def global_setup(sm_config):
init_loggers(sm_config['logs'])
if 'aws' in sm_config:
populate_aws_env_vars(sm_config['aws'])
image_storage.init(sm_config)
image_storage.configure_bucket(sm_config)
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 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)
elif args.action == 'swap':
import logging
import pandas as pd
from sm.engine.db import DB, ConnectionPool
from sm.engine.config import init_loggers
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Update molecular database molecule names')
parser.add_argument('--config',
default='conf/config.json',
help='SM config path')
parser.add_argument('file_path', help='Path to file with new names')
args = parser.parse_args()
init_loggers()
logger = logging.getLogger('engine')
logger.info(f'Importing new names from {args.file_path}')
db_config = {"host": "localhost", "database": "mol_db", "user": "******"}
with ConnectionPool(db_config):
db = DB()
names_df = pd.read_csv(args.file_path, sep='\t')[['id', 'name']]
sql = (
'WITH molecule_name AS (SELECT UNNEST(%s::text[]) as id_, UNNEST(%s::text[]) as name_) '
'UPDATE molecule SET mol_name = molecule_name.name_ '
'FROM molecule_name WHERE molecule.mol_id = molecule_name.id_')
db.alter(sql,
[names_df.id.values.tolist(),