def set_password(self, password):
"""
Sets a password on a the inbox that this instance represents.
password -- plaintext string representation of the password
"""
if self.has_password():
#We already have a password and a salt ^_^
hash, salt = parse_hash(self.password_hash)
new_hash = make_hash(settings.INBOX_SETTINGS['hash_secret'], password, salt)
self.password_hash = new_hash
self.save()
else:
#We never had a password or don't have one set atm
new_hash = make_hash(settings.INBOX_SETTINGS['hash_secret'], password)
#i = EmailUser(email_address = self.email_address, password_protected = True, password_hash = new_hash)
#i.save()
self.password_protected = True
self.password_hash = new_hash
self.save()
def wrapper(self, *args, **kwargs):
#print("Inside wrapped_f()" )
#print("Decorator arguments:", arg1, arg2, arg3 )
macro = args[0]
if 'cache_mode' in kwargs:
pass
#print(kwargs['cache_mode'])
print( make_hash(macro) )
output = f(self,*args,**kwargs)
return output
def create_user(username, email, password):
'''Register user and return user object'''
password_hash = utils.make_hash(password)
new_user = User(username=username,
password=password_hash,
email=email)
new_user.is_admin = False
try:
new_user.put()
except:
return None
new_user.user_id = new_user.key().id()
return new_user
def get_poly_quadkeys(poly, zoom, override=False, name=None, **kwargs):
if name is None:
name = utils.make_hash(':'.join([str(poly), str(kwargs)]))
filename = '_'.join(['poly', name, 'quadkeys', str(zoom)]) + '.pkl'
filePath = os.path.join(repoPath, 'resources', filename)
if os.path.isfile(filePath) and not override:
with open(filePath, 'rb') as f:
return pickle.load(f)
else:
out = make_poly_quadkey(poly, zoom, **kwargs)
with open(filePath, 'wb') as f:
pickle.dump(out, f)
return out
def post(self):
data = {}
for attr in self.request.arguments:
data_attr = self.get_argument("password", None)
if data_attr:
if attr == 'password':
data.update({'password': utils.make_hash(self.get_argument("password"))})
else:
data.update({attr: str(self.get_argument(attr))})
if data:
user = User(**data)
user.save()
self.redirect(self.reverse_url('login'))
def register():
error = None
username = ""
password1 = ""
password2 = ""
nickname = ""
gender = ""
if request.method == 'POST':
username = request.form['username']
password1 = request.form['password1']
password2 = request.form['password2']
nickname = request.form['nickname']
gender = request.form['gender']
if not username:
error = 'username is required'
elif not nickname:
error = 'nickname is required'
elif not gender:
error = 'gender is required'
elif not password1 or not password2:
error = 'password is required'
elif password1 != password2:
error = 'password is not match'
else:
cur = g.db.execute("SELECT username FROM accounts WHERE username=?", (username,))
row = cur.fetchone()
print row
if row and row[1]:
error = 'username is already exists'
else:
created_at = datetime.strftime(datetime.now(), app.config['DATE_FORMAT'])
p_hash = utils.make_hash(username, app.config['SECRET_KEY'], password2)
print 'register,username='******'password='******'hash=', p_hash
g.db.execute(
"INSERT INTO accounts (username,password,nickname,gender,created_at,created_ip) "
"VALUES (?,?,?,?,?,?)",
(username, p_hash, nickname, gender, created_at, request.remote_addr,))
g.db.commit()
result = g.db.execute('SELECT id,username,nickname FROM accounts WHERE username=?',
(username,)).fetchone()
print 'register,result=', result
if result:
session['logged_in'] = True
session['logged_user'] = request.form['username']
flash('You were logged in')
return redirect(url_for('show_entries'))
else:
error = 'register failed'
return render_template('register.html', error=error, username=username, nickname=nickname, gender=gender)
def get_intersection_weights(fromFrm,
toFrm,
override=False,
name=None,
**kwargs):
if name is None:
name = '_'.join([
utils.make_hash(str(pickle.dumps(frm)) + ':' + str(kwargs))
for frm in [fromFrm, toFrm]
])
filename = '_'.join(['intersectionWeights', name]) + '.pkl'
filePath = os.path.join(repoPath, 'resources', filename)
if os.path.isfile(filePath) and not override:
with open(filePath, 'rb') as f:
return pickle.load(f)
else:
out = make_intersection_weights(fromFrm, toFrm)
with open(filePath, 'wb') as f:
pickle.dump(out, f)
return out
def get_frm_poly(frm, override=False, name=None, **kwargs):
if name is None:
geoms = list(frm['geometry'])
geomSizes = [geom.area for geom in geoms]
geoms = [
pair[0]
for pair in sorted(zip(geoms, geomSizes), key=lambda x: x[1])
]
strGeoms = ';'.join(str(geom) for geom in geoms)
strGeoms += ':' + str(kwargs)
name = utils.make_hash(strGeoms)
filename = '_'.join(['poly', name]) + '.pkl'
filePath = os.path.join(repoPath, 'resources', filename)
if os.path.isfile(filePath) and not override:
with open(filePath, 'rb') as f:
return pickle.load(f)
else:
out = make_frm_poly(frm, **kwargs)
with open(filePath, 'wb') as f:
pickle.dump(out, f)
return out
def __init__(self, text, settings, init_from_hash=None):
"""
Creates the necessary directories and the makefile for this
text and the JSON settings.
"""
self.status = None
self.queues = []
if init_from_hash:
self.build_hash = init_from_hash
else:
self.text = text
self.makefile_contents = makefile(settings)
self.build_hash = make_hash(self.text, self.makefile_contents)
self.settings = settings
# Directories
self.directory = os.path.join(Config.directory, self.build_hash)
self.original_dir = os.path.join(self.directory, 'original')
self.annotations_dir = os.path.join(self.directory, 'annotations')
self.export_dir = os.path.join(self.directory, 'export')
self.warnings_log_file = os.path.join(self.directory,'warnings.log');
# and files
self.makefile = os.path.join(self.directory, 'Makefile')
self.settings_file = os.path.join(self.directory, 'settings.json')
self.text_file = os.path.join(self.original_dir, 'text.xml')
# Deem this build as accessed now.
self.access()
# Output from make, line by line
self.make_out = []
# Set increments to dummy values
self.command = ""
self.steps = 0
self.step = 0
def createSessionCookie(self,userId):
userHash = utils.make_hash(userId,userId)
self.response.headers.add_header("Set-Cookie", "userId = %s; Path = /" %userHash)
return userHash
def __init__(self, text, settings, files=None, init_from_hash=None, resuming=False):
"""
Create the necessary directories and the makefile for this
text and the JSON settings.
"""
self.status = None
self.queues = []
self.files = files
if init_from_hash:
self.build_hash = init_from_hash
# File upload:
if init_from_hash.endswith(Config.fileupload_ext):
original_dir = os.path.join(os.path.join(Config.builds_dir, self.build_hash), 'original')
filelist = []
for root, dirs, files in os.walk(original_dir):
for infile in files:
with open(os.path.join(root, infile), "r") as f:
text = f.read()
fname = infile[:infile.rfind(".")]
filelist.append((fname, text))
self.files = filelist
else:
self.text = text
self.filename = 'text'
else:
self.makefile_contents = makefile(settings)
self.settings = settings
# File upload
if files:
self.text = "\n".join(text for _fn, text in files)
filenames = " ".join(fn for fn, _text in files)
self.build_hash = make_hash(self.text, self.makefile_contents, filenames) + Config.fileupload_ext
else:
self.text = text
self.filename = 'text'
self.build_hash = make_hash(self.text, self.makefile_contents)
# Directories
self.directory = os.path.join(Config.builds_dir, self.build_hash)
self.original_dir = os.path.join(self.directory, 'original')
self.annotations_dir = os.path.join(self.directory, 'annotations')
self.export_dir = os.path.join(self.directory, 'export.original')
# Files
self.makefile = os.path.join(self.directory, 'Makefile')
self.warnings_log_file = os.path.join(self.directory, 'warnings.log')
self.accessed_file = os.path.join(self.directory, 'accessed')
self.settings_file = os.path.join(self.directory, 'settings.json')
self.zipfpath = os.path.join(self.directory, "export.zip")
self.zipfile = "export.zip"
if not files:
self.text_file = os.path.join(self.original_dir, self.filename + '.xml')
self.result_file_path = os.path.join(self.export_dir, self.filename + '.xml')
self.result_file = self.filename + '.xml'
# Deem this build as accessed now, unless resuming an old build
self.access(resuming)
# Output from make, line by line
self.make_out = []
# Set increments to dummy values
self.command = ""
self.steps = 0
self.step = 0
def get_hash(self):
if not self.hash:
self.hash = make_hash(self.url)
return self.hash
def hashPass(self, password):
hashedPass = utils.make_hash(password)
return hashedPass
def register():
error = None
username = ""
password1 = ""
password2 = ""
nickname = ""
gender = ""
if request.method == 'POST':
username = request.form['username']
password1 = request.form['password1']
password2 = request.form['password2']
nickname = request.form['nickname']
gender = request.form['gender']
if not username:
error = 'username is required'
elif not nickname:
error = 'nickname is required'
elif not gender:
error = 'gender is required'
elif not password1 or not password2:
error = 'password is required'
elif password1 != password2:
error = 'password is not match'
else:
cur = g.db.execute(
"SELECT username FROM accounts WHERE username=?", (username, ))
row = cur.fetchone()
print row
if row and row[1]:
error = 'username is already exists'
else:
created_at = datetime.strftime(datetime.now(),
app.config['DATE_FORMAT'])
p_hash = utils.make_hash(username, app.config['SECRET_KEY'],
password2)
print 'register,username='******'password='******'hash=', p_hash
g.db.execute(
"INSERT INTO accounts (username,password,nickname,gender,created_at,created_ip) "
"VALUES (?,?,?,?,?,?)", (
username,
p_hash,
nickname,
gender,
created_at,
request.remote_addr,
))
g.db.commit()
result = g.db.execute(
'SELECT id,username,nickname FROM accounts WHERE username=?',
(username, )).fetchone()
print 'register,result=', result
if result:
session['logged_in'] = True
session['logged_user'] = request.form['username']
flash('You were logged in')
return redirect(url_for('show_entries'))
else:
error = 'register failed'
return render_template('register.html',
error=error,
username=username,
nickname=nickname,
gender=gender)
logging.info(f"Command executed: {' '.join(sys.argv)}")
logging.info("Starting outside variant pipeline analysis")
file1 = args.case_gen
file2 = args.control_gen
pairing = args.SNP_pairs
init_file = args.init_file
p_file = args.output_folder
override_folder = args.override
odds_file = ""
logging.info("Initializing pipeline. This might take a few seconds.")
args.exec_dir = os.getcwd()
with cd(args.input_folder_path):
pipe = Pipeline.init_from_file(
init_file, file1, file2, pairing, p_file, odds_file, args)
logging.info("Making output directory")
working_dir = make_working_dir(p_file, override_folder)
pipe.working_dir = working_dir
pipe.p_value_filename = p_file.split("/")[-1]
pipe.hash = make_hash(args.input_folder_path, init_file,
file1, file2, pairing, args.unique_identifier)
with cd(args.input_folder_path):
pipe.read_input_files()
logging.info("Running pipeline...")
with cd(pipe.working_dir):
pipe.run()
def get_hash(self):
if not self.hash:
self.hash = make_hash(self.url)
return self.hash
job_dir = "%s/.job" % (output_dir)
out_dir = "%s/.out" % (output_dir)
for new_dir in [output_dir, job_dir, out_dir]:
if not os.path.exists(new_dir):
os.mkdir(new_dir)
files = [
os.path.join(trajectory_folder, f) for f in os.listdir(trajectory_folder)
if f[-3:] == 'pkl'
]
file_lists = files_by_params(files, bools, duration=50., max_seed=0)
for file_list in file_lists:
traj = ",".join(sorted(file_list))
hash_code = make_hash(traj)
output = '%s/diffusion_map_%s.pkl' % (diffusion_maps_folder, hash_code)
filey_loc = os.path.join(job_dir, "diff_map.job")
filey = open(filey_loc, "w")
filey.writelines("#!/bin/bash\n")
filey.writelines("#SBATCH --job-name=diff_map\n")
filey.writelines("#SBATCH --output=%s/diff_map_%s.out\n" %
(out_dir, hash_code))
filey.writelines("#SBATCH --error=%s/diff_map_%s.err\n" %
(out_dir, hash_code))
filey.writelines("#SBATCH --time=2-00:00\n")
filey.writelines("#SBATCH --mem=%s\n" % (memory))
if os.path.exists(output) and overwrite is False:
print("File exists and overwrite is False! Aborting diffusion map:\n" +
def cache_file(self):
# todo make this filename the hash of the url
h = utils.make_hash(self.url)
return "{}/debate_{}.json".format(self.cache_folder,h)
