Merge branch '17984-cwl-project-uuid-users' into main

refs #17984

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 04db611fbef349692bca2dd38a4988225d980917..2e491fe5ba80e0dc66d6fc69fd9d3b2df84ff895 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -22,6 +22,7 @@ import cwltool.main
 import cwltool.workflow
 import cwltool.process
 import cwltool.argparser
+from cwltool.errors import WorkflowException
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
 from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing
 
@@ -301,6 +302,9 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
         if keep_client is None:
             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
         executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
+    except WorkflowException as e:
+        logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
+        return 1
     except Exception:
         logger.exception("Error creating the Arvados CWL Executor")
         return 1

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 89176923519ee4c737d9376032463dee08a80102..13664a8dfb0d57df0477d4c627928b9be17ad8d7 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -19,9 +19,15 @@ def validate_cluster_target(arvrunner, runtimeContext):
     if runtimeContext.project_uuid:
         cluster_target = runtimeContext.submit_runner_cluster or arvrunner.api._rootDesc["uuidPrefix"]
         if not runtimeContext.project_uuid.startswith(cluster_target):
-            raise WorkflowException("Project uuid '%s' must be for target cluster '%s'" % (runtimeContext.project_uuid, cluster_target))
+            raise WorkflowException("Project uuid '%s' should start with id of target cluster '%s'" % (runtimeContext.project_uuid, cluster_target))
+
         try:
-            arvrunner.api.groups().get(uuid=runtimeContext.project_uuid).execute()
+            if runtimeContext.project_uuid[5:12] == '-tpzed-':
+                arvrunner.api.users().get(uuid=runtimeContext.project_uuid).execute()
+            else:
+                proj = arvrunner.api.groups().get(uuid=runtimeContext.project_uuid).execute()
+                if proj["group_class"] != "project":
+                    raise Exception("not a project, group_class is '%s'" % (proj["group_class"]))
         except Exception as e:
             raise WorkflowException("Invalid project uuid '%s': %s" % (runtimeContext.project_uuid, e))
 

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 12daf6b6702c906544a04c3d4ce034e2f7c01eb1..6cf59f25eed87cf6cc0c1f948d18d3234081b5f7 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -853,6 +853,7 @@ class TestSubmit(unittest.TestCase):
     @stubs
     def test_submit_container_project(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -1265,12 +1266,14 @@ class TestSubmit(unittest.TestCase):
 
     @stubs
     def test_submit_validate_project_uuid(self, stubs):
+        # Fails with bad cluster prefix
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
+        # Project lookup fails
         stubs.api.groups().get().execute.side_effect = Exception("Bad project")
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx",
@@ -1278,6 +1281,14 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
+        # It should work this time because it is looking up a user (and only group is stubbed out to fail)
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx",
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+        self.assertEqual(exited, 0)
+
+
     @mock.patch("arvados.collection.CollectionReader")
     @stubs
     def test_submit_uuid_inputs(self, stubs, collectionReader):
@@ -1382,6 +1393,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1411,6 +1423,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create_name(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1486,6 +1499,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create_collection_per_tool(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1515,6 +1529,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create_with_imports(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",
@@ -1533,6 +1548,7 @@ class TestCreateWorkflow(unittest.TestCase):
     @stubs
     def test_create_with_no_input(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        stubs.api.groups().get().execute.return_value = {"group_class": "project"}
 
         exited = arvados_cwl.main(
             ["--create-workflow", "--debug",