def biomaj_daemon_bank_update(bank):
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
if not options.user:
abort(401, 'This action requires authentication with api key')
options.update = True
options.bank = bank
params = request.get_json()
if params is None:
params = {}
if 'publish' in params:
options.publish = params['publish']
if 'fromscratch' in params:
options.fromscratch = params['fromscratch']
if 'stop_before' in params:
options.stop_before = params['stop_before']
if 'stop_after' in params:
options.stop_after = params['stop_after']
if 'from_task' in params:
options.from_task = params['from_task']
if 'process' in params:
options.process = params['process']
if 'release' in params:
options.release = params['release']
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_bank_remove(bank):
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
if not options.user:
abort(401, 'This action requires authentication with api key')
options.bank = bank
params = request.get_json()
if params is None:
params = {}
if 'all' in params and params['all']:
options.removeall = True
if 'force' in params and params['force']:
options.force = params['force']
elif 'pending' in params and params['pending']:
options.removepending = True
else:
options.remove = True
if 'release' in params:
options.release = params['release']
else:
abort(400, 'missing release')
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon():
'''
Execute a command request (bank update, removal, ...)
'''
apikey = request.headers.get('Authorization')
token = None
if apikey:
bearer = apikey.split()
if bearer[0] == 'APIKEY':
token = bearer[1]
try:
params = request.get_json()
options = params['options']
options_object = Options(options)
options_object.token = token
options_object.user = None
options_object.redis_host = config['redis']['host']
options_object.redis_port = config['redis']['port']
options_object.redis_db = config['redis']['db']
options_object.redis_prefix = config['redis']['prefix']
user = None
if token:
proxy = Utils.get_service_endpoint(config, 'user')
r = requests.get(proxy + '/api/user/info/apikey/' + token)
if not r.status_code == 200:
abort(404, {'message': 'Invalid API Key or connection issue'})
user = r.json()['user']
if user:
options_object.user = user['id']
if options_object.maintenance in ['on', 'off']:
if not options_object.user or 'admin' not in config[
'biomaj'] or options_object.user not in config['biomaj'][
'admin']:
abort(401, {
'message':
'This action requires authentication with api key'
})
if options_object.bank:
bmaj_options = BmajOptions(options_object)
BiomajConfig(options_object.bank, bmaj_options)
if not options_object.search and not options_object.show and not options_object.check and not options_object.status:
if not user:
abort(
401, {
'message':
'This action requires authentication with api key'
})
(res, msg) = biomaj_client_action(options_object, config)
except Exception as e:
logging.exception(e)
return jsonify({'status': False, 'msg': str(e)})
return jsonify({'status': res, 'msg': msg})
def biomaj_daemon_bank_status_ko():
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
options.statusko = True
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_history():
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
options.history = True
options.historyLimit = request.args.get('limit', 100)
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_bank_unpublish(bank):
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
if not options.user:
abort(401, 'This action requires authentication with api key')
options.bank = bank
options.unpublish = True
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_maintenance_off():
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
if not options.user or 'admin' not in config[
'biomaj'] or options.user not in config['biomaj']['admin']:
abort(401, 'This action requires authentication with api key')
options.maintenance = 'off'
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_bank_update_directory(bank):
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
if not options.user:
abort(401, 'This action requires authentication with api key')
params = request.get_json()
options.bank = bank
try:
options.newdir = params['path']
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_aboutme():
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
options.aboutme = True
params = request.get_json()
try:
options.userlogin = params['login']
options.userpassword = params['password']
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_bank_publish(bank):
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
if not options.user:
abort(401, 'This action requires authentication with api key')
options.bank = bank
options.publish = True
params = request.get_json()
if params is None:
params = {}
if 'release' in params:
options.release = params['release']
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def biomaj_daemon_bank_search(bank):
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
options.search = True
params = request.get_json()
if params is None:
params = {}
if 'formats' in params and params['formats']:
options.formats = ','.join(params['formats'])
if 'types' in params and params['types']:
options.types = ','.join(params['types'])
if 'query' in params and params['query']:
options.query = ','.join(params['query'])
try:
(res, msg) = biomaj_client_action(options, config)
if res:
if isinstance(msg, dict):
return jsonify(msg)
else:
return jsonify({'msg': msg})
except Exception as e:
abort(500, str(e))
def main():
parser = argparse.ArgumentParser(add_help=False)
Utils.set_args(parser)
options = Options()
parser.parse_args(namespace=options)
options.no_log = False
if options.help:
print('''
--config: global.properties file path (local install only)
--proxy: BioMAJ daemon url (http://x.y.z)
--trace: Trace workflow in Zipkin server
--api-key: User API key to authenticate against proxy
--whatsup: Get info on what biomaj is doing
--last-log: Get log file of last session
[MANDATORY]
--proxy http://x.y.z
[OPTIONAL]
--tail X number of lines to tail from log file
--about-me: Get my info
[MANDATORY]
--proxy http://x.y.z
--user-login XX
--user-password XX
--update-status: get status of an update
[MANDATORY]
--bank xx: name of the bank to check
--proxy http://x.y.z
--update-cancel: cancel current update
[MANDATORY]
--bank xx: name of the bank to cancel
--proxy http://x.y.z
--status: list of banks with published release
[OPTIONAL]
--bank xx / bank: Get status details of bank
--status-ko: list of banks in error status (last run)
--log DEBUG|INFO|WARN|ERR [OPTIONAL]: set log level in logs for this run, default is set in global.properties file
--check: Check bank property file
[MANDATORY]
--bank xx: name of the bank to check (will check xx.properties)
--owner yy: Change owner of the bank (user id)
[MANDATORY]
--bank xx: name of the bank
--visibility public|private: change visibility public/private of a bank
[MANDATORY]
--bank xx: name of the bank
--change-dbname yy: Change name of the bank to this new name
[MANDATORY]
--bank xx: current name of the bank
--move-production-directories yy: Change bank production directories location to this new path, path must exists
[MANDATORY]
--bank xx: current name of the bank
--update: Update bank
[MANDATORY]
--bank xx: name of the bank(s) to update, comma separated
[OPTIONAL]
--publish: after update set as *current* version
--from-scratch: force a new update cycle, even if release is identical, release will be incremented like (myrel_1)
--stop-before xx: stop update cycle before the start of step xx
--stop-after xx: stop update cycle after step xx has completed
--from-task xx --release yy: Force an re-update cycle for bank release *yy* or from current cycle (in production directories), skipping steps up to *xx*
--process xx: linked to from-task, optionally specify a block, meta or process name to start from
--release xx: release to update
--publish: Publish bank as current release to use
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to publish
--unpublish: Unpublish bank (remove current)
[MANDATORY]
--bank xx: name of the bank to update
--remove-all: Remove all bank releases and database records
[MANDATORY]
--bank xx: name of the bank to update
[OPTIONAL]
--force: remove freezed releases
--remove-pending: Remove pending releases
[MANDATORY]
--bank xx: name of the bank to update
--remove: Remove bank release (files and database release)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
Release must not be the *current* version. If this is the case, publish a new release before.
--freeze: Freeze bank release (cannot be removed)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
--unfreeze: Unfreeze bank release (can be removed)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
--search: basic search in bank production releases, return list of banks
--formats xx,yy : list of comma separated format
AND/OR
--types xx,yy : list of comma separated type
--query "LUCENE query syntax": search in index (if activated)
--show: Show bank files per format
[MANDATORY]
--bank xx: name of the bank to show
[OPTIONAL]
--release xx: release of the bank to show
--maintenance on/off/status: (un)set biomaj in maintenance mode to prevent updates/removal
''')
return
proxy = options.proxy
if 'BIOMAJ_PROXY' in os.environ:
proxy = os.environ['BIOMAJ_PROXY']
options.proxy = proxy
if 'BIOMAJ_APIKEY' in os.environ:
apikey = os.environ['BIOMAJ_APIKEY']
options.apikey = apikey
if not proxy:
try:
from biomaj_daemon.daemon.utils import biomaj_client_action
except Exception as e:
print(
'Failed to import biomaj libraries. Either you forgot the --proxy option, either you use a local biomaj install and did not installed it (biomaj-daemon package)'
)
try:
if not proxy:
from biomaj_daemon.daemon.utils import biomaj_client_action
options.user = getpass.getuser()
BiomajConfig.load_config(options.config)
(status, msg) = biomaj_client_action(options)
else:
headers = {}
if options.apikey:
headers = {'Authorization': 'APIKEY ' + options.apikey}
if options.lastlog:
if not options.bank:
print("--bank is missing\n")
sys.exit(1)
if options.tail:
r = requests.get(proxy + '/api/daemon/bank/' +
options.bank + '/log/' + options.tail,
headers=headers)
print(r.text)
else:
r = requests.get(proxy + '/api/daemon/bank/' +
options.bank + '/log',
headers=headers)
print(r.text)
sys.exit(0)
r = requests.post(proxy + '/api/daemon',
headers=headers,
json={'options': options.__dict__})
if not r.status_code == 200:
print('Failed to contact BioMAJ daemon')
sys.exit(1)
result = r.json()
status = result['status']
msg = result['msg']
if not status:
print('An error occured:\n')
print(str(msg))
else:
if msg:
print(str(msg))
else:
print('Done.')
except Exception as e:
logging.exception(e)
print('Error:' + str(e))
