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()