Arvbox explicitly initializes postgres with en_US.UTF-8 locale. no issue #

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

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 4db1f4f2f4d8f48739bd7ef525e9526bdd2c3b4c..20cb4677c5935b5011a66b0a958518ce42a285c3 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import os
 import json
 import copy
@@ -9,11 +13,12 @@ from cwltool.pack import pack
 from cwltool.load_tool import fetch_document
 from cwltool.process import shortname
 from cwltool.workflow import Workflow, WorkflowException
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
 
 import ruamel.yaml as yaml
 
-from .runner import upload_dependencies, trim_listing, packed_workflow, upload_workflow_collection
+from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
+from .pathmapper import trim_listing
 from .arvtool import ArvadosCommandTool
 from .perf import Perf
 
@@ -26,6 +31,8 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
     packed = packed_workflow(arvRunner, tool)
 
     adjustDirObjs(job_order, trim_listing)
+    adjustFileObjs(job_order, trim_anonymous_location)
+    adjustDirObjs(job_order, trim_anonymous_location)
 
     main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
     for inp in main["inputs"]:
@@ -106,6 +113,7 @@ class ArvadosWorkflow(Workflow):
                 joborder_keepmount = copy.deepcopy(joborder)
 
                 def keepmount(obj):
+                    remove_redundant_fields(obj)
                     with SourceLine(obj, None, WorkflowException):
                         if "location" not in obj:
                             raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
@@ -119,8 +127,7 @@ class ArvadosWorkflow(Workflow):
                         else:
                             raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
 
-                adjustFileObjs(joborder_keepmount, keepmount)
-                adjustDirObjs(joborder_keepmount, keepmount)
+                visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
 
                 if self.wf_pdh is None:
                     adjustFileObjs(packed, keepmount)