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:
print(f" Deleted {rv} 'ChEMBL Selective Compound' tdl_info rows")
else:
print(
f"Error deleting 'ChEMBL Selective Compound' tdl_info rows. See logfile {logfile} for details."
)
exit(1)
download_pmscores(args)
download_DISEASES(args)
download_mentions(args)
download_do(args)
start_time = time.time()
print("\nUpdating JensenLab PubMed Text-mining Scores...")
# delete existing pmscores
rv = dba.del_all_rows(pmscore)
if type(rv) == int:
print(f" Deleted {rv} rows from pmscore")
else:
print(f"Error deleting rows from pmscore... Exiting.")
exit(1)
# delete 'JensenLab PubMed Score' TDL Infos
rv = dba.del_tdl_infos('JensenLab PubMed Score')
if type(rv) == int:
print(f" Deleted {rv} 'JensenLab PubMed Score' tdl_info rows")
else:
print(f"Error deleting 'JensenLab PubMed Score' tdl_info rows. Exiting.")
exit(1)
# load new pmsores and TDL Infos
load_pmscores(args, dba, logger, logfile)
# update dataset
upds = {'app': PROGRAM, 'app_version': __version__,
'datetime': time.strftime("%Y-%m-%d %H:%M:%S")}
rv = upd_dataset_by_name(self, 'JensenLab PubMed Text-mining Scores', upds):
assert rv "Error updating dataset 'JensenLab PubMed Text-mining Scores'. Exiting."
print("\nUpdating JensenLab DISEASES...")
# delete existing DISEASES