allensdk.brain_observatory.argschema_utilities module

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

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: ~typing.Callable[[~typing.Any], ~typing.Any] | ~typing.Iterable[~typing.Callable[[~typing.Any], ~typing.Any]] | None = 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)[source]

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: ~typing.Callable[[~typing.Any], ~typing.Any] | ~typing.Iterable[~typing.Callable[[~typing.Any], ~typing.Any]] | None = 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)[source]

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: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool | None = None, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)[source]

Bases: DefaultSchema

class Meta[source]

Bases: object

unknown = 'raise'
opts: Any = <marshmallow.schema.SchemaOpts object>
allensdk.brain_observatory.argschema_utilities.check_read_access(path)[source]
allensdk.brain_observatory.argschema_utilities.check_write_access(filepath, allow_exists=False)[source]
allensdk.brain_observatory.argschema_utilities.check_write_access_dir(dirpath)[source]
allensdk.brain_observatory.argschema_utilities.check_write_access_overwrite(path)[source]
allensdk.brain_observatory.argschema_utilities.optional_lims_inputs(argv, input_schema, output_schema, lims_input_getter)[source]
allensdk.brain_observatory.argschema_utilities.write_or_print_outputs(data, parser)[source]