"listing": [{
"basename": "renamed.txt",
"class": "File",
- "location": "keep:99999999999999999999999999999998+99/file1.txt"
+ "location": "keep:99999999999999999999999999999998+99/file1.txt",
+ "size": 0
}],
'class': 'Directory'
},
{
'basename': 'renamed.txt',
'class': 'File', 'location':
- 'keep:99999999999999999999999999999998+99/file1.txt'
+ 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
}
]}},
'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
{'basename': 'renamed.txt',
'class': 'File',
- 'location': 'keep:99999999999999999999999999999998+99/file1.txt'
+ 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
}
]}
},
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
+ @stubs
+ def test_error_when_multiple_storage_classes_specified(self, stubs):
+ storage_classes = "foo,bar"
+ exited = arvados_cwl.main(
+ ["--debug", "--storage-classes", storage_classes,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 1)
+
@mock.patch("time.sleep")
@stubs
def test_submit_on_error(self, stubs, tm):
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ @stubs
+ def test_submit_storage_classes(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', "--debug",
+ "--storage-classes=foo", '--on-error=continue',
+ '/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(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+ @mock.patch("arvados_cwl.task_queue.TaskQueue")
+ @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+ @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
+ @stubs
+ def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ def set_final_output(job_order, output_callback, runtimeContext):
+ output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ return []
+ job.side_effect = set_final_output
+
+ try:
+ exited = arvados_cwl.main(
+ ["--debug", "--local", "--storage-classes=foo",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+
+ @mock.patch("arvados_cwl.task_queue.TaskQueue")
+ @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+ @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None))
+ @stubs
+ def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ def set_final_output(job_order, output_callback, runtimeContext):
+ output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ return []
+ job.side_effect = set_final_output
+
+ try:
+ exited = arvados_cwl.main(
+ ["--debug", "--local",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
@stubs
def test_submit_container_output_ttl(self, stubs):
@stubs
def test_submit_file_keepref(self, stubs, tm, collectionReader):
capture_stdout = cStringIO.StringIO()
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_keepref_wf.cwl"],
stubs.expect_container_request_uuid + '\n')
+ @stubs
+ def test_submit_wf_runner_resources(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["runtime_constraints"] = {
+ "API": True,
+ "vcpus": 2,
+ "ram": 2000 * 2**20
+ }
+ expect_container["name"] = "submit_wf_runner_resources.cwl"
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ {
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources",
+ "coresMin": 2,
+ "ramMin": 2000
+ }
+ ]
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ "arv": "http://arvados.org/cwl#",
+ }
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
@mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
projects / arvados.git / blobdiff