X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c2aceca339ec3a6f3d853865cebd0efe348ff518..ae92d144610446849eb568247a44f02ae985c281:/sdk/cwl/tests/test_submit.py

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 12daf6b670..5092fc4575 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -47,17 +47,22 @@ _rootDesc = None
 
 def stubs(func):
     @functools.wraps(func)
+    @mock.patch("uuid.uuid4")
     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
     @mock.patch("arvados.collection.KeepClient")
     @mock.patch("arvados.keep.KeepClient")
     @mock.patch("arvados.events.subscribe")
-    def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
+    def wrapped(self, events, keep_client1, keep_client2, keepdocker, uuid4, *args, **kwargs):
         class Stubs(object):
             pass
         stubs = Stubs()
         stubs.events = events
         stubs.keepdocker = keepdocker
 
+        uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
+                             "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
+                             "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
+
         def putstub(p, **kwargs):
             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
         keep_client1().put.side_effect = putstub
@@ -67,10 +72,10 @@ def stubs(func):
 
         stubs.keep_client = keep_client2
         stubs.docker_images = {
-            "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")],
-            "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
-            "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
-            "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
+            "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
+            "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", {})],
+            "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", {})],
+            "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", {})],
         }
         def kd(a, b, image_name=None, image_tag=None):
             return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
@@ -87,6 +92,7 @@ def stubs(func):
         stubs.api = mock.MagicMock()
         stubs.api._rootDesc = get_rootDesc()
         stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
+        stubs.api._rootDesc["revision"] = "20210628"
 
         stubs.api.users().current().execute.return_value = {
             "uuid": stubs.fake_user_uuid,
@@ -95,6 +101,11 @@ def stubs(func):
         stubs.api.containers().current().execute.return_value = {
             "uuid": stubs.fake_container_uuid,
         }
+        stubs.api.config()["StorageClasses"].items.return_value = {
+            "default": {
+                "Default": True
+            }
+        }.items()
 
         class CollectionExecute(object):
             def __init__(self, exe):
@@ -342,14 +353,12 @@ class TestSubmit(unittest.TestCase):
         cwltool.process._names = set()
         arvados_cwl.arvdocker.arv_docker_clear_cache()
 
-    @stubs
-    def test_error_when_multiple_storage_classes_specified(self, stubs):
-        storage_classes = "foo,bar"
-        exited = arvados_cwl.main(
-                ["--debug", "--storage-classes", storage_classes,
-                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-                sys.stdin, sys.stderr, api_client=stubs.api)
-        self.assertEqual(exited, 1)
+    def tearDown(self):
+        root_logger = logging.getLogger('')
+
+        # Remove existing RuntimeStatusLoggingHandlers if they exist
+        handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
+        root_logger.handlers = handlers
 
     @mock.patch("time.sleep")
     @stubs
@@ -449,7 +458,7 @@ class TestSubmit(unittest.TestCase):
                 "enableReuse": False,
             },
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
             "arv": "http://arvados.org/cwl#",
             "cwltool": "http://commonwl.org/cwltool#"
         }
@@ -526,6 +535,27 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
+    @stubs
+    def test_submit_multiple_storage_classes(self, stubs):
+        exited = arvados_cwl.main(
+            ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256", "--debug",
+                                       "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
@@ -554,6 +584,7 @@ class TestSubmit(unittest.TestCase):
     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
+        stubs.api.config().get.return_value = {"default": {"Default": True}}
 
         def set_final_output(job_order, output_callback, runtimeContext):
             output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
@@ -568,6 +599,27 @@ class TestSubmit(unittest.TestCase):
         make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
         self.assertEqual(exited, 0)
 
+    @mock.patch("cwltool.task_queue.TaskQueue")
+    @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+    @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
+    @stubs
+    def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
+        final_output_c = arvados.collection.Collection()
+        make_output.return_value = ({},final_output_c)
+
+        def set_final_output(job_order, output_callback, runtimeContext):
+            output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+            return []
+        job.side_effect = set_final_output
+
+        exited = arvados_cwl.main(
+            ["--debug", "--local",
+                "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+        self.assertEqual(exited, 0)
+
     @stubs
     def test_submit_container_output_ttl(self, stubs):
         exited = arvados_cwl.main(
@@ -853,6 +905,7 @@ 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"],
@@ -992,7 +1045,7 @@ class TestSubmit(unittest.TestCase):
                 "keep_cache": 512
             }
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
             "arv": "http://arvados.org/cwl#",
         }
         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
@@ -1007,9 +1060,6 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    def tearDown(self):
-        arvados_cwl.arvdocker.arv_docker_clear_cache()
-
     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
     @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
     @mock.patch("arvados.api")
@@ -1020,6 +1070,7 @@ class TestSubmit(unittest.TestCase):
         arvrunner.project_uuid = ""
         api.return_value = mock.MagicMock()
         arvrunner.api = api.return_value
+        arvrunner.runtimeContext.match_local_docker = False
         arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
                                                                         "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
                                                                         "link_class": "docker_image_repo+tag",
@@ -1086,9 +1137,6 @@ class TestSubmit(unittest.TestCase):
                     "content": {
                         "$graph": [
                             {
-                                "$namespaces": {
-                                    "cwltool": "http://commonwl.org/cwltool#"
-                                },
                                 "arguments": [
                                     "md5sum",
                                     "example.conf"
@@ -1177,6 +1225,9 @@ class TestSubmit(unittest.TestCase):
                                 ]
                             }
                         ],
+                        "$namespaces": {
+                            "cwltool": "http://commonwl.org/cwltool#"
+                        },
                         "cwlVersion": "v1.0"
                     },
                     "kind": "json"
@@ -1265,12 +1316,14 @@ 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 +1331,14 @@ 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):
@@ -1365,10 +1426,98 @@ class TestSubmit(unittest.TestCase):
             self.assertEqual(exited, 1)
             self.assertRegex(
                 capture_stderr.getvalue(),
-                r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
+                r"Collection\s*uuid\s*zzzzz-4zz18-zzzzzzzzzzzzzzz\s*not\s*found")
         finally:
             cwltool_logger.removeHandler(stderr_logger)
 
+    @stubs
+    def test_submit_set_process_properties(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug",
+                "tests/wf/submit_wf_process_properties.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["name"] = "submit_wf_process_properties.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+            {
+                "class": "http://arvados.org/cwl#ProcessProperties",
+                "processProperties": [
+                    {"propertyName": "baz",
+                     "propertyValue": "$(inputs.x.basename)"},
+                    {"propertyName": "foo",
+                     "propertyValue": "bar"},
+                    {"propertyName": "quux",
+                     "propertyValue": {
+                         "q1": 1,
+                         "q2": 2
+                     }
+                    }
+                ],
+            }
+        ]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+            "arv": "http://arvados.org/cwl#"
+        }
+
+        expect_container["properties"] = {
+            "baz": "blorp.txt",
+            "foo": "bar",
+            "quux": {
+                "q1": 1,
+                "q2": 2
+            }
+        }
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+
+    @stubs
+    def test_submit_enable_preemptible(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
+                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--enable-preemptible',
+                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+    @stubs
+    def test_submit_disable_preemptible(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+                        '--no-log-timestamps', '--disable-validate', '--disable-color',
+                        '--eval-timeout=20', '--thread-count=0',
+                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--disable-preemptible',
+                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
 
 class TestCreateWorkflow(unittest.TestCase):
     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
@@ -1379,9 +1528,17 @@ class TestCreateWorkflow(unittest.TestCase):
         cwltool.process._names = set()
         arvados_cwl.arvdocker.arv_docker_clear_cache()
 
+    def tearDown(self):
+        root_logger = logging.getLogger('')
+
+        # Remove existing RuntimeStatusLoggingHandlers if they exist
+        handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
+        root_logger.handlers = handlers
+
     @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 +1568,7 @@ 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",
@@ -1461,6 +1619,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          self.existing_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
+
     @stubs
     def test_update_name(self, stubs):
         exited = arvados_cwl.main(
@@ -1486,6 +1645,7 @@ 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 +1675,7 @@ 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 +1694,7 @@ 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",