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 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 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_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 ping(args):
host = config.get('host', 'selected')
user = config.username()
status = Fore.LIGHTGREEN_EX + 'Online' + Fore.RESET
try:
version = get_version()
except McmdError:
status = Fore.LIGHTRED_EX + 'Offline' + Fore.RESET
version = None
print(' Host: ' + highlight(host))
print(' Status: ' + status)
if version:
print('Version: ' + highlight(version))
print(' User: ' + highlight(user))
def give(args):
# Convert synonyms to correct permission type
if args.permission in _PERMISSION_SYNONYMS:
args.permission = _PERMISSION_SYNONYMS[args.permission]
# The PermissionManagerController always gives 200 OK so we need to validate everything ourselves
resource_type = _get_resource_type(args)
principal_type = _get_principal_type(args)
io.start('Giving %s %s permission to %s on %s %s' %
(principal_type.value, highlight(
args.receiver), highlight(args.permission),
resource_type.get_label().lower(), highlight(args.resource)))
grant(principal_type, args.receiver, resource_type, args.resource,
args.permission)
def _install(default_config):
mcmd.io.info(
"Looks like this is your first time running {}!\n "
"Let's take a moment to set things up. It's OK to leave some fields empty, you can always change "
"them later.".format(highlight("Molgenis Commander")))
mcmd.io.newline()
for configurer in property_configurers().values():
configurer(default_config)
config.set_config(default_config)
mcmd.io.newline()
mcmd.io.info('The configuration file has been created at {}'.format(
highlight(str(get_properties_file()))))
exit(0)
def _remove_script(script_name):
path = get_scripts_folder().joinpath(script_name)
_check_script_exists(path)
try:
io.start('Removing script %s' % highlight(script_name))
path.unlink()
except OSError as e:
raise McmdError('Error removing script: %s' % str(e))
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 config_set_host(args):
if args.url:
url = args.url
else:
auths = config.get('host', 'auth')
urls = [auth['url'] for auth in auths]
url = io.multi_choice('Please select a host:', urls)
io.start("Switching to host {}".format(highlight(url)))
config.set_host(url)
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 _download_attachment(attachment, issue_num):
issue_folder = get_issues_folder().joinpath(issue_num)
issue_folder.mkdir(parents=True, exist_ok=True)
file_path = issue_folder.joinpath(attachment.name)
if file_path.exists():
overwrite = io.confirm('File %s already exists. Re-download?' % file_path.name)
if not overwrite:
return file_path
io.start('Downloading %s from GitHub issue %s' % (highlight(attachment.name), highlight('#' + issue_num)))
try:
r = requests.get(attachment.url)
r.raise_for_status()
with file_path.open('wb') as f:
f.write(r.content)
except (OSError, requests.RequestException, requests.HTTPError) as e:
raise McmdError('Error downloading GitHub attachment: %s' % str(e))
io.succeed()
return file_path
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 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 _upgrade(default_config, user_config):
mcmd.io.info(
"Some properties haven't been configured yet. Let's take a moment to fix that."
)
mcmd.io.newline()
for prop, configurer in property_configurers().items():
if prop not in user_config:
configurer(default_config)
config.set_config(default_config)
mcmd.io.newline()
mcmd.io.info(
'The configuration file has been updated succesfully ({})'.format(
highlight(str(get_properties_file()))))
exit(0)
def _add_host():
url = io.input_("Enter the URL of the host", required=True)
if config.host_exists(url):
raise McmdError("A host with URL {} already exists.".format(url))
username = io.input_(
"Enter the username of the superuser (Default: admin)")
password = io.password(
"Enter the password of the superuser (Default: admin)")
username = '******' if len(username) == 0 else username
password = '******' if len(password) == 0 else password
io.start("Adding host {}".format(highlight(url)))
config.add_host(url, username, password)
io.succeed()
return url
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 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 add_group(args):
io.start('Adding group %s' % highlight(args.name))
post(config().get('api', 'group'), {
'name': args.name.lower(),
'label': args.name
})
def _switch_to_new_host(url):
if io.confirm("Do you want to switch to the new host?"):
io.start("Switching to host {}".format(highlight(url)))
config.set_host(url)
def _import_from_path(args):
io.start('Importing from path %s' % highlight(args.file))
file = Path(args.file)
if not file.is_file():
raise McmdError("File %s doesn't exist" % str(file.resolve()))
_do_import(file, args.to_package)
def _delete_entity_type(entity):
io.start('Deleting entity {}'.format(highlight(entity)))
_delete_row('sys_md_EntityType', entity)
def _delete_all_data(entity):
io.start('Deleting all data from entity {}'.format(highlight(entity)))
url = '{}{}'.format(config.api('rest1'), entity)
delete(url)
