- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
- output_name=output_name, output_tags=output_tags)
+ if "arv:on_error" in job_order_object:
+ on_error = job_order_object["arv:on_error"]
+ del job_order_object["arv:on_error"]
+
+ 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
+ arvargs.collection_cache_size = None
+
+ 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)