def on_startup(config_path: str) -> Dict:
from sm.engine import image_storage # pylint: disable=import-outside-toplevel,cyclic-import
SMConfig.set_path(config_path)
sm_config = SMConfig.get_conf()
init_loggers(sm_config['logs'])
if 'aws' in sm_config:
populate_aws_env_vars(sm_config['aws'])
image_storage.init(sm_config)
return sm_config
def main():
parser = argparse.ArgumentParser(
description='Merge mol_dbs and adducts into config')
parser.add_argument('--config',
default='conf/config.json',
help='SM config path')
args = parser.parse_args()
SMConfig.set_path(args.config)
init_loggers(SMConfig.get_conf()['logs'])
conf = SMConfig.get_conf()
with ConnectionPool(conf['db']):
db = DB()
populate_ion_formula(db)
populate_ions(db)
populate_ion_id(db)
def sm_config():
SMConfig.set_path(Path(proj_root()) / TEST_CONFIG_PATH)
SMConfig.get_conf(
update=True) # Force reload in case previous tests modified it
worker_id = os.environ.get('PYTEST_XDIST_WORKER', 'gw0')
test_id = f'sm_test_{worker_id}'
# Update the internal cached copy of the config, so independent calls to SMConfig.get_conf()
# also get the updated config
SMConfig._config_dict['db']['database'] = test_id
SMConfig._config_dict['elasticsearch']['index'] = test_id
SMConfig._config_dict['rabbitmq']['prefix'] = f'test_{worker_id}__'
for path in SMConfig._config_dict['lithops']['sm_storage'].values():
# prefix keys with test ID so they can be cleaned up later
path[1] = f'{test_id}/{path[1]}'
# __LITHOPS_SESSION_ID determines the prefix to use for anonymous cloudobjects
os.environ['__LITHOPS_SESSION_ID'] = f'{test_id}/cloudobjects'
return SMConfig.get_conf()
def main():
parser = argparse.ArgumentParser(
description='Migrate MolDB data from service to database')
parser.add_argument('--config',
default='conf/config.json',
help='SM config path')
args = parser.parse_args()
SMConfig.set_path(args.config)
config = SMConfig.get_conf()
init_loggers(config['logs'])
moldb_db_config = {
'host': 'localhost',
'database': 'mol_db',
'user': '******'
}
dump_moldb_tables(moldb_db_config)
import_moldb_tables(config['db'])
os.remove('/tmp/molecule.csv')
os.remove('/tmp/molecular_db.csv')
create_subparser = subparsers.add_parser('create')
create_subparser.add_argument('--drop',
action='store_true',
help='Delete existing index if exists')
swap_subparser = subparsers.add_parser(
'swap', help='Swap the active and inactive indexes')
drop_subparser = subparsers.add_parser(
'drop', help='Drop the index. Can only be used on the inactive index')
status_subparser = subparsers.add_parser('status',
help='Show current index mapping')
args = parser.parse_args()
SMConfig.set_path(args.config_path)
init_loggers(SMConfig.get_conf()['logs'])
es_config = SMConfig.get_conf()['elasticsearch']
es_man = ESIndexManager(es_config)
alias = es_config['index']
active_index = es_man.internal_index_name(alias)
inactive_index = es_man.another_index_name(active_index)
index = inactive_index if args.inactive else active_index
if args.action == 'create':
if args.drop:
es_man.delete_index(index)
es_man.create_index(index)
if not args.inactive:
es_man.remap_alias(index, alias)
description='Script for updating metadata in DB on per dataset basis')
parser.add_argument('--md-type',
dest='md_type',
type=str,
help='Target metadata type')
parser.add_argument(
'--ds-name',
dest='ds_name',
type=str,
help="DS name prefix mask ({} for all datasets)".format(ALL_DS_MASK),
)
parser.add_argument(
'--config',
dest='sm_config_path',
default='conf/config.json',
type=str,
help='SM config path',
)
args = parser.parse_args()
SMConfig.set_path(args.sm_config_path)
sm_config = SMConfig.get_conf()
init_loggers()
logger = logging.getLogger('engine')
if args.ds_name and args.md_type:
set_metadata_type(DB(), args.md_type, args.ds_name)
else:
parser.print_help()
