def main(gbdir, outdir):
os.makedirs(gbdir, exist_ok=True)
os.makedirs(outdir, exist_ok=True)
tempq = 'tempquery.fasta'
tempdb = 'tempdb.fasta'
for org in tqdm(Organism.objects.all()):
# get genbank and convert to fasta
fpath = os.path.join(gbdir, '{}.gb'.format(org.accession))
if not os.path.isfile(fpath):
print('\nFetching {} with accession {}'.format(
org.name, org.accession))
fetch(fpath)
SeqIO.convert(fpath, 'genbank', tempdb, 'fasta')
# get spacers of organism and convert to fasta
spacers = Spacer.objects.filter(loci__organism=org)
fastatext = ''.join([
'>{}\n{}\n'.format(spacer.id, spacer.sequence)
for spacer in spacers
])
with open(tempq, 'w') as f:
f.write(fastatext)
# run blast and save output
outpath = os.path.join(outdir, '{}.json'.format(org.accession))
commandargs = [
'blastn', '-query', tempq, '-subject', tempdb, '-out', outpath,
'-outfmt', '15'
]
subprocess.run(commandargs, stdout=subprocess.DEVNULL)
os.remove(tempq)
os.remove(tempdb)
def main(gbdir, outdir):
os.makedirs(gbdir, exist_ok=True)
os.makedirs(outdir, exist_ok=True)
tempq = 'tempquery.fasta'
tempdb = 'tempdb.fasta'
for org in tqdm(Organism.objects.all()):
# get genbank and convert to fasta
fpath = os.path.join(gbdir, '{}.gb'.format(org.accession))
if not os.path.isfile(fpath):
print('\nFetching {} with accession {}'.format(
org.name,
org.accession
))
fetch(fpath)
SeqIO.convert(fpath, 'genbank', tempdb, 'fasta')
# get spacers of organism and convert to fasta
spacers = Spacer.objects.filter(loci__organism=org)
fastatext = ''.join(['>{}\n{}\n'.format(spacer.id, spacer.sequence)
for spacer in spacers])
with open(tempq, 'w') as f:
f.write(fastatext)
# run blast and save output
outpath = os.path.join(outdir, '{}.json'.format(org.accession))
commandargs = ['blastn', '-query', tempq,
'-subject', tempdb, '-out', outpath, '-outfmt', '15']
subprocess.run(commandargs, stdout=subprocess.DEVNULL)
os.remove(tempq)
os.remove(tempdb)
def get_coupon_info(self):
"""
获取商品信息
:param url: 请求url
:param self.second_id: 商品分类id
:return:
"""
# 获取links.bin中的url
urls = read_file_to_url(LINKS_BIN)
for url in urls:
m = url.replace("\n", "").split("-")
url = m[0]
first_id = m[1]
second_id = self.get_id_for_url(url)
page = 0
while True:
try:
resp = fetch(self.get_url.format(id=second_id, page=page))
except RequestException as e:
resp = fetch(self.get_url.format(id=second_id, page=page))
log.logging.info('[warn] ineffective:{0}'.format(e))
if resp.text[0] == "<" or len(resp.json().get(
'data')['coupon_list']) == CouponList.ZERO:
log.logging.info(
'[INFO] Get {0} success'.format(second_id))
break
else:
if resp:
try:
if resp.json().get('data'):
log.logging.info('[INFO]page {0}'.format(page))
coupon = Coupon()
for info in resp.json().get(
'data')['coupon_list']:
coupon.second_id = second_id
coupon.first_id = first_id
coupon.title = info['title']
coupon.price = info['raw_price']
coupon.url = info['url']
coupon.thumbnail_pic = info[
'thumbnail_pic']
if Goods.save_coupon(coupon):
log.logging.info(
'[INFO] {0} save to database ok'.
format(coupon.title))
else:
log.logging.info(
'[INFO] {0} is existed'.format(
coupon.title))
page += 1
else:
log.logging.error('[ERROR] {0}'.format(
resp.text))
except Exception as e:
log.logging.error('[ERROR] {0}'.format(e))
else:
log.logging.info('[ERROR] resp is None')
# 一条url处理完成以后, 从文件中删除
delete_line(LINKS_BIN, url)
def get_spacerrepeatfiles():
spath = os.path.join(DATA_DIR, "spacerdatabase.txt")
surl = 'http://crispr.i2bc.paris-saclay.fr/crispr/BLAST/Spacer/Spacerdatabase'
rpath = os.path.join(DATA_DIR, "repeatdatabase.txt")
rurl = 'http://crispr.i2bc.paris-saclay.fr/crispr/BLAST/DR/DRdatabase'
fetch.fetch(spath, surl)
fetch.fetch(rpath, rurl)
return spath, rpath
def fetchgenbankfiles(gbdir='gbfiles'):
os.makedirs(gbdir, exist_ok=True)
for org in tqdm(Organism.objects.all()):
fpath = os.path.join(gbdir, '{}.gb'.format(org.accession))
if os.path.isfile(fpath):
continue
print('\nFetching {} with accession {}'.format(org.name,
org.accession))
fetch(os.path.join(fpath, '{}.gb'.format(org.accession)))
def get_spacer_repeat_files():
spath = os.path.join(DATA_DIR, "spacerdatabase.txt")
surl = ('http://crispr.i2bc.paris-saclay.fr/'
'crispr/BLAST/Spacer/Spacerdatabase')
rpath = os.path.join(DATA_DIR, "repeatdatabase.txt")
rurl = 'http://crispr.i2bc.paris-saclay.fr/crispr/BLAST/DR/DRdatabase'
fetch.fetch(spath, surl)
fetch.fetch(rpath, rurl)
return spath, rpath
def update():
if not os.path.isdir(STAT_PATH):
os.mkdir(STAT_PATH)
inputstr = '{'
result = json.loads(fetch("get", "problem?offset=0&limit=200", "{}").text)
counter_1 = 1
for i in range(0, len(result['data']['results'])):
real_id = result['data']['results'][i]['id']
display_id = result['data']['results'][i]['_id'].replace(" ", "_")
if counter_1 != 1:
inputstr += ','
inputstr += '"' + str(display_id) + '":{"_id":"' + str(real_id) + '"}'
counter_1 += 1
inputstr += '}'
f = open(os.path.join(STAT_PATH, "problem_mapping.json"), 'w')
f.write(inputstr)
f.close
print("Updated problems successfully!")
inputstr = '{'
result = json.loads(
fetch("get", "contests?offset=0&limit=10&status=0", "{}").text)
counter = 1
for i in range(0, len(result['data']['results'])):
contestid = result['data']['results'][i]['id']
payload = {"contest_id": str(contestid)}
endpoint = "contest/problem?contest_id=" + str(contestid)
result2 = json.loads(
fetch("get", "contest/problem?contest_id=" + str(contestid),
payload).text)
if result2["error"] == "error":
print("Error : " + result2["data"])
continue
q_string3 = result['data']['results'][i]["title"]
q_string2 = ""
for q1 in q_string3.split(" "):
try:
q_string2 += q1 + " "
except:
q_string2 += "XX "
q_string = result2['data'][0]['_id']
_pid = q_string.split()[0] + "+" + q_string.split()[1]
print("Found HomeWork: " + "hw" + str(counter) + " [" + q_string2 +
"]")
if counter != 1:
inputstr += ','
inputstr += '"hw' + str(counter) + '":{"contest_name":"' + str(
q_string2) + '","contest_id":' + str(
contestid) + ',"contest_problem_id":"' + str(
_pid) + '","problem_id":' + str(
result2["data"][0]["id"]) + '}'
counter += 1
inputstr += '}'
f = open(os.path.join(STAT_PATH, "assign_mapping.json"), 'w')
f.write(inputstr)
f.close
print("Updated assign successfully!")
def fetch_genbank_files(gbdir='gbfiles'):
os.makedirs(gbdir, exist_ok=True)
for org in tqdm(Organism.objects.all()):
fpath = os.path.join(gbdir, '{}.gb'.format(org.accession))
if os.path.isfile(fpath):
continue
print('\nFetching {} with accession {}'.format(
org.name,
org.accession
))
fetch(os.path.join(fpath, '{}.gb'.format(org.accession)))
def get_category(self, url):
"""
获取分类
:param url:一级分类的url
:return:
"""
try:
resp = fetch(url).text
except RequestException as e:
resp = fetch(url).text
log.logging.info('[warn] ineffective:{0}'.format(e))
html = etree.HTML(resp)
childs = html.xpath('/html/body/div[4]/div[1]/div/a')
for rc in childs[::-1]:
log.logging.info('[INFO] Get url: {0} >>> {1}'.format(
rc.attrib['href'], rc.text))
url = urllib.parse.urljoin(url, rc.attrib['href'])
url_join = url + "-" + self.first_id
if self.get_id_for_url(url): write_links(LINKS_BIN, url_join)
return
def get(assign_name):
with open(os.path.join(STAT_PATH, "assign_mapping.json"), "rt") as json_in:
assign_to_config = json.load(json_in)
if assign_name not in assign_to_config:
print("Invalid Assign Number!")
print("Available names are:")
for hwmap in assign_to_config:
print("- " + hwmap + " [" +
assign_to_config[hwmap]['contest_name'] + "]")
print(
"If you want to update latest homework assignment, type: [oj update] to update."
)
return
contest_id, problem_id = (
assign_to_config[assign_name]["contest_id"],
assign_to_config[assign_name]["contest_problem_id"],
)
endpoint = "contest/problem?contest_id={}&problem_id={}".format(
contest_id, problem_id)
result = json.loads(fetch("get", endpoint, {}).text)
data = result["data"]
if not data:
print("Unexpected Error with Server")
return
try:
samples = data["samples"]
except:
print("Unexpected Error in Parsing Response")
print(data)
return
template = None
if "C" in data["template"]:
template = data["template"]["C"]
else:
template = "#include <stdio.h>\n\nint main() {\n \n return 0;\n}\n"
dir_name = data["_id"].split(' ')[1]
print("Made a [{}] folder in your current directory.".format(dir_name))
template_path = dir_name + "/main.c"
if not os.path.isdir(dir_name):
os.mkdir(dir_name)
with open(template_path, "wt") as fout:
fout.write(template)
for idx, sample in enumerate(samples):
sample_num = idx + 1
input_sample_path = dir_name + "/" + "{}.in".format(sample_num)
input_ = sample["input"]
with open(input_sample_path, "wt") as fout:
fout.write(input_)
output_sample_path = dir_name + "/" + "{}.out".format(sample_num)
output = sample["output"]
with open(output_sample_path, "wt") as fout:
fout.write(output)
def submit(assign_number, filename):
with open(os.path.join(STAT_PATH, "assign_mapping.json"), "rt") as json_in:
assign_to_config = json.load(json_in)
if assign_number not in assign_to_config:
print("Invalid Assign Number!")
print("Available names are:")
for hwmap in assign_to_config:
print("- " + hwmap + " [" +
assign_to_config[hwmap]['contest_name'] + "]")
print(
"If you want to update latest homework assignment, type: [oj update] to update."
)
return
contest_id, problem_id = (
assign_to_config[assign_number]["contest_id"],
assign_to_config[assign_number]["problem_id"],
)
try:
with open(filename, "r") as fin:
code = fin.read()
except IOError:
print('File "' + filename + '" does not exist!')
return
payload = {
"problem_id": problem_id,
"language": "C",
"code": code,
"contest_id": contest_id,
}
try:
submission_response = json.loads(
fetch("post", "submission", payload).text)
except ValueError:
print("No response is received! Please contact class TA!")
response_data = submission_response["data"]
if response_data == "The contest have ended":
print("The contest has ended.")
return
try:
submission_id = response_data["submission_id"]
except TypeError:
if submission_response["error"] == "invalid-code":
print("You can't submit empty file.'")
return
print("Unknown error occuried!")
return
print("Submit successfully!\n" "Getting submission status...")
time.sleep(1.0)
status(submission_id)
def init_category(self):
"""
获取所有的一级分类
:return:
"""
log.logging.info('[INFO] Get category')
url = self.site_url
try:
res = fetch(url).text
except RequestException as e:
res = fetch(url).text
log.logging.info('[warn] ineffective:{0}'.format(e))
html = etree.HTML(res)
# 一级分类
root_brother = html.xpath("/html/body/div[3]/div/div/a")
# 所有的一级分类请求url
for rb in root_brother[::-1]:
log.logging.info('[INFO] Get url: {0} >>> {1}'.format(
rb.attrib['href'], rb.text))
url = urllib.parse.urljoin(url, rb.attrib['href'])
self.first_id = self.get_id_for_url(url)
self.get_category(urllib.parse.urljoin(url, rb.attrib['href']))
def login():
if not os.path.isdir(STAT_PATH):
os.makedirs(STAT_PATH)
if not os.path.isdir(COOKIE_FOLDER_PATH):
os.makedirs(COOKIE_FOLDER_PATH)
username = input("username: "******"password: "******"post", "login", value)
status = json.loads(r.text)
print(status["data"])
if not status["error"]:
f = open(os.path.join(COOKIE_FOLDER_PATH, "oj_cookies"), "w")
f.write('{"csrftoken": "' + r.cookies["csrftoken"] +
'" , "sessionid" : "' + r.cookies["sessionid"] + '"}')
f.close
