<commit_before>import datanator.config.core
from datanator.util import mongo_util
from datanator.util import file_util
from datanator.util import molecule_util
import six
import requests
from xml import etree
import libsbml
import re
import datetime
import bs4
import html
import csv
import pubchempy
import sys
import Bio.Alphabet
import Bio.SeqUtils
import math
import logging
logging.basicConfig(filename='./logs/sabiork_parser.log', level=logging.DEBUG, 
                    format='%(asctime)s %(levelname)s %(name)s %(message)s')
logger=logging.getLogger()


class SabioRk:

    def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,
                 verbose=False, max_entries=float('inf'), username=None,
                 password=<PASSWORD>, authSource='admin', webservice_batch_size=100,
                 excel_batch_size=100):
        self.cache_dirname = cache_dirname
        self.MongoDB = MongoDB
        self.replicaSet = replicaSet<commit_msg>minor modifications to sabio_rk.py<commit_after>import datanator.config.core
from datanator.util import mongo_util
from datanator.util import file_util
from datanator.util import molecule_util
import six
import requests
from xml import etree
import libsbml
import re
import datetime
import bs4
import html
import csv
import pubchempy
import sys
import Bio.Alphabet
import Bio.SeqUtils
import math
import logging
import pymongo
logging.basicConfig(filename='./logs/sabiork_parser.log', level=logging.DEBUG, 
                    format='%(asctime)s %(levelname)s %(name)s %(message)s')
logger=logging.getLogger()


class SabioRk:

    def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,
                 verbose=False, max_entries=float('inf'), username=None,
                 password=<PASSWORD>, authSource='admin', webservice_batch_size=100,
                 excel_batch_size=100):
        self.cache_dirname = cache_dirname
        self.MongoDB = MongoDB
        self.replicaSet = replicaSet
{'fraction_non_alphanumeric': 0.08333333333333333, 'fraction_numerical': 0.006986027944111776, 'mean_word_length': 4.025062656641604, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2866146', 'n_tokens_mistral': 626, 'n_tokens_neox': 591, 'n_words': 152}