def start(message):
global spinner
if config.has_option('settings', 'non_interactive') and config.get('settings', 'non_interactive') is True:
print(message)
else:
spinner = _new_spinner()
spinner.start(message)
def _get_import_action(file_name):
file_name = file_name.rstrip('.gz')
file_name = file_name.rstrip('.zip')
for file_type, action in _IMPORT_ACTIONS.items():
if file_name.endswith(file_type):
return action
return config.get('settings', 'import_action')
def raise_if_non_interactive(message: str):
if config.is_loaded() and config.get('settings', 'non_interactive'):
raise McmdError(
'User input required but running in non-interactive mode. Message: {}'
.format(message),
info=
"Please specify your command more precisely or switch to interactive mode with 'mcmd "
"config set interactive'")
def test_ping_online(capsys):
exit_code = run_commander('ping')
assert exit_code == 1
captured = capsys.readouterr().out
assert 'Online' in captured
assert 'Version' in captured
assert config.get('host', 'selected') in captured
assert config.username() in captured
def succeed():
global spinner
if spinner:
if config.has_option('settings', 'unicorn_mode') and config.get('settings', 'unicorn_mode'):
spinner.stop_and_persist(symbol='🦄'.encode('utf-8'))
else:
spinner.succeed()
spinner = None
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 = ask.multi_choice('Please select a host:', urls)
io.start("Switching to host {}".format(highlight(url)))
config.set_host(url)
def _get_version():
try:
response = requests.get(urljoin(config.get('host', 'selected'), 'api/v2/version'),
headers={'Content-Type': 'application/json'})
response.raise_for_status()
global _version
global _version_number
_version = response.json()['molgenisVersion']
_version_number = _extract_version_number(_version)
except HTTPError as e:
raise McmdError(str(e))
except requests.exceptions.ConnectionError:
raise MolgenisOfflineError()
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 _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 _do_import(file_path, package, entity_type_id, import_action):
io.start('Importing %s' % (highlight(file_path.name)))
if import_action:
action = import_action
else:
action = _get_import_action(file_path.name)
params = {'action': action, 'metadataAction': 'upsert'}
if package:
params['packageId'] = package
if entity_type_id:
params['entityTypeId'] = entity_type_id
response = post_file(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 _import_from_url(args):
file_url = args.resource
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('host', 'selected'), response.text)
status, message = _poll_for_completion(import_run_url)
if status == 'FAILED':
raise McmdError(message)
def wrapper(*args, **kwargs):
return urljoin(config.get('host', 'selected'),
quote(func(*args, **kwargs)))
def get_resource_folders(self) -> List[Path]:
return [
Path(folder)
for folder in config.get('resources', 'resource_folders')
]
def _get_dataset_folders():
return [
Path(folder) for folder in config.get('resources', 'dataset_folders')
]
def _get_import_action(file_name):
if '.owl' in file_name or '.obo' in file_name:
return 'add'
else:
return config.get('settings', 'import_action')
