<commit_before>import csv
import os
import logging
import re
import shutil
import tarfile
import glob
from datetime import datetime
from stat import ST_CTIME

import requests
from dipper.sources.Source import Source
from dipper.models.assoc.D2PAssoc import D2PAssoc
from dipper.models.Reference import Reference
from dipper.models.Model import Model
from dipper import config

LOG = logging.getLogger(__name__)

# summer 2018 PR mentioned switching to the new format
PNR = 'http://compbio.charite.de/jenkins/job/hpo.annotations.current'
HPOADL2 = PNR + '/lastSuccessfulBuild/artifact/misc_2018'

# Fall 2018 CM made a mondo version of common disease (but we decided to hold off now)
GITAPI = "https://api.github.com/repos/monarch-initiative"

ORPHANET = 'http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert='
CONF = config.get_config()


class HPOAnnotations(Source):
    """<commit_msg>can't be worse than ti one that isn't there anymore<commit_after>import csv
import os
import logging
import re
import shutil
import tarfile
import glob
from datetime import datetime
from stat import ST_CTIME

import requests
from dipper.sources.Source import Source
from dipper.models.assoc.D2PAssoc import D2PAssoc
from dipper.models.Reference import Reference
from dipper.models.Model import Model
from dipper import config

LOG = logging.getLogger(__name__)

# summer 2018 PR mentioned switching to the new format
PNR = 'http://compbio.charite.de/jenkins/job/hpo.annotations.current'
HPOADL2 = PNR + '/lastSuccessfulBuild/artifact/current'
              # '/lastSuccessfulBuild/artifact/misc_2018'   dissapeared by 2020 03

# Fall 2018 CM made a mondo version of common disease (but we decided to hold off now)
GITAPI = "https://api.github.com/repos/monarch-initiative"

ORPHANET = 'http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert='
CONF = config.get_config()


class HPOAnnotations(Source):
    """
{'fraction_non_alphanumeric': 0.08581894296180011, 'fraction_numerical': 0.018838304552590265, 'mean_word_length': 4.919504643962848, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, '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': '5915156', 'n_tokens_mistral': 637, 'n_tokens_neox': 593, 'n_words': 184}