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collect.py
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collect.py
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# -*- coding=utf-8 -*-
#!/usr/bin/env python3
"""
Inspired by [A systematic review on open source clinical software on GitHub for improving software
reuse in smart healthcare](https://www.mdpi.com/2076-3417/9/1/150) by Zhengru Shen and Marco Spruit
@author Simon Renger
"""
from typing import final
from github import Github, enable_console_debug_logging
import pandas as pd
from pathlib import Path
import argparse
import json
import math
import os
import time
from datetime import datetime, timedelta
import copy
# -- Debugger Logger
global__debugger = False
def debug__print(msg):
print("[DEBUG] {}".format(msg))
# -- utility
def split_time(timerange, splitsize):
"""
split timerange into multiple timeranges so that each timerange would only contains less than 1000
repos
@see https://github.com/ianshan0915/clinical-opensource-projects
"""
times = timerange.split('..')
start = times[0]
end = times[1]
time_format = '%Y-%m-%d'
timeranges_year = []
duration_days = (datetime.strptime(end, time_format) -
datetime.strptime(start, time_format)).days
delta_days = duration_days//splitsize
for i in range(splitsize):
if i < splitsize-1:
end_tmp = datetime.strptime(
start, time_format) + timedelta(days=delta_days)
timerange_tmp = start + '..' + end_tmp.strftime(time_format)
start_tmp = end_tmp + timedelta(days=1)
start = start_tmp.strftime(time_format)
else:
timerange_tmp = start + '..' + end
timeranges_year.append(timerange_tmp)
return timeranges_year
def search_time_range_year(type, year):
"""
get search timerange on a given year
@see https://github.com/ianshan0915/clinical-opensource-projects
"""
if type == 1:
timerange = '<' + str(year) + '-01-01'
else:
start = str(year) + '-01-01'
if year == datetime.now().year:
end = datetime.now().strftime('%Y-%m-%d')
else:
end = str(year) + '-12-31'
timerange = start + '..' + end
return timerange
# -- GitHubQuery
class GitHubQuery:
def __init__(self, token, config):
self.token = token
self.read_config(config)
if "output" in self.config:
self.output = Path(self.config['output'])
else:
self.output = Path("./")
if token is None:
self.token = self.config["token"]
def read_config(self, config):
fd = open(config, "r")
data = fd.read()
fd.close()
self.config = json.loads(data)
def connect(self):
if global__debugger:
enable_console_debug_logging()
self.conn = Github(self.token)
debug__print("Connecting to GitHub")
def time_range(self, term):
time_min = self.config['criteria']['time']['min']
time_max = self.config['criteria']['time']['max']
timeranges = []
timerange_pre = search_time_range_year(
1, time_min)
query.connect()
# double-check if the cutoff year is good or not
search_term = term + " created:"+timerange_pre
pagedlist_pre = self.conn.search_repositories(
query=search_term)
if pagedlist_pre.totalCount > 1000:
debug__print(
'the cutoff year is not correct, should choose a time before it')
elif pagedlist_pre.totalCount > 0:
timeranges.append(timerange_pre)
while time_min <= time_max:
timerange = search_time_range_year(2, time_min)
# print(timerange)
search_term = term + " created:"+timerange
pagedlist_tmp = self.conn.search_repositories(
query=search_term)
if pagedlist_tmp.totalCount > 0:
splitsize = math.ceil(pagedlist_tmp.totalCount/1000) + 2
timerange_lst = split_time(timerange, splitsize)
timeranges = timeranges + timerange_lst
time_min += 1
return timeranges
def sleep_time(self):
"""
Calculate the amount of seconds it needs to wait before remaining rate reset
"""
tdelta = datetime.fromtimestamp(
self.conn.rate_limiting_resettime) - datetime.now()
return tdelta.seconds + 30 # 30 seconds after the remaining rate reset
def fetch_content(self, repo, contentName):
"""
check if a repo has a given content
"""
url = repo.url + '/' + contentName
status = repo._requester.requestJson('GET', url)[0]
if status == 200:
content = repo.get_readme()
if "readme_dir" in self.config:
dest = self.config["readme_dir"]
isExist = os.path.exists(dest)
if not isExist:
os.makedirs(dest)
dest = os.path.join(dest, repo.name)
isExist = os.path.exists(dest)
if not isExist:
os.makedirs(dest)
dest = os.path.join(dest, "readme.md")
f = open(dest, "w")
f.write(content.content)
f.close()
return content.url
else:
return None
def query_repo(self, term, timeranges, remaining_rate):
"""
obtain repos list based on query terms
"""
# get repositories for each timerange
repos = []
iteration = 0
for timerange in timeranges:
iteration = iteration + 1
debug__print("timerange is {}".format(timerange))
debug__print("Remaining rates are {}".format(remaining_rate))
search_term = term + " created:"+timerange
paged_list = self.conn.search_repositories(
query=search_term)
if paged_list.totalCount > 1000:
debug__print(
'too many repos in this time range ({})'.format(timerange))
break
if paged_list.totalCount == 0:
debug__print("Skip()")
sleep_dur = self.sleep_time()
debug__print("sleep for {}".format(sleep_dur))
time.sleep(sleep_dur)
continue
elif remaining_rate < paged_list.totalCount*2:
debug__print("no left rates, how to break")
self.connect()
sleep_dur = self.sleep_time()
debug__print("sleep for {}".format(sleep_dur))
time.sleep(sleep_dur)
debug__print("Sleep finished()")
search_term = term + " created:"+timerange
paged_list = self.conn.search_repositories(
query=search_term)
repos_tmp = [[item._rawData[k] for k in self.config['attrs']] + [self.fetch_content(
item, 'readme')] + [item._rawData['owner']['type']] for item in paged_list]
repos = repos + repos_tmp
debug__print("remaining_rate < paged_list.totalCount*2")
else:
debug__print("process: {}".format(paged_list.totalCount))
repos_tmp = [[item._rawData[k] for k in self.config['attrs']] + [self.fetch_content(
item, 'readme')] + [item._rawData['owner']['type']] for item in paged_list]
repos = repos + repos_tmp
debug__print("finished processing batch")
time.sleep(120)
self.connect()
remaining_rate = self.conn.rate_limiting[0]
debug__print("query::else")
return repos
def process(self):
repos = []
for term in self.config["terms"]:
try:
debug__print("search for: {}".format(term))
timeranges = self.time_range(term)
# debugging print
# for timerange in timeranges:
# print(timerange)
self.connect()
remaining_rate = self.conn.rate_limiting[0]
debug__print(
"remaining rate after split big query: {}".format(remaining_rate))
# conduct small queries
repos = repos + \
self.query_repo(term, timeranges, remaining_rate)
debug__print("found repo {}".format(len(repos)))
except Exception as e:
debug__print("Oops! {} occurred.".format(e.__class__))
debug__print("repos: {}".format(len(repos)))
debug__print("Next entry.")
rindex = 0
for repoList in repos:
index = 0
for repo in repoList:
try:
if self.config['attrs'].index("license") == index:
if repo != None and "key" in repo:
repos[rindex][index] = repo["key"]
finally:
value = "Error"
index = index + 1
rindex = 1 + rindex
df_repos = pd.DataFrame(repos, columns=self.config['attrs'] +
['readme_url', 'owner_type'])
df = df_repos.drop_duplicates(subset=['id'])
df_duplicates = df_repos.loc[~df_repos.index.isin(df.index)]
self.data_output(df, "repos")
self.data_output(df_duplicates, "repos_duplicates")
def data_output(self, df, name):
isExist = os.path.exists(self.output)
if not isExist:
os.makedirs(self.output)
dt = int(time.time())
if "format" in self.config:
debug__print("File output: <{}> {}".format(
self.config["format"], "{}_{}.csv".format(name, dt)))
if self.config["format"] == "CSV":
df.to_csv(os.path.join(
self.output, "{}_{}.csv".format(name, dt)), index=False)
elif self.config["format"] == "JSON":
df.to_json(os.path.join(
self.output, "{}_{}.json".format(name, dt)))
elif self.config["format"] == "MARKDOWN":
df.to_markdown(os.path.join(
self.output, "{}_{}.mk".format(name, dt)))
elif self.config["format"] == "HTML":
df.to_html(os.path.join(
self.output, "{}_{}.html".format(name, dt)))
else:
df.to_csv(os.path.join(
self.output, "{}_{}.csv".format(name, dt)), index=False)
else:
df.to_csv(os.path.join(
self.output, "{}_{}.csv".format(name, dt)), index=False)
def check_remain_rates(self):
"""
check whether there if any remaining rates
"""
remaining = self.conn.rate_limiting[0]
debug__print("left rates: {}".format(remaining))
if remaining == 0:
debug__print('No remaining rates left!')
return False
else:
return True
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Gather information about GitHub Repositories.')
parser.add_argument('--token', type=str, dest='token',
help='Github Token')
parser.add_argument('config', metavar='config_json', type=str,
help='an integer for the accumulator')
args = parser.parse_args()
query = GitHubQuery(args.token, args.config)
query.connect()
if query.check_remain_rates():
debug__print('we have rates!')
query.process()
else:
sleep_dur = query.sleep_time()
debug__print('sleep for {}'.format(sleep_dur))
time.sleep(sleep_dur)
# double check if the rate is larger than 0
try:
query.connect()
query.process()
pass
except Exception as e:
raise e