return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
stubs.KeepClient().put.side_effect = putstub
- stubs.keepdocker.return_value = True
+ stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
stubs.api = mock.MagicMock()
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": ". 8bfd9d5a8dc1a71ab286283f9ff6fa20+153 0:153:cwl.input.json"
+ } )
+ 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,
},
'script_parameters': {
'x': {
- 'path': '99999999999999999999999999999992+99/blorp.txt',
+ 'basename': 'blorp.txt',
+ 'location': '99999999999999999999999999999994+99/blorp.txt',
'class': 'File'
},
'cwl:tool':
'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
mock.call(),
mock.call(body={
'manifest_text':
- './tool a3954c369b8924d40547ec8cf5f6a7f4+449 '
- '0:16:blub.txt 16:433:submit_tool.cwl\n./wf '
- 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364:submit_wf.cwl\n',
+ './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
+ '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
+ '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'submit_wf.cwl',
}, ensure_unique_name=True),
mock.call().execute(),
+ mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
+ '0:0:blub.txt 0:0:submit_tool.cwl\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': 'New collection',
+ 'replication_desired': None,
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
mock.call(body={
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
body=expect_body,
find_or_create=True)
+ @stubs
+ def test_submit_container(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "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([
+ mock.call(),
+ mock.call(body={
+ 'manifest_text':
+ './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
+ '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
+ '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': 'submit_wf.cwl',
+ }, ensure_unique_name=True),
+ mock.call().execute(),
+ mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
+ '0:0:blub.txt 0:0:submit_tool.cwl\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': 'New collection',
+ 'replication_desired': None,
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
+ mock.call(body={
+ 'manifest_text':
+ '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': '#',
+ }, ensure_unique_name=True),
+ mock.call().execute()])
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["owner_uuid"] = stubs.fake_user_uuid
+ stubs.api.container_requests().create.assert_called_with(
+ body=expect_container)
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
class TestCreateTemplate(unittest.TestCase):
@stubs
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--create-template", "--no-wait",
+ ["--create-template", "--no-wait", "--debug",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
'dataclass': 'File',
'required': True,
'type': 'File',
- 'value': '99999999999999999999999999999992+99/blorp.txt',
+ 'value': '99999999999999999999999999999994+99/blorp.txt',
}
expect_template = {
"components": {
expect_template["owner_uuid"] = stubs.fake_user_uuid
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
+ params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True
projects / arvados.git / blobdiff