allensdk.brain_observatory.argschema_utilities module

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

Bases: argschema.argschema_parser.ArgSchemaParser

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

Bases: marshmallow.fields.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: Any = <marshmallow.missing>, missing: Any = <marshmallow.missing>, dump_default: Any = <marshmallow.missing>, default: Any = <marshmallow.missing>, data_key: Optional[str] = None, attribute: Optional[str] = None, validate: Union[Callable[[Any], Any], Iterable[Callable[[Any], Any]], None] = None, required: bool = False, allow_none: Optional[bool] = None, load_only: bool = False, dump_only: bool = False, error_messages: Optional[Dict[str, str]] = None, metadata: Optional[Mapping[str, Any]] = None, **additional_metadata)

Bases: marshmallow.fields.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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)

Bases: argschema.schemas.DefaultSchema

class Meta

Bases: object

unknown = 'raise'

opts = <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)