dba_params = {'dbhost': args['--dbhost'], 'dbname': args['--dbname'], 'logger_name': __name__}
dba = DBAdaptor(dba_params)
dbi = dba.get_dbinfo()
logger.info("Connected to TCRD database {} (schema ver {}; data ver {})".format(args['--dbname'], dbi['schema_ver'], dbi['data_ver']))
if not args['--quiet']:
print("Connected to TCRD database {} (schema ver {}; data ver {})".format(args['--dbname'], dbi['schema_ver'], dbi['data_ver']))
start_time = time.time()
rv = dba.upd_tdls_null()
if type(rv) == int:
print(f"\nSet tdl to NULL for {rv} target rows")
else:
print(f"Error setting target.tdl values to NULL. See logfile {logfile} for details.")
exit(1)
rv = dba.del_dataset('TDLs')
if rv:
print(f"Deleted previous 'TDLs' dataset")
else:
print(f"Error deleting 'TDLs' dataset. See logfile {logfile} for details.")
exit(1)
load_tdls(dba, logfile, logger)
# Dataset
dataset_id = dba.ins_dataset( {'name': 'TDLs', 'source': 'IDG-KMC generated data by Steve Mathias at UNM.', 'app': PROGRAM, 'app_version': __version__, 'comments': 'TDLs are calculated by the loading app from data in TCRD.'} )
assert dataset_id, f"Error inserting dataset. See logfile {logfile} for details."
# Provenance
rv = dba.ins_provenance({'dataset_id': dataset_id, 'table_name': 'target', 'column_name': 'tdl'})
assert rv, f"Error inserting provenance. See logfile {logfile} for details."
if not args['--quiet']:
print(f"Connected to ChEMBL database {CHEMBL_DB}")
start_time = time.time()
# delete previous data, if any
print("\nDeleting existing ChEMBL data...")
rv = dba.del_cmpd_activities('ChEMBL')
if type(rv) == int:
print(f" Deleted {rv} 'ChEMBL' cmpd_activity rows")
else:
print(
f"Error deleting 'ChEMBL' cmpd_activity rows. See logfile {logfile} for details."
)
exit(1)
rv = dba.del_dataset('ChEMBL')
if not rv:
print(
f"Error deleting 'ChEMBL' dataset. See logfile {logfile} for details."
)
exit(1)
rv = dba.del_tdl_infos('ChEMBL First Reference Year')
if type(rv) == int:
print(f" Deleted {rv} 'ChEMBL First Reference Year' tdl_info rows")
else:
print(
f"Error deleting 'ChEMBL First Reference Year' tdl_info rows. See logfile {logfile} for details."
)
exit(1)
rv = dba.del_tdl_infos('ChEMBL Selective Compound')
if type(rv) == int: