X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2957b917aaaefc1485e1c5293d413f0931b3030a..3e5ac41e4e38e6c8fa72883b803d85fcde53e25b:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 77bef075fa..8875b7d954 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -132,7 +132,8 @@ def stubs(func): "listing": [{ "basename": "renamed.txt", "class": "File", - "location": "keep:99999999999999999999999999999998+99/file1.txt" + "location": "keep:99999999999999999999999999999998+99/file1.txt", + "size": 0 }], 'class': 'Directory' }, @@ -164,7 +165,8 @@ def stubs(func): { 'basename': 'renamed.txt', 'class': 'File', 'location': - 'keep:99999999999999999999999999999998+99/file1.txt' + 'keep:99999999999999999999999999999998+99/file1.txt', + 'size': 0 } ]}}, 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main', @@ -225,7 +227,8 @@ def stubs(func): 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ {'basename': 'renamed.txt', 'class': 'File', - 'location': 'keep:99999999999999999999999999999998+99/file1.txt' + 'location': 'keep:99999999999999999999999999999998+99/file1.txt', + 'size': 0 } ]} }, @@ -234,7 +237,6 @@ def stubs(func): }, 'secret_mounts': {}, 'state': 'Committed', - 'owner_uuid': None, 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--eval-timeout=20', '--thread-count=4', @@ -287,14 +289,14 @@ class TestSubmit(unittest.TestCase): 'manifest_text': '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies', - }), ensure_unique_name=True), + 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input', - }), ensure_unique_name=True), + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', + }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n', @@ -333,6 +335,15 @@ 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): @@ -474,14 +485,14 @@ class TestSubmit(unittest.TestCase): 'manifest_text': '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies', - }), ensure_unique_name=True), + 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input', - }), ensure_unique_name=True)]) + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', + }), ensure_unique_name=False)]) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( @@ -604,6 +615,72 @@ 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): @@ -707,6 +784,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_file_keepref(self, stubs, tm, collectionReader): capture_stdout = cStringIO.StringIO() + collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt") exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_keepref_wf.cwl"], @@ -751,7 +829,6 @@ 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__, @@ -870,7 +947,6 @@ 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__, @@ -1059,6 +1135,42 @@ 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") @@ -1236,7 +1348,6 @@ class TestSubmit(unittest.TestCase): }, "name": "secret_wf.cwl", "output_path": "/var/spool/cwl", - "owner_uuid": None, "priority": 500, "properties": {}, "runtime_constraints": { @@ -1259,6 +1370,31 @@ 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"