X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/418c57bce3aac1a22548e53e1018a1547d9efee4..6fe8e52020d421797306e5c6536afbcee761510a:/sdk/cwl/tests/test_submit.py?ds=sidebyside diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index a7f49208bf..cd46251300 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -168,6 +168,7 @@ def stubs(func): } ]}}, 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main', + 'arv:debug': True, 'arv:enable_reuse': True, 'arv:on_error': 'continue' }, @@ -233,10 +234,10 @@ def stubs(func): }, 'secret_mounts': {}, 'state': 'Committed', - 'owner_uuid': None, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'name': 'submit_wf.cwl', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, @@ -331,6 +332,15 @@ class TestSubmit(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') + @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) + @mock.patch("time.sleep") @stubs def test_submit_on_error(self, stubs, tm): @@ -444,7 +454,7 @@ class TestSubmit(unittest.TestCase): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' exited = arvados_cwl.main( - ["--submit", "--no-wait", + ["--submit", "--no-wait", "--debug", "--project-uuid", project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], sys.stdout, sys.stderr, api_client=stubs.api) @@ -503,7 +513,8 @@ class TestSubmit(unittest.TestCase): expect_container["command"] = [ 'arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--disable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--disable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False @@ -527,7 +538,8 @@ class TestSubmit(unittest.TestCase): expect_container["command"] = [ 'arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--disable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--disable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False expect_container["name"] = "submit_wf_no_reuse.cwl" @@ -563,7 +575,8 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=stop', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=stop', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -588,7 +601,9 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - "--output-name="+output_name, '--enable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', + "--output-name="+output_name, '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["output_name"] = output_name @@ -597,6 +612,72 @@ class TestSubmit(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_storage_classes(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', "--debug", + "--storage-classes=foo", '--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(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @mock.patch("arvados_cwl.task_queue.TaskQueue") + @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") + @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None)) + @stubs + def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): + def set_final_output(job_order, output_callback, runtimeContext): + output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") + return [] + job.side_effect = set_final_output + + try: + exited = arvados_cwl.main( + ["--debug", "--local", "--storage-classes=foo", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') + + @mock.patch("arvados_cwl.task_queue.TaskQueue") + @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") + @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None)) + @stubs + def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): + def set_final_output(job_order, output_callback, runtimeContext): + output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") + return [] + job.side_effect = set_final_output + + try: + exited = arvados_cwl.main( + ["--debug", "--local", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') @stubs def test_submit_container_output_ttl(self, stubs): @@ -613,8 +694,9 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', - "--intermediate-output-ttl=3600", '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', + "--intermediate-output-ttl=3600", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -637,8 +719,9 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', - "--trash-intermediate", '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', + "--trash-intermediate", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -663,7 +746,9 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', + "--output-tags="+output_tags, '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -740,13 +825,13 @@ class TestSubmit(unittest.TestCase): 'kind': 'json' } }, 'state': 'Committed', - 'owner_uuid': None, 'output_path': '/var/spool/cwl', 'name': 'expect_arvworkflow.cwl#main', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { @@ -858,13 +943,13 @@ class TestSubmit(unittest.TestCase): 'kind': 'json' } }, 'state': 'Committed', - 'owner_uuid': None, 'output_path': '/var/spool/cwl', 'name': 'a test workflow', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', '--eval-timeout=20', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { @@ -923,7 +1008,9 @@ class TestSubmit(unittest.TestCase): expect_container["owner_uuid"] = project_uuid expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid, '--eval-timeout=20', + "--eval-timeout=20", "--thread-count=4", + '--enable-reuse', '--debug', '--on-error=continue', + '--project-uuid='+project_uuid, '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -947,7 +1034,34 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', - '--enable-reuse', '--on-error=continue', '--eval-timeout=60.0', + '--eval-timeout=60.0', '--thread-count=4', + '--enable-reuse', '--debug', '--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(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + + @stubs + def test_submit_container_thread_count(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=20', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -1017,6 +1131,42 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_wf_runner_resources(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["runtime_constraints"] = { + "API": True, + "vcpus": 2, + "ram": 2000 * 2**20 + } + expect_container["name"] = "submit_wf_runner_resources.cwl" + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ + { + "class": "http://arvados.org/cwl#WorkflowRunnerResources", + "coresMin": 2, + "ramMin": 2000 + } + ] + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = { + "arv": "http://arvados.org/cwl#", + } + + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @mock.patch("arvados.commands.keepdocker.find_one_image_hash") @mock.patch("cwltool.docker.DockerCommandLineJob.get_image") @mock.patch("arvados.api") @@ -1069,9 +1219,11 @@ class TestSubmit(unittest.TestCase): "--api=containers", "--no-log-timestamps", "--disable-validate", + "--eval-timeout=20", + '--thread-count=4', "--enable-reuse", + '--debug', "--on-error=continue", - "--eval-timeout=20", "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json" ], @@ -1192,7 +1344,6 @@ class TestSubmit(unittest.TestCase): }, "name": "secret_wf.cwl", "output_path": "/var/spool/cwl", - "owner_uuid": None, "priority": 500, "properties": {}, "runtime_constraints": { @@ -1215,6 +1366,31 @@ class TestSubmit(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_request_uuid(self, stubs): + stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy" + + stubs.api.container_requests().update().execute.return_value = { + "uuid": stubs.expect_container_request_uuid, + "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", + "state": "Queued" + } + + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + stubs.api.container_requests().update.assert_called_with( + uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + class TestCreateTemplate(unittest.TestCase): existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"