pyahocorasick 1.1.1

========================================================================
pyahocorasick
========================================================================

.. contents::


Introduction
============

With an **Aho-Corasick automaton** you can efficiently search all occurences of
multiple strings (the needles) in an input string (the haystack) making a single
pass over the input string. With pyahocorasick you can eventually build large
automatons and pickle them and reuse them over and over as an index structure
for fast multi pattern string matching.

One of the advantage of an Aho-Corasick automaton is that the typical worst-case
and best-case **runtimes** are about the same and depends primarily on the size
of the input string and secondarily on the number of matches returned. While
this may not be the fastest string search algorithm in all cases, it can search
for multiple strings at once and its runtime guarantees make it rather unique.
Because pyahocorasick is based on a Trie, it stores redundant keys prefixes only
once using memory efficiently.

A drawback is that it needs to be constructed and "finalized" ahead of time
before you can search strings. In several applicatiosn where you search several
pre-defined "needles" in variable "haystacks" this is actually an advantage.

**Aho-Corasick automatons** are commonly used for fast multi-pattern matching
in intrusion detection systems (such as snort), anti-viruses and many other
applications that need fast matching against a pre-defined set of string keys.

Internally an Aho-Corasick automaton is typically based on a Trie with extra
data for failure links and an implementation of the Aho-Corasick search
procedure.

Behind the scenes the **pyahocorasick** Python library implements these two data
structures: a `Trie`__ and an `Aho-Corasick string matching automaton`__. Both
are exposed through the `Automaton` class.

In addition to Trie-like and Aho-Corasick methods and data structures,
**pyahocorasick** also implements dict-like methods: The pyahocorasick
**Automaton** is a **Trie** a dict-like structure indexed by string keys each
associated with a value object. You can use this to retrieve an associated value
in a time proportional to a string key length.

__ http://en.wikipedia.org/wiki/trie
__ http://en.wikipedia.org/wiki/Aho-Corasick%20algorithm


pyahocorasick is available in two flavors:

* a CPython **C-based extension**, compatible with Python 2 and 3.

* a simpler pure Python module, compatible with Python 2 and 3. This is only
available in the source repository (not on Pypi) under the py/ directory and
it has a slightly different API.


Some background about pyahocorasick internals
=============================================

* I wrote this article about `different trie representations`__
--- These are experiments I made while creating this module.

__ http://0x80.pl/articles/trie-representation.html


Other Aho-Corarisk implementations for Python you can consider
==============================================================

While **pyahocorasick** tries to be the finest and fastest Aho Corasick library
for Python you may consider these other libraries:

* `noaho`__ by Jeff Donner --- Written in C. Does not return overlapping matches.
Does not compile on Windows (July 2016). No support for the pickle protocol.

* `acora`__ by Stefan Behnel --- Written in Cython. Large automaton may take a
long time to build (July 2016) No support for a dict-like protocol to
associate a value to a string key.

* `ahocorasick`__ by Danny Yoo --- seems unmaintained (last update in 2005) and
is GPL-licensed. Written in C.

__ https://github.com/JDonner/NoAho
__ https://github.com/scoder/acora
__ https://hkn.eecs.berkeley.edu/~dyoo/python/ahocorasick/


API overview
============

This is the API for the C **ahocorasick** module. The pure Python module has a
slightly different interface.

Module
------

The module ``ahocorasick`` contains a few constants and the main ``Automaton`` class.


.. _Unicode and bytes:


Constants
~~~~~~~~~

* ``ahocorasick.unicode`` --- see `Unicode and bytes`_

* ``ahocorasick.STORE_ANY``, ``ahocorasick.STORE_INTS``,
``ahocorasick.STORE_LENGTH`` --- see Constructor_

* ``ahocorasick.EMPTY``, ``ahocorasick.TRIE``, ``ahocorasick.AHOCORASICK``
--- see Attributes_

* ``ahocorasick.MATCH_EXACT_LENGTH``, ``ahocorasick.MATCH_AT_MOST_PREFIX``,
``ahocorasick.MATCH_AT_LEAST_PREFIX`` --- see description of the keys_ method


Automaton class
~~~~~~~~~~~~~~~

Note: ``Automaton`` instances are pickable__ (It implements the ``__reduce__() magic method``).

__ http://docs.python.org/py3k/library/pickle.html


Constructor
###########

`Automaton(value_type)`
Create a new empty Automaton. value_type is optional and one of these constants:

``ahocorasick.STORE_ANY``
Any Python object can be stored as a value associated to a string key (default).

``ahocorasick.STORE_LENGTH``
The length of the a string key is automatically added to the trie as the
associated value for a string key.

``ahocorasick.STORE_INTS``
A 32-bit integer is used for the associated values.


Trie methods
############

The Automaton class has the following trie methods:

``add_word(key, [value]) => bool``
Add a ``key`` string to the dict-like trie and associate this key with a
``value``. ``value`` is optional or mandatory depending how the Automaton
instance was created.
Return True if the ``word`` key is inserted and did not exists in the trie
or False otherwise.

If the Automaton was created without argument (the default) as
``Automaton()`` or with ``Automaton(ahocorasik.STORE_ANY)`` then the
``value`` is required and can be any Python object.

If the Automaton was created with ``Automaton(ahocorasik.STORE_LENGTH)``
then associating a ``value`` is not allowed --- ``len(word)`` is saved
automatically as a value instead.

If the Automaton was created with ``Automaton(ahocorasik.STORE_INTS)`` then
the ``value``is optional. If provided it must be an integer, otherwise it
defaults to ``len(automaton)`` which is therefore the order index in which
keys are added to the trie.

**Calling ``add_word`` invalidates all iterators only if the new key did not
exist in the trie so far (i.e. the method returned True).**

``clear() => None``
Remove all keys from the trie.

**This method invalidates all iterators.**

``exists(key) => bool`` or ``key in ...``
Return True if the key is present in the trie. Same as using the 'in' keyword.

``match(key) => bool``
Return True if there is a prefix (or key) equal to ``key`` present in the
trie. For example if the key 'example' has been added to the trie, then
calling ``match('e')``, ``match('ex')``, ..., ``match('exampl')``,
or ``match('example')`` all return True. But ``exists()`` is True only when
calling ``exists('example')``

``longest_prefix(string) => integer``
Return the length of the longest prefix of string that exists in the trie.


Dictionary-like methods
#######################

A pyahocorasick trie behaves more or less like a Python dictionary and
implements a subset of dict-like methods.

``get(key[, default])``
Return the value associated with the ``key`` string.
Raise a ``KeyError`` exception if the key is not in the trie and no default is provided.
Return the optional ``default`` value if provided and the key is not in the trie.

.. _keys:

``keys([prefix, [wildcard, [how]]]) => yield strings``
Return an iterator on keys.

If the optional ``prefix`` string is provided, then only keys starting with
this prefix are yielded.

If the optional ``wildcard`` is provided as a single character string, then
the ``prefix`` is treated as a simple pattern using this ``wildcard`` as a wildcard.

The optional ``how`` argument is used to control how strings are matched using
one of these possible values:

``ahocorasick.MATCH_EXACT_LENGTH`` [default]
Yield matches that have the same exact length as the prefix length.

``ahocorasick.MATCH_AT_LEAST_PREFIX``
Yield matches that have a length greater or equal to the prefix length.

``ahocorasick.MATCH_AT_MOST_PREFIX``
Yield matches that have a length lesser or equal to the prefix length.

See `Example 2`_ and the section below.


``values([prefix, [wildcard, [how]]]) => yield object``
Return an iterator on values associated with each keys.
Keys are are matched optionally to the prefix using the same logic and
arguments as in the ``keys`` method.

``items([prefix, [wildcard, [how]]]) => yield tuple (string, object)``
Return an iterator on tuples of (key, value).
Keys are are matched optionally to the prefix using the same logic and
arguments as in the ``keys`` method.

``len()``
Return the number of distinct keys added to the trie.


Wildcards
^^^^^^^^^

Methods ``keys``, ``values`` and ``items`` can be called with an optional **wildcard**.
A wildcard character is equivalent to a question mark used in glob patterns (?)
or a dot from regular expressions (.). You can use any character you like as a wildcard.

Note that it is not possible to escape a wildcard to match it exactly ---
You need instead to select another wildcard character, not present in the
provided prefix. For example::

automaton.keys("hi?", "?") # would match "him", "his"
automaton.keys("XX?", "X") # would match "me?", "he?" or "it?"


Aho-Corasick methods
####################

``make_automaton()``
Finalize and create the Aho-Corasick automaton based on the keys already
added to the trie. This does not require additional memory. After successful
the ``Automaton.kind`` attribute is set to ``ahocorasick.AHOCORASICK``.

**This method invalidates all iterators.**

``iter(string, [start, [end]])``
Perform the Aho-Corasick search procedure using the provided input ``string``.
Return an iterator of tuples (end_index, value) for keys found in string where:
- ``end_index`` is the end index in the input string where a trie key string was found.
- ``value`` is the value associated with the found key string.

The start and end optional arguments can be used to limit the search to an input
string slice as in string[start:end].

``find_all(string, callback, [start, [end]])``
Perform the Aho-Corasick search procedure using the provided input ``string`` and
iterate over the matching tuples (end_index, value) for keys found in ``string``.
Invoke the ``callback`` callable with each matching tuple.
The ``callback`` callable must accept two positional arguments:
- ``end_index`` is the end index in the input string where a trie key string was found.
- ``value`` is the value associated with the found key string.

The ``start`` and ``end`` optional arguments can be used to limit the search to
a ``string`` slice as in ``string[start:end]``.

Note that the ``find_all`` method is equivalent to::

def find_all(self, string, callback):
for end_index, value in self.iter(string):
callback(end_index, value)


Attributes
##########

``kind`` [readonly]
Return the state of the ``Automaton`` instance. This is read only and is
maintained internally.
Note that some methods are not available when automaton kind is
``ahocorasick.EMPTY`` or ``ahocorasick.TRIE``. They will raise an exception
if called when not available.
Testing this property before calling these methods may be a better
(faster or more elegant) than a try/except block but you can use both
approaches.

Possible ``kind`` values are:

``ahocorasick.EMPTY``
The trie is empty.

``ahocorasick.TRIE``
Some words have been added but the Automaton has not been constructed yet:
methods related to Aho-Corasick such as ``find_all`` or ``iter`` will
not work.

``ahocorasick.AHOCORASICK``
The Aho-Corasick automaton has been constructed; all methods are available.

``store`` [readonly]
Return the type of values stored in the Automaton as specified when creating
the object. By default ``ahocorasick.STORE_ANY``is used, thus any Python
object is accepted as value. When ``ahocorasick.STORE_INTS`` or
``ahocorasick.STORE_LENGTH`` is used then values are 32-bit integers
and do not use additional memory. See the ``add_word`` documentation
for details.


Other methods
#############

``dump() => (list of nodes, list of edges, list of fail links)``
Returns a three-tuple of lists describing the Automaton as a graph of
(nodes, edges, failure links):

* nodes: each item is a pair (node id, end of word marker)
* edges: each item is a triple (node id, label char, child node id)
* failure links: each item is a pair (source node id, node if connected by fail node)

For each of these the node id is a unique number and a label is a single byte.

The source repository and source package also contains the ``dump2dot.py``
script that converts ``dump()`` results to a graphviz__ dot format.

__ http://graphviz.org


``get_stats() => dict``
Return a dictionary containing some Automaton statistics:

* ``nodes_count`` --- total number of nodes
* ``words_count`` --- same as ``len(automaton)``
* ``longest_word`` --- length of the longest word
* ``links_count`` --- number of edges
* ``sizeof_node`` --- size of single node in bytes
* ``total_size`` --- total size of trie in bytes (about
``nodes_count * size_of node + links_count * size of pointer``).
The real size occupied by the data structure could be larger because
of `internal memory fragmentation`__ that can occur in a memory manager.


__ http://en.wikipedia.org/Memory%20fragmentation


``__sizeof__() => int``
Return the approximate size in bytes occupied by the Automaton instance in
memory excluding the size of associated objects when the Automaton is
created with ``Automaton()`` or ``Automaton(ahocorasick.STORE_ANY).
Also available by calling sys.getsizeof(automaton instance).


.. _AutomatonSearchIter:

AutomatonSearchIter class
~~~~~~~~~~~~~~~~~~~~~~~~~

This class is not available directly but instances of ``AutomatonSearchIter`
are returned by the ``iter`` method of an ``Automaton``. This iterator has
the following methods:

``set(string, [reset]) => None``
Set a new string to search. When the ``reset`` argument is ``False``
(default), then the Aho-Corasick procedure is continued and the internal
state of the Automaton and index are not reset. This allow to search for
large strings in multiple chunks.
For example::

it = automaton.iter(b"")
while True:
buffer = receive(server_address, 4096)
if not buffer:
break

it.set(buffer)
for index, value in it:
print(index, '=>', value)

When ``reset`` is ``True`` then processing is restarted.
For example this code::

for string in set:
for index, value in automaton.iter(string)
print(index, '=>', value)

does the same job as::

it = automaton.iter(b"")
for string in set:
it.set(it, True)
for index, value in it:
print(index, '=>', value)


More Examples
~~~~~~~~~~~~~

::

>>> import ahocorasick
>>> A = ahocorasick.Automaton()

# add some words to trie
>>> for index, word in enumerate("he her hers she".split()):
... A.add_word(word, (index, word))

# test is word exists in set
>>> "he" in A
True
>>> "HER" in A
False
>>> A.get("he")
(0, 'he')
>>> A.get("she")
(3, 'she')
>>> A.get("cat", "<not exists>")
'<not exists>'
>>> A.get("dog")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
KeyError
>>>

# convert the trie in an Aho-Corasick automaton
A.make_automaton()

# then find all occurrences of keys in a string
for item in A.iter("_hershe_"):
... print(item)
...
(2, (0, 'he'))
(3, (1, 'her'))
(4, (2, 'hers'))
(6, (3, 'she'))
(6, (0, 'he'))


.. _example 2:


Example of the keys_ method behaviour
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

::

>>> import ahocorasick
>>> A = ahocorasick.Automaton()

# add some words to trie
>>> for index, word in enumerate("cat catastropha rat rate bat".split()):
... A.add_word(word, (index, word))

# prefix
>>> list(A.keys("cat"))
["cat", "catastropha"]

# pattern
>>> list(A.keys("?at", "?", ahocorasick.MATCH_EXACT_LENGTH))
["bat", "cat", "rat"]

>>> list(A.keys("?at?", "?", ahocorasick.MATCH_AT_MOST_PREFIX))
["bat", "cat", "rat", "rate"]

>>> list(A.keys("?at?", "?", ahocorasick.MATCH_AT_LEAST_PREFIX))
["rate"]


Build and install
=================

To install for common operating systems use pip. Pre-built wheels should be
available on Pypi::

pip install pyahocorasick

To build from sources you need to have a C compiler installed and configured
which should be standard on Linux and easy to get on MacOSX.

On Windows and Python 2.7 you need the `Microsoft Visual C++ Compiler for Python 2.7`__
(or Visual Studio 2008). There have been reports that `pyahocorasick` does not
build with MinGW. It may build with cygwin. If you get this working with these
platforms, please report!

To build from sources, clone the git repository or download and extract the
source archive.

Install `setuptools` and then run (in a `virtualenv` of course!)::

pip install .

If compilation succeeds, the module is ready to use.

__ https://www.microsoft.com/en-us/download/details.aspx?id=44266


Unicode and bytes
-----------------

The type of strings accepted and returned by ``Automaton`` methods are either
**unicode** or **bytes**, depending on a compile time settings (preprocessor
definition of ``AHOCORASICK_UNICODE`` as set in `setup.py`).

The ``Automaton.unicode`` attributes can tell you how the library was built.
On Python 3, unicode is the default. On Python 2, bytes is the default.

.. warning::

When the library is built with unicode support, an Automaton will store 2 or
4 bytes per letter, depending on your Python installation.
When built for bytes, only one byte per letter is needed.


Tests
=====

The source repository contains several tests. To run them use::

make test


Support
=======

Support is available through the `GitHub issue tracker`__ to report bugs or ask
questions.

__ https://github.com/WojciechMula/pyahocorasick/issues


Contributing
============

You can submit contributions through `GitHub pull requests`__.

__ https://github.com/WojciechMula/pyahocorasick/pull



Authors
=======

The main author: Wojciech Muła, wojciech_mula@poczta.onet.pl

This library would not be possible without help of many people, who contributed
in various ways. They created `pull requests`__, reported bugs (as `GitHub
issues`__ or via direct messages), proposed fixes, or spent their valuable time
on testing. Thank you.

__ https://github.com/WojciechMula/pyahocorasick/pull
__ https://github.com/WojciechMula/pyahocorasick/issues


License
=======

Library is licensed under very liberal BSD-3-Clause__ license.
Some portions of the code are dedicated to the public domain such as the pure
Python automaton.

Full text of license is available in LICENSE file.

__ http://spdx.org/licenses/BSD-3-Clause.html