def main(): if 'run' not in sys.argv and 'sample' not in sys.argv: print("no mode specified - use either 'run' or 'sample'") return 1 parent = argparse.ArgumentParser(add_help=False) parent.add_argument('--test', action='store_true') p = argparse.ArgumentParser() subparsers = p.add_subparsers() run_parser = subparsers.add_parser('run', parents=[parent]) run_parser.add_argument('run_id') run_parser.add_argument('--conversion_stats', nargs='?', default=None) run_parser.add_argument('--adapter_trim_file', nargs='?', default=None) run_parser.add_argument('--run_dir', help='e.g. jobs/<run_id>') run_parser.set_defaults(func=run_crawler) sample_parser = subparsers.add_parser('sample', parents=[parent]) sample_parser.add_argument('project_id') sample_parser.add_argument('sample_id') sample_parser.add_argument('--output_fileset') sample_parser.add_argument('--input_dir') sample_parser.set_defaults(func=sample_crawler) args = p.parse_args() load_config() log_cfg.default_level = logging.DEBUG log_cfg.add_handler(logging.StreamHandler(stream=sys.stdout), logging.DEBUG) return args.func(args)
def main(): a = argparser() a.add_argument('--run_name', type=str) args = a.parse_args() log_cfg.add_handler(FileHandler(args.log_file)) action = CreateReagentForRun(args.step_uri, args.username, args.password, args.run_name) return action.run()
def __init__(self, step_uri, username, password, log_file=None): split_url = urlparse.urlsplit(step_uri) self.baseuri = '%s://%s' % (split_url.scheme, split_url.netloc) self.username = username self.password = password self.step_id = split_url.path.split('/')[-1] if log_file: logging_default.add_handler(FileHandler(log_file))
def setup_dataset_logging(d): log_repo = cfg.query('logging', 'repo') if log_repo: repo_log = os.path.join(log_repo, d.name + '.log') log_cfg.add_handler(logging.FileHandler(repo_log, mode='a'), level=logging.INFO) log_cfg.add_handler( logging.FileHandler(os.path.join(cfg['jobs_dir'], d.name, 'analysis_driver.log'), mode='w'), level=logging.INFO ) log_cfg.add_handler( logging.FileHandler(os.path.join(cfg['jobs_dir'], d.name, 'analysis_driver_debug.log'), mode='w'), level=logging.DEBUG )
def main(): args = argparser().parse_args() log_cfg.add_handler(FileHandler(args.log_file)) action = FindPlateToRoute(args.step_uri, args.username, args.password, args.log_file) return action.run()