allensdk.brain_observatory.argschema_utilities module

class allensdk.brain_observatory.argschema_utilities.ArgSchemaParserPlus(*args, **kwargs)

Bases: ArgSchemaParser

class allensdk.brain_observatory.argschema_utilities.InputFile(*, load_default: typing.Any = <marshmallow.missing>, missing: typing.Any = <marshmallow.missing>, dump_default: typing.Any = <marshmallow.missing>, default: typing.Any = <marshmallow.missing>, data_key: str | None = None, attribute: str | None = None, validate: None | typing.Callable[[typing.Any], typing.Any] | typing.Iterable[typing.Callable[[typing.Any], typing.Any]] = None, required: bool = False, allow_none: bool | None = None, load_only: bool = False, dump_only: bool = False, error_messages: dict[str, str] | None = None, metadata: typing.Mapping[str, typing.Any] | None = None, **additional_metadata)

Bases: String

A marshmallow String field subclass which deserializes json str fields that represent a desired input path to pathlib.Path. Also performs read access checking.

class allensdk.brain_observatory.argschema_utilities.OutputFile(*, load_default: typing.Any = <marshmallow.missing>, missing: typing.Any = <marshmallow.missing>, dump_default: typing.Any = <marshmallow.missing>, default: typing.Any = <marshmallow.missing>, data_key: str | None = None, attribute: str | None = None, validate: None | typing.Callable[[typing.Any], typing.Any] | typing.Iterable[typing.Callable[[typing.Any], typing.Any]] = None, required: bool = False, allow_none: bool | None = None, load_only: bool = False, dump_only: bool = False, error_messages: dict[str, str] | None = None, metadata: typing.Mapping[str, typing.Any] | None = None, **additional_metadata)

Bases: String

A marshmallow String field subclass which deserializes json str fields that represent a desired output file path to a pathlib.Path. Also performs write access checking.

class allensdk.brain_observatory.argschema_utilities.RaisingSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: DefaultSchema

class Meta

Bases: object

unknown = 'raise'

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

allensdk.brain_observatory.argschema_utilities.check_read_access(path)

allensdk.brain_observatory.argschema_utilities.check_write_access(filepath, allow_exists=False)

allensdk.brain_observatory.argschema_utilities.check_write_access_dir(dirpath)

allensdk.brain_observatory.argschema_utilities.check_write_access_overwrite(path)

allensdk.brain_observatory.argschema_utilities.optional_lims_inputs(argv, input_schema, output_schema, lims_input_getter)

allensdk.brain_observatory.argschema_utilities.write_or_print_outputs(data, parser)