[ARVADOS] updated: 2.1.0-2387-gfa5d8c5af

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/runner.py |  3 ++-
 sdk/cwl/tests/test_submit.py  | 10 +++++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

       via  fa5d8c5afd6980c3e661c59e0003a3abbb752f77 (commit)
      from  29dab8e15a179ea0fb3d723986b85d355a801841 (commit)

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commit fa5d8c5afd6980c3e661c59e0003a3abbb752f77
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue May 3 18:05:43 2022 -0400

    19070: Fix most tests
    
    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 6b670c73d..10323c2be 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -402,7 +402,8 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     keeprefs = set()
     def addkeepref(k):
-        keeprefs.add(collection_pdh_pattern.match(k).group(1))
+        if k.startswith("keep:"):
+            keeprefs.add(collection_pdh_pattern.match(k).group(1))
 
     def setloc(p):
         loc = p.get("location")
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 5092fc457..b43f0268a 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -77,7 +77,7 @@ def stubs(func):
             "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", {})],
             "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", {})],
         }
-        def kd(a, b, image_name=None, image_tag=None):
+        def kd(a, b, image_name=None, image_tag=None, project_uuid=None):
             return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
         stubs.keepdocker.side_effect = kd
 
@@ -1599,6 +1599,9 @@ class TestCreateWorkflow(unittest.TestCase):
 
     @stubs
     def test_update(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
+
         exited = arvados_cwl.main(
             ["--update-workflow", self.existing_workflow_uuid,
              "--debug",
@@ -1610,6 +1613,7 @@ class TestCreateWorkflow(unittest.TestCase):
                 "name": "submit_wf.cwl",
                 "description": "",
                 "definition": self.expect_workflow,
+                "owner_uuid": project_uuid
             }
         }
         stubs.api.workflows().update.assert_called_with(
@@ -1622,6 +1626,9 @@ class TestCreateWorkflow(unittest.TestCase):
 
     @stubs
     def test_update_name(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
+
         exited = arvados_cwl.main(
             ["--update-workflow", self.existing_workflow_uuid,
              "--debug", "--name", "testing 123",
@@ -1633,6 +1640,7 @@ class TestCreateWorkflow(unittest.TestCase):
                 "name": "testing 123",
                 "description": "",
                 "definition": self.expect_workflow,
+                "owner_uuid": project_uuid
             }
         }
         stubs.api.workflows().update.assert_called_with(

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