[ARVADOS] updated: 2.1.0-1284-g432550587

Git user git at public.arvados.org
Mon Sep 13 16:23:53 UTC 2021


Summary of changes:
 sdk/cwl/arvados_cwl/arvcontainer.py                     |  2 --
 ...ge_class_wf.cwl => submit_wf_process_properties.cwl} | 17 +++++++++++++----
 2 files changed, 13 insertions(+), 6 deletions(-)
 copy sdk/cwl/tests/wf/{submit_storage_class_wf.cwl => submit_wf_process_properties.cwl} (77%)

       via  4325505873cf6da23c81ef2bbf3003777463e0df (commit)
      from  93be5ba7e96f1a62f53aee8c1e4979a99d1a9d94 (commit)

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commit 4325505873cf6da23c81ef2bbf3003777463e0df
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon Sep 13 12:23:37 2021 -0400

    14018: Add missing file.  Remove debug print()
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 3065e1a7c..1029ca0e0 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -482,9 +482,7 @@ class RunnerContainer(Runner):
         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
         if properties_req:
             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
-            print("ZZZZZZ", properties_req["processProperties"])
             for pr in properties_req["processProperties"]:
-                print("ZZZZZZ", pr)
                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 
         # --local means execute the workflow instead of submitting a container request
diff --git a/sdk/cwl/tests/wf/submit_wf_process_properties.cwl b/sdk/cwl/tests/wf/submit_wf_process_properties.cwl
new file mode 100644
index 000000000..0d669272f
--- /dev/null
+++ b/sdk/cwl/tests/wf/submit_wf_process_properties.cwl
@@ -0,0 +1,39 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# Test case for arvados-cwl-runner
+#
+# Used to test whether scanning a workflow file for dependencies
+# (e.g. submit_tool.cwl) and uploading to Keep works as intended.
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+
+class: Workflow
+cwlVersion: v1.0
+
+hints:
+  arv:ProcessProperties:
+    processProperties:
+      foo: bar
+      baz: $(inputs.x.basename)
+      quux:
+        propertyValue:
+          q1: 1
+          q2: 2
+
+inputs:
+  - id: x
+    type: File
+  - id: y
+    type: Directory
+  - id: z
+    type: Directory
+outputs: []
+steps:
+  - id: step1
+    in:
+      - { id: x, source: "#x" }
+    out: []
+    run: ../tool/submit_tool.cwl

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