[ARVADOS] updated: 2.1.0-656-g7b5adb057

[Git user]

Summary of changes:
 .licenseignore                                                 |  2 ++
 sdk/cwl/arvados_cwl/arvworkflow.py                             |  3 ++-
 sdk/cwl/tests/arvados-tests.yml                                |  5 +++++
 sdk/cwl/tests/wf/hello.txt                                     |  1 +
 sdk/cwl/tests/wf/indir1/hello2.txt                             |  1 +
 .../{secondaryFiles/example3.cwl => wf/trick_defaults2.cwl}    | 10 ++++++----
 6 files changed, 17 insertions(+), 5 deletions(-)
 create mode 100644 sdk/cwl/tests/wf/hello.txt
 create mode 100644 sdk/cwl/tests/wf/indir1/hello2.txt
 copy sdk/cwl/tests/{secondaryFiles/example3.cwl => wf/trick_defaults2.cwl} (63%)

       via  7b5adb057894123896d8b7186d767e754cc3faae (commit)
       via  cfdd62d07f704a4c982a15189071096388982b9a (commit)
       via  ffae77ee85f7a6dd4a095298aaa9dba145c98bdd (commit)
      from  64c90ad4138097404ebc315d7c36923eccb9b981 (commit)

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commit 7b5adb057894123896d8b7186d767e754cc3faae
Merge: 64c90ad41 cfdd62d07
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Apr 15 10:23:00 2021 -0400

    Merge branch '17462-secondaryfiles-regression' refs #17462
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


commit cfdd62d07f704a4c982a15189071096388982b9a
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Apr 15 10:18:07 2021 -0400

    17462: Add integration test to confirm fix
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/.licenseignore b/.licenseignore
index 7ebc82667..e3289aa7c 100644
--- a/.licenseignore
+++ b/.licenseignore
@@ -86,3 +86,5 @@ sdk/python/tests/fed-migrate/CWLFile
 sdk/python/tests/fed-migrate/*.cwl
 sdk/python/tests/fed-migrate/*.cwlex
 doc/install/*.xlsx
+sdk/cwl/tests/wf/hello.txt
+sdk/cwl/tests/wf/indir1/hello2.txt
\ No newline at end of file
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 668604f88..48255f857 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -355,3 +355,8 @@
       "size": 4
   tool: 17267-broken-schemas.cwl
   doc: "Test issue 17267 - inaccessible $schemas URL is not a fatal error"
+
+- job: null
+  output: {}
+  tool: wf/trick_defaults2.cwl
+  doc: "Test issue 17462 - secondary file objects on file defaults are not resolved"
diff --git a/sdk/cwl/tests/wf/hello.txt b/sdk/cwl/tests/wf/hello.txt
new file mode 100644
index 000000000..ce0136250
--- /dev/null
+++ b/sdk/cwl/tests/wf/hello.txt
@@ -0,0 +1 @@
+hello
diff --git a/sdk/cwl/tests/wf/indir1/hello2.txt b/sdk/cwl/tests/wf/indir1/hello2.txt
new file mode 100644
index 000000000..14be0d41c
--- /dev/null
+++ b/sdk/cwl/tests/wf/indir1/hello2.txt
@@ -0,0 +1 @@
+hello2
diff --git a/sdk/cwl/tests/wf/trick_defaults2.cwl b/sdk/cwl/tests/wf/trick_defaults2.cwl
new file mode 100644
index 000000000..9f4292218
--- /dev/null
+++ b/sdk/cwl/tests/wf/trick_defaults2.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+  inp1:
+    type: File
+    default:
+      class: File
+      location: hello.txt
+      secondaryFiles:
+        - class: Directory
+          location: indir1
+outputs: []
+baseCommand: 'true'

commit ffae77ee85f7a6dd4a095298aaa9dba145c98bdd
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Apr 14 16:13:26 2021 -0400

    Fix regression refs #17462
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 6067ae9f4..4fe82a6fe 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -17,7 +17,7 @@ from cwltool.pack import pack
 from cwltool.load_tool import fetch_document, resolve_and_validate_document
 from cwltool.process import shortname
 from cwltool.workflow import Workflow, WorkflowException, WorkflowStep
-from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class
+from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class, normalizeFilesDirs
 from cwltool.context import LoadingContext
 
 import ruamel.yaml as yaml
@@ -186,6 +186,7 @@ class ArvadosWorkflow(Workflow):
 
         discover_secondary_files(self.arvrunner.fs_access, builder,
                                  self.tool["inputs"], joborder)
+        normalizeFilesDirs(joborder)
 
         with Perf(metrics, "subworkflow upload_deps"):
             upload_dependencies(self.arvrunner,

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