import arvados
import arvados.collection
import arvados_cwl
+import arvados_cwl.executor
import arvados_cwl.runner
import arvados.keep
keep_client2.put.side_effect = putstub
stubs.keep_client = keep_client2
- stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ stubs.docker_images = {
+ "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")],
+ "debian:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
+ "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
+ "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
+ }
+ def kd(a, b, image_name=None, image_tag=None):
+ return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
+ stubs.keepdocker.side_effect = kd
+
stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+ stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
stubs.api = mock.MagicMock()
stubs.api._rootDesc = get_rootDesc()
"uuid": stubs.fake_user_uuid,
}
stubs.api.collections().list().execute.return_value = {"items": []}
+ stubs.api.containers().current().execute.return_value = {
+ "uuid": stubs.fake_container_uuid,
+ }
class CollectionExecute(object):
def __init__(self, exe):
def collection_createstub(created_collections, body, ensure_unique_name=None):
mt = body["manifest_text"]
- uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections)
+ uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
created_collections[uuid] = {
"uuid": uuid,
"uuid": "",
"portable_data_hash": "99999999999999999999999999999994+99",
"manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
+ },
+ "zzzzz-4zz18-zzzzzzzzzzzzzd3": {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3",
+ "portable_data_hash": "999999999999999999999999999999d3+99",
+ "manifest_text": ""
+ },
+ "zzzzz-4zz18-zzzzzzzzzzzzzd4": {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4",
+ "portable_data_hash": "999999999999999999999999999999d4+99",
+ "manifest_text": ""
+ },
+ "zzzzz-4zz18-zzzzzzzzzzzzzd5": {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5",
+ "portable_data_hash": "999999999999999999999999999999d5+99",
+ "manifest_text": ""
+ },
+ "zzzzz-4zz18-zzzzzzzzzzzzzd6": {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6",
+ "portable_data_hash": "999999999999999999999999999999d6+99",
+ "manifest_text": ""
}
}
stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
}
stubs.expect_job_spec = {
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': '999999999999999999999999999999d3+99',
'min_ram_mb_per_node': 1024
},
'script_parameters': {
"listing": [{
"basename": "renamed.txt",
"class": "File",
- "location": "keep:99999999999999999999999999999998+99/file1.txt"
+ "location": "keep:99999999999999999999999999999998+99/file1.txt",
+ "size": 0
}],
'class': 'Directory'
},
- 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main'
+ 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
},
'repository': 'arvados',
'script_version': 'master',
'owner_uuid': None,
"components": {
"cwl-runner": {
- 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
+ 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
'script_parameters': {
'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
'x': {"value": {
{
'basename': 'renamed.txt',
'class': 'File', 'location':
- 'keep:99999999999999999999999999999998+99/file1.txt'
+ 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
}
]}},
- 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
+ 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
+ 'arv:debug': True,
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
{'basename': 'renamed.txt',
'class': 'File',
- 'location': 'keep:99999999999999999999999999999998+99/file1.txt'
+ 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
}
]}
},
},
'secret_mounts': {},
'state': 'Committed',
- 'owner_uuid': None,
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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__,
+ 'container_image': '999999999999999999999999999999d3+99',
'output_path': '/var/spool/cwl',
'cwd': '/var/spool/cwl',
'runtime_constraints': {
class TestSubmit(unittest.TestCase):
- @mock.patch("arvados_cwl.runner.arv_docker_get_image")
+ @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image")
@mock.patch("time.sleep")
@stubs
def test_submit(self, stubs, tm, arvdock):
+ def get_image(api_client, dockerRequirement, pull_image, project_uuid):
+ if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__:
+ return '999999999999999999999999999999d3+99'
+ elif dockerRequirement["dockerPull"] == "debian:8":
+ return '999999999999999999999999999999d4+99'
+ arvdock.side_effect = get_image
+
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug",
'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',
+ ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312:workflow.cwl\n",
'replication_desired': None,
'name': 'submit_wf.cwl',
}), ensure_unique_name=True) ])
arvdock.assert_has_calls([
mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
+ mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, True, None),
mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
])
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
+ @stubs
+ def test_error_when_multiple_storage_classes_specified(self, stubs):
+ storage_classes = "foo,bar"
+ exited = arvados_cwl.main(
+ ["--debug", "--storage-classes", storage_classes,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 1)
+
@mock.patch("time.sleep")
@stubs
def test_submit_on_error(self, stubs, tm):
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["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--disable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--disable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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"
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=stop', '--eval-timeout=20',
+ '--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(
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- "--output-name="+output_name, '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ @stubs
+ def test_submit_storage_classes(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
+ "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=4',
+ '--enable-reuse', "--debug",
+ "--storage-classes=foo", '--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')
+
+ @mock.patch("arvados_cwl.task_queue.TaskQueue")
+ @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+ @stubs
+ def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ def set_final_output(job_order, output_callback, runtimeContext):
+ output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ return []
+ job.side_effect = set_final_output
+
+ try:
+ exited = arvados_cwl.main(
+ ["--debug", "--local", "--storage-classes=foo",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+
+ @mock.patch("arvados_cwl.task_queue.TaskQueue")
+ @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+ @stubs
+ def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ def set_final_output(job_order, output_callback, runtimeContext):
+ output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ return []
+ job.side_effect = set_final_output
+
+ try:
+ exited = arvados_cwl.main(
+ ["--debug", "--local",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
@stubs
def test_submit_container_output_ttl(self, stubs):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue',
- "--intermediate-output-ttl=3600", '--eval-timeout=20',
+ '--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']
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-validate',
- '--enable-reuse', '--on-error=continue',
- "--trash-intermediate", '--eval-timeout=20',
+ '--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']
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-validate',
- "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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(
@stubs
def test_submit_file_keepref(self, stubs, tm, collectionReader):
capture_stdout = cStringIO.StringIO()
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_keepref_wf.cwl"],
'kind': 'json'
}
}, 'state': 'Committed',
- 'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
- 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'container_image': '999999999999999999999999999999d3+99',
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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': {
'id': '#submit_tool.cwl/x'}
],
'requirements': [
- {'dockerPull': 'debian:8', 'class': 'DockerRequirement'}
+ {
+ 'dockerPull': 'debian:8',
+ 'class': 'DockerRequirement',
+ "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+ }
],
'id': '#submit_tool.cwl',
'outputs': [],
'kind': 'json'
}
}, 'state': 'Committed',
- 'owner_uuid': None,
'output_path': '/var/spool/cwl',
'name': 'a test workflow',
- 'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'container_image': "999999999999999999999999999999d3+99",
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--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': {
expect_container["owner_uuid"] = project_uuid
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid, '--eval-timeout=20',
+ "--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(
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=60.0',
+ '--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(
except:
logging.exception("")
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123"
+ stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
except:
logging.exception("")
- stubs.expect_container_spec["container_image"] = "arvados/jobs:123"
+ stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
stubs.expect_container_request_uuid + '\n')
+ @stubs
+ def test_submit_wf_runner_resources(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf_runner_resources.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["runtime_constraints"] = {
+ "API": True,
+ "vcpus": 2,
+ "ram": 2000 * 2**20
+ }
+ expect_container["name"] = "submit_wf_runner_resources.cwl"
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ {
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources",
+ "coresMin": 2,
+ "ramMin": 2000
+ }
+ ]
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ "arv": "http://arvados.org/cwl#",
+ }
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+ def tearDown(self):
+ arvados_cwl.arvdocker.arv_docker_clear_cache()
+
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
@mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
+ arvados_cwl.arvdocker.arv_docker_clear_cache()
+
arvrunner = mock.MagicMock()
arvrunner.project_uuid = ""
api.return_value = mock.MagicMock()
"properties": ""
}], "items_available": 1, "offset": 0},)
arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
- self.assertEqual("arvados/jobs:"+arvados_cwl.__version__,
+ arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "portable_data_hash": "9999999999999999999999999999999b+99"}
+ self.assertEqual("9999999999999999999999999999999b+99",
arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+
@stubs
def test_submit_secrets(self, stubs):
capture_stdout = cStringIO.StringIO()
"--api=containers",
"--no-log-timestamps",
"--disable-validate",
+ "--eval-timeout=20",
+ '--thread-count=4',
"--enable-reuse",
+ '--debug',
"--on-error=continue",
- "--eval-timeout=20",
"/var/lib/cwl/workflow.json#main",
"/var/lib/cwl/cwl.input.json"
],
- "container_image": "arvados/jobs:"+arvados_cwl.__version__,
+ "container_image": "999999999999999999999999999999d3+99",
"cwd": "/var/spool/cwl",
"mounts": {
"/var/lib/cwl/cwl.input.json": {
"hints": [
{
"class": "DockerRequirement",
- "dockerPull": "debian:8"
+ "dockerPull": "debian:8",
+ "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
},
{
"class": "http://commonwl.org/cwltool#Secrets",
},
"name": "secret_wf.cwl",
"output_path": "/var/spool/cwl",
- "owner_uuid": None,
"priority": 500,
"properties": {},
"runtime_constraints": {
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), cluster_id="zzzzz")
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+ @stubs
+ def test_submit_container_cluster_id(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
+ "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)
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+ @stubs
+ def test_submit_validate_cluster_id(self, stubs):
+ capture_stdout = cStringIO.StringIO()
+ stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
+ "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, 1)
+
class TestCreateTemplate(unittest.TestCase):
existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
"components": {
"inputs_test.cwl": {
'runtime_constraints': {
- 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__,
+ 'docker_image': '999999999999999999999999999999d3+99',
'min_ram_mb_per_node': 1024
},
'script_parameters': {
'cwl:tool':
- '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main',
+ 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
- params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main'
+ params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True