_rootDesc = None
-def stubs(func):
- @functools.wraps(func)
- @mock.patch("arvados_cwl.arvdocker.determine_image_id")
- @mock.patch("uuid.uuid4")
- @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
- @mock.patch("arvados.collection.KeepClient")
- @mock.patch("arvados.keep.KeepClient")
- @mock.patch("arvados.events.subscribe")
- def wrapped(self, events, keep_client1, keep_client2, keepdocker,
- uuid4, determine_image_id, *args, **kwargs):
- class Stubs(object):
- pass
- stubs = Stubs()
- stubs.events = events
- stubs.keepdocker = keepdocker
-
- uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
- "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
- "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
-
- determine_image_id.return_value = None
-
- def putstub(p, **kwargs):
- return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
- keep_client1().put.side_effect = putstub
- keep_client1.put.side_effect = putstub
- keep_client2().put.side_effect = putstub
- keep_client2.put.side_effect = putstub
-
- stubs.keep_client = keep_client2
- stubs.docker_images = {
- "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
- "debian:buster-slim": [("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, project_uuid=None):
- return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
- stubs.keepdocker.side_effect = kd
+def stubs(wfname='submit_wf.cwl'):
+ def outer_wrapper(func, *rest):
+ @functools.wraps(func)
+ @mock.patch("arvados_cwl.arvdocker.determine_image_id")
+ @mock.patch("uuid.uuid4")
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ @mock.patch("arvados.collection.KeepClient")
+ @mock.patch("arvados.keep.KeepClient")
+ @mock.patch("arvados.events.subscribe")
+ def wrapped(self, events, keep_client1, keep_client2, keepdocker,
+ uuid4, determine_image_id, *args, **kwargs):
+ class Stubs(object):
+ pass
+ stubs = Stubs()
+ stubs.events = events
+ stubs.keepdocker = keepdocker
+
+ uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
+ "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
+ "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
+
+ determine_image_id.return_value = None
+
+ def putstub(p, **kwargs):
+ return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
+ keep_client1().put.side_effect = putstub
+ keep_client1.put.side_effect = putstub
+ keep_client2().put.side_effect = putstub
+ keep_client2.put.side_effect = putstub
+
+ stubs.keep_client = keep_client2
+ stubs.docker_images = {
+ "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})],
+ "debian:buster-slim": [("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, project_uuid=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.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+ stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
- if sys.version_info[0] < 3:
- stubs.capture_stdout = BytesIO()
- else:
- stubs.capture_stdout = StringIO()
+ if sys.version_info[0] < 3:
+ stubs.capture_stdout = BytesIO()
+ else:
+ stubs.capture_stdout = StringIO()
- stubs.api = mock.MagicMock()
- stubs.api._rootDesc = get_rootDesc()
- stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
- stubs.api._rootDesc["revision"] = "20210628"
+ stubs.api = mock.MagicMock()
+ stubs.api._rootDesc = get_rootDesc()
+ stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
+ stubs.api._rootDesc["revision"] = "20210628"
- stubs.api.users().current().execute.return_value = {
- "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,
- }
- stubs.api.config()["StorageClasses"].items.return_value = {
- "default": {
- "Default": True
- }
- }.items()
-
- class CollectionExecute(object):
- def __init__(self, exe):
- self.exe = exe
- def execute(self, num_retries=None):
- return self.exe
-
- def collection_createstub(created_collections, body, ensure_unique_name=None):
- mt = body["manifest_text"].encode('utf-8')
- uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
- pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
- created_collections[uuid] = {
- "uuid": uuid,
- "portable_data_hash": pdh,
- "manifest_text": mt.decode('utf-8')
+ stubs.api.users().current().execute.return_value = {
+ "uuid": stubs.fake_user_uuid,
}
- return CollectionExecute(created_collections[uuid])
-
- def collection_getstub(created_collections, uuid):
- for v in viewvalues(created_collections):
- if uuid in (v["uuid"], v["portable_data_hash"]):
- return CollectionExecute(v)
-
- created_collections = {
- "99999999999999999999999999999998+99": {
- "uuid": "",
- "portable_data_hash": "99999999999999999999999999999998+99",
- "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
- },
- "99999999999999999999999999999997+99": {
- "uuid": "",
- "portable_data_hash": "99999999999999999999999999999997+99",
- "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
- },
- "99999999999999999999999999999994+99": {
- "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().list().execute.return_value = {"items": []}
+ stubs.api.containers().current().execute.return_value = {
+ "uuid": stubs.fake_container_uuid,
}
- }
- stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
- stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
-
- stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
- stubs.api.jobs().create().execute.return_value = {
- "uuid": stubs.expect_job_uuid,
- "state": "Queued",
- }
-
- stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
- stubs.api.container_requests().create().execute.return_value = {
- "uuid": stubs.expect_container_request_uuid,
- "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
- "state": "Queued"
- }
-
- stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
- stubs.api.pipeline_templates().create().execute.return_value = {
- "uuid": stubs.expect_pipeline_template_uuid,
- }
- stubs.expect_job_spec = {
- 'runtime_constraints': {
- 'docker_image': '999999999999999999999999999999d3+99',
- 'min_ram_mb_per_node': 1024
- },
- 'script_parameters': {
- 'x': {
- 'basename': 'blorp.txt',
- 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- 'class': 'File'
+ stubs.api.config()["StorageClasses"].items.return_value = {
+ "default": {
+ "Default": True
+ }
+ }.items()
+
+ class CollectionExecute(object):
+ def __init__(self, exe):
+ self.exe = exe
+ def execute(self, num_retries=None):
+ return self.exe
+
+ def collection_createstub(created_collections, body, ensure_unique_name=None):
+ mt = body["manifest_text"].encode('utf-8')
+ uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
+ pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
+ created_collections[uuid] = {
+ "uuid": uuid,
+ "portable_data_hash": pdh,
+ "manifest_text": mt.decode('utf-8')
+ }
+ return CollectionExecute(created_collections[uuid])
+
+ def collection_getstub(created_collections, uuid):
+ for v in viewvalues(created_collections):
+ if uuid in (v["uuid"], v["portable_data_hash"]):
+ return CollectionExecute(v)
+
+ created_collections = {
+ "99999999999999999999999999999998+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999998+99",
+ "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
},
- 'y': {
- 'basename': '99999999999999999999999999999998+99',
- 'location': 'keep:99999999999999999999999999999998+99',
- 'class': 'Directory'
+ "99999999999999999999999999999997+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999997+99",
+ "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
},
- 'z': {
- 'basename': 'anonymous',
- "listing": [{
- "basename": "renamed.txt",
- "class": "File",
- "location": "keep:99999999999999999999999999999998+99/file1.txt",
- "size": 0
- }],
- 'class': 'Directory'
+ "99999999999999999999999999999994+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999994+99",
+ "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
},
- 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner'
- }
- stubs.pipeline_component = stubs.expect_job_spec.copy()
- stubs.expect_pipeline_instance = {
- 'name': 'submit_wf.cwl',
- 'state': 'RunningOnServer',
- 'owner_uuid': None,
- "components": {
- "cwl-runner": {
- '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': 'blorp.txt',
- 'class': 'File',
- 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- "size": 16
- }},
- 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
- 'listing': [
- {
- 'basename': 'renamed.txt',
- 'class': 'File', 'location':
- 'keep:99999999999999999999999999999998+99/file1.txt',
- 'size': 0
- }
- ]}},
- 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
- 'arv:debug': True,
- 'arv:enable_reuse': True,
- 'arv:on_error': 'continue'
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner',
- 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
+ "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.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
- stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
- stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
- stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
- stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
- "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
- "state": "Queued"
- }
- stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
- stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
+ stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
+ stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
- with open("tests/wf/submit_wf_packed.cwl") as f:
- expect_packed_workflow = yaml.round_trip_load(f)
+ stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ stubs.api.jobs().create().execute.return_value = {
+ "uuid": stubs.expect_job_uuid,
+ "state": "Queued",
+ }
- stubs.expect_container_spec = {
- 'priority': 500,
- 'mounts': {
- '/var/spool/cwl': {
- 'writable': True,
- 'kind': 'collection'
- },
- '/var/lib/cwl/workflow.json': {
- 'content': expect_packed_workflow,
- 'kind': 'json'
+ stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+ stubs.api.container_requests().create().execute.return_value = {
+ "uuid": stubs.expect_container_request_uuid,
+ "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz",
+ "state": "Queued"
+ }
+
+ stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
+ stubs.api.pipeline_templates().create().execute.return_value = {
+ "uuid": stubs.expect_pipeline_template_uuid,
+ }
+ stubs.expect_job_spec = {
+ 'runtime_constraints': {
+ 'docker_image': '999999999999999999999999999999d3+99',
+ 'min_ram_mb_per_node': 1024
},
- 'stdout': {
- 'path': '/var/spool/cwl/cwl.output.json',
- 'kind': 'file'
+ 'script_parameters': {
+ 'x': {
+ 'basename': 'blorp.txt',
+ 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ 'class': 'File'
+ },
+ 'y': {
+ 'basename': '99999999999999999999999999999998+99',
+ 'location': 'keep:99999999999999999999999999999998+99',
+ 'class': 'Directory'
+ },
+ 'z': {
+ 'basename': 'anonymous',
+ "listing": [{
+ "basename": "renamed.txt",
+ "class": "File",
+ "location": "keep:99999999999999999999999999999998+99/file1.txt",
+ "size": 0
+ }],
+ 'class': 'Directory'
+ },
+ 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
},
- '/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:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- "size": 16
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
+ 'script': 'cwl-runner'
+ }
+ stubs.pipeline_component = stubs.expect_job_spec.copy()
+ stubs.expect_pipeline_instance = {
+ 'name': 'submit_wf.cwl',
+ 'state': 'RunningOnServer',
+ 'owner_uuid': None,
+ "components": {
+ "cwl-runner": {
+ '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': 'blorp.txt',
+ 'class': 'File',
+ 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ "size": 16
+ }},
+ 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
+ 'listing': [
+ {
+ 'basename': 'renamed.txt',
+ 'class': 'File', 'location':
+ 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
+ }
+ ]}},
+ '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',
- 'size': 0
- }
- ]}
- },
- 'kind': 'json'
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
+ 'script': 'cwl-runner',
+ 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
+ }
}
- },
- 'secret_mounts': {},
- 'state': 'Committed',
- 'command': ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
- 'name': 'submit_wf.cwl',
- 'container_image': '999999999999999999999999999999d3+99',
- 'output_path': '/var/spool/cwl',
- 'cwd': '/var/spool/cwl',
- 'runtime_constraints': {
- 'API': True,
- 'vcpus': 1,
- 'ram': (1024+256)*1024*1024
- },
- 'use_existing': False,
- 'properties': {},
- 'secret_mounts': {}
- }
-
- stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
- 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,
- }
+ }
+ stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
+ stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
+ stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
+ stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
+ stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
+ "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "state": "Queued"
+ }
+ stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
+ stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
+
+ with open("tests/wf/submit_wf_packed.cwl") as f:
+ expect_packed_workflow = yaml.round_trip_load(f)
+
+ stubs.expect_container_spec = {
+ 'priority': 500,
+ 'mounts': {
+ '/var/spool/cwl': {
+ 'writable': True,
+ 'kind': 'collection'
+ },
+ '/var/lib/cwl/workflow.json': {
+ 'content': expect_packed_workflow,
+ 'kind': 'json'
+ },
+ 'stdout': {
+ 'path': '/var/spool/cwl/cwl.output.json',
+ 'kind': 'file'
+ },
+ '/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:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ "size": 16
+ },
+ 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
+ {'basename': 'renamed.txt',
+ 'class': 'File',
+ 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+ 'size': 0
+ }
+ ]}
+ },
+ 'kind': 'json'
+ }
+ },
+ 'secret_mounts': {},
+ 'state': 'Committed',
+ 'command': ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow '+wfname,
+ '--debug', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+ 'name': wfname,
+ 'container_image': '999999999999999999999999999999d3+99',
+ 'output_name': 'Output from workflow '+wfname,
+ 'output_path': '/var/spool/cwl',
+ 'cwd': '/var/spool/cwl',
+ 'runtime_constraints': {
+ 'API': True,
+ 'vcpus': 1,
+ 'ram': (1024+256)*1024*1024
+ },
+ 'use_existing': False,
+ 'properties': {},
+ 'secret_mounts': {}
+ }
- return func(self, stubs, *args, **kwargs)
- return wrapped
+ stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
+ 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
+ return outer_wrapper
class TestSubmit(unittest.TestCase):
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--disable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl",
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs('submit_wf_no_reuse.cwl')
def test_submit_container_reuse_disabled_by_workflow(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--disable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf_no_reuse.cwl', '--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["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
{
"class": "http://arvados.org/cwl#ReuseRequirement",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl",
'--debug', '--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', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", "--debug",
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl',
+ "--debug",
"--storage-classes=foo", '--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', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", "--debug",
+ '--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl",
+ "--debug",
"--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
make_output.return_value = ({},final_output_c)
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
stubs.api.config().get.return_value = {"default": {"Default": True}}
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
make_output.return_value = ({},final_output_c)
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
"tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@stubs
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug',
+ '--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl", '--debug',
'--on-error=continue',
"--intermediate-output-ttl=3600",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl",
"--output-tags="+output_tags, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
}, 'state': 'Committed',
'output_path': '/var/spool/cwl',
'name': 'expect_arvworkflow.cwl#main',
+ 'output_name': 'Output from workflow expect_arvworkflow.cwl#main',
'container_image': '999999999999999999999999999999d3+99',
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow expect_arvworkflow.cwl#main',
+ '--debug', '--on-error=continue',
'/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs('hello container 123')
def test_submit_container_name(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_container["name"] = "hello container 123"
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
"--eval-timeout=20", "--thread-count=0",
- '--enable-reuse', "--collection-cache-size=256", '--debug',
+ '--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl", '--debug',
'--on-error=continue',
'--project-uuid='+project_uuid,
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs('submit_wf_runner_resources.cwl')
def test_submit_wf_runner_resources(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"vcpus": 2,
"ram": (2000+512) * 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",
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
+ '--enable-reuse', "--collection-cache-size=512",
+ '--output-name=Output from workflow submit_wf_runner_resources.cwl',
+ '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
'--thread-count=0',
"--enable-reuse",
"--collection-cache-size=256",
+ '--output-name=Output from workflow secret_wf.cwl'
'--debug',
"--on-error=continue",
"/var/lib/cwl/workflow.json#main",
}
},
"name": "secret_wf.cwl",
+ "output_name": "Output from workflow secret_wf.cwl",
"output_path": "/var/spool/cwl",
"priority": 500,
"properties": {},
finally:
cwltool_logger.removeHandler(stderr_logger)
- @stubs
+ @stubs('submit_wf_process_properties.cwl')
def test_submit_set_process_properties(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_container["name"] = "submit_wf_process_properties.cwl"
+
expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
{
"class": "http://arvados.org/cwl#ProcessProperties",
projects / arvados.git / commitdiff