[FlattenedIsaJsonDataset]
              omnipy.data.dataset.Dataset[Dataset]
              omnipy.data._mixins.display.DatasetDisplayMixin[DatasetDisplayMixin]
              omnipy.data._mixins.display.BaseDisplayMixin[BaseDisplayMixin]
              omnipy.data._mixins.task.TaskDatasetMixin[TaskDatasetMixin]
              omnipy.data._data_class_creator.DataClassBase[DataClassBase]

                              omnipy.data.dataset.Dataset --> omnipy.components.isa.FlattenedIsaJsonDataset
                                omnipy.data._mixins.display.DatasetDisplayMixin --> omnipy.data.dataset.Dataset
                                omnipy.data._mixins.display.BaseDisplayMixin --> omnipy.data._mixins.display.DatasetDisplayMixin
                

                omnipy.data._mixins.task.TaskDatasetMixin --> omnipy.data.dataset.Dataset
                
                omnipy.data._data_class_creator.DataClassBase --> omnipy.data.dataset.Dataset
                
                omnipy.util.pydantic.GenericModel --> omnipy.data.dataset.Dataset
                



              click omnipy.components.isa.FlattenedIsaJsonDataset href "" "omnipy.components.isa.FlattenedIsaJsonDataset"
              click omnipy.data.dataset.Dataset href "" "omnipy.data.dataset.Dataset"
              click omnipy.data._mixins.display.DatasetDisplayMixin href "" "omnipy.data._mixins.display.DatasetDisplayMixin"
              click omnipy.data._mixins.display.BaseDisplayMixin href "" "omnipy.data._mixins.display.BaseDisplayMixin"
              click omnipy.data._mixins.task.TaskDatasetMixin href "" "omnipy.data._mixins.task.TaskDatasetMixin"
              click omnipy.data._data_class_creator.DataClassBase href "" "omnipy.data._data_class_creator.DataClassBase"

Dataset containing flattened ISA-JSON records.

Records in this dataset follow :class:FlattenedIsaJsonModel and are intended for tabular-style processing after ISA structures are flattened.

Returned by:

Reference Code reference
- omnipy flatten_isa_json
- omnipy components
  - isa flatten_isa_json
  - isa flows flatten_isa_json

Source code in src/omnipy/components/isa/datasets.py

class FlattenedIsaJsonDataset(Dataset[FlattenedIsaJsonModel]):
    """Dataset containing flattened ISA-JSON records.

    Records in this dataset follow :class:`FlattenedIsaJsonModel` and are
    intended for tabular-style processing after ISA structures are flattened.
    """
    ...

FlattenedIsaJsonModel

Bases: Model[JsonScalarColumnWiseTableWithColNamesModel], PrintableTable


              flowchart BT
              omnipy.components.isa.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.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.FlattenedIsaJsonModel
                


              click omnipy.components.isa.FlattenedIsaJsonModel href "" "omnipy.components.isa.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):
    ...

IsaAssayJsonSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaAssayJsonSchema[IsaAssayJsonSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaAssayJsonSchema
                


              click omnipy.components.isa.IsaAssayJsonSchema href "" "omnipy.components.isa.IsaAssayJsonSchema"

Schema describing an assay block in ISA-JSON.

ATTRIBUTE	DESCRIPTION
`filename`	Source filename for the assay metadata. TYPE: `str \| None`
`measurementType`	Ontology term describing what is measured. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`technologyType`	Ontology term describing the assay technology. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`dataFiles`	Data files produced or referenced by the assay. TYPE: `list[data_schema.IsaDataModel] \| None`
`processSequence`	Ordered process applications for the assay workflow. TYPE: `list[process_schema.IsaProcessOrProtocolApplicationModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaAssayJsonModel
- omnipy components isa models assay_schema IsaAssayJsonModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA assay schema parsing.

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

class IsaAssayJsonSchema(pyd.BaseModel):
    """Schema describing an assay block in ISA-JSON.

    Attributes:
        filename: Source filename for the assay metadata.
        measurementType: Ontology term describing what is measured.
        technologyType: Ontology term describing the assay technology.
        dataFiles: Data files produced or referenced by the assay.
        processSequence: Ordered process applications for the assay workflow.
    """
    class Config:
        """Validation settings for ISA assay schema parsing.

        Attributes:
            extra: Rejects keys not defined in the schema.
            use_enum_values: Serializes enum members 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')
    filename: Optional[str] = None
    measurementType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = (None)
    technologyType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = (None)
    technologyPlatform: Optional[str] = None
    dataFiles: Optional[List[data_schema.IsaDataModel]] = None
    materials: Optional[_MaterialsModel] = None
    characteristicCategories: Optional[List[material_attribute_schema.IsaMaterialAttributeModel]] =\
        pyd.Field(
            None,
            description='List of all the characteristics categories (or material attributes) '
            'defined in the study, used to avoid duplication of their declaration '
            'when each material_attribute_value is created. ')
    unitCategories: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]] = \
        pyd.Field(
            None,
            description='List of all the units defined in the study, used to avoid duplication '
                        'of their declaration when each value is created. ')
    processSequence: Optional[List[process_schema.IsaProcessOrProtocolApplicationModel]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

characteristicCategories `class-attribute` `instance-attribute`

characteristicCategories: list[material_attribute_schema.IsaMaterialAttributeModel] | None = (
    pyd.Field(
        None,
        description="List of all the characteristics categories (or material attributes) defined in the study, used to avoid duplication of their declaration when each material_attribute_value is created. ",
    )
)

comments `class-attribute` `instance-attribute`

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

dataFiles `class-attribute` `instance-attribute`

dataFiles: list[data_schema.IsaDataModel] | 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')

filename `class-attribute` `instance-attribute`

filename: str | None = None

materials `class-attribute` `instance-attribute`

materials: _MaterialsModel | None = None

measurementType `class-attribute` `instance-attribute`

measurementType: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

processSequence `class-attribute` `instance-attribute`

processSequence: list[process_schema.IsaProcessOrProtocolApplicationModel] | None = None

technologyPlatform `class-attribute` `instance-attribute`

technologyPlatform: str | None = None

technologyType `class-attribute` `instance-attribute`

technologyType: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

unitCategories `class-attribute` `instance-attribute`

unitCategories: list[ontology_annotation_schema.IsaOntologyReferenceModel] | None = pyd.Field(
    None,
    description="List of all the units defined in the study, used to avoid duplication of their declaration when each value is created. ",
)

Config

Validation settings for ISA assay schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys not defined in the schema.
`use_enum_values`	Serializes enum members as their value strings.

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

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

    Attributes:
        extra: Rejects keys not defined in the schema.
        use_enum_values: Serializes enum members 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

IsaCommentSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaCommentSchema[IsaCommentSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaCommentSchema
                


              click omnipy.components.isa.IsaCommentSchema href "" "omnipy.components.isa.IsaCommentSchema"

Schema for comments attached to ISA objects.

ATTRIBUTE	DESCRIPTION
`name`	Comment key or label. TYPE: `str \| None`
`value`	Comment text associated with `name`. TYPE: `str \| None`

Subclassed by:

Reference Code reference
- omnipy IsaCommentModel
- omnipy components isa models comment_schema IsaCommentModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA comment schema parsing.

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

class IsaCommentSchema(pyd.BaseModel):
    """Schema for comments attached to ISA objects.

    Attributes:
        name: Comment key or label.
        value: Comment text associated with ``name``.
    """
    class Config:
        """Validation settings for ISA comment schema parsing.

        Attributes:
            extra: Rejects unknown keys in input data.
            use_enum_values: Emits enum members as raw 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')
    name: Optional[str] = None
    value: Optional[str] = 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

value `class-attribute` `instance-attribute`

value: str | None = None

Config

Validation settings for ISA comment schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects unknown keys in input data.
`use_enum_values`	Emits enum members as raw value strings.

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

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

    Attributes:
        extra: Rejects unknown keys in input data.
        use_enum_values: Emits enum members as raw 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

IsaDataSchema

Bases: pyd.BaseModel


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

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


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

IsaFactorSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaFactorSchema[IsaFactorSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaFactorSchema
                


              click omnipy.components.isa.IsaFactorSchema href "" "omnipy.components.isa.IsaFactorSchema"

Schema for an experimental factor defined in a study.

ATTRIBUTE	DESCRIPTION
`factorName`	Human-readable factor label. TYPE: `str \| None`
`factorType`	Ontology term describing the factor category. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`comments`	Optional comments attached to the factor definition. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaFactorModel
- omnipy components isa models factor_schema IsaFactorModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA factor schema parsing.

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

class IsaFactorSchema(pyd.BaseModel):
    """Schema for an experimental factor defined in a study.

    Attributes:
        factorName: Human-readable factor label.
        factorType: Ontology term describing the factor category.
        comments: Optional comments attached to the factor definition.
    """
    class Config:
        """Validation settings for ISA factor schema parsing.

        Attributes:
            extra: Rejects unknown keys in incoming data.
            use_enum_values: Serializes enums as 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')
    factorName: Optional[str] = None
    factorType: 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

factorName `class-attribute` `instance-attribute`

factorName: str | None = None

factorType `class-attribute` `instance-attribute`

factorType: ontology_annotation_schema.IsaOntologyReferenceModel | 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')

Config

Validation settings for ISA factor schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects unknown keys in incoming data.
`use_enum_values`	Serializes enums as value strings.

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

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

    Attributes:
        extra: Rejects unknown keys in incoming data.
        use_enum_values: Serializes enums as 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

IsaFactorValueSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaFactorValueSchema[IsaFactorValueSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaFactorValueSchema
                


              click omnipy.components.isa.IsaFactorValueSchema href "" "omnipy.components.isa.IsaFactorValueSchema"

Schema for values assigned to study factors.

ATTRIBUTE	DESCRIPTION
`category`	Factor definition that this value belongs to. TYPE: `factor_schema.IsaFactorModel \| None`
`value`	Actual assigned value, either ontology-backed or scalar. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| str \| float \| None`
`unit`	Unit ontology term for numeric values when applicable. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`comments`	Optional comments describing the assignment. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaFactorValueModel
- omnipy components isa models factor_value_schema IsaFactorValueModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA factor-value schema parsing.

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

class IsaFactorValueSchema(pyd.BaseModel):
    """Schema for values assigned to study factors.

    Attributes:
        category: Factor definition that this value belongs to.
        value: Actual assigned value, either ontology-backed or scalar.
        unit: Unit ontology term for numeric values when applicable.
        comments: Optional comments describing the assignment.
    """
    class Config:
        """Validation settings for ISA factor-value schema parsing.

        Attributes:
            extra: Rejects keys not declared in the schema.
            use_enum_values: Converts enum members to raw 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')
    category: Optional[factor_schema.IsaFactorModel] = None
    value: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]] = None
    unit: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

category `class-attribute` `instance-attribute`

category: factor_schema.IsaFactorModel | 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')

unit `class-attribute` `instance-attribute`

unit: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

value `class-attribute` `instance-attribute`

value: ontology_annotation_schema.IsaOntologyReferenceModel | str | float | None = None

Config

Validation settings for ISA factor-value schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys not declared in the schema.
`use_enum_values`	Converts enum members to raw value strings.

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

class Config:
    """Validation settings for ISA factor-value schema parsing.

    Attributes:
        extra: Rejects keys not declared in the schema.
        use_enum_values: Converts enum members to raw 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

IsaInvestigationSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaInvestigationSchema[IsaInvestigationSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaInvestigationSchema
                


              click omnipy.components.isa.IsaInvestigationSchema href "" "omnipy.components.isa.IsaInvestigationSchema"

Schema for an ISA investigation document.

ATTRIBUTE	DESCRIPTION
`identifier`	Stable identifier for the investigation. TYPE: `str \| None`
`title`	Human-readable investigation title. TYPE: `str \| None`
`studies`	Study entries included in this investigation. TYPE: `list[study_schema.IsaStudyModel] \| None`
`submissionDate`	Submission date value for the investigation metadata. TYPE: `datetime \| date \| pyd.constr(max_length=0) \| None`
`publicReleaseDate`	Public release date for the investigation. TYPE: `datetime \| date \| pyd.constr(max_length=0) \| None`

Subclassed by:

Reference Code reference
- omnipy
  - IsaInvestigationModel
  - IsaJsonModel
- omnipy components
  - isa IsaJsonModel
  - isa
    - models IsaJsonModel
    - models investigation_schema IsaInvestigationModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA investigation schema parsing.

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

class IsaInvestigationSchema(pyd.BaseModel):
    """Schema for an ISA investigation document.

    Attributes:
        identifier: Stable identifier for the investigation.
        title: Human-readable investigation title.
        studies: Study entries included in this investigation.
        submissionDate: Submission date value for the investigation metadata.
        publicReleaseDate: Public release date for the investigation.
    """
    class Config:
        """Validation settings for ISA investigation schema parsing.

        Attributes:
            extra: Rejects undeclared keys in incoming payloads.
            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')
    filename: Optional[str] = None
    identifier: Optional[str] = None
    title: Optional[str] = None
    description: Optional[str] = None
    submissionDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None
    publicReleaseDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None
    ontologySourceReferences: Optional[List[
        ontology_source_reference_schema.IsaOntologySourceReferenceModel]] = None
    publications: Optional[List[publication_schema.IsaPublicationModel]] = None
    people: Optional[List[person_schema.IsaPersonModel]] = None
    studies: Optional[List[study_schema.IsaStudyModel]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

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

comments `class-attribute` `instance-attribute`

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

description `class-attribute` `instance-attribute`

description: str | 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')

filename `class-attribute` `instance-attribute`

filename: str | None = None

identifier `class-attribute` `instance-attribute`

identifier: str | None = None

ontologySourceReferences `class-attribute` `instance-attribute`

ontologySourceReferences: (
    list[ontology_source_reference_schema.IsaOntologySourceReferenceModel] | None
) = None

people `class-attribute` `instance-attribute`

people: list[person_schema.IsaPersonModel] | None = None

publicReleaseDate `class-attribute` `instance-attribute`

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

publications `class-attribute` `instance-attribute`

publications: list[publication_schema.IsaPublicationModel] | None = None

studies `class-attribute` `instance-attribute`

studies: list[study_schema.IsaStudyModel] | None = None

submissionDate `class-attribute` `instance-attribute`

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

title `class-attribute` `instance-attribute`

title: str | None = None

Config

Validation settings for ISA investigation schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects undeclared keys in incoming payloads.
`use_enum_values`	Emits enum fields as their value strings.

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

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

    Attributes:
        extra: Rejects undeclared keys in incoming payloads.
        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

IsaJsonDataset

Bases: Dataset[IsaJsonModel]


              flowchart BT
              omnipy.components.isa.IsaJsonDataset[IsaJsonDataset]
              omnipy.data.dataset.Dataset[Dataset]
              omnipy.data._mixins.display.DatasetDisplayMixin[DatasetDisplayMixin]
              omnipy.data._mixins.display.BaseDisplayMixin[BaseDisplayMixin]
              omnipy.data._mixins.task.TaskDatasetMixin[TaskDatasetMixin]
              omnipy.data._data_class_creator.DataClassBase[DataClassBase]

                              omnipy.data.dataset.Dataset --> omnipy.components.isa.IsaJsonDataset
                                omnipy.data._mixins.display.DatasetDisplayMixin --> omnipy.data.dataset.Dataset
                                omnipy.data._mixins.display.BaseDisplayMixin --> omnipy.data._mixins.display.DatasetDisplayMixin
                

                omnipy.data._mixins.task.TaskDatasetMixin --> omnipy.data.dataset.Dataset
                
                omnipy.data._data_class_creator.DataClassBase --> omnipy.data.dataset.Dataset
                
                omnipy.util.pydantic.GenericModel --> omnipy.data.dataset.Dataset
                



              click omnipy.components.isa.IsaJsonDataset href "" "omnipy.components.isa.IsaJsonDataset"
              click omnipy.data.dataset.Dataset href "" "omnipy.data.dataset.Dataset"
              click omnipy.data._mixins.display.DatasetDisplayMixin href "" "omnipy.data._mixins.display.DatasetDisplayMixin"
              click omnipy.data._mixins.display.BaseDisplayMixin href "" "omnipy.data._mixins.display.BaseDisplayMixin"
              click omnipy.data._mixins.task.TaskDatasetMixin href "" "omnipy.data._mixins.task.TaskDatasetMixin"
              click omnipy.data._data_class_creator.DataClassBase href "" "omnipy.data._data_class_creator.DataClassBase"

Dataset containing validated ISA-JSON documents.

Each record in the dataset is validated by :class:IsaJsonModel, allowing downstream ISA flows and tasks to operate on a consistent document shape.

Used by:

Reference Code reference
- omnipy flatten_isa_json
- omnipy components
  - isa flatten_isa_json
  - isa flows flatten_isa_json

Source code in src/omnipy/components/isa/datasets.py

class IsaJsonDataset(Dataset[IsaJsonModel]):
    """Dataset containing validated ISA-JSON documents.

    Each record in the dataset is validated by :class:`IsaJsonModel`, allowing
    downstream ISA flows and tasks to operate on a consistent document shape.
    """
    ...

IsaJsonModel

Bases: Model[IsaInvestigationSchema | IsaTopLevelModel]


              flowchart BT
              omnipy.components.isa.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.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.IsaJsonModel href "" "omnipy.components.isa.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

IsaMaterialAttributeSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaMaterialAttributeSchema[IsaMaterialAttributeSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaMaterialAttributeSchema
                


              click omnipy.components.isa.IsaMaterialAttributeSchema href "" "omnipy.components.isa.IsaMaterialAttributeSchema"

Schema for material attribute categories in ISA.

ATTRIBUTE	DESCRIPTION
`characteristicType`	Ontology term describing the attribute category. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`

Subclassed by:

Reference Code reference
- omnipy IsaMaterialAttributeModel
- omnipy components isa models material_attribute_schema IsaMaterialAttributeModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA material-attribute schema parsing.

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

class IsaMaterialAttributeSchema(pyd.BaseModel):
    """Schema for material attribute categories in ISA.

    Attributes:
        characteristicType: Ontology term describing the attribute category.
    """
    class Config:
        """Validation settings for ISA material-attribute schema parsing.

        Attributes:
            extra: Rejects keys not present in the schema.
            use_enum_values: Serializes enums with raw 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')
    characteristicType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

characteristicType `class-attribute` `instance-attribute`

characteristicType: ontology_annotation_schema.IsaOntologyReferenceModel | 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')

Config

Validation settings for ISA material-attribute schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys not present in the schema.
`use_enum_values`	Serializes enums with raw value strings.

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

class Config:
    """Validation settings for ISA material-attribute schema parsing.

    Attributes:
        extra: Rejects keys not present in the schema.
        use_enum_values: Serializes enums with raw 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

IsaMaterialAttributeValueSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaMaterialAttributeValueSchema[IsaMaterialAttributeValueSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaMaterialAttributeValueSchema
                


              click omnipy.components.isa.IsaMaterialAttributeValueSchema href "" "omnipy.components.isa.IsaMaterialAttributeValueSchema"

Schema for assigned material attribute values.

ATTRIBUTE	DESCRIPTION
`category`	Attribute definition that this value belongs to. TYPE: `material_attribute_schema.IsaMaterialAttributeModel \| None`
`value`	Scalar or ontology-backed attribute value. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| str \| float \| None`
`unit`	Unit ontology term when the value is quantitative. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`comments`	Optional comments attached to the value. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaMaterialAttributeValueModel
- omnipy components isa models material_attribute_value_schema IsaMaterialAttributeValueModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA attribute-value schema parsing.

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

class IsaMaterialAttributeValueSchema(pyd.BaseModel):
    """Schema for assigned material attribute values.

    Attributes:
        category: Attribute definition that this value belongs to.
        value: Scalar or ontology-backed attribute value.
        unit: Unit ontology term when the value is quantitative.
        comments: Optional comments attached to the value.
    """
    class Config:
        """Validation settings for ISA attribute-value schema parsing.

        Attributes:
            extra: Rejects undeclared keys from input data.
            use_enum_values: Emits enum members 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')
    category: Optional[material_attribute_schema.IsaMaterialAttributeModel] = None
    value: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]] = None
    unit: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

category `class-attribute` `instance-attribute`

category: material_attribute_schema.IsaMaterialAttributeModel | 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')

unit `class-attribute` `instance-attribute`

unit: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

value `class-attribute` `instance-attribute`

value: ontology_annotation_schema.IsaOntologyReferenceModel | str | float | None = None

Config

Validation settings for ISA attribute-value schema parsing.

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

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

class Config:
    """Validation settings for ISA attribute-value schema parsing.

    Attributes:
        extra: Rejects undeclared keys from input data.
        use_enum_values: Emits enum members 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

IsaMaterialSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaMaterialSchema[IsaMaterialSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaMaterialSchema
                


              click omnipy.components.isa.IsaMaterialSchema href "" "omnipy.components.isa.IsaMaterialSchema"

Schema for non-sample materials in ISA studies.

ATTRIBUTE	DESCRIPTION
`name`	Material name or identifier. TYPE: `str \| None`
`type`	Controlled label for material category. TYPE: `Type \| None`
`characteristics`	Assigned material attribute values. TYPE: `list[material_attribute_value_schema.IsaMaterialAttributeValueModel] \| None`
`derivesFrom`	Parent materials from which this material was derived. TYPE: `list[IsaMaterialModel] \| None`
`comments`	Optional comments attached to the material. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaMaterialModel
- omnipy components isa models material_schema IsaMaterialModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA material schema parsing.

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

class IsaMaterialSchema(pyd.BaseModel):
    """Schema for non-sample materials in ISA studies.

    Attributes:
        name: Material name or identifier.
        type: Controlled label for material category.
        characteristics: Assigned material attribute values.
        derivesFrom: Parent materials from which this material was derived.
        comments: Optional comments attached to the material.
    """
    class Config:
        """Validation settings for ISA material schema parsing.

        Attributes:
            extra: Rejects unknown fields.
            use_enum_values: Serializes enum fields by 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
    type: Optional[Type] = None
    characteristics: Optional[List[
        material_attribute_value_schema.IsaMaterialAttributeValueModel]] = None
    derivesFrom: Optional[List['IsaMaterialModel']] = 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

derivesFrom `class-attribute` `instance-attribute`

derivesFrom: list[IsaMaterialModel] | 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 material schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects unknown fields.
`use_enum_values`	Serializes enum fields by raw values.

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

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

    Attributes:
        extra: Rejects unknown fields.
        use_enum_values: Serializes enum fields by 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

IsaOntologyReferenceSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaOntologyReferenceSchema[IsaOntologyReferenceSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaOntologyReferenceSchema
                


              click omnipy.components.isa.IsaOntologyReferenceSchema href "" "omnipy.components.isa.IsaOntologyReferenceSchema"

Schema for ontology terms referenced in ISA metadata.

ATTRIBUTE	DESCRIPTION
`annotationValue`	Free-text or numeric value associated with the term. TYPE: `str \| float \| None`
`termSource`	Short name of the ontology source. TYPE: `str \| None`
`termAccession`	Accession identifier for the ontology term. TYPE: `str \| None`
`comments`	Optional comments attached to the annotation. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaOntologyReferenceModel
- omnipy components isa models ontology_annotation_schema IsaOntologyReferenceModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA ontology-annotation parsing.

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

class IsaOntologyReferenceSchema(pyd.BaseModel):
    """Schema for ontology terms referenced in ISA metadata.

    Attributes:
        annotationValue: Free-text or numeric value associated with the term.
        termSource: Short name of the ontology source.
        termAccession: Accession identifier for the ontology term.
        comments: Optional comments attached to the annotation.
    """
    class Config:
        """Validation settings for ISA ontology-annotation parsing.

        Attributes:
            extra: Rejects keys that are not defined by the schema.
            use_enum_values: Outputs enum fields as 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')
    annotationValue: Optional[Union[str, float]] = None
    termSource: Optional[str] = pyd.Field(
        None,
        description='The abbreviated ontology name. It should correspond to one of the sources as '
        'specified in the ontologySourceReference section of the Investigation.',
    )
    termAccession: Optional[str] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

annotationValue `class-attribute` `instance-attribute`

annotationValue: str | float | 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')

termAccession `class-attribute` `instance-attribute`

termAccession: str | None = None

termSource `class-attribute` `instance-attribute`

termSource: str | None = pyd.Field(
    None,
    description="The abbreviated ontology name. It should correspond to one of the sources as specified in the ontologySourceReference section of the Investigation.",
)

Config

Validation settings for ISA ontology-annotation parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys that are not defined by the schema.
`use_enum_values`	Outputs enum fields as value strings.

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

class Config:
    """Validation settings for ISA ontology-annotation parsing.

    Attributes:
        extra: Rejects keys that are not defined by the schema.
        use_enum_values: Outputs enum fields as 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

IsaOntologySourceReferenceSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaOntologySourceReferenceSchema[IsaOntologySourceReferenceSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaOntologySourceReferenceSchema
                


              click omnipy.components.isa.IsaOntologySourceReferenceSchema href "" "omnipy.components.isa.IsaOntologySourceReferenceSchema"

Schema for ontology source references in ISA metadata.

ATTRIBUTE	DESCRIPTION
`name`	Short source name used by ontology term references. TYPE: `str \| None`
`version`	Version string for the ontology source. TYPE: `str \| None`
`file`	Optional URI or file reference for the ontology. TYPE: `str \| None`
`description`	Human-readable source description. TYPE: `str \| None`

Subclassed by:

Reference Code reference
- omnipy IsaOntologySourceReferenceModel
- omnipy components isa models ontology_source_reference_schema IsaOntologySourceReferenceModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA ontology-source schema parsing.

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

class IsaOntologySourceReferenceSchema(pyd.BaseModel):
    """Schema for ontology source references in ISA metadata.

    Attributes:
        name: Short source name used by ontology term references.
        version: Version string for the ontology source.
        file: Optional URI or file reference for the ontology.
        description: Human-readable source description.
    """
    class Config:
        """Validation settings for ISA ontology-source schema parsing.

        Attributes:
            extra: Rejects undeclared keys in input payloads.
            use_enum_values: Serializes enum values as 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')
    comments: Optional[List[comment_schema.IsaCommentModel]] = None
    description: Optional[str] = None
    file: Optional[str] = None
    name: Optional[str] = None
    version: Optional[str] = None

comments `class-attribute` `instance-attribute`

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

description `class-attribute` `instance-attribute`

description: str | 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')

file `class-attribute` `instance-attribute`

file: str | None = None

name `class-attribute` `instance-attribute`

name: str | None = None

version `class-attribute` `instance-attribute`

version: str | None = None

Config

Validation settings for ISA ontology-source schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects undeclared keys in input payloads.
`use_enum_values`	Serializes enum values as strings.

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

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

    Attributes:
        extra: Rejects undeclared keys in input payloads.
        use_enum_values: Serializes enum values as 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

IsaOrganizationSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaOrganizationSchema[IsaOrganizationSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaOrganizationSchema
                


              click omnipy.components.isa.IsaOrganizationSchema href "" "omnipy.components.isa.IsaOrganizationSchema"

Schema for organization entries referenced in ISA metadata.

ATTRIBUTE	DESCRIPTION
`name`	Organization name. TYPE: `str \| None`

Subclassed by:

Reference Code reference
- omnipy IsaOrganizationModel
- omnipy components isa models organization_schema IsaOrganizationModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA organization schema parsing.

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

class IsaOrganizationSchema(pyd.BaseModel):
    """Schema for organization entries referenced in ISA metadata.

    Attributes:
        name: Organization name.
    """
    class Config:
        """Validation settings for ISA organization schema parsing.

        Attributes:
            extra: Rejects unknown keys.
            use_enum_values: Emits enum members as 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')
    name: Optional[str] = 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 organization schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects unknown keys.
`use_enum_values`	Emits enum members as value strings.

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

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

    Attributes:
        extra: Rejects unknown keys.
        use_enum_values: Emits enum members as 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

IsaPersonSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaPersonSchema[IsaPersonSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaPersonSchema
                


              click omnipy.components.isa.IsaPersonSchema href "" "omnipy.components.isa.IsaPersonSchema"

Schema for people associated with ISA investigations.

ATTRIBUTE	DESCRIPTION
`firstName`	Given name. TYPE: `str \| None`
`lastName`	Family name. TYPE: `str \| None`
`email`	Contact email for the person. TYPE: `pyd.EmailStr \| None`
`affiliation`	Organizational affiliation text. TYPE: `str \| None`
`roles`	Ontology terms describing investigation roles. TYPE: `list[ontology_annotation_schema.IsaOntologyReferenceModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaPersonModel
- omnipy components isa models person_schema IsaPersonModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA person schema parsing.

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

class IsaPersonSchema(pyd.BaseModel):
    """Schema for people associated with ISA investigations.

    Attributes:
        firstName: Given name.
        lastName: Family name.
        email: Contact email for the person.
        affiliation: Organizational affiliation text.
        roles: Ontology terms describing investigation roles.
    """
    class Config:
        """Validation settings for ISA person schema parsing.

        Attributes:
            extra: Rejects keys not listed in the schema.
            use_enum_values: Converts enum members to raw 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')
    lastName: Optional[str] = None
    firstName: Optional[str] = None
    midInitials: Optional[str] = None
    email: Optional[pyd.EmailStr] = None
    phone: Optional[str] = None
    fax: Optional[str] = None
    address: Optional[str] = None
    affiliation: Optional[str] = None
    roles: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

address `class-attribute` `instance-attribute`

address: str | None = None

affiliation `class-attribute` `instance-attribute`

affiliation: str | None = None

comments `class-attribute` `instance-attribute`

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

email `class-attribute` `instance-attribute`

email: pyd.EmailStr | None = None

fax `class-attribute` `instance-attribute`

fax: str | 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')

firstName `class-attribute` `instance-attribute`

firstName: str | None = None

lastName `class-attribute` `instance-attribute`

lastName: str | None = None

midInitials `class-attribute` `instance-attribute`

midInitials: str | None = None

phone `class-attribute` `instance-attribute`

phone: str | None = None

roles `class-attribute` `instance-attribute`

roles: list[ontology_annotation_schema.IsaOntologyReferenceModel] | None = None

Config

Validation settings for ISA person schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys not listed in the schema.
`use_enum_values`	Converts enum members to raw strings.

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

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

    Attributes:
        extra: Rejects keys not listed in the schema.
        use_enum_values: Converts enum members to raw 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

IsaProcessOrProtocolApplicationSchema

Bases: pyd.BaseModel


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

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


              click omnipy.components.isa.IsaProcessOrProtocolApplicationSchema href "" "omnipy.components.isa.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:

Reference Code reference
- omnipy IsaProcessOrProtocolApplicationModel
- omnipy components isa models process_schema IsaProcessOrProtocolApplicationModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA process-step schema parsing.

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

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

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

IsaProcessParameterValueSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaProcessParameterValueSchema[IsaProcessParameterValueSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaProcessParameterValueSchema
                


              click omnipy.components.isa.IsaProcessParameterValueSchema href "" "omnipy.components.isa.IsaProcessParameterValueSchema"

Schema for protocol parameter values applied in process steps.

ATTRIBUTE	DESCRIPTION
`category`	Protocol parameter definition this value belongs to. TYPE: `protocol_parameter_schema.IsaProtocolParameterModel \| None`
`value`	Scalar or ontology-backed assigned value. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| str \| float \| None`
`unit`	Unit ontology annotation for quantitative values. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`comments`	Optional comments attached to the value. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaProcessParameterValueModel
- omnipy components isa models process_parameter_value_schema IsaProcessParameterValueModel

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

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

class IsaProcessParameterValueSchema(pyd.BaseModel):
    """Schema for protocol parameter values applied in process steps.

    Attributes:
        category: Protocol parameter definition this value belongs to.
        value: Scalar or ontology-backed assigned value.
        unit: Unit ontology annotation for quantitative values.
        comments: Optional comments attached to the value.
    """
    class Config:
        """Validation settings for ISA process-parameter schema parsing.

        Attributes:
            extra: Rejects unknown keys in input payloads.
            use_enum_values: Emits enum members by value string.
        """

        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')
    category: Optional[protocol_parameter_schema.IsaProtocolParameterModel] = None
    value: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]] = None
    unit: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

category `class-attribute` `instance-attribute`

category: protocol_parameter_schema.IsaProtocolParameterModel | 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')

unit `class-attribute` `instance-attribute`

unit: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

value `class-attribute` `instance-attribute`

value: ontology_annotation_schema.IsaOntologyReferenceModel | str | float | None = None

Config

Validation settings for ISA process-parameter schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects unknown keys in input payloads.
`use_enum_values`	Emits enum members by value string.

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

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

    Attributes:
        extra: Rejects unknown keys in input payloads.
        use_enum_values: Emits enum members by value string.
    """

    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

IsaProtocolParameterSchema

Bases: pyd.BaseModel


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

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


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

IsaProtocolSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaProtocolSchema[IsaProtocolSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaProtocolSchema
                


              click omnipy.components.isa.IsaProtocolSchema href "" "omnipy.components.isa.IsaProtocolSchema"

Schema for protocols referenced by ISA process workflows.

ATTRIBUTE	DESCRIPTION
`name`	Protocol name. TYPE: `str \| None`
`protocolType`	Ontology term describing protocol category. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`
`description`	Human-readable protocol description. TYPE: `str \| None`
`parameters`	Parameter definitions accepted by the protocol. TYPE: `list[protocol_parameter_schema.IsaProtocolParameterModel] \| None`
`components`	Reusable protocol components and materials. TYPE: `list[Component] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaProtocolModel
- omnipy components isa models protocol_schema IsaProtocolModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA protocol schema parsing.

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

class IsaProtocolSchema(pyd.BaseModel):
    """Schema for protocols referenced by ISA process workflows.

    Attributes:
        name: Protocol name.
        protocolType: Ontology term describing protocol category.
        description: Human-readable protocol description.
        parameters: Parameter definitions accepted by the protocol.
        components: Reusable protocol components and materials.
    """
    class Config:
        """Validation settings for ISA protocol schema parsing.

        Attributes:
            extra: Rejects keys that are not defined in the schema.
            use_enum_values: Serializes enum members by value.
        """

        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
    protocolType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None
    description: Optional[str] = None
    uri: Optional[str] = None
    version: Optional[str] = None
    parameters: Optional[List[protocol_parameter_schema.IsaProtocolParameterModel]] = (None)
    components: Optional[List[Component]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

comments `class-attribute` `instance-attribute`

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

components `class-attribute` `instance-attribute`

components: list[Component] | None = None

description `class-attribute` `instance-attribute`

description: str | 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

parameters `class-attribute` `instance-attribute`

parameters: list[protocol_parameter_schema.IsaProtocolParameterModel] | None = None

protocolType `class-attribute` `instance-attribute`

protocolType: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

uri `class-attribute` `instance-attribute`

uri: str | None = None

version `class-attribute` `instance-attribute`

version: str | None = None

Config

Validation settings for ISA protocol schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys that are not defined in the schema.
`use_enum_values`	Serializes enum members by value.

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

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

    Attributes:
        extra: Rejects keys that are not defined in the schema.
        use_enum_values: Serializes enum members by value.
    """

    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

IsaPublicationSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaPublicationSchema[IsaPublicationSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaPublicationSchema
                


              click omnipy.components.isa.IsaPublicationSchema href "" "omnipy.components.isa.IsaPublicationSchema"

Schema for publication metadata linked to ISA investigations.

ATTRIBUTE	DESCRIPTION
`pubMedID`	PubMed identifier, when available. TYPE: `str \| None`
`doi`	DOI string for the publication. TYPE: `str \| None`
`authorList`	Free-form list of publication authors. TYPE: `str \| None`
`title`	Publication title. TYPE: `str \| None`
`status`	Ontology term describing publication status. TYPE: `ontology_annotation_schema.IsaOntologyReferenceModel \| None`

Subclassed by:

Reference Code reference
- omnipy IsaPublicationModel
- omnipy components isa models publication_schema IsaPublicationModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA publication schema parsing.

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

class IsaPublicationSchema(pyd.BaseModel):
    """Schema for publication metadata linked to ISA investigations.

    Attributes:
        pubMedID: PubMed identifier, when available.
        doi: DOI string for the publication.
        authorList: Free-form list of publication authors.
        title: Publication title.
        status: Ontology term describing publication status.
    """
    class Config:
        """Validation settings for ISA publication schema parsing.

        Attributes:
            extra: Rejects undeclared keys from payloads.
            use_enum_values: Emits enum fields as 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')
    pubMedID: Optional[str] = None
    doi: Optional[str] = None
    authorList: Optional[str] = None
    title: Optional[str] = None
    status: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

authorList `class-attribute` `instance-attribute`

authorList: str | None = None

comments `class-attribute` `instance-attribute`

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

doi `class-attribute` `instance-attribute`

doi: str | 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')

pubMedID `class-attribute` `instance-attribute`

pubMedID: str | None = None

status `class-attribute` `instance-attribute`

status: ontology_annotation_schema.IsaOntologyReferenceModel | None = None

title `class-attribute` `instance-attribute`

title: str | None = None

Config

Validation settings for ISA publication schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects undeclared keys from payloads.
`use_enum_values`	Emits enum fields as value strings.

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

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

    Attributes:
        extra: Rejects undeclared keys from payloads.
        use_enum_values: Emits enum fields as 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

IsaSampleSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaSampleSchema[IsaSampleSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaSampleSchema
                


              click omnipy.components.isa.IsaSampleSchema href "" "omnipy.components.isa.IsaSampleSchema"

Schema for sample entities in ISA study materials.

ATTRIBUTE	DESCRIPTION
`name`	Sample name or identifier. TYPE: `str \| None`
`characteristics`	Material attribute values describing the sample. TYPE: `list[material_attribute_value_schema.IsaMaterialAttributeValueModel] \| None`
`factorValues`	Factor assignments associated with the sample. TYPE: `list[factor_value_schema.IsaFactorValueModel] \| None`
`derivesFrom`	Source materials from which the sample originates. TYPE: `list[source_schema.IsaSourceModel] \| None`
`comments`	Optional comments attached to the sample. TYPE: `list[comment_schema.IsaCommentModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaSampleModel
- omnipy components isa models sample_schema IsaSampleModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA sample schema parsing.

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

class IsaSampleSchema(pyd.BaseModel):
    """Schema for sample entities in ISA study materials.

    Attributes:
        name: Sample name or identifier.
        characteristics: Material attribute values describing the sample.
        factorValues: Factor assignments associated with the sample.
        derivesFrom: Source materials from which the sample originates.
        comments: Optional comments attached to the sample.
    """
    class Config:
        """Validation settings for ISA sample schema parsing.

        Attributes:
            extra: Rejects unknown keys in input payloads.
            use_enum_values: Serializes enums to their 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
    characteristics: Optional[List[
        material_attribute_value_schema.IsaMaterialAttributeValueModel]] = None
    factorValues: Optional[List[factor_value_schema.IsaFactorValueModel]] = None
    derivesFrom: Optional[List[source_schema.IsaSourceModel]] = 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

derivesFrom `class-attribute` `instance-attribute`

derivesFrom: list[source_schema.IsaSourceModel] | None = None

factorValues `class-attribute` `instance-attribute`

factorValues: list[factor_value_schema.IsaFactorValueModel] | 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 sample schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects unknown keys in input payloads.
`use_enum_values`	Serializes enums to their raw values.

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

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

    Attributes:
        extra: Rejects unknown keys in input payloads.
        use_enum_values: Serializes enums to their 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

IsaSourceSchema

Bases: pyd.BaseModel


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

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


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

IsaStudyGroupSchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaStudyGroupSchema[IsaStudyGroupSchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaStudyGroupSchema
                


              click omnipy.components.isa.IsaStudyGroupSchema href "" "omnipy.components.isa.IsaStudyGroupSchema"

Schema for study groups used to organize related samples.

ATTRIBUTE	DESCRIPTION
`name`	Study group label. TYPE: `str \| None`
`factor_levels`	Factor-value assignments that define the group. TYPE: `list[factor_value_schema.IsaFactorValueModel] \| None`
`study_group_size`	Number of members in the group. TYPE: `int \| None`
`members`	Sample entries assigned to the group. TYPE: `list[sample_schema.IsaSampleModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaStudyGroupModel
- omnipy components isa models study_group IsaStudyGroupModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA study-group schema parsing.

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

class IsaStudyGroupSchema(pyd.BaseModel):
    """Schema for study groups used to organize related samples.

    Attributes:
        name: Study group label.
        factor_levels: Factor-value assignments that define the group.
        study_group_size: Number of members in the group.
        members: Sample entries assigned to the group.
    """
    class Config:
        """Validation settings for ISA study-group schema parsing.

        Attributes:
            extra: Rejects keys not declared by the schema.
            use_enum_values: Converts enum members to 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')
    name: Optional[str] = None
    factor_levels: Optional[List[factor_value_schema.IsaFactorValueModel]] = None
    study_group_size: Optional[int] = None
    members: Optional[List[sample_schema.IsaSampleModel]] = None
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

comments `class-attribute` `instance-attribute`

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

factor_levels `class-attribute` `instance-attribute`

factor_levels: list[factor_value_schema.IsaFactorValueModel] | 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')

members `class-attribute` `instance-attribute`

members: list[sample_schema.IsaSampleModel] | None = None

name `class-attribute` `instance-attribute`

name: str | None = None

study_group_size `class-attribute` `instance-attribute`

study_group_size: int | None = None

Config

Validation settings for ISA study-group schema parsing.

ATTRIBUTE	DESCRIPTION
`extra`	Rejects keys not declared by the schema.
`use_enum_values`	Converts enum members to value strings.

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

class Config:
    """Validation settings for ISA study-group schema parsing.

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

IsaStudySchema

Bases: pyd.BaseModel


              flowchart BT
              omnipy.components.isa.IsaStudySchema[IsaStudySchema]

                              omnipy.util.pydantic.BaseModel --> omnipy.components.isa.IsaStudySchema
                


              click omnipy.components.isa.IsaStudySchema href "" "omnipy.components.isa.IsaStudySchema"

Schema for study entries inside an ISA investigation.

ATTRIBUTE	DESCRIPTION
`identifier`	Stable identifier for the study. TYPE: `str \| None`
`title`	Human-readable study title. TYPE: `str \| None`
`materials`	Sources, samples, and other materials in the study. TYPE: `_Materials \| None`
`processSequence`	Ordered list of process steps. TYPE: `list[process_schema.IsaProcessOrProtocolApplicationModel] \| None`
`assays`	Assay entries defined for the study. TYPE: `list[assay_schema.IsaAssayJsonModel] \| None`
`factors`	Experimental factors used to structure comparisons. TYPE: `list[factor_schema.IsaFactorModel] \| None`

Subclassed by:

Reference Code reference
- omnipy IsaStudyModel
- omnipy components isa models study_schema IsaStudyModel

CLASS	DESCRIPTION
`Config`	Validation settings for ISA study schema parsing.

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

class IsaStudySchema(pyd.BaseModel):
    """Schema for study entries inside an ISA investigation.

    Attributes:
        identifier: Stable identifier for the study.
        title: Human-readable study title.
        materials: Sources, samples, and other materials in the study.
        processSequence: Ordered list of process steps.
        assays: Assay entries defined for the study.
        factors: Experimental factors used to structure comparisons.
    """
    class Config:
        """Validation settings for ISA study schema parsing.

        Attributes:
            extra: Rejects undeclared keys from input data.
            use_enum_values: Emits enum fields as 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')
    filename: Optional[str] = None
    identifier: Optional[str] = None
    title: Optional[str] = None
    description: Optional[str] = None
    submissionDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None
    publicReleaseDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None
    publications: Optional[List[publication_schema.IsaPublicationModel]] = None
    people: Optional[List[person_schema.IsaPersonModel]] = None
    studyDesignDescriptors: Optional[List[
        ontology_annotation_schema.IsaOntologyReferenceModel]] = None
    protocols: Optional[List[protocol_schema.IsaProtocolModel]] = None
    materials: Optional[_Materials] = None
    processSequence: Optional[List[process_schema.IsaProcessOrProtocolApplicationModel]] = None
    assays: Optional[List[assay_schema.IsaAssayJsonModel]] = None
    factors: Optional[List[factor_schema.IsaFactorModel]] = None
    characteristicCategories: Optional[List[
        material_attribute_schema.IsaMaterialAttributeModel]] = \
        pyd.Field(
            None,
            description='List of all the characteristics categories (or material attributes) '
                        'defined in the study, used to avoid duplication of their declaration '
                        'when each material_attribute_value is created. ')
    unitCategories: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]] = \
        pyd.Field(
            None,
            description='List of all the units defined in the study, used to avoid duplication '
                        'of their declaration when each value is created. ')
    comments: Optional[List[comment_schema.IsaCommentModel]] = None

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

assays `class-attribute` `instance-attribute`

assays: list[assay_schema.IsaAssayJsonModel] | None = None

characteristicCategories `class-attribute` `instance-attribute`

characteristicCategories: list[material_attribute_schema.IsaMaterialAttributeModel] | None = (
    pyd.Field(
        None,
        description="List of all the characteristics categories (or material attributes) defined in the study, used to avoid duplication of their declaration when each material_attribute_value is created. ",
    )
)

comments `class-attribute` `instance-attribute`

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

description `class-attribute` `instance-attribute`

description: str | None = None

factors `class-attribute` `instance-attribute`

factors: list[factor_schema.IsaFactorModel] | 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')

filename `class-attribute` `instance-attribute`

filename: str | None = None

identifier `class-attribute` `instance-attribute`

identifier: str | None = None

materials `class-attribute` `instance-attribute`

materials: _Materials | None = None

people `class-attribute` `instance-attribute`

people: list[person_schema.IsaPersonModel] | None = None

processSequence `class-attribute` `instance-attribute`

processSequence: list[process_schema.IsaProcessOrProtocolApplicationModel] | None = None

protocols `class-attribute` `instance-attribute`

protocols: list[protocol_schema.IsaProtocolModel] | None = None

publicReleaseDate `class-attribute` `instance-attribute`

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

publications `class-attribute` `instance-attribute`

publications: list[publication_schema.IsaPublicationModel] | None = None

studyDesignDescriptors `class-attribute` `instance-attribute`

studyDesignDescriptors: list[ontology_annotation_schema.IsaOntologyReferenceModel] | None = None

submissionDate `class-attribute` `instance-attribute`

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

title `class-attribute` `instance-attribute`

title: str | None = None

unitCategories `class-attribute` `instance-attribute`

unitCategories: list[ontology_annotation_schema.IsaOntologyReferenceModel] | None = pyd.Field(
    None,
    description="List of all the units defined in the study, used to avoid duplication of their declaration when each value is created. ",
)

Config

Validation settings for ISA study schema parsing.

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

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

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

    Attributes:
        extra: Rejects undeclared keys from input data.
        use_enum_values: Emits enum fields as 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

flatten_isa_json

flatten_isa_json(dataset: IsaJsonDataset) -> FlattenedIsaJsonDataset

Flatten ISA-JSON documents into tabular-like records.

The flow converts each ISA document to an intermediate dictionary-of-dictionaries representation, transposes that structure into record lists, and then flattens nested keys into scalar columns.

PARAMETER	DESCRIPTION
`dataset`	Dataset with ISA-JSON documents to flatten. TYPE: `IsaJsonDataset`

RETURNS	DESCRIPTION
`FlattenedIsaJsonDataset`	A dataset containing flattened ISA records suitable for tabular workflows.

Source code in src/omnipy/components/isa/flows.py

@LinearFlowTemplate(
    convert_dataset.refine(fixed_params=dict(dataset_cls=JsonDictOfDictsDataset)),
    transpose_dict_of_dicts_2_list_of_dicts,
    flatten_nested_json,
    convert_dataset.refine(fixed_params=dict(dataset_cls=FlattenedIsaJsonDataset)))
def flatten_isa_json(dataset: IsaJsonDataset) -> FlattenedIsaJsonDataset:
    """Flatten ISA-JSON documents into tabular-like records.

    The flow converts each ISA document to an intermediate dictionary-of-dictionaries
    representation, transposes that structure into record lists, and then flattens
    nested keys into scalar columns.

    Args:
        dataset: Dataset with ISA-JSON documents to flatten.

    Returns:
        A dataset containing flattened ISA records suitable for tabular workflows.
    """
    ...

omnipy.components.isa

FlattenedIsaJsonDataset

FlattenedIsaJsonModel

IsaAssayJsonSchema

characteristicCategories class-attribute instance-attribute

comments class-attribute instance-attribute

dataFiles class-attribute instance-attribute

field_context class-attribute instance-attribute

field_id class-attribute instance-attribute

field_type class-attribute instance-attribute

filename class-attribute instance-attribute

materials class-attribute instance-attribute

measurementType class-attribute instance-attribute

processSequence class-attribute instance-attribute

technologyPlatform class-attribute instance-attribute

technologyType class-attribute instance-attribute

unitCategories class-attribute instance-attribute

Config

extra class-attribute instance-attribute

use_enum_values class-attribute instance-attribute

IsaCommentSchema

field_context class-attribute instance-attribute

field_id class-attribute instance-attribute

field_type class-attribute instance-attribute

name class-attribute instance-attribute

value class-attribute instance-attribute

Config

extra class-attribute instance-attribute

use_enum_values class-attribute instance-attribute

IsaDataSchema

comments class-attribute instance-attribute

field_context class-attribute instance-attribute

field_id class-attribute instance-attribute

field_type class-attribute instance-attribute

name class-attribute instance-attribute

type class-attribute instance-attribute

Config

extra class-attribute instance-attribute

use_enum_values class-attribute instance-attribute

IsaFactorSchema

comments class-attribute instance-attribute

factorName class-attribute instance-attribute

factorType class-attribute instance-attribute

field_context class-attribute instance-attribute

field_id class-attribute instance-attribute

field_type class-attribute instance-attribute

Config

extra class-attribute instance-attribute

use_enum_values class-attribute instance-attribute

IsaFactorValueSchema

category class-attribute instance-attribute

comments class-attribute instance-attribute

field_context class-attribute instance-attribute

field_id class-attribute instance-attribute

field_type class-attribute instance-attribute

unit class-attribute instance-attribute

value class-attribute instance-attribute

Config

extra class-attribute instance-attribute

use_enum_values class-attribute instance-attribute

IsaInvestigationSchema

comments class-attribute instance-attribute

description class-attribute instance-attribute

field_context class-attribute instance-attribute

field_id class-attribute instance-attribute

field_type class-attribute instance-attribute

filename class-attribute instance-attribute

identifier class-attribute instance-attribute

ontologySourceReferences class-attribute instance-attribute

people class-attribute instance-attribute

publicReleaseDate class-attribute instance-attribute

publications class-attribute instance-attribute

studies class-attribute instance-attribute

submissionDate class-attribute instance-attribute

title class-attribute instance-attribute

Config

extra class-attribute instance-attribute

use_enum_values class-attribute instance-attribute

IsaJsonDataset

IsaJsonModel

characteristicCategories `class-attribute` `instance-attribute`

comments `class-attribute` `instance-attribute`

dataFiles `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

filename `class-attribute` `instance-attribute`

materials `class-attribute` `instance-attribute`

measurementType `class-attribute` `instance-attribute`

processSequence `class-attribute` `instance-attribute`

technologyPlatform `class-attribute` `instance-attribute`

technologyType `class-attribute` `instance-attribute`

unitCategories `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

name `class-attribute` `instance-attribute`

value `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

comments `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

name `class-attribute` `instance-attribute`

type `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

comments `class-attribute` `instance-attribute`

factorName `class-attribute` `instance-attribute`

factorType `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

category `class-attribute` `instance-attribute`

comments `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

unit `class-attribute` `instance-attribute`

value `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

comments `class-attribute` `instance-attribute`

description `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

filename `class-attribute` `instance-attribute`

identifier `class-attribute` `instance-attribute`

ontologySourceReferences `class-attribute` `instance-attribute`

people `class-attribute` `instance-attribute`

publicReleaseDate `class-attribute` `instance-attribute`

publications `class-attribute` `instance-attribute`

studies `class-attribute` `instance-attribute`

submissionDate `class-attribute` `instance-attribute`

title `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

smart_union `class-attribute` `instance-attribute`

characteristicType `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

category `class-attribute` `instance-attribute`

comments `class-attribute` `instance-attribute`

field_context `class-attribute` `instance-attribute`

field_id `class-attribute` `instance-attribute`

field_type `class-attribute` `instance-attribute`

unit `class-attribute` `instance-attribute`

value `class-attribute` `instance-attribute`

extra `class-attribute` `instance-attribute`

use_enum_values `class-attribute` `instance-attribute`

characteristics `class-attribute` `instance-attribute`