def setUp(self,
data_dir='example01',
bgen_names='chr{:d}impv1.bgen',
bgenix_path='bgenix',
user_pass_line=None):
super(TestRestApiGenotype, self).setUp()
# Load data
genoq = GenoQuery(get_repository_path(data_dir),
bgen_names=bgen_names,
bgenix_path=bgenix_path)
# Configure
app.app.config['testing'] = True
app.app.config['auth'] = None
app.app.config['genoquery'] = genoq
if user_pass_line is not None:
f = tempfile.NamedTemporaryFile(delete=False)
f.close()
with open(f.name, 'w') as fi:
fi.write(user_pass_line)
ph = PasswordHasher(f.name, method='pbkdf2:sha256')
app.app.config['auth'] = ph.setup_http_basic_auth()
self.app = app.app.test_client()
def test_process_users_file_file_does_not_exist_test00(self):
# prepare
users_file = get_repository_path('no/existing/file/here.txt')
# run
ph = PasswordHasher(users_file, method='pbkdf2:sha256')
ph.process_users_file()
def test_process_users_file_one_password_hashed_rest_not_test01(self):
# prepare
orig_user_file = get_repository_path('wsgi/test01/users.txt')
users_file = orig_user_file + '.bak'
copyfile(orig_user_file, users_file)
orig_users = self.load_data(orig_user_file)
# run
ph = PasswordHasher(users_file, method='pbkdf2:sha256')
ph.process_users_file()
# evaluate
assert os.path.isfile(users_file)
users = self.load_data(users_file)
assert len(users) == 3
for user, password in users.items():
assert user in orig_users.keys(), user
if user != 'adams':
assert password != orig_users[user], user + ' / ' + password + ' / ' + orig_users[user]
else:
assert password == users[user], user + password + ' / ' + users[user]
assert len(password) == 93, len(password)
os.remove(users_file)
def test_process_users_file_already_hashed_test00(self):
# prepare
orig_user_file = get_repository_path('wsgi/test00/users.txt')
users_file = orig_user_file + '.bak'
copyfile(orig_user_file, users_file)
orig_users = self.load_data(orig_user_file)
ph = PasswordHasher(users_file, method='pbkdf2:sha256')
ph.process_users_file()
users = self.load_data(users_file)
# run
ph = PasswordHasher(users_file, method='pbkdf2:sha256')
ph.process_users_file()
# evaluate
assert os.path.isfile(users_file)
new_users = self.load_data(users_file)
assert len(users) == 3
for user, password in new_users.items():
assert user in orig_users.keys(), user
assert password == users[user], password + ' / ' + users[user]
assert len(password) == 93, len(password)
os.remove(users_file)
def test_verify_password_users_file_none_test01(self):
# prepare
ph = PasswordHasher(None, method='pbkdf2:sha256')
ph.process_users_file()
# evaluate
assert ph.verify_password('milton', 'whatever')
assert ph.verify_password('john', 'mypassword')
assert ph.verify_password('adams', 'anotherpassword')
assert ph.verify_password('james', 'mypassword')
def test_verify_password_users_file_does_not_exist_test01(self):
# prepare
users_file = get_repository_path('no/existing/file/here.txt')
ph = PasswordHasher(users_file, method='pbkdf2:sha256')
ph.process_users_file()
# evaluate
assert not ph.verify_password('milton', 'whatever')
assert not ph.verify_password('john', 'mypassword')
assert not ph.verify_password('adams', 'anotherpassword')
assert not ph.verify_password('james', 'mypassword')
def test_verify_password_users_file_empty_test01(self):
# prepare
orig_user_file = get_repository_path('wsgi/test02/users.txt')
users_file = orig_user_file + '.bak'
ph = PasswordHasher(users_file, method='pbkdf2:sha256')
ph.process_users_file()
# evaluate
assert not ph.verify_password('milton', 'whatever')
assert not ph.verify_password('john', 'mypassword')
assert not ph.verify_password('adams', 'anotherpassword')
assert not ph.verify_password('james', 'mypassword')
genoq_parameters = config.get_genoquery_parameters()
genoq_parameters = update_parameters_from_args(genoq_parameters, args)
if parameter_empty(genoq_parameters, 'genotype_path'):
logger.warning('--genotype-path missing')
genoq = GenoQuery(**genoq_parameters)
app.config.update({'genoquery': genoq})
# Pheno2SQL
pheno2sql_parameters = config.get_pheno2sql_parameters()
pheno2sql_parameters = update_parameters_from_args(pheno2sql_parameters,
args)
if parameter_empty(pheno2sql_parameters, 'db_uri'):
parser.error('--db-uri missing')
p2sql = Pheno2SQL(**pheno2sql_parameters)
app.config.update({'pheno2sql': p2sql})
ph = PasswordHasher(args.users_file, method='pbkdf2:sha256')
ph.process_users_file()
auth = ph.setup_http_basic_auth()
app.config.update({'auth': auth})
app.run(host=str(args.host),
port=args.port,
debug=args.debug,
ssl_context='adhoc' if args.ssl_mode else None)
from ukbrest import config
from ukbrest.app import app
from ukbrest.common.genoquery import GenoQuery
from ukbrest.common.pheno2sql import Pheno2SQL
from ukbrest.common.utils.auth import PasswordHasher
def setup_app(app, ph):
# Add GenoQuery object
genoq = GenoQuery(**config.get_genoquery_parameters())
app.config.update({'genoquery': genoq})
# Add Pheno2SQL object
p2sql = Pheno2SQL(**config.get_pheno2sql_parameters())
app.config.update({'pheno2sql': p2sql})
# Add auth object
auth = ph.setup_http_basic_auth()
app.config.update({'auth': auth})
ph = PasswordHasher(config.http_auth_users_file, method='pbkdf2:sha256')
ph.process_users_file()
setup_app(app, ph)