allensdk.config.manifest module

class allensdk.config.manifest.Manifest(config=None, relative_base_dir='.', version=None)

Bases: object

Manages the location of external files referenced in an Allen SDK configuration

DIR = 'dir'

DIRNAME = 'dir_name'

FILE = 'file'

VERSION = 'manifest_version'

add_file(file_key, file_name, dir_key=None, path_format=None)

Insert a new file entry.

Parameters:

file_key : string

Reference to the entry.

file_name : string

Subtitutions of the %s, %d style allowed.

dir_key : string

Reference to the parent directory entry.

path_format : string, optional

File type for further parsing.

add_path(key, path, path_type='dir', absolute=True, path_format=None, parent_key=None)

Insert a new entry.

Parameters:

key : string

Identifier for referencing the entry.

path : string

Specification for a path using %s, %d style substitution.

path_type : string enumeration

‘dir’ (default) or ‘file’

absolute : boolean

Is the spec relative to the process current directory.

path_format : string, optional

Indicate a known file type for further parsing.

parent_key : string

Refer to another entry.

add_paths(path_info)

add information about paths stored in the manifest.

Parameters

path_info : dict

Information about the new paths

as_dataframe()

check_dir(path_key, do_exit=False)

Verify a directories existence or optionally exit.

Parameters:

path_key : string

Reference to the entry.

do_exit : boolean

What to do if the directory is not present.

create_dir(path_key)

Make a directory for an entry.

Parameters:

path_key : string

Reference to the entry.

get_format(path_key)

Retrieve the type of a path entry.

Parameters:

path_key : string

reference to the entry

Returns:

string

File type.

get_path(path_key, *args)

Retrieve an entry with substitutions.

Parameters:

path_key : string

Refer to the entry to retrieve.

args : any types, optional

arguments to be substituted into the path spec for %s, %d, etc.

Returns:

string

Path with parent structure and substitutions applied.

load_config(config, version=None)

Load paths into the manifest from an Allen SDK config section.

Parameters:

config : Config

Manifest section of an Allen SDK config.

log = <logging.Logger object>

resolve_paths(description_dict, suffix='_key')

Walk input items and expand those that refer to a manifest entry.

Parameters:

description_dict : dict

Any entries with key names ending in suffix will be expanded.

suffix : string

Indicates the entries to be expanded.

classmethod safe_make_parent_dirs(file_name)

Create a parent directories for file.

Parameters:

file_name : string

classmethod safe_mkdir(directory)

Create path if not already there.

Parameters:

directory : string

create it if it doesn’t exist

exception allensdk.config.manifest.ManifestVersionError(message, version, found_version)

Bases: exceptions.Exception