- toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
- t = load_tool(toolpath, runner.arv_make_tool)
+ if "arv:debug" in job_order_object:
+ debug = job_order_object["arv:debug"]
+ del job_order_object["arv:debug"]
+
+ arvargs = argparse.Namespace()
+ arvargs.work_api = "jobs"
+ arvargs.output_name = output_name
+ arvargs.output_tags = output_tags
+ arvargs.thread_count = 1
+
+ runner = arvados_cwl.ArvCwlExecutor(api_client=arvados.safeapi.ThreadSafeApiCache(
+ api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
+ arvargs=arvargs)
+
+ make_fs_access = functools.partial(CollectionFsAccess,
+ collection_cache=runner.collection_cache)
+
+ t = load_tool(toolpath, runner.loadingContext)
+
+ if debug:
+ logger.setLevel(logging.DEBUG)
+ logging.getLogger('arvados').setLevel(logging.DEBUG)
+ logging.getLogger("cwltool").setLevel(logging.DEBUG)