sic

(Latin) so, thus, such, in such a way, in this way

(English) spelling is correct

sic is a module for string normalization. Given a string, it separates sequences of alphabetical, numeric, and punctuation characters, as well as performs more complex transformation (i.e. separates or replaces specific words or individual symbols). It comes with set of default normalization rules to transliterate and tokenize greek letters and replace accented characters with their base form. It also allows using custom normalization configurations.

Basic usage:

import sic

builder = sic.Builder()
machine = builder.build_normalizer()
x = machine.normalize('abc123xyzalphabetagammag')
print(x)

The output will be:

abc 123 xyz alpha beta gamma g

Installation

• sic is designed to work in Python 3 environment.
• sic only needs Python Standard Library (no other packages).

To get wheel for Windows (Python >= 3.6) or source code package for Linux:

pip install sic

To get source code package regardless the OS:

pip install sic --no-binary sic

Wheels and .tar.gz can also be downloaded from the project's repository.

Wheels contain binaries compiled from cythonized code. Source code package is pure Python. Cythonized version performs better on short strings, while non-cythonized version performs better on long strings, so one may be preferred over another depending on usage scenario. The benchmark is below.

STRING LENGTH	REPEATS	VERSION	MEAN TIME (s)
71	10000	.tar.gz	1.8
71	10000	wheel	0.5
710000	1	.tar.gz	2.7
710000	1	wheel	15.9

Tokenization configs

sic implements tokenization, i.e. it splits a given string into tokens and processes those tokens according to the rules specified in a configuration file. Basic tokenization includes separating groups of alphabetical, numerical, and punctuation characters within a string, thus turning them into separate words (for future reference, we'll call such words tokens). For instance, abc-123 will be transformed into abc - 123, having tokens abc, -, and 123.

What happens next to initially tokenized string must be defined using XML in configuration file(s). Entry point to default tokenizer applied to a string is sic/tokenizer.standard.xml.

Below is the template and description for tokenizer config.

<!-- tokenizer.config.xml -->
<!--
  This is the description of config file for tokenizer.
  General structure:
  <tokenizer>
  +-<import>
  +-...
  +-<import>
  +-<setting>
  +-...
  +-<setting>
  +-<split>
  +-...
  +-<split>
  +-<token>
  +-...
  +-<token>
  +-<character>
  +-...
  +-<character>
-->

<?xml version="1.0" encoding="UTF-8"?>

<!-- There must be single root element, and it must be <tokenizer>: -->
<tokenizer name="$name">
<!-- $name: string label for this tokenizer -->
  
  <!--
    Direct children of <tokenizer> are <import>, <setting>, <split>,
      <token>, and/or <character> elements (there can be zero to many
      declarations of any of those)
  -->

  <!-- <import> elements point at other tokenizer configs to merge with -->
  <import file="$file" />
  <!-- $file: path to file with another tokenizer config -->

  <!-- <setting> elements define high-level tokenizer settings -->
  <setting name="$name" value="$value" />
  <!--
    Names and value requirements for /tokenizer/setting elements:
    $name="cs": $value="0"|"1" (if "1", this tokenizer will be case-sensitive)
    $name="bypass": $value="0"|"1" (if "1", this tokenizer will do nothing,
      regardless the rest content of this file)
  -->

  <!--
    <split> elements define substrings that should be separated from text as
      tokens
  -->
  <split where="$where" value="$value" />
  <!--
    $where="l"|"r"|"m" ("l" for left, "r" for right, "m" for middle)
    $value: string that will be handled as token when it's either in the
      beginning of word ($where="l"), at the end of word ($where="r"), or in
      the middle ($where="m")
  -->

  <!--
    <token> elements define tokens that should be replaced with other tokens
      (or with nothing => removed)
  -->
  <token to="$to" from="$from" />
  <!--
    $to: string that should replace the token specified in $from
    $from: string that is the token to be replaced by another string specified
      in $to
  -->

  <!--
    <character> elements define single characters that should be replaced with
      other single characters
  -->
  <character to="$to" from="$from" />
  <!--
    $to: character that should replace the another character specified in $from
    $from: character that should be replaced by another character specified in
      $to
  -->

</tokenizer>

Below are descriptions and examples of tokenizer config elements.

ELEMENT	ATTRIBUTES	DESCRIPTION	EXAMPLE
<import>	file="path/to/another/config.xml"	Import tokenization rules from another tokenizer config.
<setting>	name="bypass" value="?"	If present and value="1", all tokenization rules are ignored, as if there was no tokenization at all (left for debug purposes).
<setting>	name="cs" value="?"	If value="1", string is processed case-sensitively; if value="0" - case-insensitively; if not present, tokenizer is case-insensitive.
<split>	where="l" value="?"	Separates token specified in value from left part of a bigger token.	where="l" value="kappa": nf kappab --> nf kappa b
<split>	where="m" value="?"	Separates token specified in value when it is found in the middle of a bigger token.	where="m" value="kappa": nfkappab --> nf kappa b
<split>	where="r" value="?"	Separates token specified in value from right part of a bigger token.	where="r" value="gamma": ifngamma --> ifn gamma
<token>	to="?" from="?"	Replaces token specified in from with another token specified in to.	to="protein" from="gene": nf kappa b gene --> nf kappa b protein
<character>	to="?" from="?"	Replaces character specified in from with another character specified in to.	to="e" from="ë": citroën --> citroen

Attribute where of <split> element may have any combination of l, m, or r literals if the specified substring is required to be separated in different places of a bigger string. So, instead of three different elements

<split where="l" value="word" />
<split where="m" value="word" />
<split where="r" value="word" />

using the following single one

<split where="lmr" value="word" />

will achieve the same result.

Transformation is applied in the following order:

1. Replacing characters
2. Splitting tokens
3. Replacing tokens

When splitting tokens, longer ones shadow shorter ones. Token replacement instructions may contradict each other locally, but in entire set they must converge so that each token has only one replacement option (otherwise ValueError exception will be thrown).

Usage

import sic

For detailed description of all function and methods, see comments in the source code.

Class sic.Model

This class is designed to instanly create tokenization rules directly in Python. It is neither convenient nor recommended for complex normalization tasks, but can be handy for small ones where using external XML config might seem an overkill.

# instantiate Model
model = sic.Model()

# model is case-sensitive
model.case_sensitive = True

# model will do nothing
model.bypass = True

Method sic.Model.add_rule adds single tokenization instruction to the Model instance:

# equivalent to XML <split where="lmr" value="beta" />
model.add_rule(sic.SplitToken('beta', 'lmr'))

# equivalent to XML <token to="good" from="bad" />
model.add_rule(sic.ReplaceToken('bad', 'good'))

# equivalent to XML <character to="z" from="a" />
model.add_rule(sic.ReplaceCharacter('a', 'z'))

NB: in case new sic.ReplaceToken or sic.ReplaceChar instruction contradicts something that is already in the model, the newer instruction overrides older instruction:

model.add_rule(sic.ReplaceToken('bad', 'good'))
model.add_rule(sic.ReplaceToken('bad', 'better'))

"bad" --> "good" will not be used; "bad" --> "better" will be used instead

Method sic.Model.remove_rule removes single tokenization instruction from Model instance if it is there:

model.remove_rule(sic.ReplaceToken('bad', 'good'))
# tokenization rule that fits definition above will be removed from model

Class sic.Builder

Function sic.Builder.build_normalizer() reads tokenization config, instantiates sic.Normalizer class that would perform tokenization according to rules specified in a given config, and returns this sic.Normalizer class instance.

ARGUMENT	TYPE	DEFAULT	DESCRIPTION
endpoint	str, Model	None	Path to tokenizer configuration file.

# create Builder object
builder = sic.Builder()

# create Normalizer object with default set of rules
machine = builder.build_normalizer()

# create Normalizer object with custom set of rules
machine = builder.build_normalizer('/path/to/config.xml')

# create Normalizer object using ad hoc model
model = sic.Model()
model.add_rule(sic.SplitToken('beta', 'lmr'))
machine = builder.build_normalizer(model)

Class sic.Normalizer

Method sic.Normalizer.save() saves data structure from instance of sic.Normalizer class to a specified file (pickle).

ARGUMENT	TYPE	DEFAULT	DESCRIPTION
filename	str	n/a	Path and name of file to write.

Function sic.Normalizer.load() reads specified file (pickle) and places data structure in sic.Normalizer instance.

ARGUMENT	TYPE	DEFAULT	DESCRIPTION
filename	str	n/a	Path and name of file to read.

Function sic.Normalizer.normalize() performs string normalization according to the rules ingested at the time of class initialization, and returns normalized string.

ARGUMENT	TYPE	DEFAULT	DESCRIPTION
source_string	str	n/a	String to normalize.
word_separator	str	' '	Word delimiter (single character).
normalizer_option	int	0	Mode of post-processing.
control_character	str	'\x00'	Character masking word delimiter (single character)

word_separator: Specified character will be considered a boundary between tokens. The default value is ' ' (space) which seems reasonable choice for natural language. However any character can be specified, which might be more useful in certain context.

normalizer_option: The value can be either one of 0, 1, 2, or 3 and controls the way tokenized string is post-processed:

VALUE	MODE
0	No post-processing.
1	Rearrange tokens in alphabetical order.
2	Rearrange tokens in alphabetical order and remove duplicates.
3	Remove all added word separators.

control_character: Implementation detail - character that used as word delimiter inserted in a parsed string at the run time. If parsed string initially included this character somewhere, normalization will return error. The value is set to \x00 by default.

Property sic.Normalizer.result retains the result of last call for sic.Normalizer.normalize function as dict object with the following keys:

KEY	VALUE TYPE	DESCRIPTION
'original'	str	Original string value that was processed.
'normalized'	str	Returned normalized string value.
'map'	list(int)	Map between original and normalized strings.
'r_map'	list(list(int))	Reverse map between original and normalized strings.

sic.Normalizer.result['map']: Not only sic.Normalizer.normalize() generates normalized string out of originally provided, it also tries to map character indexes in normalized string back on those in the original one. This map is represented as list of integers where item index is character position in normalized string and item value is character position in original string. This is only valid when normalizer_option argument for sic.Normalizer.normalize() call has been set to 0.

sic.Normalizer.result['r_map']: Reverse map between character locations in original string and its normalized reflection (item index is character position in original string; item value is list [x, y] where x and y are respectively lowest and highest indexes of mapped character in normalized string).

Method sic.build_normalizer()

sic.build_normalizer() implicitly creates single instance of sic.Normalizer class accessible globally from sic namespace. Arguments are same as for sic.Builder.build_normalizer() function.

Method sic.save()

sic.save() saves data structure stored in global instance of sic.Normalizer class to a specified file (pickle). Arguments are same as for sic.Normalizer.save() method.

Function sic.load()

sic.load() reads specified file (pickle) and places data structure in global instance of sic.Normalizer class stored in that file. Arguments are same as for sic.Normalizer.load() function.

Function sic.normalize()

sic.normalize(*args, **kwargs) either uses global class sic.Normalizer or instantly creates new local sic.Normalizer class, and uses it to perform requested string normalization.

ARGUMENT	TYPE	DEFAULT	DESCRIPTION
source_string	str	n/a	String to normalize.
word_separator	str	' '	Word delimiter (single character).
normalizer_option	int	0	Mode of post-processing.
control_character	str	'\x00'	Character masking word delimiter (single character)
tokenizer_config	str	None	Path to tokenizer configuration file.

If tokenizer_config argument is not provided, the function will use global instance of sic.Normalizer class (will create it if it is not initialized).

Method sic.reset()

sic.reset() resets global sic.Normalizer instance to None, forcing subsequently called sic.normalize() to create new global instance again if it needs it.

Attribute sic.result, function sic.result()

sic.result attribute retains the value of sic.Normalizer.result property that belonged to most recently used sic.Normalizer instance accessed from sic.normalize() function (either global or local).

Python 3.6 does not support PEP-562 (module attributes). So in Python 3.6, use function sic.result() rather than attribute sic.result:

sic.result() # will work in Python >= 3.6
sic.result   # will work in Python >= 3.7

Examples

Basic usage

import sic

# create Builder object
builder = sic.Builder()
# create Normalizer object with default set of rules
machine = builder.build_normalizer()

# using default word_separator and normalizer_option
x = machine.normalize('alpha-2-macroglobulin-p')
print(x) # 'alpha - 2 - macroglobulin - p'
print(machine.result)
"""
{
  'original': 'alpha-2-macroglobulin-p',
  'normalized': 'alpha - 2 - macroglobulin - p',
  'map': [
    0, 1, 2, 3, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 21, 22, 22
  ],
  'r_map: [
    [0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 6], [7, 8], [9, 10], [11, 12], [13, 13], [14, 14], [15, 15], [16, 16], [17, 17], [18, 18], [19, 19], [20, 20], [21, 21], [22, 22], [23, 23], [24, 24], [25, 26], [27, 28]
  ]
}
"""

Custom word separator

x = machine.normalize('alpha-2-macroglobulin-p', word_separator='|')
print(x) # 'alpha|-|2|-|macroglobulin|-|p'

Post-processing options

# using normalizer_option=1
x = machine.normalize('alpha-2-macroglobulin-p', normalizer_option=1)
print(x) # '- - - 2 alpha macroglobulin p'

# using normalizer_option=2
x = machine.normalize('alpha-2-macroglobulin-p', normalizer_option=2)
print(x) # '- 2 alpha macroglobulin p'

# using normalizer_option=3
# assuming normalization config includes the following:
# <setting name="cs" value="0" />
# <split value="mis" where="l" />
# <token to="spelling" from="speling" />
x = machine.normalize('Misspeling')
print(x) # 'Misspelling'

Using implicitly instantiated classes

# normalize() with default instance
x = sic.normalize('alpha-2-macroglobulin-p', word_separator='|')
print(x) # 'alpha|-|2|-|macroglobulin|-|p'

# custom configuration for implicitly instantiated normalizer
sic.build_normalizer('/path/to/config.xml')
x = sic.normalize('some string')
print(x) # will be normalized according to config at /path/to/config.xml

# custom config and normalization in one line
x = sic.normalize('some string', tokenizer_config='/path/to/another/config.xml')
print(x) # will be normalized according to config at /path/to/another/config.xml

Saving and loading compiled normalizer to/from disk

machine.save('/path/to/file') # will write /path/to/file
another_machine = sic.Normalizer()
another_machine.load('/path/to/file') # will read /path/to/file

Adding normalization rules to already compiled model

# (assuming `machine` is sic.Normalizer instance armed with tokenization ruleset)
new_ruleset = [sic.ReplaceToken('from', 'to'), sic.SplitToken('token', 'r')]
new_ruleset_string = ''.join([rule.decode() for rule in new_ruleset])
machine.make_tokenizer(new_ruleset_string, update=True) # rules from `new_ruleset` will be added to the normalizer