def test_use_hardlinks_config(self):
"""
Test that hardlinks are disabled by default and can be overridden.
"""
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
# Must be disabled in local.properties
config = BiomajConfig('local')
self.assertFalse(config.get_bool("use_hardlinks"))
# Must be enabled for hardlinks.properties (override)
config = BiomajConfig('hardlinks')
self.assertTrue(config.get_bool("use_hardlinks"))
# Reload file with use_hardlinks=1
BiomajConfig.load_config(self.utils.global_properties_hl,
allow_user_config=False)
config = BiomajConfig('local')
self.assertTrue(config.get_bool("use_hardlinks"))
def biomaj_daemon():
'''
Execute a command request (bank update, removal, ...)
'''
apikey = request.headers.get('Authorization')
token = None
if apikey:
bearer = apikey.split()
if bearer[0] == 'APIKEY':
token = bearer[1]
try:
params = request.get_json()
options = params['options']
options_object = Options(options)
options_object.token = token
options_object.user = None
options_object.redis_host = config['redis']['host']
options_object.redis_port = config['redis']['port']
options_object.redis_db = config['redis']['db']
options_object.redis_prefix = config['redis']['prefix']
user = None
if token:
proxy = Utils.get_service_endpoint(config, 'user')
r = requests.get(proxy + '/api/user/info/apikey/' + token)
if not r.status_code == 200:
abort(404, {'message': 'Invalid API Key or connection issue'})
user = r.json()['user']
if user:
options_object.user = user['id']
if options_object.maintenance in ['on', 'off']:
if not options_object.user or 'admin' not in config[
'biomaj'] or options_object.user not in config['biomaj'][
'admin']:
abort(401, {
'message':
'This action requires authentication with api key'
})
if options_object.bank:
bmaj_options = BmajOptions(options_object)
BiomajConfig(options_object.bank, bmaj_options)
if not options_object.search and not options_object.show and not options_object.check and not options_object.status:
if not user:
abort(
401, {
'message':
'This action requires authentication with api key'
})
(res, msg) = biomaj_client_action(options_object, config)
except Exception as e:
logging.exception(e)
return jsonify({'status': False, 'msg': str(e)})
return jsonify({'status': res, 'msg': msg})
def tearDown(self):
# Delete lock files
for bank_name in self.BANKS:
config = BiomajConfig(bank_name)
data_dir = config.get('data.dir')
lock_file = os.path.join(data_dir, 'local.lock')
if os.path.exists(lock_file):
os.remove(lock_file)
self.utils.clean()
def test_properties_override(self):
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
config = BiomajConfig('local')
ldap_host = config.get('ldap.host')
self.assertTrue(ldap_host == 'localhost')
os.environ['BIOMAJ_LDAP_HOST'] = 'someserver'
ldap_host = config.get('ldap.host')
self.assertTrue(ldap_host == 'someserver')
def test_check_method(self):
"""Check .name, .exe and .args are well check during bank configuration
checking"""
BiomajConfig.load_config(self.utils.global_properties)
for conf in [
'noname', 'noexe', 'noargs', 'prenoname', 'prenoexe',
'prenoargs', 'rmnoname', 'rmnoexe', 'rmnoargs'
]:
config = BiomajConfig(conf)
self.assertFalse(config.check())
def setUp(self):
self.utils = UtilsForTest()
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
self.config = BiomajConfig('testhttp')
self.http_parse = HTTPParse(
self.config.get('http.parse.dir.line'),
self.config.get('http.parse.file.line'),
int(self.config.get('http.group.dir.name')),
int(self.config.get('http.group.dir.date')),
int(self.config.get('http.group.file.name')),
int(self.config.get('http.group.file.date')),
self.config.get('http.group.file.date_format', None),
int(self.config.get('http.group.file.size')))
def setUp(self):
self.utils = UtilsForTest()
curdir = os.path.dirname(os.path.realpath(__file__))
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
# Delete all banks
b = Bank('alu')
b.banks.remove({})
self.config = BiomajConfig('alu')
data_dir = self.config.get('data.dir')
lock_file = os.path.join(data_dir, 'alu.lock')
if os.path.exists(lock_file):
os.remove(lock_file)
def setUp(self):
self.utils = UtilsForTest()
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
# Clean banks used in tests
for bank_name in self.BANKS:
# Delete all releases
b = Bank(bank_name)
b.banks.remove({})
# Delete lock files
config = BiomajConfig(bank_name)
data_dir = config.get('data.dir')
lock_file = os.path.join(data_dir, 'local.lock')
if os.path.exists(lock_file):
os.remove(lock_file)
def biomaj_daemon():
'''
List users
'''
apikey = request.headers.get('Authorization')
token = None
if apikey:
bearer = apikey.split()
if bearer[0] == 'APIKEY':
token = bearer[1]
try:
params = request.get_json()
options = params['options']
options_object = Options(options)
options_object.token = token
options_object.user = None
options_object.redis_host = config['redis']['host']
options_object.redis_port = config['redis']['port']
options_object.redis_db = config['redis']['db']
options_object.redis_prefix = config['redis']['prefix']
user = None
if token:
r = requests.get(config['web']['local_endpoint'] + '/api/user/info/apikey/' + token)
if not r.status_code == 200:
abort(404, {'message': 'Invalid API Key or connection issue'})
user = r.json()['user']
if user:
options_object.user = user['id']
if options_object.bank:
bmaj_options = BmajOptions(options_object)
BiomajConfig(options_object.bank, bmaj_options)
if not options_object.search and not options_object.show and not options_object.check and not options_object.status:
if not user:
abort(403, {'message': 'This action requires authentication with api key'})
(res, msg) = biomaj_client_action(options_object)
except Exception as e:
logging.exception(e)
return jsonify({'status': False, 'msg': str(e)})
return jsonify({'status': res, 'msg': msg})
def setUp(self):
BmajIndex.es = None
self.utils = UtilsForTest()
curdir = os.path.dirname(os.path.realpath(__file__))
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
if BmajIndex.do_index == False:
self.skipTest(
"Skipping indexing tests due to elasticsearch not available")
# Delete all banks
b = Bank('local')
b.banks.remove({})
BmajIndex.delete_all_bank('local')
self.config = BiomajConfig('local')
data_dir = self.config.get('data.dir')
lock_file = os.path.join(data_dir, 'local.lock')
if os.path.exists(lock_file):
os.remove(lock_file)