allensdk.api.cache module

class allensdk.api.cache.Cache(manifest=None, cache=True, version=None, **kwargs)

Bases: object

add_manifest_paths(manifest_builder)

Add cache-class specific paths to the manifest. In derived classes, should call super.

build_manifest(file_name)

Creation of default path specifications.

Parameters:

file_name : string

where to save it

static cache_csv()

static cache_csv_dataframe()

static cache_csv_json()

static cache_json()

static cache_json_dataframe()

static cacher(fn, *args, **kwargs)

make an rma query, save it and return the dataframe.

Parameters:

fn : function reference

makes the actual query using kwargs.

path : string

where to save the data

strategy : string or None, optional

‘create’ always generates the data, ‘file’ loads from disk, ‘lazy’ queries the server if no file exists, None generates the data and bypasses all caching behavior

pre : function

df|json->df|json, takes one data argument and returns filtered version, None for pass-through

post : function

df|json->?, takes one data argument and returns Object

reader : function, optional

path -> data, default NOP

writer : function, optional

path, data -> None, default NOP

kwargs : objects

passed through to the query function

Returns:

Object or None

data type depends on fn, reader and/or post methods.

static csv_writer(pth, gen)

get_cache_path(file_name, manifest_key, *args)

Helper method for accessing path specs from manifest keys.

Parameters:

file_name : string

manifest_key : string

args : ordered parameters

Returns:

string or None

path

static json_remove_keys(data, keys)

static json_rename_columns(data, new_old_name_tuples=None)

Convenience method to rename columns in a pandas dataframe.

Parameters:

data : dataframe

edited in place.

new_old_name_tuples : list of string tuples (new, old)

load_csv(path, rename=None, index=None)

Read a csv file as a pandas dataframe.

Parameters:

rename : list of string tuples (new old), optional

columns to rename

index : string, optional

post-rename column to use as the row label.

load_json(path, rename=None, index=None)

Read a json file as a pandas dataframe.

Parameters:

rename : list of string tuples (new old), optional

columns to rename

index : string, optional

post-rename column to use as the row label.

load_manifest(file_name, version=None)

Read a keyed collection of path specifications.

Parameters:

file_name : string

path to the manifest file

Returns:

Manifest

manifest_dataframe()

Convenience method to view manifest as a pandas dataframe.

static nocache_dataframe()

static nocache_json()

static pathfinder(file_name_position, secondary_file_name_position=None, path_keyword=None)

helper method to find path argument in legacy methods written prior to the @cacheable decorator. Do not use for new @cacheable methods.

Parameters:

file_name_position : integer

zero indexed position in the decorated method args where file path may be found.

secondary_file_name_position : integer

zero indexed position in the decorated method args where tha file path may be found.

path_keyword : string

kwarg that may have the file path.

Notes

This method is only intended to provide backward-compatibility for some methods that otherwise do not follow the path conventions of the @cacheable decorator.

static remove_keys(data, keys=None)

DataFrame version

static rename_columns(data, new_old_name_tuples=None)

Convenience method to rename columns in a pandas dataframe.

Parameters:

data : dataframe

edited in place.

new_old_name_tuples : list of string tuples (new, old)

wrap(**kwargs)

make an rma query, save it and return the dataframe.

Parameters:

fn : function reference

makes the actual query using kwargs.

path : string

where to save the data

cache : boolean

True will make the query, False just loads from disk

save_as_json : boolean, optional

True (default) will save data as json, False as csv

return_dataframe : boolean, optional

True will cast the return value to a pandas dataframe, False (default) will not

index : string, optional

column to use as the pandas index

rename : list of string tuples, optional

(new, old) columns to rename

kwargs : objects

passed through to the query function

Returns:

dict or DataFrame

data type depends on return_dataframe option.

Notes

Column renaming happens after the file is reloaded for json

allensdk.api.cache.cacheable(strategy=None, pre=None, writer=None, reader=None, post=None, pathfinder=None)

decorator for rma queries, save it and return the dataframe.

Parameters:

fn : function reference

makes the actual query using kwargs.

path : string

where to save the data

strategy : string or None, optional

‘create’ always gets the data from the source (server or generated), ‘file’ loads from disk, ‘lazy’ creates the data and saves to file if no file exists, None queries the server and bypasses all caching behavior

pre : function

df|json->df|json, takes one data argument and returns filtered version, None for pass-through

post : function

df|json->?, takes one data argument and returns Object

reader : function, optional

path -> data, default NOP

writer : function, optional

path, data -> None, default NOP

kwargs : objects

passed through to the query function

Returns:

dict or DataFrame

data type depends on dataframe option.

Notes

Column renaming happens after the file is reloaded for json

allensdk.api.cache.memoize(f)