def load_job(workflow, job, cwl_args=None, cwd=None):
"""
Tries to load json object from "job". If failed, assumes that
"job" has been already parsed into Object. Inits loaded "job_data"
based on the "workflow" (mostly for setting defaults from the workflow
inputs; never fails). "cwl_args" can be used to update parameters for
loading and runtime contexts.
If "job" was file, resolves relative paths based on the job file location.
If "job" was already parsed into Object, resolves relative paths based on
"cwd". If "cwd" was None uses "inputs_folder" value from "cwl_args" or
its default value returned from "get_default_cwl_args" function.
Checking links after relative paths are resolved is disabled (checklinks
is set to False in both places). This will prevent rasing an exception by
schema salad in those cases when an input file will be created from the
provided content during workflow execution.
Always returns CommentedMap
"""
cwl_args = {} if cwl_args is None else cwl_args
default_cwl_args = get_default_cwl_args(cwl_args)
cwd = default_cwl_args["inputs_folder"] if cwd is None else cwd
loading_context = setup_loadingContext(
LoadingContext(default_cwl_args), RuntimeContext(default_cwl_args),
argparse.Namespace(**default_cwl_args))
job_copy = deepcopy(job)
try:
job_data, _ = loading_context.loader.resolve_ref(job_copy,
checklinks=False)
except (FileNotFoundError, SchemaSaladException) as err:
job_data = load_yaml(json.dumps(job_copy))
job_data["id"] = file_uri(cwd) + "/"
job_data, metadata = loading_context.loader.resolve_all(
job_data, job_data["id"], checklinks=False)
initialized_job_data = init_job_order(
job_order_object=job_data,
args=argparse.Namespace(**default_cwl_args),
process=slow_cwl_load(workflow=workflow, cwl_args=default_cwl_args),
loader=loading_context.loader,
stdout=os.devnull)
return initialized_job_data
def __load(location):
return load_tool(
location,
setup_loadingContext(LoadingContext(default_cwl_args),
RuntimeContext(default_cwl_args),
argparse.Namespace(**default_cwl_args)))
