[ARVADOS] updated: 2.3.0-29-gcd034042a

[Git user]

Summary of changes:
 sdk/python/arvados/commands/arv_copy.py | 36 ++++++++++++++++++++++++++-------
 sdk/python/tests/test_arv_copy.py       | 13 ++++++++----
 2 files changed, 38 insertions(+), 11 deletions(-)

       via  cd034042a1ea9950ebea9109ce857eee72adc249 (commit)
      from  bbc934a55d42bcd46ad0a7d33456b37c0be18f61 (commit)

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commit cd034042a1ea9950ebea9109ce857eee72adc249
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Wed Nov 17 17:03:57 2021 -0500

    Merge branch '17962-check-wf-definition' refs #17962
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/python/arvados/commands/arv_copy.py b/sdk/python/arvados/commands/arv_copy.py
index d10234ca6..7951842ac 100755
--- a/sdk/python/arvados/commands/arv_copy.py
+++ b/sdk/python/arvados/commands/arv_copy.py
@@ -113,7 +113,7 @@ def main():
     copy_opts.set_defaults(recursive=True)
 
     parser = argparse.ArgumentParser(
-        description='Copy a workflow, collection or project from one Arvados instance to another.',
+        description='Copy a workflow, collection or project from one Arvados instance to another.  On success, the uuid of the copied object is printed to stdout.',
         parents=[copy_opts, arv_cmd.retry_opt])
     args = parser.parse_args()
 
@@ -161,7 +161,12 @@ def main():
         logger.error("API server returned an error result: {}".format(result))
         exit(1)
 
-    logger.info("")
+    print(result['uuid'])
+
+    if result.get('partial_error'):
+        logger.warning("Warning: created copy with uuid {} but failed to copy some items: {}".format(result['uuid'], result['partial_error']))
+        exit(1)
+
     logger.info("Success: created copy with uuid {}".format(result['uuid']))
     exit(0)
 
@@ -292,8 +297,11 @@ def copy_workflow(wf_uuid, src, dst, args):
     # fetch the workflow from the source instance
     wf = src.workflows().get(uuid=wf_uuid).execute(num_retries=args.retries)
 
+    if not wf["definition"]:
+        logger.warning("Workflow object {} has an empty or null definition, it won't do anything.".format(wf_uuid))
+
     # copy collections and docker images
-    if args.recursive:
+    if args.recursive and wf["definition"]:
         wf_def = yaml.safe_load(wf["definition"])
         if wf_def is not None:
             locations = []
@@ -683,17 +691,31 @@ def copy_project(obj_uuid, src, dst, owner_uuid, args):
 
     logger.debug('Copying %s to %s', obj_uuid, project_record["uuid"])
 
+
+    partial_error = ""
+
     # Copy collections
-    copy_collections([col["uuid"] for col in arvados.util.list_all(src.collections().list, filters=[["owner_uuid", "=", obj_uuid]])],
-                     src, dst, args)
+    try:
+        copy_collections([col["uuid"] for col in arvados.util.list_all(src.collections().list, filters=[["owner_uuid", "=", obj_uuid]])],
+                         src, dst, args)
+    except Exception as e:
+        partial_error += "\n" + str(e)
 
     # Copy workflows
     for w in arvados.util.list_all(src.workflows().list, filters=[["owner_uuid", "=", obj_uuid]]):
-        copy_workflow(w["uuid"], src, dst, args)
+        try:
+            copy_workflow(w["uuid"], src, dst, args)
+        except Exception as e:
+            partial_error += "\n" + "Error while copying %s: %s" % (w["uuid"], e)
 
     if args.recursive:
         for g in arvados.util.list_all(src.groups().list, filters=[["owner_uuid", "=", obj_uuid]]):
-            copy_project(g["uuid"], src, dst, project_record["uuid"], args)
+            try:
+                copy_project(g["uuid"], src, dst, project_record["uuid"], args)
+            except Exception as e:
+                partial_error += "\n" + "Error while copying %s: %s" % (g["uuid"], e)
+
+    project_record["partial_error"] = partial_error
 
     return project_record
 
diff --git a/sdk/python/tests/test_arv_copy.py b/sdk/python/tests/test_arv_copy.py
index b560018d3..b853b3304 100644
--- a/sdk/python/tests/test_arv_copy.py
+++ b/sdk/python/tests/test_arv_copy.py
@@ -61,10 +61,13 @@ class ArvCopyVersionTestCase(run_test_server.TestCaseWithServers, tutil.VersionC
             contents = api.groups().list(filters=[["owner_uuid", "=", dest_proj]]).execute()
             assert len(contents["items"]) == 0
 
-            try:
-                self.run_copy(["--project-uuid", dest_proj, "--storage-classes", "foo", src_proj])
-            except SystemExit as e:
-                assert e.code == 0
+            with tutil.redirected_streams(
+                    stdout=tutil.StringIO, stderr=tutil.StringIO) as (out, err):
+                try:
+                    self.run_copy(["--project-uuid", dest_proj, "--storage-classes", "foo", src_proj])
+                except SystemExit as e:
+                    assert e.code == 0
+                copy_uuid_from_stdout = out.getvalue().strip()
 
             contents = api.groups().list(filters=[["owner_uuid", "=", dest_proj]]).execute()
             assert len(contents["items"]) == 1
@@ -72,6 +75,8 @@ class ArvCopyVersionTestCase(run_test_server.TestCaseWithServers, tutil.VersionC
             assert contents["items"][0]["name"] == "arv-copy project"
             copied_project = contents["items"][0]["uuid"]
 
+            assert copied_project == copy_uuid_from_stdout
+
             contents = api.collections().list(filters=[["owner_uuid", "=", copied_project]]).execute()
             assert len(contents["items"]) == 1
 

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