def main_runner(argv, parser, exe_runner_func,
level=logging.DEBUG, str_formatter=_LOG_FORMAT):
"""
Fundamental interface to commandline applications
"""
started_at = time.time()
args = parser.parse_args(argv)
console_or_file = getattr(args, 'log_file', None)
if hasattr(args, 'log_level'):
level = getattr(args, 'log_level')
# Debug will override
if hasattr(args, 'debug'):
if args.debug:
if args.debug is True:
level = logging.DEBUG
# Quiet will override everything
if hasattr(args, 'quiet'):
if args.quiet:
level = logging.ERROR
setup_logger(console_or_file, level, formatter=str_formatter)
log.debug(args)
log.info("Starting tool version {v}".format(v=parser.version))
rcode = exe_runner_func(args)
run_time = time.time() - started_at
_d = dict(r=rcode, s=run_time)
log.info("exiting with return code {r} in {s:.2f} sec.".format(**_d))
return rcode
def main_runner(argv, parser, exe_runner_func,
level=logging.DEBUG, str_formatter=_LOG_FORMAT):
"""
Fundamental interface to commandline applications
"""
dep_msg = "The `pbservice` commandline is deprecated and will be removed " \
"in a future version. Please using the scala implementation in smrtflow " \
"at https://github.com/PacificBiosciences/smrtflow"
started_at = time.time()
args = parser.parse_args(argv)
level = get_parsed_args_log_level(args, default_level=level)
console_or_file = args.log_file
setup_logger(console_or_file, level, formatter=str_formatter)
log.warn(dep_msg)
log.debug(args)
log.info("Starting tool version {v}".format(v=parser.version))
rcode = exe_runner_func(args)
run_time = time.time() - started_at
_d = dict(r=rcode, s=run_time)
log.info("exiting with return code {r} in {s:.2f} sec.".format(**_d))
return rcode
def main_runner(argv, parser, exe_runner_func,
level=logging.DEBUG, str_formatter=_LOG_FORMAT):
"""
Fundamental interface to commandline applications
"""
dep_msg = "The `pbservice` commandline is deprecated and will be removed " \
"in a future version. Please using the scala implementation in smrtflow " \
"at https://github.com/PacificBiosciences/smrtflow"
started_at = time.time()
args = parser.parse_args(argv)
level = get_parsed_args_log_level(args, default_level=level)
console_or_file = args.log_file
setup_logger(console_or_file, level, formatter=str_formatter)
warnings.warn(dep_msg, DeprecationWarning)
log.warn(dep_msg)
log.debug(args)
log.info("Starting tool version {v}".format(v=parser.version))
rcode = exe_runner_func(args)
run_time = time.time() - started_at
_d = dict(r=rcode, s=run_time)
log.info("exiting with return code {r} in {s:.2f} sec.".format(**_d))
return rcode
def _args_run_butler(args):
butler = B.config_parser_to_butler(args.testkit_cfg)
test_cases = L.parse_cfg_file(args.testkit_cfg)
if not os.path.exists(butler.output_dir):
os.mkdir(butler.output_dir)
output_xml = args.output_xml
if output_xml is None:
output_xml = os.path.join(butler.output_dir, 'testkit_xunit.xml')
if args.log_file is None:
log_file = os.path.join(butler.output_dir, 'testkit.log')
else:
log_file = args.log_file
force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
log_level = args.log_level
# Short hand for --log-level=DEBUG
if args.debug:
log_level = logging.DEBUG
if log_level == logging.DEBUG:
# The logger isn't setup yet
print "Args", args
if args.only_tests:
# in test only mode, only emit to stdout (to avoid overwritten the
# log file
setup_logger(None, level=log_level)
return run_butler_tests(test_cases, butler.output_dir, output_xml,
butler.job_id, butler.requirements)
else:
rcode = run_butler(butler,
test_cases,
output_xml,
log_file,
log_level=log_level,
force_distribute=force_distribute,
force_chunk=force_chunk,
ignore_test_failures=args.ignore_test_failures)
return rcode
def _w(args):
started_at = time.time()
def run_time():
return time.time() - started_at
def exit_msg(rcode_):
return "Completed running {r} exitcode {e} in {t:.2f} sec.".format(
r=rtc, e=rcode_, t=run_time())
level = get_parsed_args_log_level(args)
setup_logger(None, level=level)
log.info("Loading pbcommand {v}".format(v=pbcommand.get_version()))
log.info("Registry {r}".format(r=registry))
log.info("Setting log-level to {d}".format(d=level))
log.debug("args {a}".format(a=args))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {
t.task.task_id: func
for t, func in registry.rtc_runners.iteritems()
}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
rcode = 1
log.error(
"Unknown tool contract id '{x}' Registered TC ids {i}".format(
x=rtc.task.task_id, i=id_funcs.keys()))
log.error(exit_msg(rcode))
return rcode
else:
log.info("Running id:{i} Resolved Tool Contract {r}".format(
r=rtc, i=rtc.task.task_id))
log.info("Runner func {f}".format(f=func))
exit_code = func(rtc)
if exit_code == 0:
log.info(exit_msg(exit_code))
else:
log.error(exit_msg(exit_code))
return exit_code
def _args_run_butler(args):
butler = B.config_parser_to_butler(args.testkit_cfg)
test_cases = L.parse_cfg_file(args.testkit_cfg)
if not os.path.exists(butler.output_dir):
os.mkdir(butler.output_dir)
output_xml = args.output_xml
if output_xml is None:
output_xml = os.path.join(butler.output_dir, 'testkit_xunit.xml')
if args.log_file is None:
log_file = os.path.join(butler.output_dir, 'testkit.log')
else:
log_file = args.log_file
force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
log_level = args.log_level
# Short hand for --log-level=DEBUG
if args.debug:
log_level = logging.DEBUG
if log_level == logging.DEBUG:
# The logger isn't setup yet
print "Args", args
if args.only_tests:
# in test only mode, only emit to stdout (to avoid overwritten the
# log file
setup_logger(None, level=log_level)
return run_butler_tests(test_cases, butler.output_dir, output_xml, butler.job_id)
else:
rcode = run_butler(butler, test_cases, output_xml, log_file,
log_level=log_level,
force_distribute=force_distribute,
force_chunk=force_chunk,
ignore_test_failures=args.ignore_test_failures)
return rcode
def main_runner(argv, parser, exe_runner_func,
level=logging.DEBUG, str_formatter=_LOG_FORMAT):
"""
Fundamental interface to commandline applications
"""
started_at = time.time()
args = parser.parse_args(argv)
level = get_parsed_args_log_level(args, default_level=level)
console_or_file = args.log_file
setup_logger(console_or_file, level, formatter=str_formatter)
log.debug(args)
log.info("Starting tool version {v}".format(v=parser.version))
rcode = exe_runner_func(args)
run_time = time.time() - started_at
_d = dict(r=rcode, s=run_time)
log.info("exiting with return code {r} in {s:.2f} sec.".format(**_d))
return rcode
def _w(args):
started_at = time.time()
def run_time():
return time.time() - started_at
def exit_msg(rcode_):
return "Completed running {r} exitcode {e} in {t:.2f} sec.".format(r=rtc, e=rcode_, t=run_time())
level = get_parsed_args_log_level(args)
setup_logger(None, level=level)
log.info("Loading pbcommand {v}".format(v=pbcommand.get_version()))
log.info("Registry {r}".format(r=registry))
log.info("Setting log-level to {d}".format(d=level))
log.debug("args {a}".format(a=args))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {t.task.task_id: func for t, func in registry.rtc_runners.iteritems()}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
rcode = 1
log.error("Unknown tool contract id '{x}' Registered TC ids {i}".format(x=rtc.task.task_id, i=id_funcs.keys()))
log.error(exit_msg(rcode))
return rcode
else:
log.info("Running id:{i} Resolved Tool Contract {r}".format(r=rtc, i=rtc.task.task_id))
log.info("Runner func {f}".format(f=func))
exit_code = func(rtc)
if exit_code == 0:
log.info(exit_msg(exit_code))
else:
log.error(exit_msg(exit_code))
return exit_code
def main_runner(argv,
parser,
exe_runner_func,
level=logging.DEBUG,
str_formatter=_LOG_FORMAT):
"""
Fundamental interface to commandline applications
"""
started_at = time.time()
args = parser.parse_args(argv)
level = get_parsed_args_log_level(args, default_level=level)
console_or_file = args.log_file
setup_logger(console_or_file, level, formatter=str_formatter)
log.debug(args)
log.info("Starting tool version {v}".format(v=parser.version))
rcode = exe_runner_func(args)
run_time = time.time() - started_at
_d = dict(r=rcode, s=run_time)
log.info("exiting with return code {r} in {s:.2f} sec.".format(**_d))
return rcode
