def wrapper(args):
global token
if args.as_user is None:
username = config().get('auth', 'username')
else:
username = args.as_user
if args.with_password is None:
if args.as_user is None:
password = config().get('auth', 'password')
else:
password = args.as_user
else:
password = args.with_password
login_url = config().get('api', 'login')
io.debug('Logging in as user %s' % username)
response = post(login_url,
data={
"username": username,
"password": password
})
token = response.json()['token']
func(args)
def succeed():
global spinner
if spinner:
if config().has_option('set', 'unicorn_mode') and config().getboolean(
'set', 'unicorn_mode'):
spinner.stop_and_persist(symbol='🦄'.encode('utf-8'))
else:
spinner.succeed()
spinner = None
def add_token(args):
io.start('Adding token %s for user %s' %
(highlight(args.token), highlight(args.user)))
user = get(config().get('api', 'rest2') +
'sys_sec_User?attrs=id&q=username==%s' % args.user)
if user.json()['total'] == 0:
raise McmdError('Unknown user %s' % args.user)
user_id = user.json()['items'][0]['id']
data = {'User': user_id, 'token': args.token}
post(config().get('api', 'rest1') + 'sys_sec_Token', data)
def _do_import(file_path, package):
io.start('Importing %s' % (highlight(file_path.name)))
params = {'action': _get_import_action(file_path.name),
'metadataAction': 'upsert'}
if package:
params['packageId'] = package
response = post_file(config().get('api', 'import'), file_path.resolve(), params)
import_run_url = urljoin(config().get('api', 'host'), response.text)
status, message = _poll_for_completion(import_run_url)
if status == 'FAILED':
raise McmdError(message)
def make(args):
io.start('Making user %s a member of role %s' %
(highlight(args.user), highlight(args.role.upper())))
group_name = _find_group(args.role)
url = config().get('api', 'member') % group_name
post(url, {'username': args.user, 'roleName': args.role.upper()})
def add_package(args):
io.start('Adding package %s' % highlight(args.id))
data = {'id': args.id, 'label': args.id}
if args.parent:
data['parent'] = args.parent
post(config().get('api', 'rest1') + 'sys_md_Package', data)
def enable_rls(args):
io.start('Enabling row level security on entity type %s' %
highlight(args.entity))
ensure_resource_exists(args.entity, ResourceType.ENTITY_TYPE)
post(config().get('api', 'rls'),
data={
'id': args.entity,
'rlsEnabled': True
})
def _find_group(role):
io.debug('Fetching groups')
groups = get(config().get('api', 'rest2') + 'sys_sec_Group?attrs=name')
role = lower_kebab(role)
matches = {
len(group['name']): group['name']
for group in groups.json()['items'] if role.startswith(group['name'])
}
if not matches:
raise McmdError('No group found for role %s' % upper_snake(role))
return matches[max(matches, key=int)]
def enable_rls(args):
if not io.confirm(
'Are you sure you want to disable row level security on %s?' %
args.entity):
return
io.start('Disabling row level security on entity type %s' %
highlight(args.entity))
ensure_resource_exists(args.entity, ResourceType.ENTITY_TYPE)
post(config().get('api', 'rls'),
data={
'id': args.entity,
'rlsEnabled': False
})
def add_user(args):
io.start('Adding user %s' % highlight(args.username))
password = args.set_password if args.set_password else args.username
email = args.with_email if args.with_email else args.username + '@molgenis.org'
active = not args.is_inactive
superuser = args.is_superuser
ch_pwd = args.change_password
post(
config().get('api', 'rest1') + 'sys_sec_User', {
'username': args.username,
'password_': password,
'changePassword': ch_pwd,
'Email': email,
'active': active,
'superuser': superuser
})
def _import_from_url(args):
file_url = args.from_url
file_name = file_url.split("/")[-1]
io.start('Importing from URL %s' % highlight(file_url))
params = {'action': _get_import_action(file_name),
'metadataAction': 'upsert'}
if args.to_package:
params['packageId'] = args.to_package
params['url'] = file_url
response = import_by_url(params)
import_run_url = urljoin(config().get('api', 'host'), response.text)
status, message = _poll_for_completion(import_run_url)
if status == 'FAILED':
raise McmdError(message)
def grant(principal_type, principal_name, resource_type, identifier,
permission):
data = {'radio-' + identifier: permission}
if principal_type == PrincipalType.USER:
data['username'] = principal_name
elif principal_type == PrincipalType.ROLE:
data['rolename'] = principal_name.upper()
else:
raise McmdError('Unknown principal type: %s' % principal_type)
url = config().get('api', 'perm') + resource_type.get_resource_name(
) + '/' + principal_type.value
return _handle_request(lambda: requests.post(
url,
headers={
'Content-Type': 'application/x-www-form-urlencoded; charset=UTF-8',
'x-molgenis-token': token
},
data=data))
def user_exists(username):
log.debug('Checking if user %s exists' % username)
response = get(config().get('api', 'rest2') + 'sys_sec_User?q=username==' +
username)
return int(response.json()['total']) > 0
def _get_import_action(file_name):
if '.owl' in file_name or '.obo' in file_name:
return 'add'
else:
return config().get('set', 'import_action')
def add_group(args):
io.start('Adding group %s' % highlight(args.name))
post(config().get('api', 'group'), {
'name': args.name.lower(),
'label': args.name
})
def _get_molgenis_folders():
if not config().has_option('data', 'git_root') or not config().has_option('data', 'git_paths'):
io.info('Molgenis git paths not configured. Edit the mcmd.properties file to include the test data.')
return list()
else:
return config_string_to_paths(config().get('data', 'git_paths'))
def _get_quick_folders():
if not config().has_option('data', 'quick_folders'):
return list()
else:
return config_string_to_paths(config().get('data', 'quick_folders'))
def role_exists(rolename):
log.debug('Checking if role %s exists' % rolename)
response = get(config().get('api', 'rest2') + 'sys_sec_Role?q=name==' +
rolename.upper())
return int(response.json()['total']) > 0
def import_by_url(params):
return _handle_request(
lambda: requests.post(config().get('api', 'import_url'),
headers=_get_default_headers(),
params=params))
def resource_exists(resource_id, resource_type):
log.debug('Checking if %s %s exists' %
(resource_type.get_label(), resource_id))
response = get(config().get('api', 'rest2') +
resource_type.get_entity_id() + '?q=id==' + resource_id)
return int(response.json()['total']) > 0