arg_parser.add_argument('-s',
'--sleeptime',
type=int,
default=10,
help='time to sleep before checking for new files')
arg_parser.add_argument('-f', '--logfile', help='path to log file')
arg_parser.add_argument('-l',
'--loglevel',
default='info',
help='log level (default: info)')
arg_parser.add_argument('-q',
'--quiet',
action='store_true',
default=False,
help='disable console logging')
args = arg_parser.parse_args()
nimsutil.configure_log(args.logfile, not args.quiet, args.loglevel)
nimsgears.model.init_model(sqlalchemy.create_engine(args.db_uri))
sorter = Sorter(args.stage_path, args.preserve_path, args.nims_path,
args.sleeptime)
def term_handler(signum, stack):
sorter.halt()
log.info('Receieved SIGTERM - shutting down...')
signal.signal(signal.SIGTERM, term_handler)
sorter.run()
log.warning('Process halted')
def __init__(self):
super(ArgumentParser, self).__init__()
self.add_argument('reap_path', help='path to reaping stage')
self.add_argument('sort_path', help='path to sorting stage')
self.add_argument('data_path', help='path to data source')
self.add_argument('-p', '--patid', help='glob for patient IDs to reap (default: "*")')
self.add_argument('-d', '--discard', default='discard', help='space-separated list of Patient IDs to discard')
self.add_argument('-s', '--sleeptime', type=int, default=30, help='time to sleep before checking for new data')
self.add_argument('-f', '--logfile', help='path to log file')
self.add_argument('-l', '--loglevel', default='info', help='log level (default: info)')
self.add_argument('-q', '--quiet', action='store_true', default=False, help='disable console logging')
if __name__ == '__main__':
args = ArgumentParser().parse_args()
reaper_id = args.data_path.strip('/').replace('/', '_')
nimsutil.configure_log(args.logfile, not args.quiet, args.loglevel)
datetime_file = os.path.join(os.path.dirname(__file__), '.%s.datetime' % reaper_id)
reaper = PFileReaper(reaper_id, args.patid, args.discard.split(), args.data_path, args.reap_path, args.sort_path, datetime_file, args.sleeptime)
def term_handler(signum, stack):
reaper.halt()
log.info('Received SIGTERM - shutting down...')
signal.signal(signal.SIGTERM, term_handler)
reaper.run()
log.warning('Process halted')
