type=str, required=True)
parser.add_argument('--fastrun', dest='fastrun', action='store_true')
parser.add_argument('--no-fastrun', dest='fastrun', action='store_false')
parser.add_argument('--entrez', help="Run only this one gene")
parser.set_defaults(fastrun=True)
args = parser.parse_args()
log_dir = args.log_dir if args.log_dir else "./logs"
run_id = datetime.now().strftime('%Y%m%d_%H:%M')
__metadata__['run_id'] = run_id
taxon = args.taxon
fast_run = args.fastrun
mcb = MicrobialChromosomeBot()
# get metadata about sources
mgd = MyGeneDownloader()
metadata = mgd.get_metadata()['src_version']
if args.entrez:
main(taxon, metadata, run_id=run_id, log_dir=log_dir, fast_run=fast_run,
write=not args.dummy, entrez=args.entrez)
sys.exit(0)
if "microbe" in taxon:
microbe_taxa = mcb.get_all_taxids()
taxon = taxon.replace("microbe", ','.join(map(str, microbe_taxa)))
for taxon1 in taxon.split(","):
try:
main(taxon1, metadata, run_id=run_id, log_dir=log_dir, fast_run=fast_run, write=not args.dummy)
except Exception as e:
# if one taxon fails, still try to run the others
parser = argparse.ArgumentParser(description='run wikidata gene bot')
parser.add_argument('--log-dir', help='directory to store logs', type=str)
parser.add_argument('--dummy',
help='do not actually do write',
action='store_true')
parser.add_argument('--fastrun', dest='fastrun', action='store_true')
parser.add_argument('--no-fastrun', dest='fastrun', action='store_false')
parser.set_defaults(fastrun=True)
args = parser.parse_args()
log_dir = args.log_dir if args.log_dir else "./logs"
run_id = datetime.now().strftime('%Y%m%d_%H:%M')
__metadata__['run_id'] = run_id
fast_run = args.fastrun
# get metadata about sources
mgd = MyGeneDownloader()
metadata = dict()
src = mgd.get_metadata()['src']
for source in src.keys():
metadata[source] = src[source]["version"]
log_name = '{}-{}.log'.format(__metadata__['name'], run_id)
if wdi_core.WDItemEngine.logger is not None:
wdi_core.WDItemEngine.logger.handles = []
wdi_core.WDItemEngine.setup_logging(log_dir=log_dir,
log_name=log_name,
header=json.dumps(__metadata__),
logger_name='orthologs')
main(metadata, log_dir=log_dir, fast_run=fast_run, write=not args.dummy)