13627: a-c-r migration to cwltool loading/runtimeContext API

[arvados.git] / sdk / cwl / arvados_cwl / crunch_script.py

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index bf940eca4ba92fad7e01ccd06e70564cb2fa0103..94e9c8fc84abcd2511935d63b7c413e77da38948 100644 (file)
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -27,6 +27,7 @@ from cwltool.process import shortname
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
 from cwltool.load_tool import load_tool
 from cwltool.errors import WorkflowException
+from cwltool.context import RuntimeContext
 
 from .fsaccess import CollectionFetcher, CollectionFsAccess
 
@@ -115,7 +116,7 @@ def run():
             logging.getLogger('arvados').setLevel(logging.DEBUG)
             logging.getLogger("cwltool").setLevel(logging.DEBUG)
 
-        args = argparse.Namespace()
+        args = RuntimeContext()
         args.project_uuid = arvados.current_job()["owner_uuid"]
         args.enable_reuse = enable_reuse
         args.on_error = on_error
@@ -132,8 +133,9 @@ def run():
         args.priority = arvados_cwl.DEFAULT_PRIORITY
         args.do_validate = True
         args.disable_js_validation = False
+        args.tmp_outdir_prefix = "tmp"
 
-        runner.arv_executor(t, job_order_object, **vars(args))
+        runner.arv_executor(t, job_order_object, args)
     except Exception as e:
         if isinstance(e, WorkflowException):
             logging.info("Workflow error %s", e)