X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c8e58cb205933c32ead3bc416e8eeeade12fc974..ba34a22d9918ae97306472c04701e69090821c82:/sdk/cwl/tests/test_container.py diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py index 3de90c8d88..75371e2b78 100644 --- a/sdk/cwl/tests/test_container.py +++ b/sdk/cwl/tests/test_container.py @@ -63,6 +63,13 @@ class TestContainer(unittest.TestCase): cwltool.process._names = set() 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 + def helper(self, runner, enable_reuse=True): document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION) @@ -171,7 +178,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_'+str(enable_reuse), + 'output_name': 'Output from step test_run_'+str(enable_reuse), 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -179,7 +186,7 @@ class TestContainer(unittest.TestCase): 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["default"] })) @@ -194,6 +201,7 @@ class TestContainer(unittest.TestCase): runner.intermediate_output_ttl = 3600 runner.secret_store = cwltool.secrets.SecretStore() runner.api._rootDesc = {"revision": "20210628"} + runner.api.config.return_value = {"Containers": {"DefaultKeepCacheDisk": 0}} keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { @@ -260,7 +268,7 @@ class TestContainer(unittest.TestCase): "capacity": 5242880000 } }, 'state': 'Committed', - 'output_name': 'Output for step test_resource_requirements', + 'output_name': 'Output from step test_resource_requirements', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 7200, @@ -270,7 +278,7 @@ class TestContainer(unittest.TestCase): 'scheduling_parameters': { 'partitions': ['blurb'] }, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["default"] } @@ -394,7 +402,7 @@ class TestContainer(unittest.TestCase): } }, 'state': 'Committed', - 'output_name': 'Output for step test_initial_work_dir', + 'output_name': 'Output from step test_initial_work_dir', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -403,7 +411,7 @@ class TestContainer(unittest.TestCase): 'cwd': '/var/spool/cwl', 'scheduling_parameters': { }, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["default"] } @@ -482,7 +490,7 @@ class TestContainer(unittest.TestCase): }, }, 'state': 'Committed', - "output_name": "Output for step test_run_redirect", + "output_name": "Output from step test_run_redirect", 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -490,7 +498,7 @@ class TestContainer(unittest.TestCase): 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["default"] })) @@ -527,6 +535,7 @@ class TestContainer(unittest.TestCase): arvjob.successCodes = [0] arvjob.outdir = "/var/spool/cwl" arvjob.output_ttl = 3600 + arvjob.uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzz1" arvjob.collect_outputs.return_value = {"out": "stuff"} @@ -536,7 +545,8 @@ class TestContainer(unittest.TestCase): "output_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", "uuid": "zzzzz-xvhdp-zzzzzzzzzzzzzzz", "container_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", - "modified_at": "2017-05-26T12:01:22Z" + "modified_at": "2017-05-26T12:01:22Z", + "properties": {} }) self.assertFalse(api.collections().create.called) @@ -546,6 +556,10 @@ class TestContainer(unittest.TestCase): arvjob.output_callback.assert_called_with({"out": "stuff"}, "success") runner.add_intermediate_output.assert_called_with("zzzzz-4zz18-zzzzzzzzzzzzzz2") + runner.api.container_requests().update.assert_called_with(uuid="zzzzz-xvhdp-zzzzzzzzzzzzzz1", + body={'container_request': {'properties': {'cwl_output': {'out': 'stuff'}}}}) + + # Test to make sure we dont call runtime_status_update if we already did # some where higher up in the call stack @mock.patch("arvados_cwl.util.get_current_container") @@ -629,7 +643,8 @@ class TestContainer(unittest.TestCase): "output_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", "uuid": "zzzzz-xvhdp-zzzzzzzzzzzzzzz", "container_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", - "modified_at": "2017-05-26T12:01:22Z" + "modified_at": "2017-05-26T12:01:22Z", + "properties": {} }) rts_mock.assert_called_with( @@ -718,7 +733,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_mounts', + 'output_name': 'Output from step test_run_mounts', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -726,7 +741,38 @@ class TestContainer(unittest.TestCase): 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': { + "p1": { + "basename": "99999999999999999999999999999994+44", + "class": "Directory", + "dirname": "/keep", + "http://arvados.org/cwl#collectionUUID": "zzzzz-4zz18-zzzzzzzzzzzzzzz", + "listing": [ + { + "basename": "file1", + "class": "File", + "dirname": "/keep/99999999999999999999999999999994+44", + "location": "keep:99999999999999999999999999999994+44/file1", + "nameext": "", + "nameroot": "file1", + "path": "/keep/99999999999999999999999999999994+44/file1", + "size": 0 + }, + { + "basename": "file2", + "class": "File", + "dirname": "/keep/99999999999999999999999999999994+44", + "location": "keep:99999999999999999999999999999994+44/file2", + "nameext": "", + "nameroot": "file2", + "path": "/keep/99999999999999999999999999999994+44/file2", + "size": 0 + } + ], + "location": "keep:99999999999999999999999999999994+44", + "path": "/keep/99999999999999999999999999999994+44" + } + }}, 'secret_mounts': {}, 'output_storage_classes': ["default"] })) @@ -812,7 +858,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_secrets', + 'output_name': 'Output from step test_secrets', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -820,7 +866,7 @@ class TestContainer(unittest.TestCase): 'command': ['md5sum', 'example.conf'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': job_order}, "secret_mounts": { "/var/spool/cwl/example.conf": { "content": "username: user\npassword: blorp\n", @@ -934,7 +980,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_True', + 'output_name': 'Output from step test_run_True', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -942,7 +988,7 @@ class TestContainer(unittest.TestCase): 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["foo_sc", "bar_sc"] })) @@ -1020,7 +1066,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_True', + 'output_name': 'Output from step test_run_True', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -1030,6 +1076,7 @@ class TestContainer(unittest.TestCase): 'scheduling_parameters': {}, 'properties': { "baz": "blorp", + "cwl_input": {"x": "blorp"}, "foo": "bar", "quux": { "q1": 1, @@ -1130,7 +1177,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_True' + ("" if test_case == 0 else "_"+str(test_case+1)), + 'output_name': 'Output from step test_run_True' + ("" if test_case == 0 else "_"+str(test_case+1)), 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -1138,7 +1185,7 @@ class TestContainer(unittest.TestCase): 'command': ['nvidia-smi'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["default"] })) @@ -1204,7 +1251,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_True', + 'output_name': 'Output from step test_run_True', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -1212,7 +1259,7 @@ class TestContainer(unittest.TestCase): 'command': ['echo'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'secret_mounts': {}, 'output_storage_classes': ["default"] } @@ -1227,13 +1274,161 @@ class TestContainer(unittest.TestCase): runtimeContext.match_local_docker = True container_request['container_image'] = '99999999999999999999999999999993+99' container_request['name'] = 'test_run_True_2' - container_request['output_name'] = 'Output for step test_run_True_2' + container_request['output_name'] = 'Output from step test_run_True_2' for j in arvtool.job({}, mock.MagicMock(), runtimeContext): j.run(runtimeContext) runner.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(container_request)) + # The test passes no builder.resources + # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + def test_run_preemptible_hint(self, keepdocker): + arvados_cwl.add_arv_hints() + for enable_preemptible in (None, True, False): + for preemptible_hint in (None, True, False): + arv_docker_clear_cache() + + runner = mock.MagicMock() + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": "20210628"} + + keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + runner.api.collections().get().execute.return_value = { + "portable_data_hash": "99999999999999999999999999999993+99"} + + if preemptible_hint is not None: + hints = [{ + "class": "http://arvados.org/cwl#UsePreemptible", + "usePreemptible": preemptible_hint + }] + else: + hints = [] + + tool = cmap({ + "inputs": [], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2", + "hints": hints + }) + + loadingContext, runtimeContext = self.helper(runner) + + runtimeContext.name = 'test_run_enable_preemptible_'+str(enable_preemptible)+str(preemptible_hint) + runtimeContext.enable_preemptible = enable_preemptible + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + # Test the interactions between --enable/disable-preemptible + # and UsePreemptible hint + + if enable_preemptible is None: + if preemptible_hint is None: + sched = {} + else: + sched = {'preemptible': preemptible_hint} + else: + if preemptible_hint is None: + sched = {'preemptible': enable_preemptible} + else: + sched = {'preemptible': enable_preemptible and preemptible_hint} + + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + runner.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher({ + 'environment': { + 'HOME': '/var/spool/cwl', + 'TMPDIR': '/tmp' + }, + 'name': runtimeContext.name, + 'runtime_constraints': { + 'vcpus': 1, + 'ram': 268435456 + }, + 'use_existing': True, + 'priority': 500, + 'mounts': { + '/tmp': {'kind': 'tmp', + "capacity": 1073741824 + }, + '/var/spool/cwl': {'kind': 'tmp', + "capacity": 1073741824 } + }, + 'state': 'Committed', + 'output_name': 'Output from step '+runtimeContext.name, + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', + 'output_path': '/var/spool/cwl', + 'output_ttl': 0, + 'container_image': '99999999999999999999999999999993+99', + 'command': ['ls', '/var/spool/cwl'], + 'cwd': '/var/spool/cwl', + 'scheduling_parameters': sched, + 'properties': {'cwl_input': {}}, + 'secret_mounts': {}, + 'output_storage_classes': ["default"] + })) + + + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + def test_output_properties(self, keepdocker): + arvados_cwl.add_arv_hints() + for rev in ["20210628", "20220510"]: + runner = mock.MagicMock() + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": rev} + + keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + runner.api.collections().get().execute.return_value = { + "portable_data_hash": "99999999999999999999999999999993+99"} + + tool = cmap({ + "inputs": [{ + "id": "inp", + "type": "string" + }], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "", + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "hints": [ + { + "class": "http://arvados.org/cwl#OutputCollectionProperties", + "outputProperties": { + "foo": "bar", + "baz": "$(inputs.inp)" + } + } + ] + }) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_timelimit" + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + for j in arvtool.job({"inp": "quux"}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + + _, kwargs = runner.api.container_requests().create.call_args + if rev == "20220510": + self.assertEqual({"foo": "bar", "baz": "quux"}, kwargs['body'].get('output_properties')) + else: + self.assertEqual(None, kwargs['body'].get('output_properties')) + class TestWorkflow(unittest.TestCase): def setUp(self): @@ -1288,6 +1483,8 @@ class TestWorkflow(unittest.TestCase): runner.api.collections().list().execute.return_value = {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999993+99"}]} + runner.api.containers().current().execute.return_value = {} + runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 @@ -1360,11 +1557,23 @@ class TestWorkflow(unittest.TestCase): } }, "name": "scatterstep", - "output_name": "Output for step scatterstep", + "output_name": "Output from step scatterstep", "output_path": "/var/spool/cwl", "output_ttl": 0, "priority": 500, - "properties": {}, + "properties": {'cwl_input': { + "fileblub": { + "basename": "token.txt", + "class": "File", + "dirname": "/keep/99999999999999999999999999999999+118", + "location": "keep:99999999999999999999999999999999+118/token.txt", + "nameext": ".txt", + "nameroot": "token", + "path": "/keep/99999999999999999999999999999999+118/token.txt", + "size": 0 + }, + "sleeptime": 5 + }}, "runtime_constraints": { "ram": 1073741824, "vcpus": 1 @@ -1437,7 +1646,7 @@ class TestWorkflow(unittest.TestCase): 'name': u'echo-subwf', 'secret_mounts': {}, 'runtime_constraints': {'API': True, 'vcpus': 3, 'ram': 1073741824}, - 'properties': {}, + 'properties': {'cwl_input': {}}, 'priority': 500, 'mounts': { '/var/spool/cwl/cwl.input.yml': { @@ -1474,7 +1683,7 @@ class TestWorkflow(unittest.TestCase): u'cwl.input.yml' ], 'use_existing': True, - 'output_name': u'Output for step echo-subwf', + 'output_name': u'Output from step echo-subwf', 'cwd': '/var/spool/cwl', 'output_storage_classes': ["default"] }))