[ARVADOS] updated: 2.1.0-2360-ga1e644bd3

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/executor.py                    |  3 +-
 sdk/cwl/arvados_cwl/pathmapper.py                  | 52 +++++++++++++---------
 sdk/cwl/arvados_cwl/runner.py                      | 30 ++++++-------
 sdk/cwl/tests/18994-basename/check.cwl             | 22 +++++++++
 sdk/cwl/tests/18994-basename/rename.cwl            | 16 +++++++
 sdk/cwl/tests/18994-basename/wf_ren.cwl            | 33 ++++++++++++++
 .../cwl/tests/18994-basename/whale.txt             |  2 +-
 sdk/cwl/tests/arvados-tests.yml                    |  5 +++
 8 files changed, 123 insertions(+), 40 deletions(-)
 create mode 100644 sdk/cwl/tests/18994-basename/check.cwl
 create mode 100644 sdk/cwl/tests/18994-basename/rename.cwl
 create mode 100644 sdk/cwl/tests/18994-basename/wf_ren.cwl
 copy tools/salt-install/tests/test.txt => sdk/cwl/tests/18994-basename/whale.txt (94%)

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       via  5d039c344850dfc5fedd03c1050fa51eec404d72 (commit)
       via  faf47b57391a6e704b82623e997d9213ffc9442c (commit)
       via  4d212400b51fc73c1b21db30f90c6714d244b777 (commit)
       via  adc0f36eeab40f4b8e0603247392b3c804d7272a (commit)
       via  29e3fe60d22218d122a1a3448a144bfcfd64785a (commit)
       via  bf95fa077c79c6bd4ac548ec534b618e97e3f00b (commit)
       via  aade42c825f24882d9421893a1447f87708b2f33 (commit)
      from  e426e643b34e2d39507daf9e0d768ecea58dfa26 (commit)

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commit a1e644bd3b63d97fab7ed1a1d66e00e6dea5fa1e
Merge: e426e643b 97fc7b68a
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue Apr 19 10:13:32 2022 -0400

    Merge branch '18994-cwl-basename' refs #18994
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


commit 97fc7b68a8777794e1beb2c93a1c5c7880f1f0df
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue Apr 19 10:12:36 2022 -0400

    18994: Remove commented out code
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index ddd1d2bac..e5a81cdc7 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -353,25 +353,13 @@ def upload_dependencies(arvrunner, name, document_loader,
     if include_primary and "id" in workflowobj:
         sc.append({"class": "File", "location": workflowobj["id"]})
 
-    #if "$schemas" in workflowobj:
-    #    for s in workflowobj["$schemas"]:
-    #        sc.append({"class": "File", "location": s})
-
     def visit_default(obj):
-        #remove = [False]
-        def ensure_default_location(f):
+        def defaults_are_optional(f):
             if "location" not in f and "path" in f:
                 f["location"] = f["path"]
                 del f["path"]
             optional_deps.append(f)
-            #if "location" in f and not arvrunner.fs_access.exists(f["location"]):
-            #    # Doesn't exist, remove from list of dependencies to upload
-            #    sc[:] = [x for x in sc if x["location"] != f["location"]]
-            #    # Delete "default" from workflowobj
-            #    remove[0] = True
-        visit_class(obj["default"], ("File", "Directory"), ensure_default_location)
-        #if remove[0]:
-        #    del obj["default"]
+        visit_class(obj["default"], ("File", "Directory"), defaults_are_optional)
 
     find_defaults(workflowobj, visit_default)
 

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