def _poll_for_completion(url):
def step_function(step):
"""Increases time between polls with one second each time, with a maximum of 10 seconds."""
step += 1
return min(step, 10)
polling.poll(lambda: get(url).json()['status'] != 'RUNNING',
step=0,
step_function=step_function,
poll_forever=True)
import_run = get(url).json()
return import_run['status'], import_run['message']
def _get_settings():
molgenis_settings = get(api.rest2('sys_md_EntityType'),
params={
'q': 'extends==sys_set_settings',
'attrs': '~id'
}).json()['items']
return [setting['id'] for setting in molgenis_settings]
def _get_group_id(group_name) -> str:
groups = get(api.rest2('sys_sec_Group'),
params={
'attrs': 'id',
'q': 'name=={}'.format(group_name)
}).json()['items']
if len(groups) == 0:
raise McmdError('No group found with name {}'.format(groups))
else:
return groups[0]['id']
def _get_user(user_name: str) -> User:
users = get(api.rest2('sys_sec_User'),
params={
'attrs': 'id,username',
'q': 'username=={}'.format(user_name)
}).json()['items']
if len(users) == 0:
raise McmdError('Unknown user {}'.format(user_name))
else:
return map_to_user(users[0])
def _get_role(role_name: str) -> Role:
roles = get(api.rest2('sys_sec_Role'),
params={
'attrs': 'id,name,label,group(id,name)',
'q': 'name=={}'.format(role_name)
}).json()['items']
if len(roles) == 0:
raise McmdError('No role found with name {}'.format(role_name))
else:
return map_to_role(roles[0])
def _get_group_roles(group: Group) -> List[Role]:
roles = get(api.rest2('sys_sec_Role'),
params={
'attrs': 'id,name,label,group(id,name)',
'q': 'group=={}'.format(group.id)
}).json()['items']
if len(roles) == 0:
raise McmdError('No roles found for group {}'.format(group.name))
return [map_to_role(role) for role in roles]
def _is_member(user: User, role: Role) -> bool:
memberships = get(api.rest2('sys_sec_RoleMembership'),
params={
'attrs':
'id',
'q':
"user=={};role=={};(to=='',to=ge={})".format(
user.id, role.id, timestamp())
}).json()['items']
return len(memberships) > 0
def _delete_packages_in_package(package_id):
response = client.get(api.rest2(ResourceType.PACKAGE.get_entity_id()),
params={
'attrs': 'id',
'q': 'parent==' + package_id
})
package_ids = [
entity_type['id'] for entity_type in response.json()['items']
]
if len(package_ids) > 0:
_delete_rows(ResourceType.PACKAGE.get_entity_id(), package_ids)
def _delete_entity_type_attribute(args):
if args.force or (not args.force and mcmd.io.ask.confirm(
'Are you sure you want to delete attribute {} of entity type {}?'.
format(args.attribute, args.resource))):
io.start('Deleting attribute {} of entity {}'.format(
highlight(args.attribute), highlight(args.resource)))
response = client.get(api.rest2('sys_md_Attribute'),
params={
'q':
'entity=={};name=={}'.format(
args.resource, args.attribute)
})
attribute_id = response.json()['items'][0]['id']
client.delete(api.rest2('sys_md_Attribute/{}'.format(attribute_id)))
def add_token(args):
io.start('Adding token %s for user %s' %
(highlight(args.token), highlight(args.user)))
user = get(api.rest2('sys_sec_User'),
params={
'attrs': 'id',
'q': 'username=={}'.format(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(api.rest1('sys_sec_Token'), data=data)
def _get_role_ids(role_names) -> List[str]:
roles = get(api.rest2('sys_sec_Role'),
params={
'attrs': 'id,name',
'q': 'name=in=({})'.format(','.join(role_names))
}).json()['items']
name_to_id = {role['name']: role['id'] for role in roles}
not_found = list()
for role_name in role_names:
if role_name not in name_to_id:
not_found.append(role_name)
if len(not_found) > 0:
raise McmdError("Couldn't find role(s) {}".format(
' and '.join(not_found)))
else:
return list(name_to_id.values())
def _get_group_membership(user: User,
group: Group) -> Optional[RoleMembership]:
group_roles = _get_group_roles(group)
group_role_ids = [role.id for role in group_roles]
memberships = get(
api.rest2('sys_sec_RoleMembership'),
params={
'attrs':
'id,user(id,username),role(id,name,label,group(id,name))',
'q':
"user=={};role=in=({});(to=='',to=ge={})".format(
user.id, ','.join(group_role_ids), timestamp())
}).json()['items']
if len(memberships) == 0:
return None
else:
return map_to_role_membership(memberships[0])
def _get_first_row_id(entity):
settings = get(api.rest2(entity), params={'attrs': '~id'}).json()['items']
return settings[0]['id']
def role_exists(role_input):
log.debug('Checking if role %s exists' % role_input)
response = get(api.rest2('sys_sec_Role'),
params={'q': 'name==' + to_role_name(role_input)})
return int(response.json()['total']) > 0
def user_exists(username):
log.debug('Checking if user %s exists' % username)
response = get(api.rest2('sys_sec_User'),
params={'q': 'username==' + username})
return int(response.json()['total']) > 0
