}
]}},
'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
+ 'arv:debug': True,
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
expect_packed_workflow = yaml.round_trip_load(f)
stubs.expect_container_spec = {
- 'priority': 1,
+ 'priority': 500,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'kind': 'json'
}
},
+ 'secret_mounts': {},
'state': 'Committed',
- 'owner_uuid': None,
- 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
- '--enable-reuse', '--on-error=continue',
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'ram': 1024*1024*1024
},
'use_existing': True,
- 'properties': {}
+ 'properties': {},
+ 'secret_mounts': {}
}
stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
'replication_desired': None,
- 'name': 'submit_tool.cwl dependencies',
- }), ensure_unique_name=True),
+ 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+ }), ensure_unique_name=False),
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),
+ 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+ }), ensure_unique_name=False),
mock.call(body=JsonDiffMatcher({
'manifest_text':
'. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
- ["--submit", "--no-wait",
+ ["--submit", "--no-wait", "--debug",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stdout, sys.stderr, api_client=stubs.api)
'manifest_text':
'. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
'replication_desired': None,
- 'name': 'submit_tool.cwl dependencies',
- }), ensure_unique_name=True),
+ 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+ }), ensure_unique_name=False),
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)])
+ 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+ }), ensure_unique_name=False)])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = [
- 'arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
- '--disable-reuse', '--on-error=continue',
+ 'arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--disable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = [
- 'arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
- '--disable-reuse', '--on-error=continue',
+ 'arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--disable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
expect_container["name"] = "submit_wf_no_reuse.cwl"
"enableReuse": False,
},
]
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ "arv": "http://arvados.org/cwl#",
+ "cwltool": "http://commonwl.org/cwltool#"
+ }
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
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']
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--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))
logging.exception("")
expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
- "--output-name="+output_name, '--enable-reuse', '--on-error=continue',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse',
+ "--output-name="+output_name, '--debug', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["output_name"] = output_name
stubs.api.container_requests().create.assert_called_with(
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=continue',
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
"--intermediate-output-ttl=3600",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
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=continue',
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
"--trash-intermediate",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
logging.exception("")
expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
- "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse',
+ "--output-tags="+output_tags, '--debug', '--on-error=continue',
+ '/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(exited, 0)
expect_container = {
- 'priority': 1,
+ 'priority': 500,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'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',
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'ram': 1073741824
},
'use_existing': True,
- 'properties': {}
+ 'properties': {},
+ 'secret_mounts': {}
}
stubs.api.container_requests().create.assert_called_with(
self.assertEqual(exited, 0)
expect_container = {
- 'priority': 1,
+ 'priority': 500,
'mounts': {
'/var/spool/cwl': {
'writable': True,
'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',
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'use_existing': True,
'properties': {
"template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
- }
+ },
+ 'secret_mounts': {}
}
stubs.api.container_requests().create.assert_called_with(
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["owner_uuid"] = project_uuid
- expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
- '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid,
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ "--eval-timeout=20", "--thread-count=4",
+ '--enable-reuse', '--debug', '--on-error=continue',
+ '--project-uuid='+project_uuid,
+ '/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')
+
+ @stubs
+ def test_submit_container_eval_timeout(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
+ "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', '--disable-validate',
+ '--eval-timeout=60.0', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
+ '/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')
+
+
+ @stubs
+ def test_submit_container_thread_count(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
+ "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', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=20',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ @stubs
+ def test_submit_priority(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
+ "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["priority"] = 669
+
+ 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')
+
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
- @mock.patch("cwltool.docker.get_image")
+ @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
arvrunner = mock.MagicMock()
self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+ @stubs
+ def test_submit_secrets(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+
+ expect_container = {
+ "command": [
+ "arvados-cwl-runner",
+ "--local",
+ "--api=containers",
+ "--no-log-timestamps",
+ "--disable-validate",
+ "--eval-timeout=20",
+ '--thread-count=4',
+ "--enable-reuse",
+ '--debug',
+ "--on-error=continue",
+ "/var/lib/cwl/workflow.json#main",
+ "/var/lib/cwl/cwl.input.json"
+ ],
+ "container_image": "arvados/jobs:"+arvados_cwl.__version__,
+ "cwd": "/var/spool/cwl",
+ "mounts": {
+ "/var/lib/cwl/cwl.input.json": {
+ "content": {
+ "pw": {
+ "$include": "/secrets/s0"
+ }
+ },
+ "kind": "json"
+ },
+ "/var/lib/cwl/workflow.json": {
+ "content": {
+ "$graph": [
+ {
+ "$namespaces": {
+ "cwltool": "http://commonwl.org/cwltool#"
+ },
+ "arguments": [
+ "md5sum",
+ "example.conf"
+ ],
+ "class": "CommandLineTool",
+ "hints": [
+ {
+ "class": "http://commonwl.org/cwltool#Secrets",
+ "secrets": [
+ "#secret_job.cwl/pw"
+ ]
+ }
+ ],
+ "id": "#secret_job.cwl",
+ "inputs": [
+ {
+ "id": "#secret_job.cwl/pw",
+ "type": "string"
+ }
+ ],
+ "outputs": [
+ {
+ "id": "#secret_job.cwl/out",
+ "type": "stdout"
+ }
+ ],
+ "stdout": "hashed_example.txt",
+ "requirements": [
+ {
+ "class": "InitialWorkDirRequirement",
+ "listing": [
+ {
+ "entry": "username: user\npassword: $(inputs.pw)\n",
+ "entryname": "example.conf"
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "class": "Workflow",
+ "hints": [
+ {
+ "class": "DockerRequirement",
+ "dockerPull": "debian:8"
+ },
+ {
+ "class": "http://commonwl.org/cwltool#Secrets",
+ "secrets": [
+ "#main/pw"
+ ]
+ }
+ ],
+ "id": "#main",
+ "inputs": [
+ {
+ "id": "#main/pw",
+ "type": "string"
+ }
+ ],
+ "outputs": [
+ {
+ "id": "#main/out",
+ "outputSource": "#main/step1/out",
+ "type": "File"
+ }
+ ],
+ "steps": [
+ {
+ "id": "#main/step1",
+ "in": [
+ {
+ "id": "#main/step1/pw",
+ "source": "#main/pw"
+ }
+ ],
+ "out": [
+ "#main/step1/out"
+ ],
+ "run": "#secret_job.cwl"
+ }
+ ]
+ }
+ ],
+ "cwlVersion": "v1.0"
+ },
+ "kind": "json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": True
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ }
+ },
+ "name": "secret_wf.cwl",
+ "output_path": "/var/spool/cwl",
+ "priority": 500,
+ "properties": {},
+ "runtime_constraints": {
+ "API": True,
+ "ram": 1073741824,
+ "vcpus": 1
+ },
+ "secret_mounts": {
+ "/secrets/s0": {
+ "content": "blorp",
+ "kind": "text"
+ }
+ },
+ "state": "Committed",
+ "use_existing": True
+ }
+
+ 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_request_uuid(self, stubs):
+ stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
+
+ stubs.api.container_requests().update().execute.return_value = {
+ "uuid": stubs.expect_container_request_uuid,
+ "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
+ "state": "Queued"
+ }
+
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
+ "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.container_requests().update.assert_called_with(
+ uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
class TestCreateTemplate(unittest.TestCase):
existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
projects / arvados.git / blobdiff