Pickle versus shelve storing large dictionaries in Python

Question

If I am storing a large directory as a pickle file, does loading it via cPickle mean that it will all be consumed into memory at once?

If s

Answer 1

If you want a module that's more robust than shelve, you might look at klepto. klepto is built to provide a dictionary interface to platform-agnostic storage on disk or database, and is built to work with large data.

Here, we first create some pickled objects stored on disk. They use the dir_archive, which stores one object per file.

>>> d = dict(zip('abcde',range(5)))
>>> d['f'] = max
>>> d['g'] = lambda x:x**2
>>> 
>>> import klepto
>>> help(klepto.archives.dir_archive)       

>>> print klepto.archives.dir_archive.__new__.__doc__
initialize a dictionary with a file-folder archive backend

    Inputs:
        name: name of the root archive directory [default: memo]
        dict: initial dictionary to seed the archive
        cached: if True, use an in-memory cache interface to the archive
        serialized: if True, pickle file contents; otherwise save python objects
        compression: compression level (0 to 9) [default: 0 (no compression)]
        memmode: access mode for files, one of {None, 'r+', 'r', 'w+', 'c'}
        memsize: approximate size (in MB) of cache for in-memory compression

>>> a = klepto.archives.dir_archive(dict=d)
>>> a
dir_archive('memo', {'a': 0, 'c': 2, 'b': 1, 'e': 4, 'd': 3, 'g': <function <lambda> at 0x102f562a8>, 'f': <built-in function max>}, cached=True)
>>> a.dump()
>>> del a

Now, the data is all on disk, let's pick and choose which ones we want to load in to memory. b is the dict in memory, while b.archive maps the collection of files into a dictionary view.

>>> b = klepto.archives.dir_archive('memo')
>>> b
dir_archive('memo', {}, cached=True)
>>> b.keys()   
[]
>>> b.archive.keys()
['a', 'c', 'b', 'e', 'd', 'g', 'f']
>>> b.load('a')
>>> b
dir_archive('memo', {'a': 0}, cached=True)
>>> b.load('b')
>>> b.load('f')
>>> b.load('g')
>>> b['g'](b['f'](b['a'],b['b']))
1

klepto also provides the same interface to a sql archive.

>>> print klepto.archives.sql_archive.__new__.__doc__
initialize a dictionary with a sql database archive backend

    Connect to an existing database, or initialize a new database, at the
    selected database url. For example, to use a sqlite database 'foo.db'
    in the current directory, database='sqlite:///foo.db'. To use a mysql
    database 'foo' on localhost, database='mysql://user:pass@localhost/foo'.
    For postgresql, use database='postgresql://user:pass@localhost/foo'. 
    When connecting to sqlite, the default database is ':memory:'; otherwise,
    the default database is 'defaultdb'. If sqlalchemy is not installed,
    storable values are limited to strings, integers, floats, and other
    basic objects. If sqlalchemy is installed, additional keyword options
    can provide database configuration, such as connection pooling.
    To use a mysql or postgresql database, sqlalchemy must be installed.

    Inputs:
        name: url for the sql database [default: (see note above)]
        dict: initial dictionary to seed the archive
        cached: if True, use an in-memory cache interface to the archive
        serialized: if True, pickle table contents; otherwise cast as strings

>>> c = klepto.archives.sql_archive('database')
>>> c.update(b)
>>> c
sql_archive('sqlite:///database', {'a': 0, 'b': 1, 'g': <function <lambda> at 0x10446b1b8>, 'f': <built-in function max>}, cached=True)
>>> c.dump()

Where now the same objects on disk are also in a sql archive. We can add new objects to either archive.

>>> b['x'] = 69
>>> c['y'] = 96
>>> b.dump('x')
>>> c.dump('y')

Get klepto here: https://github.com/uqfoundation

Answer 2

I know shelve is supposed to do this: is that as portable as pickle though?

Yes. shelve is part of The Python Standard Library and is written in Python.

Edit

So if you have a large dictionary:

bigd = {'a': 1, 'b':2, # . . .
}

And you want to save it without having to read the whole thing in later then don't save it as a pickle, it would be better to save it as a shelf, a sort of on disk dictionary.

import shelve

myShelve = shelve.open('my.shelve')
myShelve.update(bigd)
myShelve.close()

Then later you can:

import shelve

myShelve = shelve.open('my.shelve')
value = myShelve['a']
value += 1
myShelve['a'] = value

You basically treat the shelve object like a dict, but the items are stored on disk (as individual pickles) and read in as needed.

If your objects could be stored as a list of properties, then sqlite may be a good alternative. Shelves and pickles are convenient, but can only be accessed by Python, but a sqlite database can by read from most languages.