omnipy.components.isa.models.study_schema

CLASS	DESCRIPTION
FieldType
IsaStudyModel
IsaStudySchema

FieldType

Bases: Enum

ATTRIBUTE	DESCRIPTION
Study

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

class FieldType(Enum):
    Study = 'Study'

Study class-attribute instance-attribute

Study = 'Study'

IsaStudyModel

Bases: Model[IsaStudySchema]

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

class IsaStudyModel(Model[IsaStudySchema]):
    ...

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