X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/35658af99f09f2f6768583d65246429f789fc5a2..1c95615a417b6435dc86f80e3f02563196449611:/sdk/cwl/tests/test_container.py?ds=sidebyside diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py index 3374e1c13f..1a2bd112f3 100644 --- a/sdk/cwl/tests/test_container.py +++ b/sdk/cwl/tests/test_container.py @@ -18,6 +18,7 @@ import os import functools import cwltool.process import cwltool.secrets +from cwltool.update import INTERNAL_VERSION from schema_salad.ref_resolver import Loader from schema_salad.sourceline import cmap @@ -58,9 +59,10 @@ class TestContainer(unittest.TestCase): def setUp(self): cwltool.process._names = set() + arv_docker_clear_cache() def helper(self, runner, enable_reuse=True): - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1") + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION) make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) @@ -69,7 +71,7 @@ class TestContainer(unittest.TestCase): "basedir": "", "make_fs_access": make_fs_access, "loader": Loader({}), - "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}}) + "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}}) runtimeContext = arvados_cwl.context.ArvRuntimeContext( {"work_api": "containers", "basedir": "", @@ -110,6 +112,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -121,7 +124,7 @@ class TestContainer(unittest.TestCase): "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], "id": "#", - "class": "CommandLineTool" + "class": "org.w3id.cwl.cwl.CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner, enable_reuse) @@ -161,18 +164,19 @@ class TestContainer(unittest.TestCase): 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, 'properties': {}, - 'secret_mounts': {} + 'secret_mounts': {}, + 'output_storage_classes': ["default"] })) # The test passes some fields in builder.resources # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch("arvados.commands.keepdocker.list_images_in_arv") def test_resource_requirements(self, keepdocker): - arv_docker_clear_cache() runner = mock.MagicMock() runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 3600 runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": "20210628"} keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { @@ -204,7 +208,7 @@ class TestContainer(unittest.TestCase): }], "baseCommand": "ls", "id": "#", - "class": "CommandLineTool" + "class": "org.w3id.cwl.cwl.CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner) @@ -249,7 +253,8 @@ class TestContainer(unittest.TestCase): 'partitions': ['blurb'] }, 'properties': {}, - 'secret_mounts': {} + 'secret_mounts': {}, + 'output_storage_classes': ["default"] } call_body = call_kwargs.get('body', None) @@ -263,11 +268,11 @@ class TestContainer(unittest.TestCase): @mock.patch("arvados.commands.keepdocker.list_images_in_arv") @mock.patch("arvados.collection.Collection") def test_initial_work_dir(self, collection_mock, keepdocker): - 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 = { @@ -312,7 +317,7 @@ class TestContainer(unittest.TestCase): }], "baseCommand": "ls", "id": "#", - "class": "CommandLineTool" + "class": "org.w3id.cwl.cwl.CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner) @@ -379,7 +384,8 @@ class TestContainer(unittest.TestCase): 'scheduling_parameters': { }, 'properties': {}, - 'secret_mounts': {} + 'secret_mounts': {}, + 'output_storage_classes': ["default"] } call_body = call_kwargs.get('body', None) @@ -391,18 +397,17 @@ class TestContainer(unittest.TestCase): # Test redirecting stdin/stdout/stderr @mock.patch("arvados.commands.keepdocker.list_images_in_arv") def test_redirects(self, keepdocker): - 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"} - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1") + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION) tool = cmap({ "inputs": [], @@ -413,7 +418,7 @@ class TestContainer(unittest.TestCase): "stdin": "/keep/99999999999999999999999999999996+99/file.txt", "arguments": [{"valueFrom": "$(runtime.outdir)"}], "id": "#", - "class": "CommandLineTool" + "class": "org.w3id.cwl.cwl.CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner) @@ -465,7 +470,8 @@ class TestContainer(unittest.TestCase): 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, 'properties': {}, - 'secret_mounts': {} + 'secret_mounts': {}, + 'output_storage_classes': ["default"] })) @mock.patch("arvados.collection.Collection") @@ -534,6 +540,25 @@ class TestContainer(unittest.TestCase): except RuntimeError: self.fail("RuntimeStatusLoggingHandler should not be called recursively") + + # Test to make sure that an exception raised from + # get_current_container doesn't cause the logger to raise an + # exception + @mock.patch("arvados_cwl.util.get_current_container") + def test_runtime_status_get_current_container_exception(self, gcc_mock): + self.setup_and_test_container_executor_and_logging(gcc_mock) + root_logger = logging.getLogger('') + + # get_current_container is invoked when we call + # runtime_status_update, it is going to also raise an + # exception. + gcc_mock.side_effect = Exception("Second Error") + try: + root_logger.error("First Error") + except Exception: + self.fail("Exception in logger should not propagate") + self.assertTrue(gcc_mock.called) + @mock.patch("arvados_cwl.ArvCwlExecutor.runtime_status_update") @mock.patch("arvados_cwl.util.get_current_container") @mock.patch("arvados.collection.CollectionReader") @@ -597,12 +622,11 @@ class TestContainer(unittest.TestCase): # 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_mounts(self, keepdocker): - 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 = { @@ -620,7 +644,7 @@ class TestContainer(unittest.TestCase): "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], "id": "#", - "class": "CommandLineTool" + "class": "org.w3id.cwl.cwl.CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner) @@ -681,19 +705,19 @@ class TestContainer(unittest.TestCase): 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, 'properties': {}, - 'secret_mounts': {} + 'secret_mounts': {}, + 'output_storage_classes': ["default"] })) # 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_secrets(self, keepdocker): - 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 = { @@ -702,7 +726,7 @@ class TestContainer(unittest.TestCase): document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1") tool = cmap({"arguments": ["md5sum", "example.conf"], - "class": "CommandLineTool", + "class": "org.w3id.cwl.cwl.CommandLineTool", "hints": [ { "class": "http://commonwl.org/cwltool#Secrets", @@ -778,19 +802,19 @@ class TestContainer(unittest.TestCase): "content": "username: user\npassword: blorp\n", "kind": "text" } - } + }, + 'output_storage_classes': ["default"] })) # 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_timelimit(self, keepdocker): - 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 = { @@ -802,7 +826,7 @@ class TestContainer(unittest.TestCase): "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], "id": "#", - "class": "CommandLineTool", + "class": "org.w3id.cwl.cwl.CommandLineTool", "hints": [ { "class": "ToolTimeLimit", @@ -824,12 +848,179 @@ class TestContainer(unittest.TestCase): self.assertEqual(42, kwargs['body']['scheduling_parameters'].get('max_run_time')) + # 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_setting_storage_class(self, keepdocker): + 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"} + + tool = cmap({ + "inputs": [], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "#", + "class": "org.w3id.cwl.cwl.CommandLineTool", + "hints": [ + { + "class": "http://arvados.org/cwl#OutputStorageClass", + "finalStorageClass": ["baz_sc", "qux_sc"], + "intermediateStorageClass": ["foo_sc", "bar_sc"] + } + ] + }) + + loadingContext, runtimeContext = self.helper(runner, True) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool.formatgraph = None + + 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': 'test_run_True', + 'runtime_constraints': { + 'vcpus': 1, + 'ram': 1073741824 + }, + 'use_existing': True, + 'priority': 500, + 'mounts': { + '/tmp': {'kind': 'tmp', + "capacity": 1073741824 + }, + '/var/spool/cwl': {'kind': 'tmp', + "capacity": 1073741824 } + }, + 'state': 'Committed', + 'output_name': 'Output for step test_run_True', + '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': {}, + 'properties': {}, + 'secret_mounts': {}, + 'output_storage_classes': ["foo_sc", "bar_sc"] + })) + + + # 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_setting_process_properties(self, keepdocker): + 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"} + + tool = cmap({ + "inputs": [ + {"id": "x", "type": "string"}], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "#", + "class": "org.w3id.cwl.cwl.CommandLineTool", + "hints": [ + { + "class": "http://arvados.org/cwl#ProcessProperties", + "processProperties": [ + {"propertyName": "foo", + "propertyValue": "bar"}, + {"propertyName": "baz", + "propertyValue": "$(inputs.x)"}, + {"propertyName": "quux", + "propertyValue": { + "q1": 1, + "q2": 2 + } + } + ], + } + ] + }) + + loadingContext, runtimeContext = self.helper(runner, True) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool.formatgraph = None + + for j in arvtool.job({"x": "blorp"}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + runner.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher({ + 'environment': { + 'HOME': '/var/spool/cwl', + 'TMPDIR': '/tmp' + }, + 'name': 'test_run_True', + 'runtime_constraints': { + 'vcpus': 1, + 'ram': 1073741824 + }, + 'use_existing': True, + 'priority': 500, + 'mounts': { + '/tmp': {'kind': 'tmp', + "capacity": 1073741824 + }, + '/var/spool/cwl': {'kind': 'tmp', + "capacity": 1073741824 } + }, + 'state': 'Committed', + 'output_name': 'Output for step test_run_True', + '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': {}, + 'properties': { + "baz": "blorp", + "foo": "bar", + "quux": { + "q1": 1, + "q2": 2 + } + }, + 'secret_mounts': {}, + 'output_storage_classes': ["default"] + })) + + class TestWorkflow(unittest.TestCase): def setUp(self): cwltool.process._names = set() + arv_docker_clear_cache() def helper(self, runner, enable_reuse=True): - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1") + document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) @@ -844,7 +1035,7 @@ class TestWorkflow(unittest.TestCase): "basedir": "", "make_fs_access": make_fs_access, "loader": document_loader, - "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}, + "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}, "construct_tool_object": runner.arv_make_tool}) runtimeContext = arvados_cwl.context.ArvRuntimeContext( {"work_api": "containers", @@ -863,7 +1054,6 @@ class TestWorkflow(unittest.TestCase): @mock.patch("arvados.collection.Collection") @mock.patch('arvados.commands.keepdocker.list_images_in_arv') def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader): - arv_docker_clear_cache() arvados_cwl.add_arv_hints() api = mock.MagicMock() @@ -885,6 +1075,8 @@ class TestWorkflow(unittest.TestCase): loadingContext, runtimeContext = self.helper(runner) runner.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir) + mockcollectionreader().exists.return_value = True + tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl") metadata["cwlVersion"] = tool["cwlVersion"] @@ -909,7 +1101,7 @@ class TestWorkflow(unittest.TestCase): "--no-container", "--move-outputs", "--preserve-entire-environment", - "workflow.cwl#main", + "workflow.cwl", "cwl.input.yml" ], "container_image": "99999999999999999999999999999993+99", @@ -959,7 +1151,8 @@ class TestWorkflow(unittest.TestCase): "scheduling_parameters": {}, "secret_mounts": {}, "state": "Committed", - "use_existing": True + "use_existing": True, + 'output_storage_classes': ["default"] })) mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)]) mockc.open().__enter__().write.assert_has_calls([mock.call( @@ -979,7 +1172,6 @@ class TestWorkflow(unittest.TestCase): @mock.patch("arvados.collection.Collection") @mock.patch('arvados.commands.keepdocker.list_images_in_arv') def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader): - arv_docker_clear_cache() arvados_cwl.add_arv_hints() api = mock.MagicMock() @@ -1057,12 +1249,13 @@ class TestWorkflow(unittest.TestCase): u'--no-container', u'--move-outputs', u'--preserve-entire-environment', - u'workflow.cwl#main', + u'workflow.cwl', u'cwl.input.yml' ], 'use_existing': True, 'output_name': u'Output for step echo-subwf', - 'cwd': '/var/spool/cwl' + 'cwd': '/var/spool/cwl', + 'output_storage_classes': ["default"] })) def test_default_work_api(self):