def main():
parser = arg_parser()
parsed_args = parser.parse_args(sys.argv[1:])
# Load the requested parsl configuration
if parsed_args.parsl == 'cori':
parsl.load(cori_regular_config)
elif parsed_args.parsl == 'cori-debug':
parsl.load(cori_debug_config)
else:
parsl.load(threads_config)
# Trigger the argparse message if the cwl file is missing
# Otherwise cwltool will use the default argparser
if not parsed_args.workflow:
if os.path.isfile("CWLFile"):
setattr(parsed_args, "workflow", "CWLFile")
else:
_logger.error("")
_logger.error("CWL document required, no input file was provided")
parser.print_help()
sys.exit(1)
elif not parsed_args.basedir:
_logger.error("")
_logger.error("Basedir is required for storing itermediate results")
parser.print_help()
sys.exit(1)
rc = RuntimeContext(vars(parsed_args))
rc.shifter = False
parsed_args.__dict__['parallel'] = True
rc.tmpdir_prefix = rc.basedir + '/tmp/tmp'
rc.tmp_outdir_prefix = rc.basedir + '/out/out' # type: Text
if parsed_args.shifter:
rc.shifter = True
rc.docker_outdir = '/spooldir'
rc.docker_stagedir = rc.basedir + '/stage'
rc.docker_tmpdir = '/tmpdir'
lc = LoadingContext(vars(parsed_args))
lc.construct_tool_object = customMakeTool
sys.exit(
cwltool.main.main(args=parsed_args,
loadingContext=lc,
runtimeContext=rc))
def run_native(config_object: 'ConfigBase', workflow: str, run_directory: str = '.', verbosity="normal") -> int:
"""Executes the workflow using native Python rather than subprocess "command line"
Args:
config_object: a constructed ConfigBase-derived object
workflow: the path to the workflow to be executed
run_directory: the destination folder for workflow output subdirectories (default: CWD)
parallel: process libraries in parallel where possible
verbosity: controls the depth of information written to terminal by cwltool
Returns: None
"""
def furnish_if_file_record(file_dict):
if isinstance(file_dict, dict) and file_dict.get('class', None) == 'File':
file_dict['basename'] = os.path.basename(file_dict['path'])
file_dict['location'] = file_dict['path']
file_dict['contents'] = None
# Upgrade file entries in Run Config with extra descriptors cwltool expects
for _, config_param in config_object.config.items():
if isinstance(config_param, list):
for config_dict in config_param:
furnish_if_file_record(config_dict)
else:
furnish_if_file_record(config_param)
# Set overall config for cwltool
runtime_context = RuntimeContext({
'secret_store': cwltool.secrets.SecretStore(),
'outdir': run_directory,
'on_error': "continue",
'js_console': verbosity == "debug",
'debug': verbosity == "debug"
})
# Set proper temp directory for Mac users
if sys.platform == "darwin":
default_mac_path = "/private/tmp/docker_tmp"
if runtime_context.tmp_outdir_prefix == DEFAULT_TMP_PREFIX:
runtime_context.tmp_outdir_prefix = default_mac_path
if runtime_context.tmpdir_prefix == DEFAULT_TMP_PREFIX:
runtime_context.tmpdir_prefix = default_mac_path
# Enable rich terminal output (timestamp, color, formatting)
logger = logging.getLogger("cwltool")
logger.handlers.clear() # executors.py loads a default handler; outputs are printed twice if we don't clear it
level = 'DEBUG' if verbosity == 'debug' else 'WARN' if verbosity == "quiet" else "INFO"
coloredlogs.install(logger=logger, stream=sys.stderr, fmt="[%(asctime)s] %(levelname)s %(message)s",
datefmt="%Y-%m-%d %H:%M:%S", level=level, isatty=True)
# Create a wrapper for the executors so that we may pass our logger to them (unsupported by Factory)
parallel: MultithreadedJobExecutor = functools.partial(MultithreadedJobExecutor(), logger=logger)
serial: SingleJobExecutor = functools.partial(SingleJobExecutor(), logger=logger)
# Instantiate Factory with our run preferences
cwl = cwltool.factory.Factory(
runtime_context=runtime_context,
loading_context=LoadingContext({'relax_path_checks': True}),
executor=parallel if parallel else serial
)
try:
# Load the workflow document and execute
pipeline = cwl.make(workflow)
pipeline(**config_object.config)
except cwltool.factory.WorkflowStatus:
# For now, return non-zero if workflow did not complete
return 1
return 0