import arvados
import arvados.collection
import arvados_cwl
+import arvados_cwl.runner
import arvados.keep
from .matcher import JsonDiffMatcher
stubs.expect_pipeline_instance = {
'name': 'submit_wf.cwl',
'state': 'RunningOnServer',
+ 'owner_uuid': None,
"components": {
"cwl-runner": {
'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__},
}
},
'state': 'Committed',
- 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ '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'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
stubs.api.workflows().create().execute.return_value = {
"uuid": stubs.expect_workflow_uuid,
}
+ def update_mock(**kwargs):
+ stubs.updated_uuid = kwargs.get('uuid')
+ return mock.DEFAULT
+ stubs.api.workflows().update.side_effect = update_mock
+ stubs.api.workflows().update().execute.side_effect = lambda **kwargs: {
+ "uuid": stubs.updated_uuid,
+ }
return func(self, stubs, *args, **kwargs)
return wrapped
'./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',
+ 'owner_uuid': None,
'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',
'replication_desired': None,
'name': 'New collection'
}, ensure_unique_name=True),
mock.call(body={
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'owner_uuid': None,
'name': '#',
}, ensure_unique_name=True),
mock.call().execute()])
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["owner_uuid"] = stubs.fake_user_uuid
stubs.api.pipeline_instances().create.assert_called_with(
body=expect_pipeline)
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["owner_uuid"] = stubs.fake_user_uuid
+ stubs.api.pipeline_instances().create.assert_called_with(
+ body=expect_pipeline)
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_pipeline_uuid + '\n')
+
+ @mock.patch("time.sleep")
+ @stubs
+ def test_submit_output_name(self, stubs, tm):
+ output_name = "test_output_name"
+
+ capture_stdout = cStringIO.StringIO()
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--debug", "--output-name", output_name,
+ "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_name"] = output_name
+
+ 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')
+
+ @mock.patch("time.sleep")
+ @stubs
+ 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=expect_pipeline)
self.assertEqual(capture_stdout.getvalue(),
'./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',
+ 'owner_uuid': None,
'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(body={
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'owner_uuid': None,
'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_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
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')
+ @stubs
+ def test_submit_container_output_name(self, stubs):
+ output_name = "test_output_name"
+
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
+ "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', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+
+ 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')
+
+ @stubs
+ def test_submit_container_output_tags(self, stubs):
+ output_tags = "tag0,tag1,tag2"
+
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
+ "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', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+
+ 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')
+
+ @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
+ @mock.patch("cwltool.docker.get_image")
+ @mock.patch("arvados.api")
+ def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
+ arvrunner = mock.MagicMock()
+ arvrunner.project_uuid = ""
+ api.return_value = mock.MagicMock()
+ arvrunner.api = api.return_value
+ arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
+ {"items": [], "items_available": 0, "offset": 0},
+ {"items": [], "items_available": 0, "offset": 0},
+ {"items": [{"created_at": "",
+ "head_uuid": "",
+ "link_class": "docker_image_hash",
+ "name": "123456",
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
+ {"items": [], "items_available": 0, "offset": 0},
+ {"items": [{"created_at": "",
+ "head_uuid": "",
+ "link_class": "docker_image_repo+tag",
+ "name": "arvados/jobs:"+arvados_cwl.__version__,
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
+ {"items": [{"created_at": "",
+ "head_uuid": "",
+ "link_class": "docker_image_hash",
+ "name": "123456",
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} ,
+ )
+ find_one_image_hash.return_value = "123456"
+
+ arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0},
+ {"items": [{"uuid": "",
+ "owner_uuid": "",
+ "manifest_text": "",
+ "properties": ""
+ }], "items_available": 1, "offset": 0},
+ {"items": [{"uuid": ""}], "items_available": 1, "offset": 0})
+ arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
+ self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner))
class TestCreateTemplate(unittest.TestCase):
@stubs
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--create-template", "--debug",
+ ["--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)
class TestCreateWorkflow(unittest.TestCase):
+ existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
+ expect_workflow = open("tests/wf/expect_packed.cwl").read()
+
@stubs
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
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)
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
- }
+ "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()
+ 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))
+
+ @stubs
+ def test_update(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+
+ exited = arvados_cwl.main(
+ ["--update-workflow", self.existing_workflow_uuid,
+ "--debug",
+ "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": "submit_wf.cwl",
+ "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 = {
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- expect_template = copy.deepcopy(self.expect_template)
- expect_template["owner_uuid"] = stubs.fake_user_uuid
-
stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+ body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
@stubs
def test_inputs(self, stubs):
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- self.expect_template["owner_uuid"] = stubs.fake_user_uuid
-
expect_template = copy.deepcopy(self.expect_template)
- expect_template["owner_uuid"] = stubs.fake_user_uuid
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
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