X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/98d6c8c5743e0fd6be85af3b9f30286a358bd1d4..81693ee04f18e68558c9206705ef589cca2460b0:/sdk/cwl/tests/test_container.py diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py index cd555a72ca..d7aa193fe5 100644 --- a/sdk/cwl/tests/test_container.py +++ b/sdk/cwl/tests/test_container.py @@ -2,26 +2,101 @@ # # SPDX-License-Identifier: Apache-2.0 +from builtins import str +from builtins import object + import arvados_cwl +import arvados_cwl.context +import arvados_cwl.util from arvados_cwl.arvdocker import arv_docker_clear_cache +import copy +import arvados.config import logging import mock import unittest import os import functools import cwltool.process +import cwltool.secrets from schema_salad.ref_resolver import Loader from schema_salad.sourceline import cmap from .matcher import JsonDiffMatcher +from .mock_discovery import get_rootDesc if not os.getenv('ARVADOS_DEBUG'): logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN) logging.getLogger('arvados.arv-run').setLevel(logging.WARN) +class CollectionMock(object): + def __init__(self, vwdmock, *args, **kwargs): + self.vwdmock = vwdmock + self.count = 0 + + def open(self, *args, **kwargs): + self.count += 1 + return self.vwdmock.open(*args, **kwargs) + + def copy(self, *args, **kwargs): + self.count += 1 + self.vwdmock.copy(*args, **kwargs) + + def save_new(self, *args, **kwargs): + pass + + def __len__(self): + return self.count + + def portable_data_hash(self): + if self.count == 0: + return arvados.config.EMPTY_BLOCK_LOCATOR + else: + return "99999999999999999999999999999996+99" + class TestContainer(unittest.TestCase): + def helper(self, runner, enable_reuse=True): + 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)) + loadingContext = arvados_cwl.context.ArvLoadingContext( + {"avsc_names": avsc_names, + "basedir": "", + "make_fs_access": make_fs_access, + "loader": Loader({}), + "metadata": {"cwlVersion": "v1.0"}}) + runtimeContext = arvados_cwl.context.ArvRuntimeContext( + {"work_api": "containers", + "basedir": "", + "name": "test_run_"+str(enable_reuse), + "make_fs_access": make_fs_access, + "tmpdir": "/tmp", + "enable_reuse": enable_reuse, + "priority": 500, + "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + }) + + return loadingContext, runtimeContext + + # Helper function to set up the ArvCwlExecuture to use the containers api + # and test that the RuntimeStatusLoggingHandler is set up correctly + def setup_and_test_container_executor_and_logging(self, gcc_mock) : + api = mock.MagicMock() + api._rootDesc = copy.deepcopy(get_rootDesc()) + del api._rootDesc.get('resources')['jobs']['methods']['create'] + + # Make sure ArvCwlExecutor thinks it's running inside a container so it + # adds the logging handler that will call runtime_status_update() mock + self.assertFalse(gcc_mock.called) + runner = arvados_cwl.ArvCwlExecutor(api) + self.assertEqual(runner.work_api, 'containers') + root_logger = logging.getLogger('') + handlerClasses = [h.__class__ for h in root_logger.handlers] + self.assertTrue(arvados_cwl.RuntimeStatusLoggingHandler in handlerClasses) + return runner + # 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") @@ -30,16 +105,14 @@ class TestContainer(unittest.TestCase): arv_docker_clear_cache() runner = mock.MagicMock() - runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() 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("v1.0") - tool = cmap({ "inputs": [], "outputs": [], @@ -48,14 +121,14 @@ class TestContainer(unittest.TestCase): "id": "#", "class": "CommandLineTool" }) - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names, - basedir="", make_fs_access=make_fs_access, loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner, enable_reuse) + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_"+str(enable_reuse), - make_fs_access=make_fs_access, tmpdir="/tmp"): - j.run(enable_reuse=enable_reuse, priority=500) + + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.container_requests().create.assert_called_with( body=JsonDiffMatcher({ 'environment': { @@ -77,14 +150,16 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', + 'output_name': 'Output for step test_run_'+str(enable_reuse), 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, - 'container_image': 'arvados/jobs', + 'container_image': '99999999999999999999999999999993+99', 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, 'properties': {}, + 'secret_mounts': {} })) # The test passes some fields in builder.resources @@ -93,10 +168,9 @@ class TestContainer(unittest.TestCase): def test_resource_requirements(self, keepdocker): arv_docker_clear_cache() runner = mock.MagicMock() - runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 3600 - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + runner.secret_store = cwltool.secrets.SecretStore() keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { @@ -130,15 +204,14 @@ class TestContainer(unittest.TestCase): "id": "#", "class": "CommandLineTool" }) - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", - avsc_names=avsc_names, make_fs_access=make_fs_access, - loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_resource_requirements" + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements", - make_fs_access=make_fs_access, tmpdir="/tmp"): - j.run(enable_reuse=True, priority=500) + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) call_args, call_kwargs = runner.api.container_requests().create.call_args @@ -163,16 +236,18 @@ class TestContainer(unittest.TestCase): "capacity": 5242880000 } }, 'state': 'Committed', + 'output_name': 'Output for step test_resource_requirements', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 7200, - 'container_image': 'arvados/jobs', + 'container_image': '99999999999999999999999999999993+99', 'command': ['ls'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': { 'partitions': ['blurb'] }, - 'properties': {} + 'properties': {}, + 'secret_mounts': {} } call_body = call_kwargs.get('body', None) @@ -188,10 +263,9 @@ class TestContainer(unittest.TestCase): def test_initial_work_dir(self, collection_mock, keepdocker): arv_docker_clear_cache() runner = mock.MagicMock() - runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 0 - document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") + runner.secret_store = cwltool.secrets.SecretStore() keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { @@ -206,8 +280,7 @@ class TestContainer(unittest.TestCase): runner.fs_access.get_collection.side_effect = get_collection_mock vwdmock = mock.MagicMock() - collection_mock.return_value = vwdmock - vwdmock.portable_data_hash.return_value = "99999999999999999999999999999996+99" + collection_mock.side_effect = lambda *args, **kwargs: CollectionMock(vwdmock, *args, **kwargs) tool = cmap({ "inputs": [], @@ -239,15 +312,14 @@ class TestContainer(unittest.TestCase): "id": "#", "class": "CommandLineTool" }) - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", - avsc_names=avsc_names, make_fs_access=make_fs_access, - loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_initial_work_dir" + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_initial_work_dir", - make_fs_access=make_fs_access, tmpdir="/tmp"): - j.run(priority=500) + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) call_args, call_kwargs = runner.api.container_requests().create.call_args @@ -295,15 +367,17 @@ class TestContainer(unittest.TestCase): } }, 'state': 'Committed', + 'output_name': 'Output for step test_initial_work_dir', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, - 'container_image': 'arvados/jobs', + 'container_image': '99999999999999999999999999999993+99', 'command': ['ls'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': { }, - 'properties': {} + 'properties': {}, + 'secret_mounts': {} } call_body = call_kwargs.get('body', None) @@ -318,9 +392,9 @@ class TestContainer(unittest.TestCase): arv_docker_clear_cache() runner = mock.MagicMock() - runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { @@ -339,14 +413,14 @@ class TestContainer(unittest.TestCase): "id": "#", "class": "CommandLineTool" }) - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names, - basedir="", make_fs_access=make_fs_access, loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_run_redirect" + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None - for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_redirect", - make_fs_access=make_fs_access, tmpdir="/tmp"): - j.run(priority=500) + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.container_requests().create.assert_called_with( body=JsonDiffMatcher({ 'environment': { @@ -380,14 +454,16 @@ class TestContainer(unittest.TestCase): }, }, 'state': 'Committed', + "output_name": "Output for step test_run_redirect", 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, - 'container_image': 'arvados/jobs', + 'container_image': '99999999999999999999999999999993+99', 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, 'properties': {}, + 'secret_mounts': {} })) @mock.patch("arvados.collection.Collection") @@ -396,10 +472,10 @@ class TestContainer(unittest.TestCase): runner = mock.MagicMock() runner.api = api - runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.num_retries = 0 runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() runner.api.containers().get().execute.return_value = {"state":"Complete", "output": "abc+123", @@ -407,9 +483,16 @@ class TestContainer(unittest.TestCase): col().open.return_value = [] - arvjob = arvados_cwl.ArvadosContainer(runner) - arvjob.name = "testjob" - arvjob.builder = mock.MagicMock() + loadingContext, runtimeContext = self.helper(runner) + + arvjob = arvados_cwl.ArvadosContainer(runner, + runtimeContext, + mock.MagicMock(), + {}, + None, + [], + [], + "testjob") arvjob.output_callback = mock.MagicMock() arvjob.collect_outputs = mock.MagicMock() arvjob.successCodes = [0] @@ -428,11 +511,86 @@ class TestContainer(unittest.TestCase): }) self.assertFalse(api.collections().create.called) + self.assertFalse(runner.runtime_status_error.called) arvjob.collect_outputs.assert_called_with("keep:abc+123") arvjob.output_callback.assert_called_with({"out": "stuff"}, "success") runner.add_intermediate_output.assert_called_with("zzzzz-4zz18-zzzzzzzzzzzzzz2") + # 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") + def test_recursive_runtime_status_update(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 + # so try and log again! + gcc_mock.side_effect = lambda *args: root_logger.error("Second Error") + try: + root_logger.error("First Error") + except RuntimeError: + self.fail("RuntimeStatusLoggingHandler should not be called recursively") + + @mock.patch("arvados_cwl.ArvCwlExecutor.runtime_status_update") + @mock.patch("arvados_cwl.util.get_current_container") + @mock.patch("arvados.collection.CollectionReader") + @mock.patch("arvados.collection.Collection") + def test_child_failure(self, col, reader, gcc_mock, rts_mock): + runner = self.setup_and_test_container_executor_and_logging(gcc_mock) + + gcc_mock.return_value = {"uuid" : "zzzzz-dz642-zzzzzzzzzzzzzzz"} + self.assertTrue(gcc_mock.called) + + runner.num_retries = 0 + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.label = mock.MagicMock() + runner.label.return_value = '[container testjob]' + + runner.api.containers().get().execute.return_value = { + "state":"Complete", + "output": "abc+123", + "exit_code": 1, + "log": "def+234" + } + + col().open.return_value = [] + + loadingContext, runtimeContext = self.helper(runner) + + arvjob = arvados_cwl.ArvadosContainer(runner, + runtimeContext, + mock.MagicMock(), + {}, + None, + [], + [], + "testjob") + arvjob.output_callback = mock.MagicMock() + arvjob.collect_outputs = mock.MagicMock() + arvjob.successCodes = [0] + arvjob.outdir = "/var/spool/cwl" + arvjob.output_ttl = 3600 + arvjob.collect_outputs.return_value = {"out": "stuff"} + + arvjob.done({ + "state": "Final", + "log_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1", + "output_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", + "uuid": "zzzzz-xvhdp-zzzzzzzzzzzzzzz", + "container_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", + "modified_at": "2017-05-26T12:01:22Z" + }) + + rts_mock.assert_called_with( + 'error', + 'arvados.cwl-runner: [container testjob] (zzzzz-xvhdp-zzzzzzzzzzzzzzz) error log:', + ' ** log is empty **' + ) + arvjob.output_callback.assert_called_with({"out": "stuff"}, "permanentFail") + # 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") @@ -440,13 +598,14 @@ class TestContainer(unittest.TestCase): arv_docker_clear_cache() runner = mock.MagicMock() - runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { - "portable_data_hash": "99999999999999999999999999999993+99"} + "portable_data_hash": "99999999999999999999999999999994+99", + "manifest_text": ". 99999999999999999999999999999994+99 0:0:file1 0:0:file2"} document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0") @@ -461,10 +620,11 @@ class TestContainer(unittest.TestCase): "id": "#", "class": "CommandLineTool" }) - make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, - collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names, - basedir="", make_fs_access=make_fs_access, loader=Loader({})) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_run_mounts" + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None job_order = { "p1": { @@ -482,9 +642,8 @@ class TestContainer(unittest.TestCase): ] } } - for j in arvtool.job(job_order, mock.MagicMock(), basedir="", name="test_run_mounts", - make_fs_access=make_fs_access, tmpdir="/tmp"): - j.run(priority=500) + for j in arvtool.job(job_order, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) runner.api.container_requests().create.assert_called_with( body=JsonDiffMatcher({ 'environment': { @@ -509,12 +668,153 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', + 'output_name': 'Output for step test_run_mounts', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, - 'container_image': 'arvados/jobs', + 'container_image': '99999999999999999999999999999994+99', 'command': ['ls', '/var/spool/cwl'], 'cwd': '/var/spool/cwl', 'scheduling_parameters': {}, 'properties': {}, + 'secret_mounts': {} })) + + # 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() + + 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("v1.0") + + tool = cmap({"arguments": ["md5sum", "example.conf"], + "class": "CommandLineTool", + "hints": [ + { + "class": "http://commonwl.org/cwltool#Secrets", + "secrets": [ + "#secret_job.cwl/pw" + ] + } + ], + "id": "#secret_job.cwl", + "inputs": [ + { + "id": "#secret_job.cwl/pw", + "type": "string" + } + ], + "outputs": [ + ], + "requirements": [ + { + "class": "InitialWorkDirRequirement", + "listing": [ + { + "entry": "username: user\npassword: $(inputs.pw)\n", + "entryname": "example.conf" + } + ] + } + ]}) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_secrets" + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool.formatgraph = None + + job_order = {"pw": "blorp"} + runner.secret_store.store(["pw"], job_order) + + for j in arvtool.job(job_order, 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_secrets', + '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_secrets', + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', + 'output_path': '/var/spool/cwl', + 'output_ttl': 0, + 'container_image': '99999999999999999999999999999993+99', + 'command': ['md5sum', 'example.conf'], + 'cwd': '/var/spool/cwl', + 'scheduling_parameters': {}, + 'properties': {}, + "secret_mounts": { + "/var/spool/cwl/example.conf": { + "content": "username: user\npassword: blorp\n", + "kind": "text" + } + } + })) + + # 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() + + 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": "CommandLineTool", + "hints": [ + { + "class": "http://commonwl.org/cwltool#TimeLimit", + "timelimit": 42 + } + ] + }) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_timelimit" + + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool.formatgraph = None + + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + + _, kwargs = runner.api.container_requests().create.call_args + self.assertEqual(42, kwargs['body']['scheduling_parameters'].get('max_run_time'))