15028: Update cwltool/schema-salad deps, fix tests
[arvados.git] / sdk / cwl / tests / test_container.py
index 2295e934ac77de76182d04749715a57f730874b4..2ddd06535e6628ae83514a49c1e0a71df840a4d1 100644 (file)
@@ -2,8 +2,15 @@
 #
 # 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
@@ -15,14 +22,81 @@ 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("v1.1.0-dev1")
+
+        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": "v1.1.0-dev1", "http://commonwl.org/cwltool#original_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 ArvCwlExecutor 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")
@@ -31,7 +105,6 @@ 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()
@@ -40,8 +113,6 @@ class TestContainer(unittest.TestCase):
             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": [],
@@ -50,15 +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({}),
-                                                     metadata={"cwlVersion": "v1.0"})
+
+            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': {
@@ -80,10 +150,11 @@ 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': {},
@@ -97,13 +168,10 @@ 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
         runner.secret_store = cwltool.secrets.SecretStore()
 
-        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
-
         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
         runner.api.collections().get().execute.return_value = {
             "portable_data_hash": "99999999999999999999999999999993+99"}
@@ -136,15 +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({}), metadata={"cwlVersion": "v1.0"})
+
+        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
 
@@ -169,10 +236,11 @@ 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': {
@@ -195,13 +263,10 @@ 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
         runner.secret_store = cwltool.secrets.SecretStore()
 
-        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
-
         keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
         runner.api.collections().get().execute.return_value = {
             "portable_data_hash": "99999999999999999999999999999993+99"}
@@ -215,8 +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": [],
@@ -248,15 +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({}), metadata={"cwlVersion": "v1.0"})
+
+        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
 
@@ -304,10 +367,11 @@ 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': {
@@ -328,7 +392,6 @@ 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()
@@ -337,7 +400,7 @@ class TestContainer(unittest.TestCase):
         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")
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
 
         tool = cmap({
             "inputs": [],
@@ -350,15 +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({}),
-                                                 metadata={"cwlVersion": "v1.0"})
+
+        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': {
@@ -392,10 +454,11 @@ 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': {},
@@ -409,7 +472,6 @@ 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
@@ -421,9 +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]
@@ -442,11 +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")
@@ -454,16 +598,16 @@ 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")
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
 
         tool = cmap({
             "inputs": [
@@ -476,16 +620,17 @@ 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({}),
-                                                 metadata={"cwlVersion": "v1.0"})
+
+        loadingContext, runtimeContext = self.helper(runner)
+        runtimeContext.name = "test_run_mounts"
+
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
         arvtool.formatgraph = None
         job_order = {
             "p1": {
                 "class": "Directory",
                 "location": "keep:99999999999999999999999999999994+44",
+                "http://arvados.org/cwl#collectionUUID": "zzzzz-4zz18-zzzzzzzzzzzzzzz",
                 "listing": [
                     {
                         "class": "File",
@@ -498,9 +643,8 @@ 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': {
@@ -517,7 +661,8 @@ class TestContainer(unittest.TestCase):
                     'mounts': {
                         "/keep/99999999999999999999999999999994+44": {
                             "kind": "collection",
-                            "portable_data_hash": "99999999999999999999999999999994+44"
+                            "portable_data_hash": "99999999999999999999999999999994+44",
+                            "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz"
                         },
                         '/tmp': {'kind': 'tmp',
                                  "capacity": 1073741824 },
@@ -525,10 +670,11 @@ 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': {},
@@ -543,7 +689,6 @@ 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()
@@ -552,7 +697,7 @@ class TestContainer(unittest.TestCase):
         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")
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1.0-dev1")
 
         tool = cmap({"arguments": ["md5sum", "example.conf"],
                      "class": "CommandLineTool",
@@ -584,19 +729,18 @@ class TestContainer(unittest.TestCase):
                              ]
                          }
                      ]})
-        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({}),
-                                                 metadata={"cwlVersion": "v1.0"})
+
+        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(), basedir="", name="test_secrets",
-                             make_fs_access=make_fs_access, tmpdir="/tmp"):
-            j.run(enable_reuse=True, 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': {
@@ -618,10 +762,11 @@ class TestContainer(unittest.TestCase):
                                            "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': 'arvados/jobs',
+                    'container_image': '99999999999999999999999999999993+99',
                     'command': ['md5sum', 'example.conf'],
                     'cwd': '/var/spool/cwl',
                     'scheduling_parameters': {},
@@ -633,3 +778,45 @@ class TestContainer(unittest.TestCase):
                         }
                     }
                 }))
+
+    # 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": "ToolTimeLimit",
+                    "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'))