"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']))
# for the time being, this has to be done manually because Lars is forcing https
# -SLM 20210227
#print("\nDownloading new JensenLab files...")
#download_pmscores(args)
#download_DISEASES(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)
# set all existing 'JensenLab PubMed Score' TDL Infos to zero
# This is so we don't have to redo inserting zero values for proteins with no score
rv = dba.upd_pmstdlis_zero()
if type(rv) == int:
print(
f" Reset {rv} 'JensenLab PubMed Score' tdl_info values to zero.")
else:
print(
f"Error updating 'JensenLab PubMed Score' tdl_info values. Exiting."
)
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']))
print("\nDownloading update files...")
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