- keep().put.side_effect = putstub
- keepdocker.return_value = True
- api.users().current().execute.return_value = {"uuid": "zzzzz-tpzed-zzzzzzzzzzzzzzz"}
- api.collections().list().execute.return_value = {"items": []}
- api.collections().create().execute.side_effect = ({"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
- "portable_data_hash": "99999999999999999999999999999991+99"},
- {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
- "portable_data_hash": "99999999999999999999999999999992+99"})
- api.jobs().create().execute.return_value = {"uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", "state": "Queued"}
-
- arvados_cwl.main(["--debug", "--submit", "--no-wait", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdout, sys.stderr, api_client=api)
-
- api.collections().create.assert_has_calls([
+ stubs.KeepClient().put.side_effect = putstub
+
+ stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+
+ stubs.api = mock.MagicMock()
+ stubs.api.users().current().execute.return_value = {
+ "uuid": stubs.fake_user_uuid,
+ }
+ stubs.api.collections().list().execute.return_value = {"items": []}
+ stubs.api.collections().create().execute.side_effect = ({
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
+ "portable_data_hash": "99999999999999999999999999999991+99",
+ "manifest_text": ""
+ }, {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
+ "portable_data_hash": "99999999999999999999999999999992+99",
+ "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
+ },
+ {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
+ "portable_data_hash": "99999999999999999999999999999994+99",
+ "manifest_text": ""
+ },
+ {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
+ "portable_data_hash": "99999999999999999999999999999995+99",
+ "manifest_text": ""
+ } )
+ stubs.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
+
+ stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ stubs.api.jobs().create().execute.return_value = {
+ "uuid": stubs.expect_job_uuid,
+ "state": "Queued",
+ }
+
+ stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+ stubs.api.container_requests().create().execute.return_value = {
+ "uuid": stubs.expect_container_request_uuid,
+ "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
+ "state": "Queued"
+ }
+
+ stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
+ stubs.api.pipeline_templates().create().execute.return_value = {
+ "uuid": stubs.expect_pipeline_template_uuid,
+ }
+ stubs.expect_job_spec = {
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs'
+ },
+ 'script_parameters': {
+ 'x': {
+ 'basename': 'blorp.txt',
+ 'location': '99999999999999999999999999999994+99/blorp.txt',
+ 'class': 'File'
+ },
+ 'cwl:tool':
+ '99999999999999999999999999999991+99/wf/submit_wf.cwl'
+ },
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'cwl-runner'
+ }
+
+ stubs.expect_container_spec = {
+ 'priority': 1,
+ 'mounts': {
+ '/var/spool/cwl': {
+ 'writable': True,
+ 'kind': 'collection'
+ },
+ '/var/lib/cwl/workflow': {
+ 'portable_data_hash': '99999999999999999999999999999991+99',
+ 'kind': 'collection'
+ },
+ 'stdout': {
+ 'path': '/var/spool/cwl/cwl.output.json',
+ 'kind': 'file'
+ },
+ '/var/lib/cwl/job/cwl.input.json': {
+ 'portable_data_hash': '765fda0d9897729ff467a4609879c00a+60/cwl.input.json',
+ 'kind': 'collection'
+ }
+ },
+ 'state': 'Committed',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+ 'name': 'submit_wf.cwl',
+ 'container_image': '99999999999999999999999999999993+99',
+ 'output_path': '/var/spool/cwl',
+ 'cwd': '/var/spool/cwl',
+ 'runtime_constraints': {
+ 'API': True,
+ 'vcpus': 1,
+ 'ram': 268435456
+ }
+ }
+ return func(self, stubs, *args, **kwargs)
+ return wrapped
+
+
+class TestSubmit(unittest.TestCase):
+ @stubs
+ def test_submit(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 0)
+
+ stubs.api.collections().create.assert_has_calls([