def create_user():
try:
username = request.json["username"]
password = request.json["password"]
first_name = request.json["first_name"]
last_name = request.json["last_name"]
email = request.json["email"]
val = validate(username, password, first_name, last_name, email)
if val is not None:
return jsonify(val[0]), val[1]
# Encypt password
encrypted_password = bcrypt_sha256.encrypt(password)
user = User(username, encrypted_password, first_name, last_name, email)
user_dao.save(user)
return jsonify('User successfully created'), 201
except KeyError as ke:
user_sessionDB.rollback()
user_sessionDB.close()
return jsonify('Attribute ' + ke.args[0] + ' missing!'), 400
except IntegrityError as ie:
user_sessionDB.rollback()
user_sessionDB.close()
error = ie.args[0].split("\"")
print error[1]
return jsonify(error[1]), 500
def newPassword():
if request.method == 'POST':
dao.save(passwordItem(request.form['websiteName'],request.form['websiteLoginUrl'],request.form['userName'],encryptPasswordItem(request.form['password']),
datetime.now().strftime('%Y-%m-%d %H:%M:%S'),datetime.now().strftime('%Y-%m-%d %H:%M:%S'),request.form['securityLevel'],flask_login.current_user.__dict__['mobile']))
return redirect('/')
else:
return render_template('new_password.html',sites = dao.getAllSiteConfigs())
def register():
mobile = request.form['mobile']
if(dao.containsUser(mobile)):
return 'BAD REQUEST'
nickName = request.form['nickName']
masterPassword=request.form['masterPassword']
newUser = user(nickName,encrypt(masterPassword),mobile,'',True,datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
dao.save(newUser)
newUser.id=mobile
flask_login.login_user(newUser)
return redirect('/')
def new_security_notes():
result = {}
title = request.form['title']
detail = request.form['detail']
current_user = flask_login.current_user
eid = dao.save(securityNotes(title,detail,current_user.__dict__['mobile'],datetime.now().strftime('%Y-%m-%d %H:%M:%S'),datetime.now().strftime('%Y-%m-%d %H:%M:%S')))
result['id'] = eid
result['status'] = 'success'
return jsonify(**result)
def process(f):
df = pcl.pd_dataFrame(f)
msg = dao.save(df)
if msg == 'success':
return df
elif msg == 'error 1':
return 'error in connection'
elif msg == 'error 2':
return 'error in insert'
def process(f):
masterDataList = mapper.mapMasterData(f)
msg1 = dao.saveMasterData(masterDataList)
df = pcl.calc(f)
msg2 = dao.save(df)
if msg1 == 'success' and msg2 == 'success':
return "success"
else:
return "MASTER DATA UPLOAD : " + msg1 + " |###| PD SAVE : " + msg2
def check_watching():
if cfg.get('other', 'is_watching') == '1':
result = subprocess.Popen(['sudo iptables -L -v -n -x'],
stdout=subprocess.PIPE,
shell=True).communicate()
stdout = result[0]
stderr = result[1]
if stderr is None:
try:
# print stdout
length = len(user_list)
current_time = int(round(time.time() * 1000))
result = stdout.split("\n")[-length - 1:-1]
for i in range(length):
result[i] = Output(result[i].split()[-1].split(':')[1],
result[i].split()[1], current_time)
save(result[i])
# for item in result:
# print item
except Exception, e:
print str(e)
else:
print "check_watching error: " + stderr
def init_site() :
# remove('site_config')
for each_site in global_site:
if not containsSiteConfig(each_site.site_name) :
save(each_site)
def handlePair(foutdir,
sep=',',
dbname=None,
checkTMP=True,
jumpStep=None,
fin=None,
f2tmp_nonTtmp_info_qualified=None,
keepOne=False):
'''
数据量较少，直接逐行查询，很多蛋白被查询了多次
:param foutdir:
:param sep: sep of fin file
:parameter dbname: name of mongodb
:parameter jumpStep: skip some step in this method [1,2,3,4]
:parameter fin:ignore this parameter when 1 in jumpStep
:parameter f2tmp_nonTtmp_info_qualified: sign this path in the dir
:return:
fin = 'file/1intAct_pair_norepeat.txt'
foutdir = 'file/1positive'
handlePair(fin,foutdir)
'''
'''
config path
'''
f1tmp_nontmp_info = os.path.join(foutdir, '1tmp_nontmp_info.tsv')
f1TMP_nonTMP = os.path.join(foutdir, '1tmp_nontmp.tsv')
if not f2tmp_nonTtmp_info_qualified:
f2tmp_nonTtmp_info_qualified = os.path.join(
foutdir, '2tmp_nontmp_info_qualified.tsv')
fout_fasta = os.path.join(foutdir, '2pair.fasta')
fout_tmp_fasta = os.path.join(foutdir, '2tmp.fasta')
fout_nontmp_fasta = os.path.join(foutdir, '2nontmp.fasta')
f2positive = os.path.join(foutdir, '2pair.tsv')
f2tmp = os.path.join(foutdir, '2tmp.list')
f2nontmp = os.path.join(foutdir, '2nontmp.list')
f2all = os.path.join(foutdir, '2all.list')
f2tmp_info = os.path.join(foutdir, '2tmp_info.tsv')
f2nontmp_info = os.path.join(foutdir, '2nontmp_info.tsv')
f2all_info = os.path.join(foutdir, '2all_info.tsv')
f3subcell = os.path.join(foutdir, '3subcellular.tsv')
'''
1. get tmp nontmp pair
time 1766.4131457805634
'''
if jumpStep == None or 1 not in jumpStep:
getPairInfo_TMP_nonTMP(fin,
f1tmp_nontmp_info,
sep=sep,
checkTMP=checkTMP,
keepOne=keepOne)
simplifyTable(f1tmp_nontmp_info, f1TMP_nonTMP)
'''
2. get qualified tmp nontmp pair
'''
if jumpStep == None or 2 not in jumpStep:
saveQualified(f1tmp_nontmp_info, f2tmp_nonTtmp_info_qualified)
'''
3. get related list,fasta,pair
'''
if jumpStep == None or 3 not in jumpStep:
simplifyTable(f2tmp_nonTtmp_info_qualified, f2positive)
extractPairAndFasta(f2tmp_nonTtmp_info_qualified,
fout_fasta,
fout_tmp_fasta=fout_tmp_fasta,
fout_nontmp_fasta=fout_nontmp_fasta)
getproteinlist(f2tmp_nonTtmp_info_qualified,
ftmp=f2tmp,
fnontmp=f2nontmp,
fall=f2all,
ftmp_info=f2tmp_info,
ftmp_nontmp_info=f2nontmp_info,
fall_info=f2all_info)
'''
4. save to mongodb
'''
if jumpStep == None or (4 not in jumpStep and dbname):
notsvaelist = save(readIDlist(f2all), dbname)
print('those protein not save in the mongodb', notsvaelist)
'''
5. calcu subcellular
'''
if jumpStep == None or 5 not in jumpStep:
handleRow(f2tmp_nonTtmp_info_qualified, f3subcell, calcuSubcell)
