cleanse_wiki_data.py

'''
Script on Cleansing Wikipedia Data that has been extracted from extract_raw_wiki_data.py
'''
#core functionality modules
import os, gc
import logging
import argparse
import warnings

from functools import partial

#text preprocess modules
import re
import urllib
from xml.etree import ElementTree as ET

#dataset related modules
import numpy as np
import pandas as pd


### MODULES DEFINITION ###
#create custom type-checking of incoming ArgParse
def argparse_bool_check(value: str):
    #cast str with value like float into actual float
    try:
        value = float(value)
    #can't be parsed as float, keep as it is
    except ValueError:
        pass

    #cast float-like value (incl int) into str
    if isinstance(value, float) and int(value) == value:
        value = str(int(value))
    #raise ArgumentTypeError if the value isn't in string already
    else:
        if not isinstance(value, str):
            raise argparse.ArgumentTypeError(f"Not the correct value (args: {value})! Expected is cast-able to '1' or '0' or already in string. Please rectify!")
    #check for these combinations of values
    if value.lower() in ("yes", "true", "t", "y", "1"):
        return True
    elif value.lower() in ("no", "false", "f", "n", "0"):
        return False
    else:
        raise argparse.ArgumentTypeError(f"Value Error! Not the correct value (args: {value})! Please rectify!")


def set_logger():
    # Set up the logger
    logging.basicConfig(
        level=logging.INFO,  # Set the desired logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL)
        format='%(asctime)s [%(levelname)s]: %(message)s',  # Customize the log message format
        datefmt='%Y-%m-%d %H:%M:%S'  # Customize the date/time format
    )

    # Create a file handler to write logs into a file
    file_handler = logging.FileHandler('app.log')

    # Set the log level for the file handler
    file_handler.setLevel(logging.INFO) 

    # Create a formatter for the file handler (customize the log format for the file)
    file_formatter = logging.Formatter('%(asctime)s [%(levelname)s]: %(message)s', datefmt='%Y-%m-%d %H:%M:%S')
    file_handler.setFormatter(file_formatter)

    logger = logging.getLogger("Wiki Dataset Generation")
    logger.addHandler(file_handler)

    return logger


#wrapper fn of text-cleansing
def text_cleansing_wrapper(fn, exception_class_names = []):

    #ensure caught exception class names passed to decorator is a list (if provided)
    if not isinstance(exception_class_names, list):
        raise TypeError("Exception Class Name for Wrapper is not a list!")
    #ensure all values of caught exception class name list is a string
    if not all([isinstance(val, str) for val in exception_class_names]):
        raise ValueError("Found an element of Exception Class Name for Wrapper that is not a string!")

    #lowercase all exception class name
    exception_class_names = [val.lower() for val in exception_class_names]
    if len(exception_class_names) == 0:
        warnings.warn("The wrapper receives 0 `exception_class_names` to be warned! Will return the function value with its input!")

    def text_fn_wrapper(text: str):
        try:
            return fn(text)
        except Exception as e:
            _exc_name = type(e).__name__
            if _exc_name.lower() not in exception_class_names and len(exception_class_names)>0:
                raise Exception(f"Exception Occured of {_exc_name}!") from e
            else:
                _followup_msg = "Returning the input as it is..."
                _text_warn = f"An exception of {_exc_name} occured! {_followup_msg}"
                warnings.warn(_text_warn)
                return text

    return text_fn_wrapper


#create html tags cleanser of a given text
partial_decorator = partial(text_cleansing_wrapper, exception_class_names=["parseerror"])
@partial_decorator
def remove_html_tags(text: str):
    #extracted from "https://stackoverflow.com/a/9662410", w/ additional decorator of error handler
    return ''.join(ET.fromstring(text).itertext())


#create non-ascii removal of text
@text_cleansing_wrapper
def decode_url_and_remove_non_ascii(text: str):
    # return (urllib.parse.unquote(text)).encode('utf8', errors='ignore').decode().strip()
    return (urllib.parse.unquote(text)).encode('ascii', errors='ignore').decode().strip()

#create excessive whitespace removal of text
@text_cleansing_wrapper
def remove_excessive_whitespace(text: str):
    return re.sub("(\s)(\s+)", "\1", text).strip()

#create non-alphanumeric removal of text
@text_cleansing_wrapper
def remove_non_alphanumeric(text: str):
    return re.sub("[^a-z0-9\s]", "", text, flags=re.I).strip()

def cleanse_wiki_text(text: str):
    return remove_html_tags(decode_url_and_remove_non_ascii(text))

def normalize_wiki_title(text: str):
    return remove_non_alphanumeric(remove_excessive_whitespace(text.lower()))


### MAIN CODE ###
if __name__ == "__main__":
    parser = argparse.ArgumentParser()

    parser.add_argument("--raw-csv-path", help="Relative location of csv file containing raw Wikipedia data")
    parser.add_argument("--drop-hard-dupl", help="""Flag whether to drop hard duplicates
                        (exact values of data of relevant text fields, Titles & Desc)""",
          default=True, type=argparse_bool_check)
    parser.add_argument("--drop-soft-dupl", help="""Flag whether to drop soft duplicates
                        (duplicates after cleansed and normalized relevant text fields, Titles & Desc)""",
          default=True, type=argparse_bool_check)
    parser.add_argument("--save-dir-path", help="""Relative dir path of saved Wikipedia CSV data
                        to the `cleanse_wiki_data.py` script dir""",
            default=os.path.dirname(os.path.abspath(__file__)))

    args = parser.parse_args()


    expected_colnames = ["id", "url", "title", "text"]

    logger = set_logger()
    logger.info("Parsing arguments...")

    raw_data_path = args.raw_csv_path
    drop_hard_dupl = args.drop_hard_dupl
    drop_soft_dupl = args.drop_soft_dupl
    save_dir = args.save_dir_path

    df = pd.read_csv(raw_data_path)
    if len(set(df.columns).difference(set(expected_colnames))) != 0 or len(set(expected_colnames).difference(set(df.columns))) != 0:
        raise ValueError(f"The data schema expected, consist of columns: {', '.join(df.columns.to_list())} doesn't match with expected column values of {', '.join(expected_colnames)}!")

    if (not drop_hard_dupl) and (not drop_soft_dupl):
        raise AssertionError("The script won't run with both `drop-hard-dupl` and `drop-soft-dupl` args turned off!")
    elif (not drop_hard_dupl):
        warnings.warn("The args of `drop_hard_dupl` isn't turned off! Possibly the data will contain one template value of Wikipedia (usually no contribution text!)")

    #will save id identifier colname first (popping first list val)
    id_colname = expected_colnames.pop(0)

    # if any of the data has duplicate values from columns checked (url, title, or text),
    # it means the data integrity is questionable
    # i.e. copied from other article or filled with template text
    # hence, we will delete those duplicated datasets

    suffix_file = "_dedup_cleansed"
    #hard duplicate drop (drop all duplicate values that has exact same text on expected unique colnames)
    if drop_hard_dupl:

        for colname in expected_colnames:
            logger.info(f"Checking data integrity on column {colname} on removing hard-duplicate(s)...")
            dupl_text_df = df[df.duplicated(subset=colname,keep=False)]
            shape_of_dupl_data = dupl_text_df.shape[0]

            if shape_of_dupl_data > 0:
                logger.info(f"Found {shape_of_dupl_data} data duplicated! Will be dropped")
                df.drop_duplicates(subset=colname, keep=False, inplace=True)


        #check id/idx of the cleansed data, whether it has duplicate
        # (the duplication of id/idx should came from the very first extraction, not from the cleansing)

        if df[df.duplicated(subset=id_colname,keep=False)].shape[0] > 0:
            logger.info("Duplicated ID found! Re-assigning ID to the new ones based on `df.reset_index` method!")
            df[id_colname] = df.reset_index().index

    #soft duplicate drop (drop all except one duplicate values that has exact same text on expected unique colnames)
    #keep the data that has longest value of its raw form
    if drop_soft_dupl:

        idx_to_keep = set(df.index.to_list())
        #clean from text & title only, url isn't needed for this process
        expected_colnames.remove("url")

        for colname in expected_colnames:
            logger.info(f"Checking data integrity on column {colname} on removing soft-duplicate(s)...")
            _df = df.copy(deep=True)

            #define text processing fn for soft-duplicate cleansing
            #text processing for all colums (text & title)
            _df = _df[[colname]]
            _df[colname] = _df[colname].astype("str")
            logger.info(f"Cleansing the data based on {colname}")
            _df[colname+"_raw_len"] = _df[colname].apply(len)
            _df[colname+"_cleansed"] = _df[colname].apply(cleanse_wiki_text)
            if colname == "title":
                # title text has been cleansed by `cleanse_wiki_text` fn, but needs to normalized on
                # whitespaces, non alphanum syms (incl. punctuations), and case (all lowercased)
                _df[colname+"_cleansed"] = _df[colname+"_cleansed"].apply(normalize_wiki_title)

            #choose the data to keep by "ranking" it according to len of its raw text (greatest to keep)
            logger.info(f"Ranking and grouping the data based on {colname}")
            _df["rk"] = _df.groupby(colname+"_cleansed")[colname+"_raw_len"].rank(method="min", ascending=False)
            shape_of_dupl_data = _df[_df["rk"]>1].shape[0]

            if shape_of_dupl_data > 0:
                logger.info(f"Found {shape_of_dupl_data} data duplicated! Will be dropped")
                _idx_to_keep = _df[_df["rk"]==1].index.to_list()
                if len(_idx_to_keep)+shape_of_dupl_data != df.shape[0]:
                    raise AssertionError("Mismatch of data number!")
                idx_to_keep = idx_to_keep.intersection(set(_idx_to_keep))
            del _df
            gc.collect()

        logger.info(f"The final data kept is {len(idx_to_keep)} from {df.shape[0]}")
        df = df.loc[list(idx_to_keep),:]

    logger.info("Saving dataset cleansed form...")
    #input path splitted by ("/") for the last entry should return filename
    #whereas the filename splitted by (".") except the last value should return the filename w/o ".csv" extension
    
    _save_fn = ".".join(raw_data_path.split("/")[-1].split(".")[:-1]) + suffix_file + ".csv"
    df.to_csv(f"{save_dir}/{_save_fn}", index=False)