'99999999999999999999999999999991+99/wf/submit_wf.cwl'
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner'
}
stubs.pipeline_component = stubs.expect_job_spec.copy()
'arv:enable_reuse': True
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner',
'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
}
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
- 'kind': 'collection'
+ '/var/lib/cwl/cwl.input.json': {
+ 'kind': 'json',
+ 'content': {
+ 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
+ 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999994+99/blorp.txt'},
+ 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ ]}
+ },
+ 'kind': 'json'
}
},
'state': 'Committed',
'owner_uuid': None,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'output_path': '/var/spool/cwl',
'API': True,
'vcpus': 1,
'ram': 1024*1024*1024
- }
+ },
+ "properties": {}
}
stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
+ 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')
+
+
+ @mock.patch("time.sleep")
+ @stubs
+ 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)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["owner_uuid"] = project_uuid
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
@stubs
def test_submit_container(self, stubs):
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
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/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--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=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-name="+output_name, '--enable-reuse',
+ '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json']
+ stubs.expect_container_spec["output_name"] = output_name
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
except:
logging.exception("")
- stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+ stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ "--output-tags="+output_tags, '--enable-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=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
- body=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
'portable_data_hash': '99999999999999999999999999999994+99',
'kind': 'collection'
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json',
- '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/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--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=expect_container)
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
@mock.patch("time.sleep")
@stubs
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()}
+ stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
]
}
},
- '/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json',
- 'kind': 'collection'}
+ '/var/lib/cwl/cwl.input.json': {
+ 'content': {
+ 'x': 'XxX'
+ },
+ 'kind': 'json'
+ }
}, 'state': 'Committed',
'owner_uuid': None,
'output_path': '/var/spool/cwl',
- 'name': 'arvwf:962eh-7fd4e-gkbzl62qqtfig37#main',
+ '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/job/cwl.input.json'],
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+ '--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')
+
+
+ @stubs
+ 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(),
self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner))
class TestCreateTemplate(unittest.TestCase):
- @stubs
- def test_create(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- capture_stdout = cStringIO.StringIO()
+ existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
- 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_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
-
- expect_component = copy.deepcopy(stubs.expect_job_spec)
+ def _adjust_script_params(self, expect_component):
expect_component['script_parameters']['x'] = {
'dataclass': 'File',
'required': True,
'required': True,
'type': 'Directory',
}
+
+ @stubs
+ def test_create(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=jobs",
+ "--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)
+ self._adjust_script_params(expect_component)
expect_template = {
"components": {
"submit_wf.cwl": expect_component,
stubs.expect_pipeline_template_uuid + '\n')
+ @stubs
+ def test_create_name(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--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.assert_called_with(
+ body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_template_uuid + '\n')
+
+
+ @stubs
+ 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')
+
+
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = open("tests/wf/expect_packed.cwl").read()
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
+
+ @stubs
+ def test_create_name(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "--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_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "testing 123",
+ "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')
+
@stubs
def test_incompatible_api(self, stubs):
capture_stderr = cStringIO.StringIO()
self.existing_workflow_uuid + '\n')
+ @stubs
+ 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')
+
+
class TestTemplateInputs(unittest.TestCase):
expect_template = {
"components": {
},
},
'repository': 'arvados',
- 'script_version': arvados_cwl.__version__,
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
'script': 'cwl-runner',
},
},
@stubs
def test_inputs_empty(self, stubs):
exited = arvados_cwl.main(
- ["--create-template", "--no-wait",
+ ["--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
def test_inputs(self, stubs):
exited = arvados_cwl.main(
- ["--create-template", "--no-wait",
+ ["--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)
projects / arvados.git / blobdiff