omnipy.components.isa

MODULE	DESCRIPTION
datasets
flows
models

CLASS	DESCRIPTION
FlattenedIsaJsonDataset
FlattenedIsaJsonModel
IsaAssayJsonSchema
IsaCommentSchema
IsaDataSchema
IsaFactorSchema
IsaFactorValueSchema
IsaInvestigationSchema
IsaJsonDataset
IsaJsonModel
IsaMaterialAttributeSchema
IsaMaterialAttributeValueSchema
IsaMaterialSchema
IsaOntologyReferenceSchema
IsaOntologySourceReferenceSchema
IsaOrganizationSchema
IsaPersonSchema
IsaProcessOrProtocolApplicationSchema
IsaProcessParameterValueSchema
IsaProtocolParameterSchema
IsaProtocolSchema
IsaPublicationSchema
IsaSampleSchema
IsaSourceSchema
IsaStudyGroupSchema
IsaStudySchema

FUNCTION	DESCRIPTION
flatten_isa_json

FlattenedIsaJsonDataset

Bases: Dataset[FlattenedIsaJsonModel]

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

class FlattenedIsaJsonDataset(Dataset[FlattenedIsaJsonModel]):
    ...

FlattenedIsaJsonModel

Bases: Model[JsonListOfDictsOfScalarsModel]

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

class FlattenedIsaJsonModel(Model[JsonListOfDictsOfScalarsModel]):
    ...

IsaAssayJsonSchema

Bases: pyd.BaseModel

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
characteristicCategories	TYPE: Optional[List[material_attribute_schema.IsaMaterialAttributeModel]]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
dataFiles	TYPE: Optional[List[data_schema.IsaDataModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
filename	TYPE: Optional[str]
materials	TYPE: Optional[_MaterialsModel]
measurementType	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
processSequence	TYPE: Optional[List[process_schema.IsaProcessOrProtocolApplicationModel]]
technologyPlatform	TYPE: Optional[str]
technologyType	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
unitCategories	TYPE: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]]

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

class IsaAssayJsonSchema(pyd.BaseModel):
    class Config:
        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: 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. ",
    )
)

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

dataFiles class-attribute instance-attribute

dataFiles: Optional[List[data_schema.IsaDataModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

filename class-attribute instance-attribute

filename: Optional[str] = None

materials class-attribute instance-attribute

materials: Optional[_MaterialsModel] = None

measurementType class-attribute instance-attribute

measurementType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

processSequence class-attribute instance-attribute

processSequence: Optional[List[process_schema.IsaProcessOrProtocolApplicationModel]] = None

technologyPlatform class-attribute instance-attribute

technologyPlatform: Optional[str] = None

technologyType class-attribute instance-attribute

technologyType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

unitCategories class-attribute instance-attribute

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. ",
)

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]
value	TYPE: Optional[str]

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

class IsaCommentSchema(pyd.BaseModel):
    class Config:
        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: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

value class-attribute instance-attribute

value: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]
type	TYPE: Optional[Type]

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

class IsaDataSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

type class-attribute instance-attribute

type: Optional[Type] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
factorName	TYPE: Optional[str]
factorType	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]

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

class IsaFactorSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

factorName class-attribute instance-attribute

factorName: Optional[str] = None

factorType class-attribute instance-attribute

factorType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
category	TYPE: Optional[factor_schema.IsaFactorModel]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
unit	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
value	TYPE: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]]

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

class IsaFactorValueSchema(pyd.BaseModel):
    class Config:
        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: Optional[factor_schema.IsaFactorModel] = None

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

unit class-attribute instance-attribute

unit: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

value class-attribute instance-attribute

value: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
description	TYPE: Optional[str]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
filename	TYPE: Optional[str]
identifier	TYPE: Optional[str]
ontologySourceReferences	TYPE: Optional[List[ontology_source_reference_schema.IsaOntologySourceReferenceModel]]
people	TYPE: Optional[List[person_schema.IsaPersonModel]]
publicReleaseDate	TYPE: Optional[Union[datetime, date, pyd.constr(max_length=0)]]
publications	TYPE: Optional[List[publication_schema.IsaPublicationModel]]
studies	TYPE: Optional[List[study_schema.IsaStudyModel]]
submissionDate	TYPE: Optional[Union[datetime, date, pyd.constr(max_length=0)]]
title	TYPE: Optional[str]

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

class IsaInvestigationSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

description class-attribute instance-attribute

description: Optional[str] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

filename class-attribute instance-attribute

filename: Optional[str] = None

identifier class-attribute instance-attribute

identifier: Optional[str] = None

ontologySourceReferences class-attribute instance-attribute

ontologySourceReferences: Optional[
    List[ontology_source_reference_schema.IsaOntologySourceReferenceModel]
] = None

people class-attribute instance-attribute

people: Optional[List[person_schema.IsaPersonModel]] = None

publicReleaseDate class-attribute instance-attribute

publicReleaseDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None

publications class-attribute instance-attribute

publications: Optional[List[publication_schema.IsaPublicationModel]] = None

studies class-attribute instance-attribute

studies: Optional[List[study_schema.IsaStudyModel]] = None

submissionDate class-attribute instance-attribute

submissionDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None

title class-attribute instance-attribute

title: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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]

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

class IsaJsonDataset(Dataset[IsaJsonModel]):
    ...

IsaJsonModel

Bases: Model[IsaInvestigationSchema | IsaTopLevelModel]

CLASS	DESCRIPTION
Config

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

class IsaJsonModel(Model[IsaInvestigationSchema | IsaTopLevelModel]):
    class Config:
        smart_union = False

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

Config

ATTRIBUTE	DESCRIPTION
smart_union

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

class Config:
    smart_union = False

smart_union class-attribute instance-attribute

smart_union = False

IsaMaterialAttributeSchema

Bases: pyd.BaseModel

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
characteristicType	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]

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

class IsaMaterialAttributeSchema(pyd.BaseModel):
    class Config:
        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: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
category	TYPE: Optional[material_attribute_schema.IsaMaterialAttributeModel]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
unit	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
value	TYPE: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]]

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

class IsaMaterialAttributeValueSchema(pyd.BaseModel):
    class Config:
        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: Optional[material_attribute_schema.IsaMaterialAttributeModel] = None

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

unit class-attribute instance-attribute

unit: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

value class-attribute instance-attribute

value: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
characteristics	TYPE: Optional[List[material_attribute_value_schema.IsaMaterialAttributeValueModel]]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
derivesFrom	TYPE: Optional[List[IsaMaterialModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]
type	TYPE: Optional[Type]

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

class IsaMaterialSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[material_attribute_value_schema.IsaMaterialAttributeValueModel]] = (
    None
)

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

derivesFrom class-attribute instance-attribute

derivesFrom: Optional[List[IsaMaterialModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

type class-attribute instance-attribute

type: Optional[Type] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
annotationValue	TYPE: Optional[Union[str, float]]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
termAccession	TYPE: Optional[str]
termSource	TYPE: Optional[str]

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

class IsaOntologyReferenceSchema(pyd.BaseModel):
    class Config:
        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: Optional[Union[str, float]] = None

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

termAccession class-attribute instance-attribute

termAccession: Optional[str] = None

termSource class-attribute instance-attribute

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.",
)

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
description	TYPE: Optional[str]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
file	TYPE: Optional[str]
name	TYPE: Optional[str]
version	TYPE: Optional[str]

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

class IsaOntologySourceReferenceSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

description class-attribute instance-attribute

description: Optional[str] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

file class-attribute instance-attribute

file: Optional[str] = None

name class-attribute instance-attribute

name: Optional[str] = None

version class-attribute instance-attribute

version: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]

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

class IsaOrganizationSchema(pyd.BaseModel):
    class Config:
        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: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
address	TYPE: Optional[str]
affiliation	TYPE: Optional[str]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
email	TYPE: Optional[pyd.EmailStr]
fax	TYPE: Optional[str]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
firstName	TYPE: Optional[str]
lastName	TYPE: Optional[str]
midInitials	TYPE: Optional[str]
phone	TYPE: Optional[str]
roles	TYPE: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]]

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

class IsaPersonSchema(pyd.BaseModel):
    class Config:
        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: Optional[str] = None

affiliation class-attribute instance-attribute

affiliation: Optional[str] = None

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

email class-attribute instance-attribute

email: Optional[pyd.EmailStr] = None

fax class-attribute instance-attribute

fax: Optional[str] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

firstName class-attribute instance-attribute

firstName: Optional[str] = None

lastName class-attribute instance-attribute

lastName: Optional[str] = None

midInitials class-attribute instance-attribute

midInitials: Optional[str] = None

phone class-attribute instance-attribute

phone: Optional[str] = None

roles class-attribute instance-attribute

roles: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
date	TYPE: Optional[Union[datetime, date, pyd.constr(max_length=0)]]
executesProtocol	TYPE: Optional[protocol_schema.IsaProtocolModel]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
inputs	TYPE: Optional[List[Union[source_schema.IsaSourceModel, sample_schema.IsaSampleModel, data_schema.IsaDataModel, material_schema.IsaMaterialModel]]]
name	TYPE: Optional[str]
nextProcess	TYPE: Optional[IsaProcessOrProtocolApplicationModel]
outputs	TYPE: Optional[List[Union[sample_schema.IsaSampleModel, data_schema.IsaDataModel, material_schema.IsaMaterialModel]]]
parameterValues	TYPE: Optional[List[process_parameter_value_schema.IsaProcessParameterValueModel]]
performer	TYPE: Optional[str]
previousProcess	TYPE: Optional[IsaProcessOrProtocolApplicationModel]

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

class IsaProcessOrProtocolApplicationSchema(pyd.BaseModel):
    class Config:
        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, 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: Optional[List[comment_schema.IsaCommentModel]] = None

date class-attribute instance-attribute

date: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None

executesProtocol class-attribute instance-attribute

executesProtocol: Optional[protocol_schema.IsaProtocolModel] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

inputs class-attribute instance-attribute

inputs: Optional[
    List[
        Union[
            source_schema.IsaSourceModel,
            sample_schema.IsaSampleModel,
            data_schema.IsaDataModel,
            material_schema.IsaMaterialModel,
        ]
    ]
] = None

name class-attribute instance-attribute

name: Optional[str] = None

nextProcess class-attribute instance-attribute

nextProcess: Optional[IsaProcessOrProtocolApplicationModel] = None

outputs class-attribute instance-attribute

outputs: Optional[
    List[
        Union[
            sample_schema.IsaSampleModel, data_schema.IsaDataModel, material_schema.IsaMaterialModel
        ]
    ]
] = None

parameterValues class-attribute instance-attribute

parameterValues: Optional[List[process_parameter_value_schema.IsaProcessParameterValueModel]] = None

performer class-attribute instance-attribute

performer: Optional[str] = None

previousProcess class-attribute instance-attribute

previousProcess: Optional[IsaProcessOrProtocolApplicationModel] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
category	TYPE: Optional[protocol_parameter_schema.IsaProtocolParameterModel]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
unit	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
value	TYPE: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]]

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

class IsaProcessParameterValueSchema(pyd.BaseModel):
    class Config:
        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: Optional[protocol_parameter_schema.IsaProtocolParameterModel] = None

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

unit class-attribute instance-attribute

unit: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

value class-attribute instance-attribute

value: Optional[Union[ontology_annotation_schema.IsaOntologyReferenceModel, str, float]] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
parameterName	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]

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

class IsaProtocolParameterSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

parameterName class-attribute instance-attribute

parameterName: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
components	TYPE: Optional[List[Component]]
description	TYPE: Optional[str]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]
parameters	TYPE: Optional[List[protocol_parameter_schema.IsaProtocolParameterModel]]
protocolType	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
uri	TYPE: Optional[str]
version	TYPE: Optional[str]

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

class IsaProtocolSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

components class-attribute instance-attribute

components: Optional[List[Component]] = None

description class-attribute instance-attribute

description: Optional[str] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

parameters class-attribute instance-attribute

parameters: Optional[List[protocol_parameter_schema.IsaProtocolParameterModel]] = None

protocolType class-attribute instance-attribute

protocolType: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

uri class-attribute instance-attribute

uri: Optional[str] = None

version class-attribute instance-attribute

version: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
authorList	TYPE: Optional[str]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
doi	TYPE: Optional[str]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
pubMedID	TYPE: Optional[str]
status	TYPE: Optional[ontology_annotation_schema.IsaOntologyReferenceModel]
title	TYPE: Optional[str]

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

class IsaPublicationSchema(pyd.BaseModel):
    class Config:
        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: Optional[str] = None

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

doi class-attribute instance-attribute

doi: Optional[str] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

pubMedID class-attribute instance-attribute

pubMedID: Optional[str] = None

status class-attribute instance-attribute

status: Optional[ontology_annotation_schema.IsaOntologyReferenceModel] = None

title class-attribute instance-attribute

title: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
characteristics	TYPE: Optional[List[material_attribute_value_schema.IsaMaterialAttributeValueModel]]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
derivesFrom	TYPE: Optional[List[source_schema.IsaSourceModel]]
factorValues	TYPE: Optional[List[factor_value_schema.IsaFactorValueModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]

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

class IsaSampleSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[material_attribute_value_schema.IsaMaterialAttributeValueModel]] = (
    None
)

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

derivesFrom class-attribute instance-attribute

derivesFrom: Optional[List[source_schema.IsaSourceModel]] = None

factorValues class-attribute instance-attribute

factorValues: Optional[List[factor_value_schema.IsaFactorValueModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
characteristics	TYPE: Optional[List[material_attribute_value_schema.IsaMaterialAttributeValueModel]]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
name	TYPE: Optional[str]

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

class IsaSourceSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[material_attribute_value_schema.IsaMaterialAttributeValueModel]] = (
    None
)

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

name class-attribute instance-attribute

name: Optional[str] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
factor_levels	TYPE: Optional[List[factor_value_schema.IsaFactorValueModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
members	TYPE: Optional[List[sample_schema.IsaSampleModel]]
name	TYPE: Optional[str]
study_group_size	TYPE: Optional[int]

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

class IsaStudyGroupSchema(pyd.BaseModel):
    class Config:
        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: Optional[List[comment_schema.IsaCommentModel]] = None

factor_levels class-attribute instance-attribute

factor_levels: Optional[List[factor_value_schema.IsaFactorValueModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

members class-attribute instance-attribute

members: Optional[List[sample_schema.IsaSampleModel]] = None

name class-attribute instance-attribute

name: Optional[str] = None

study_group_size class-attribute instance-attribute

study_group_size: Optional[int] = None

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

CLASS	DESCRIPTION
Config

ATTRIBUTE	DESCRIPTION
assays	TYPE: Optional[List[assay_schema.IsaAssayJsonModel]]
characteristicCategories	TYPE: Optional[List[material_attribute_schema.IsaMaterialAttributeModel]]
comments	TYPE: Optional[List[comment_schema.IsaCommentModel]]
description	TYPE: Optional[str]
factors	TYPE: Optional[List[factor_schema.IsaFactorModel]]
field_context	TYPE: Optional[str]
field_id	TYPE: Optional[str]
field_type	TYPE: Optional[FieldType]
filename	TYPE: Optional[str]
identifier	TYPE: Optional[str]
materials	TYPE: Optional[_Materials]
people	TYPE: Optional[List[person_schema.IsaPersonModel]]
processSequence	TYPE: Optional[List[process_schema.IsaProcessOrProtocolApplicationModel]]
protocols	TYPE: Optional[List[protocol_schema.IsaProtocolModel]]
publicReleaseDate	TYPE: Optional[Union[datetime, date, pyd.constr(max_length=0)]]
publications	TYPE: Optional[List[publication_schema.IsaPublicationModel]]
studyDesignDescriptors	TYPE: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]]
submissionDate	TYPE: Optional[Union[datetime, date, pyd.constr(max_length=0)]]
title	TYPE: Optional[str]
unitCategories	TYPE: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]]

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

class IsaStudySchema(pyd.BaseModel):
    class Config:
        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: Optional[List[assay_schema.IsaAssayJsonModel]] = None

characteristicCategories class-attribute instance-attribute

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. ",
    )
)

comments class-attribute instance-attribute

comments: Optional[List[comment_schema.IsaCommentModel]] = None

description class-attribute instance-attribute

description: Optional[str] = None

factors class-attribute instance-attribute

factors: Optional[List[factor_schema.IsaFactorModel]] = None

field_context class-attribute instance-attribute

field_context: Optional[str] = pyd.Field(None, alias='@context')

field_id class-attribute instance-attribute

field_id: Optional[str] = pyd.Field(None, alias='@id')

field_type class-attribute instance-attribute

field_type: Optional[FieldType] = pyd.Field(None, alias='@type')

filename class-attribute instance-attribute

filename: Optional[str] = None

identifier class-attribute instance-attribute

identifier: Optional[str] = None

materials class-attribute instance-attribute

materials: Optional[_Materials] = None

people class-attribute instance-attribute

people: Optional[List[person_schema.IsaPersonModel]] = None

processSequence class-attribute instance-attribute

processSequence: Optional[List[process_schema.IsaProcessOrProtocolApplicationModel]] = None

protocols class-attribute instance-attribute

protocols: Optional[List[protocol_schema.IsaProtocolModel]] = None

publicReleaseDate class-attribute instance-attribute

publicReleaseDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None

publications class-attribute instance-attribute

publications: Optional[List[publication_schema.IsaPublicationModel]] = None

studyDesignDescriptors class-attribute instance-attribute

studyDesignDescriptors: Optional[List[ontology_annotation_schema.IsaOntologyReferenceModel]] = None

submissionDate class-attribute instance-attribute

submissionDate: Optional[Union[datetime, date, pyd.constr(max_length=0)]] = None

title class-attribute instance-attribute

title: Optional[str] = None

unitCategories class-attribute instance-attribute

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. ",
)

Config

ATTRIBUTE	DESCRIPTION
extra
use_enum_values

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

class Config:
    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

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:
    ...