def stubs(func):
@functools.wraps(func)
+ @mock.patch("arvados_cwl.arvdocker.determine_image_id")
+ @mock.patch("uuid.uuid4")
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
@mock.patch("arvados.collection.KeepClient")
@mock.patch("arvados.keep.KeepClient")
@mock.patch("arvados.events.subscribe")
- def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
+ def wrapped(self, events, keep_client1, keep_client2, keepdocker,
+ uuid4, determine_image_id, *args, **kwargs):
class Stubs(object):
pass
stubs = Stubs()
stubs.events = events
stubs.keepdocker = keepdocker
+ uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
+ "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
+ "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
+
+ determine_image_id.return_value = None
+
def putstub(p, **kwargs):
return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
keep_client1().put.side_effect = putstub
stubs.keep_client = keep_client2
stubs.docker_images = {
- "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")],
- "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
- "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
- "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
+ "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
+ "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", {})],
+ "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", {})],
+ "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", {})],
}
- def kd(a, b, image_name=None, image_tag=None):
+ def kd(a, b, image_name=None, image_tag=None, project_uuid=None):
return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
stubs.keepdocker.side_effect = kd
stubs.api = mock.MagicMock()
stubs.api._rootDesc = get_rootDesc()
stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
+ stubs.api._rootDesc["revision"] = "20210628"
stubs.api.users().current().execute.return_value = {
"uuid": stubs.fake_user_uuid,
cwltool.process._names = set()
arvados_cwl.arvdocker.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
@mock.patch("time.sleep")
@stubs
"enableReuse": False,
},
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
"arv": "http://arvados.org/cwl#",
"cwltool": "http://commonwl.org/cwltool#"
}
make_output.return_value = ({},final_output_c)
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
+ stubs.api.config().get.return_value = {"default": {"Default": True}}
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
make_output.return_value = ({},final_output_c)
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
"tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@stubs
"keep_cache": 512
}
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
"arv": "http://arvados.org/cwl#",
}
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- def tearDown(self):
- arvados_cwl.arvdocker.arv_docker_clear_cache()
-
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
@mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
arvrunner.project_uuid = ""
api.return_value = mock.MagicMock()
arvrunner.api = api.return_value
+ arvrunner.runtimeContext.match_local_docker = False
arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
"head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"link_class": "docker_image_repo+tag",
"name": "arvados/jobs:"+arvados_cwl.__version__,
"owner_uuid": "",
"properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
+ {"items": [{"created_at": "",
+ "head_uuid": "",
+ "link_class": "docker_image_hash",
+ "name": "123456",
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
+ {"items": [{"created_at": "",
+ "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "link_class": "docker_image_repo+tag",
+ "name": "arvados/jobs:"+arvados_cwl.__version__,
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
{"items": [{"created_at": "",
"head_uuid": "",
"link_class": "docker_image_hash",
"owner_uuid": "",
"manifest_text": "",
"properties": ""
- }], "items_available": 1, "offset": 0},)
+ }], "items_available": 1, "offset": 0},
+ {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "owner_uuid": "",
+ "manifest_text": "",
+ "properties": ""
+ }], "items_available": 1, "offset": 0})
arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"portable_data_hash": "9999999999999999999999999999999b+99"}
+
self.assertEqual("9999999999999999999999999999999b+99",
- arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+ arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
@stubs
"content": {
"$graph": [
{
- "$namespaces": {
- "cwltool": "http://commonwl.org/cwltool#"
- },
"arguments": [
"md5sum",
"example.conf"
]
}
],
+ "$namespaces": {
+ "cwltool": "http://commonwl.org/cwltool#"
+ },
"cwlVersion": "v1.0"
},
"kind": "json"
self.assertEqual(exited, 1)
self.assertRegex(
capture_stderr.getvalue(),
- r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
+ r"Collection\s*uuid\s*zzzzz-4zz18-zzzzzzzzzzzzzzz\s*not\s*found")
finally:
cwltool_logger.removeHandler(stderr_logger)
{
"class": "http://arvados.org/cwl#ProcessProperties",
"processProperties": [
- {"propertyName": "foo",
- "propertyValue": "bar"},
{"propertyName": "baz",
"propertyValue": "$(inputs.x.basename)"},
+ {"propertyName": "foo",
+ "propertyValue": "bar"},
{"propertyName": "quux",
"propertyValue": {
"q1": 1,
],
}
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
"arv": "http://arvados.org/cwl#"
}
self.assertEqual(exited, 0)
+ @stubs
+ def test_submit_enable_preemptible(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--enable-preemptible',
+ '/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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs
+ def test_submit_disable_preemptible(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--disable-preemptible',
+ '/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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = StripYAMLComments(
cwltool.process._names = set()
arvados_cwl.arvdocker.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
+
@stubs
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
@stubs
def test_update(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
+
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug",
"name": "submit_wf.cwl",
"description": "",
"definition": self.expect_workflow,
+ "owner_uuid": project_uuid
}
}
stubs.api.workflows().update.assert_called_with(
self.existing_workflow_uuid + '\n')
self.assertEqual(exited, 0)
+
@stubs
def test_update_name(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
+
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug", "--name", "testing 123",
"name": "testing 123",
"description": "",
"definition": self.expect_workflow,
+ "owner_uuid": project_uuid
}
}
stubs.api.workflows().update.assert_called_with(
projects / arvados.git / blobdiff