def run_svc(service_url, module, command, param_file, token=None, level=logging.INFO, logger=None):
"""
Narrative Job Service Genome util service wrapper.
Args:
ws_url: A url for the KBase workspace service.
param_file: A file name for the input parameters.
output_filename: A file name where the output JSON string should be stored.
level: Logging level, defaults to logging.INFO.
"""
if logger is None:
logger = script_util.stderrlogger(__file__)
if service_url != "impl":
logger.error("Only 'impl' is accepted as svc_url")
raise
# TODO:
#TODO: Dynamically load required module, for now direct import
config = get_config(module = module, cfg_path = None)
if config is None:
logger.error("Could not find deployment.cfg to configure the service\n\tPlease ensure {0},{1},or{2} to be defined".format(DEPLOY, DEPLOYMENT, TOP))
raise
gu_hndlr = KBaseGenomeUtil(config)
with open(param_file) as paramh:
param = json.load(paramh)
if token is None:
token = environ.get('KB_AUTH_TOKEN', None)
if token is None: logger.error("Could not retrieve user token from KB_AUTH_TOKEN")
#TODO: May add full call ctx
try:
logger.info("Execute {0}.{1} with {2}".format(module,command, pprint.pformat(param)))
output = getattr(gu_hndlr,command)({'token' : token },param)
logger.info("Output: {0}".format(pprint.pformat(output)))
except:
logger.exception("".join(traceback.format_exc()))
sys.exit(1)
return output
# called only if script is run from command line
if __name__ == "__main__":
import sys
parser = argparse.ArgumentParser(prog='njs-run-genome-util.py',
description='NJS Service Wrapper Script',
epilog='Authors: Shinjae Yoo')
parser.add_argument('-s', '--service_url', help='Service url', action='store', type=str, default='impl', nargs='?', required=False)
parser.add_argument('-w', '--ws_url', help='Workspace url', action='store', type=str, default='https://kbase.us/services/ws/', nargs='?', required=False)
parser.add_argument('-m', '--module', help='Module name', action='store', type=str, default='KBaseGenomeUtil', nargs='?', required=False)
parser.add_argument('-c','--command', help ='Command name', action='store', type=str, nargs='?', required=True)
parser.add_argument('-p','--param_file', help ='Input parameter file name', action='store', type=str, nargs='?', required=True)
parser.add_argument('-t','--token', help ='token', action='store', type=str, nargs='?', default=None, required=False)
args = parser.parse_args()
logger = script_util.stderrlogger(__file__)
try:
ret_json = run_svc(args.service_url, args.module, args.command, args.param_file, logger=logger)
#logger.info("Writing out JSON.")
#with open(args.output_filename, "w") as outFile:
# outFile.write(json.dumps(ret_json,sort_keys = True, indent = 4))
logger.info("Execution completed.")
except:
logger.exception("".join(traceback.format_exc()))
sys.exit(1)
sys.exit(0)