def add_token(args):
io.start('Adding token %s for user %s' %
(highlight(args.token), highlight(args.user)))
user = get(
config.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.api('rest1') + 'sys_sec_Token', data)
def wrapper(args):
global token
if args.as_user is None:
username = config.username()
else:
username = args.as_user
if args.with_password is None:
if args.as_user is None:
password = config.password()
else:
password = args.as_user
else:
password = args.with_password
login_url = config.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 resource_exists(resource_id, resource_type):
log.debug('Checking if %s %s exists' %
(resource_type.get_label(), resource_id))
response = get(
config.api('rest2') + resource_type.get_entity_id() + '?q=id==' +
resource_id)
return int(response.json()['total']) > 0
def add_theme(args):
"""
add_theme adds a theme to the stylesheet table
:param args: commandline arguments containing bootstrap3_theme and optionally bootstrap4_theme
:return: None
"""
_validate_args(args)
valid_types = {'text/css'}
api = config.api('add_theme')
paths = []
bs3_name = args.bootstrap3
bs4 = args.bootstrap4
paths = [bs3_name]
names = ['bootstrap3-style']
if bs4:
paths.append(bs4)
names.append('bootstrap4-style')
bs4_name = get_file_name_from_path(bs4)
io.start(
'Adding bootstrap 3 theme {} and bootstrap 4 theme {} to bootstrap themes'
.format(highlight(bs3_name), highlight(bs4_name)))
else:
io.start('Adding bootstrap 3 theme {} to bootstrap themes'.format(
highlight(bs3_name)))
if not args.from_path:
paths = [_get_path_from_quick_folders(theme) for theme in paths]
files = _prepare_files_for_upload(paths, names, valid_types)
post_files(files, api)
def one_resource_exists(resources, resource_type):
log.debug('Checking if one of [{}] exists in [{}]'.format(
','.join(resources), resource_type.get_label()))
response = get(
config.api('rest2') + resource_type.get_entity_id() +
'?q=id=in=({})'.format(','.join(resources)))
return int(response.json()['total']) > 0
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.api('member').format(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.api('rest1') + 'sys_md_Package', data)
def enable_theme(args):
"""
enable_theme enables a bootstrap theme
:param args: commandline arguments containing the id of the theme (without .css)
:exception McmdError: when applying the theme fails
:return None
"""
theme = args.theme.replace('.css', '').replace('.min', '')
io.start('Applying theme {}'.format(highlight(theme)))
# Resource can be bootstrap-name.min.css (if molgenis theme), or name.min.css (if uploaded .min.css), or
# name.css (if uploaded as .css).
if one_resource_exists([theme + '.min.css', theme + '.css', 'bootstrap-' + theme + '.min.css'], ResourceType.THEME):
# Molgenis themes start with bootstrap- but this is stripped from the name in the theme manager
try:
post(config.api('set_theme'), theme)
except:
post(config.api('set_theme'), theme.split('bootstrap-')[1])
else:
raise McmdError(
'Applying theme failed. No themes found containing {} in the name'.format(args.theme, 'sys_set_StyleSheet'))
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.api('rls'), data={'id': args.entity, 'rlsEnabled': False})
def add_logo(args):
"""
add_logo uploads a logo to add to the left top of the menu
:param args: commandline arguments containing path to logo
:return: None
"""
io.start('Adding logo from path {}'.format(highlight(args.logo)))
api = config.api('logo')
valid_types = {'image/jpeg', 'image/png', 'image/gif'}
logo = [args.logo]
if not args.from_path:
logo = [_get_path_from_quick_folders(args.logo)]
files = _prepare_files_for_upload(logo, ['logo'], valid_types)
post_files(files, api)
def _find_group(role):
io.debug('Fetching groups')
groups = get(config.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 _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.api('import'), file_path.resolve(), params)
import_run_url = urljoin(config.get('host', 'selected'), response.text)
status, message = _poll_for_completion(import_run_url)
if status == 'FAILED':
raise McmdError(message)
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.api('rest1') + 'sys_sec_User', {
'username': args.username,
'password_': password,
'changePassword': ch_pwd,
'Email': email,
'active': active,
'superuser': superuser
})
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.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 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.api('rls'), data={'id': args.entity,
'rlsEnabled': True})
def _delete_row(entity, row):
url = '{}{}'.format(config.api('rest2'), entity)
delete_data(url, [row])
def _delete_all_data(entity):
io.start('Deleting all data from entity {}'.format(highlight(entity)))
url = '{}{}'.format(config.api('rest1'), entity)
delete(url)
def import_by_url(params):
return _handle_request(
lambda: requests.post(config.api('import_url'),
headers=_get_default_headers(),
params=params))
def get_version():
response = get(urljoin(config.api('rest2'), 'version'))
return response.json()['molgenisVersion']
def user_exists(username):
log.debug('Checking if user %s exists' % username)
response = get(
config.api('rest2') + 'sys_sec_User?q=username==' + username)
return int(response.json()['total']) > 0
def role_exists(rolename):
log.debug('Checking if role %s exists' % rolename)
response = get(
config.api('rest2') + 'sys_sec_Role?q=name==' + rolename.upper())
return int(response.json()['total']) > 0
def add_group(args):
io.start('Adding group %s' % highlight(args.name))
post(config.api('group'), {'name': args.name.lower(), 'label': args.name})
