pymamba

A Fast ACID Database solution for Python

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This package has now been obsoleted in favour of Pynndb

Pynndb is built on the same base as Pymamba, and is mostly compatible, but contains numerous bugfixes and is where ongoing development will happen. https://github.com/oddjobz/pynndb

PyMamba

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PyMamba is a Python library designed to turn the LMDB storage engine into a relatively complete Database package for use in Python3 applications. In the spirit of the language title, this package is named after the fastest snake on the planet (Black Mamba) as a nod to the speed of the LMDB storage engine we’re leaning on.

The logic behind a Python only database is simply that most modern applications tend to be written in higher level languages such as Python, and access speeds when measured from the likes of ‘C’ are in context irrelevant. The driving force behind this development was my conclusion that using MySQL for web based applications is outdated, and the performance of my preferred alternative (Mongo) is really pretty poor. When I stopped to think in more depth, the Python MySQL interface leaves things to be desired, and the Mongo interface is primarily JS orientated rather than Pythonic, so definitely a gap in the market so to speak.

Anyway, without wanting to bore you, PyMamba should be noticeably faster than Mongo, and considerably ligther in terms of resource usage. (so by implication far easier to deploy and maintain)

PyMamba ORM (New!) :information_source:

There is now a native ORM style interface now available. It’s very new and there are some features that haven’t yet been implemented, so be gentle with it. There’s some initial documentation here;

Features

  • LMDB mmapped storage engine, arguably the best solution for small to medium DB’s
  • Data is mapped directly to Python objects (ujson) so you read and write dict’s
  • Transparent indexes are keyed by Python ‘expression’
  • There is no schema, DDL, query language, just Python
  • Everything is transactional with ACI[D] by default
  • LMDB provides multi-thread and multi-process access which defeats GIL limitations

Examples

This is an example of how to create a new database called my-database, then within that database to create a table called people, then to add some people. (this is all from the Python shell)

from pymamba import Database
db = Database('my-database')
people = db.table('people')
people.append({'name': 'Fred Bloggs', 'age': 21})
people.append({'name': 'Joe Smith', 'age': 22})
people.append({'name': 'John Doe', 'age': 19})

Now there are lots of different ways of recovering information from the database, the simplest is just to use find() which can be used to scan through the entire table. As find returns a generator, you can either use it within a for-loop, or use list to recover the results as a single list object.

>>> list(people.find())
[{'_id': b'58ed69161839fc5e5a57bc35', 'name': 'Fred Bloggs', 'age': 21}, {'_id': b'58ed69211839fc5e5a57bc36', 'name': 'Joe Smith', 'age': 22}, {'_id': b'58ed69301839fc5e5a57bc37', 'name': 'John Doe', 'age': 19}]

>>> for doc in people.find():
...     print(doc)
... 
{'_id': b'58ed69161839fc5e5a57bc35', 'name': 'Fred Bloggs', 'age': 21}
{'_id': b'58ed69211839fc5e5a57bc36', 'name': 'Joe Smith', 'age': 22}
{'_id': b'58ed69301839fc5e5a57bc37', 'name': 'John Doe', 'age': 19}

Note that the returned record includes an _id field, this is almost identical to the ObjectId field used by Mongo, except we’re returning a simple byte-string rather than an ObjectId class. A nice feature of dealing with data in this form when matched with Python’s new ‘format’ function is the ability to easily format this data like so;

>>> for doc in people.find():
...     print('Name: {name:20} Age:{age:3}'.format(**doc))
... 
Name: Fred Bloggs          Age: 21
Name: Joe Smith            Age: 22
Name: John Doe             Age: 19

Or if we just want a subset of the data, we can use an anonymous function to filter our results; (note that this is a linear / sequential scan with a filter)

>>> for doc in people.find(expression=lambda doc: doc['age'] > 21):
...     print('Name: {name:20} Age:{age:3}'.format(**doc))
... 
Name: Joe Smith            Age: 22

Indexing

Transparent indexes are a key part of any database system, and I struggled for a while trying to decide which mechanism to use. On the one hand I wanted the functionality of being able to index tables by compound fields and functions, and on the other I just wanted to be able to simply index based on a single clean field. In the end I settled on the following;

>>> people.index('by_name', '{name}')
>>> people.index('by_age_name', '{age:03}{name}')

If you’re really familiar with Python format strings, you’re going to see fairly quickly what’s going on here, essentially we’re indexing by expression only, but the expression comes from a Python format string when supplied with the record in dict format. So you can’t directly use a function to do anything with regards to key generation, but you can do an awful lot with the Python format mini-language. (and adding actual functions is relatively easy for anyone who can think of a must-have use-case)

So, once we have an index we can search using the index and also find records in order based on the index, so we can re-use find but this time give it an index to use;

>>> for doc in people.find('by_age_name'):
...     print('Name: {name:20} Age:{age:3}'.format(**doc))
... 
Name: John Doe             Age: 19
Name: Fred Bloggs          Age: 21
Name: Joe Smith            Age: 22

Or we can look for specific records;

>>> people.seek_one('by_name', {'name': 'Joe Smith'})
{'_id': b'58ed69211839fc5e5a57bc36', 'name': 'Joe Smith', 'age': 22}

Or we can look for a range of records;

>>> for doc in people.range('by_name', {'name': 'J'}, {'name': 'K'}):
...     print('Name: {name:20} Age:{age:3}'.format(**doc))
... 
Name: Joe Smith            Age: 22
Name: John Doe             Age: 19

Updating Records

We’ve already covered adding new records to the database, so that leaves us with updating and deleting records. How about this;

>>> person = people.seek_one('by_name', {'name': 'Joe Smith'})
>>> person['age'] += 1
>>> people.save(person)
>>> people.seek_one('by_name', {'name': 'Joe Smith'})
{'_id': b'58ed69211839fc5e5a57bc36', 'name': 'Joe Smith', 'age': 23}

And to delete;

>>> person = people.seek_one('by_name', {'name': 'Fred Bloggs'})
>>> people.delete(person['_id'])
>>> for doc in people.find():
...     print('Name: {name:20} Age:{age:3}'.format(**doc))
... 
Name: Joe Smith            Age: 23
Name: John Doe             Age: 19
>>> 

There’s a lot more to come, but so far it’s looking pretty promising. On my workstation a for-loop based on a find yields around 200k results per second, and an append yields around 30k new items per second. This seems to be fairly respectable for a high level language database and seems to be much faster than Mongo when used with either Python or Node.

** SINGLE Threaded benchmark **
** Probably better throughput with multiple processes

* No Indecies
  -     0: 5000 - Append Speed/sec = 48882
  -  5000: 5000 - Append Speed/sec = 52778
  - 10000: 5000 - Append Speed/sec = 52882
* Indexed by sid, day, hour
  -     0: 5000 - Append Speed/sec = 34420
  -  5000: 5000 - Append Speed/sec = 36096
  - 10000: 5000 - Append Speed/sec = 35885
* Indexed by function
  -     0: 5000 - Append Speed/sec = 39235
  -  5000: 5000 - Append Speed/sec = 39822
  - 10000: 5000 - Append Speed/sec = 41116
* Linear scan through most recent index
  -     0:15000 - Read Speed/sec   = 234615

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