root_logger.handlers = handlers
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_invalid_runner_ram(self, stubs, tm):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_container(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_tool(self, stubs):
# test for issue #16139
exited = arvados_cwl.main(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_no_reuse(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
stubs.expect_container_request_uuid + '\n')
- @stubs
+ @stubs()
def test_submit_container_on_error(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_name(self, stubs):
output_name = "test_output_name"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_multiple_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_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)
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
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)
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_ttl(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_trash_intermediate(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_tags(self, stubs):
output_tags = "tag0,tag1,tag2"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_runner_ram(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_file_keepref(self, stubs, tm, collectionReader):
collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_keepref(self, stubs, tm, reader):
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
self.assertEqual(exited, 0)
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_arvworkflow(self, stubs, tm):
with open("tests/wf/expect_arvworkflow.cwl") as f:
stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_missing_input(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_container_project(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_eval_timeout(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_collection_cache(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_thread_count(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_runner_image(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_priority(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
- @stubs
+ @stubs()
def test_submit_secrets(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_request_uuid(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_cluster_id(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_validate_cluster_id(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
exited = arvados_cwl.main(
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_validate_project_uuid(self, stubs):
# Fails with bad cluster prefix
exited = arvados_cwl.main(
@mock.patch("arvados.collection.CollectionReader")
- @stubs
+ @stubs()
def test_submit_uuid_inputs(self, stubs, collectionReader):
collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_mismatched_uuid_inputs(self, stubs):
def list_side_effect(**kwargs):
m = mock.MagicMock()
cwltool_logger.removeHandler(stderr_logger)
@mock.patch("arvados.collection.CollectionReader")
- @stubs
+ @stubs()
def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
capture_stderr = StringIO()
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_enable_preemptible(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_disable_preemptible(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
root_logger.handlers = handlers
- @stubs
+ @stubs()
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_update(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_update_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
self.existing_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_collection_per_tool(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_with_imports(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_with_no_input(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}