def test_submit_with_project_uuid(self, events, keep, keepdocker):
api = mock.MagicMock()
def putstub(p, **kwargs):
return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
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"
}
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
arvados_cwl.main([
"--debug", "--submit", "--project-uuid", project_uuid, "--no-wait",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"
],
sys.stdout,
sys.stderr,
api_client=api)
api.jobs().create.assert_called_with(body={
'owner_uuid': project_uuid,
'runtime_constraints': {
'docker_image': 'arvados/jobs'
},
'script_parameters': {
'x': {
'path': '99999999999999999999999999999992+99/blorp.txt',
'class': 'File'
},
'cwl:tool':
'99999999999999999999999999999991+99/wf/submit_wf.cwl'
},
'repository': 'arvados',
'script_version': 'master',
'script': 'cwl-runner'
},
find_or_create=True)
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_templates().create.refute_called()
stubs.api.container_requests().create.refute_called()
body = {
"workflow": {
"owner_uuid": project_uuid,
"name": "submit_wf.cwl",
"description": "",
"definition": self.expect_workflow,
}
}
stubs.api.workflows().create.assert_called_with(
body=JsonDiffMatcher(body))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
def test_submit_container(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
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, keep_client=stubs.keep_client)
self.assertEqual(exited, 0)
except:
logging.exception("")
stubs.api.collections().create.assert_has_calls([
mock.call(),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
'replication_desired': None,
'name': 'submit_tool.cwl dependencies',
}), ensure_unique_name=True),
mock.call().execute(num_retries=4),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
'name': 'submit_wf.cwl input',
}), ensure_unique_name=True),
mock.call().execute(num_retries=4)])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_file_keepref(self, stubs, tm, collectionReader):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_keepref_wf.cwl"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
def test_update_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--update-workflow", self.existing_template_uuid,
"--debug",
"--project-uuid", project_uuid,
"--api=jobs",
"--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
expect_component = copy.deepcopy(stubs.expect_job_spec)
self._adjust_script_params(expect_component)
expect_template = {
"components": {
"testing 123": expect_component,
},
"name": "testing 123",
"owner_uuid": project_uuid,
}
stubs.api.pipeline_templates().create.refute_called()
stubs.api.pipeline_templates().update.assert_called_with(
body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
self.assertEqual(capture_stdout.getvalue(),
self.existing_template_uuid + '\n')
def test_update_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--update-workflow", self.existing_template_uuid,
"--debug",
"--project-uuid", project_uuid,
"--api=jobs",
"--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
expect_component = copy.deepcopy(stubs.expect_job_spec)
self._adjust_script_params(expect_component)
expect_template = {
"components": {
"testing 123": expect_component,
},
"name": "testing 123",
"owner_uuid": project_uuid,
}
stubs.api.pipeline_templates().create.refute_called()
stubs.api.pipeline_templates().update.assert_called_with(
body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
self.assertEqual(capture_stdout.getvalue(),
self.existing_template_uuid + '\n')
def test_submit_file_keepref(self, stubs, tm, collectionReader):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_keepref_wf.cwl"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--create-template", "--no-wait",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
expect_component = copy.deepcopy(stubs.expect_job_spec)
expect_component['script_parameters']['x'] = {
'dataclass': 'File',
'required': True,
'type': 'File',
'value': '99999999999999999999999999999992+99/blorp.txt',
}
expect_template = {
"components": {
"submit_wf.cwl": expect_component,
},
"name": "submit_wf.cwl",
"owner_uuid": project_uuid,
}
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_template_uuid + '\n')
def test_submit_invalid_runner_ram(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
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([
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',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'submit_wf.cwl',
}, ensure_unique_name=True),
mock.call().execute(),
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_job = copy.deepcopy(stubs.expect_job_spec)
expect_job["owner_uuid"] = stubs.fake_user_uuid
stubs.api.jobs().create.assert_called_with(
body=expect_job,
find_or_create=True)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_job_uuid + '\n')
def test_submit_invalid_runner_ram(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main([
"--create-workflow", "--debug", "--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"
],
capture_stdout,
sys.stderr,
api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_templates().create.refute_called()
stubs.api.container_requests().create.refute_called()
with open("tests/wf/expect_packed.cwl") as f:
expect_workflow = f.read()
body = {
"workflow": {
"owner_uuid": project_uuid,
"name": "submit_wf.cwl",
"description": "",
"definition": expect_workflow
}
}
stubs.api.workflows().create.assert_called_with(
body=JsonDiffMatcher(body))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
def test_submit(self, stubs, tm, arvdock):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--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=JsonDiffMatcher({
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
'replication_desired': None,
'name': 'submit_tool.cwl dependencies',
}), ensure_unique_name=True),
mock.call().execute(num_retries=4),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
'name': 'submit_wf.cwl input',
}), ensure_unique_name=True),
mock.call().execute(num_retries=4)])
arvdock.assert_has_calls([
mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
])
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_inputs_empty(self, stubs):
exited = arvados_cwl.main(
["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
def test_inputs_empty(self, stubs):
exited = arvados_cwl.main(
["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
def test_submit_keepref(self, stubs, tm, reader):
capture_stdout = cStringIO.StringIO()
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_container = {
'priority': 1,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'kind': 'collection'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
'/var/lib/cwl/workflow': {
'portable_data_hash': '99999999999999999999999999999994+99',
'kind': 'collection'
},
'/var/lib/cwl/cwl.input.json': {
'content': {
'x': 'XxX'
},
'kind': 'json'
}
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
'--enable-reuse', '--on-error=continue',
'/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
'vcpus': 1,
'ram': 1073741824
},
"properties": {}
}
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_container(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
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,
keep_client=stubs.keep_client)
self.assertEqual(exited, 0)
except:
logging.exception("")
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 '
'cc2ffb940e60adf1b2b282c67587e43d+413 0:413: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')
def test_submit_keepref(self, stubs, tm, reader):
capture_stdout = cStringIO.StringIO()
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_container = {
'priority': 1,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'kind': 'collection'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
'/var/lib/cwl/workflow': {
'portable_data_hash': '99999999999999999999999999999994+99',
'kind': 'collection'
},
'/var/lib/cwl/cwl.input.json': {
'content': {
'x': 'XxX'
},
'kind': 'json'
}
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
'vcpus': 1,
'ram': 1073741824
},
"properties": {}
}
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_with_project_uuid(self, stubs, tm):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
["--submit", "--no-wait",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["owner_uuid"] = project_uuid
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
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([
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_job = copy.deepcopy(stubs.expect_job_spec)
expect_job["owner_uuid"] = stubs.fake_user_uuid
stubs.api.jobs().create.assert_called_with(body=expect_job,
find_or_create=True)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_job_uuid + '\n')
def test_submit_with_project_uuid(self, stubs, tm):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
["--submit", "--no-wait",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["owner_uuid"] = project_uuid
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
def test_submit_on_error(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_incompatible_api(self, stubs):
capture_stderr = cStringIO.StringIO()
logging.getLogger('arvados.cwl-runner').addHandler(
logging.StreamHandler(capture_stderr))
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--api=jobs",
"--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stderr, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
self.assertRegexpMatches(
capture_stderr.getvalue(),
"--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
def test_submit_runner_ram(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_submit_no_reuse(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--disable-reuse",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_submit_runner_ram(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_submit_pipeline_name(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--name=hello job 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.expect_pipeline_instance["name"] = "hello job 123"
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=expect_pipeline)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_submit_with_project_uuid(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
["--submit", "--no-wait",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_body = copy.deepcopy(stubs.expect_job_spec)
expect_body["owner_uuid"] = project_uuid
stubs.api.jobs().create.assert_called_with(
body=expect_body,
find_or_create=True)
def test_submit_pipeline_name(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--name=hello job 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["name"] = "hello job 123"
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_incompatible_api(self, stubs):
capture_stderr = cStringIO.StringIO()
logging.getLogger('arvados.cwl-runner').addHandler(
logging.StreamHandler(capture_stderr))
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--api=jobs",
"--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stderr, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
self.assertRegexpMatches(
capture_stderr.getvalue(),
"--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
def test_inputs(self, stubs):
exited = arvados_cwl.main(
["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_template = copy.deepcopy(self.expect_template)
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
def test_submit_with_project_uuid(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main([
"--submit", "--no-wait", "--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"
],
sys.stdout,
sys.stderr,
api_client=stubs.api)
self.assertEqual(exited, 0)
expect_body = copy.deepcopy(stubs.expect_job_spec)
expect_body["owner_uuid"] = project_uuid
stubs.api.jobs().create.assert_called_with(body=expect_body,
find_or_create=True)
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main([
"--create-template", "--debug", "--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"
],
capture_stdout,
sys.stderr,
api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
expect_component = copy.deepcopy(stubs.expect_job_spec)
expect_component['script_parameters']['x'] = {
'dataclass': 'File',
'required': True,
'type': 'File',
'value': '99999999999999999999999999999994+99/blorp.txt',
}
expect_component['script_parameters']['y'] = {
'dataclass': 'Collection',
'required': True,
'type': 'Directory',
'value': '99999999999999999999999999999998+99',
}
expect_component['script_parameters']['z'] = {
'dataclass': 'Collection',
'required': True,
'type': 'Directory',
}
expect_template = {
"components": {
"submit_wf.cwl": expect_component,
},
"name": "submit_wf.cwl",
"owner_uuid": project_uuid,
}
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_template_uuid + '\n')
def test_submit_output_tags(self, stubs, tm):
output_tags = "tag0,tag1,tag2"
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_inputs(self, stubs):
exited = arvados_cwl.main(
["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_template = copy.deepcopy(self.expect_template)
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
params["cwl:tool"] = '99999999999999999999999999999994+99/workflow.cwl#main'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
def test_submit_container_runner_image(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
"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("")
stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_job_runner_image(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
"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("")
stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
def test_submit_container_no_reuse(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
"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("")
stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_container_runner_ram(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
"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("")
stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_container_name(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
"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("")
stubs.expect_container_spec["name"] = "hello container 123"
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=expect_container)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_jobs_keepref(self, stubs, tm, reader):
capture_stdout = cStringIO.StringIO()
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug",
"keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
def test_submit_container_on_error(self, stubs):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
"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',
'--enable-reuse', '--on-error=stop',
'/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')
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([
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_job = copy.deepcopy(stubs.expect_job_spec)
expect_job["owner_uuid"] = stubs.fake_user_uuid
stubs.api.jobs().create.assert_called_with(
body=expect_job,
find_or_create=True)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_job_uuid + '\n')
def test_update_name(self, stubs):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug", "--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
body = {
"workflow": {
"name": "testing 123",
"description": "",
"definition": self.expect_workflow,
}
}
stubs.api.workflows().update.assert_called_with(
uuid=self.existing_workflow_uuid,
body=JsonDiffMatcher(body))
self.assertEqual(capture_stdout.getvalue(),
self.existing_workflow_uuid + '\n')
def test_update_name(self, stubs):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug", "--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
body = {
"workflow": {
"name": "testing 123",
"description": "",
"definition": self.expect_workflow,
}
}
stubs.api.workflows().update.assert_called_with(
uuid=self.existing_workflow_uuid,
body=JsonDiffMatcher(body))
self.assertEqual(capture_stdout.getvalue(),
self.existing_workflow_uuid + '\n')
def test_submit_arvworkflow(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
with open("tests/wf/expect_arvworkflow.cwl") as f:
stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_container = {
'priority': 1,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'kind': 'collection'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
'/var/lib/cwl/workflow.json': {
'kind': 'json',
'content': {
'cwlVersion': 'v1.0',
'$graph': [
{
'id': '#main',
'inputs': [
{'type': 'string', 'id': '#main/x'}
],
'steps': [
{'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
'run': '#submit_tool.cwl',
'id': '#main/step1',
'out': []}
],
'class': 'Workflow',
'outputs': []
},
{
'inputs': [
{
'inputBinding': {'position': 1},
'type': 'string',
'id': '#submit_tool.cwl/x'}
],
'requirements': [
{'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
],
'id': '#submit_tool.cwl',
'outputs': [],
'baseCommand': 'cat',
'class': 'CommandLineTool'
}
]
}
},
'/var/lib/cwl/cwl.input.json': {
'content': {
'x': 'XxX'
},
'kind': 'json'
}
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'a test workflow',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
'--enable-reuse', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
'vcpus': 1,
'ram': 1073741824
},
"properties": {
"template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
}
}
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit_arvworkflow(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
with open("tests/wf/expect_arvworkflow.cwl") as f:
stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_container = {
'priority': 1,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'kind': 'collection'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
'/var/lib/cwl/workflow.json': {
'kind': 'json',
'json': {
'cwlVersion': 'v1.0',
'$graph': [
{
'inputs': [
{
'inputBinding': {'position': 1},
'type': 'string',
'id': '#submit_tool.cwl/x'}
],
'requirements': [
{'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
],
'id': '#submit_tool.cwl',
'outputs': [],
'baseCommand': 'cat',
'class': 'CommandLineTool'
}, {
'id': '#main',
'inputs': [
{'type': 'string', 'id': '#main/x'}
],
'steps': [
{'in': [{'source': '#main/x', 'id': '#main/step1/x'}],
'run': '#submit_tool.cwl',
'id': '#main/step1',
'out': []}
],
'class': 'Workflow',
'outputs': []
}
]
}
},
'/var/lib/cwl/cwl.input.json': {
'content': {
'x': 'XxX'
},
'kind': 'json'
}
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'a test workflow',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
'vcpus': 1,
'ram': 1073741824
},
"properties": {
"template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
}
}
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
def test_submit(self, events, keep, keepdocker):
api = mock.MagicMock()
def putstub(p, **kwargs):
return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
keep().put.side_effect = putstub
keepdocker.return_value = True
user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
api.users().current().execute.return_value = {"uuid": user_uuid}
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([
mock.call(),
mock.call(body={
'manifest_text':
'./tool 84ec4df683711de31b782505389a8843+429 0:16:blub.txt 16:413:submit_tool.cwl\n./wf 81d977a245a41b8e79859fbe00623fd0+344 0:344: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':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': '#'
},
ensure_unique_name=True),
mock.call().execute()
])
api.jobs().create.assert_called_with(body={
'owner_uuid': user_uuid,
'runtime_constraints': {
'docker_image': 'arvados/jobs'
},
'script_parameters': {
'x': {
'path': '99999999999999999999999999999992+99/blorp.txt',
'class': 'File'
},
'cwl:tool':
'99999999999999999999999999999991+99/wf/submit_wf.cwl'
},
'repository': 'arvados',
'script_version': 'master',
'script': 'cwl-runner'
},
find_or_create=True)