[ARVADOS] updated: 2.1.0-1181-g82c5c20ba
Git user
git at public.arvados.org
Thu Aug 12 19:24:48 UTC 2021
Summary of changes:
sdk/cwl/arvados_cwl/executor.py | 4 +-
sdk/cwl/tests/test_container.py | 97 ++++++++++++++++++++--
sdk/cwl/tests/test_submit.py | 55 ++++++++++--
...r_resources.cwl => submit_storage_class_wf.cwl} | 6 +-
4 files changed, 140 insertions(+), 22 deletions(-)
copy sdk/cwl/tests/wf/{submit_wf_runner_resources.cwl => submit_storage_class_wf.cwl} (87%)
via 82c5c20ba8966a23fdfb040aac46a25ff74cfc7b (commit)
from cb33e4c24bd396b223c455ad91a18691e0d59f72 (commit)
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commit 82c5c20ba8966a23fdfb040aac46a25ff74cfc7b
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Thu Aug 12 15:24:14 2021 -0400
17390: Add unit tests for storage classes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 6d4f1bd52..edb9d5b52 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -42,7 +42,7 @@ from .context import ArvLoadingContext, ArvRuntimeContext
from ._version import __version__
from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
-from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class
+from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class, aslist
from cwltool.command_line_tool import compute_checksums
from cwltool.load_tool import load_tool
@@ -549,7 +549,7 @@ The 'jobs' API is no longer supported.
if runtimeContext.submit_request_uuid and self.work_api != "containers":
raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
- default_storage_classes = [k for k,v in self.api.config()["StorageClasses"].items() if v.get("Default") is True].join(",")
+ default_storage_classes = ",".join([k for k,v in self.api.config()["StorageClasses"].items() if v.get("Default") is True])
if runtimeContext.storage_classes == "default":
runtimeContext.storage_classes = default_storage_classes
if runtimeContext.intermediate_storage_classes == "default":
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 09983f87a..2b46b89c6 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -163,7 +163,8 @@ class TestContainer(unittest.TestCase):
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}))
# The test passes some fields in builder.resources
@@ -250,7 +251,8 @@ class TestContainer(unittest.TestCase):
'partitions': ['blurb']
},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}
call_body = call_kwargs.get('body', None)
@@ -379,7 +381,8 @@ class TestContainer(unittest.TestCase):
'scheduling_parameters': {
},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}
call_body = call_kwargs.get('body', None)
@@ -463,7 +466,8 @@ class TestContainer(unittest.TestCase):
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}))
@mock.patch("arvados.collection.Collection")
@@ -696,7 +700,8 @@ class TestContainer(unittest.TestCase):
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}))
# The test passes no builder.resources
@@ -791,7 +796,8 @@ class TestContainer(unittest.TestCase):
"content": "username: user\npassword: blorp\n",
"kind": "text"
}
- }
+ },
+ 'output_storage_classes': ["default"]
}))
# The test passes no builder.resources
@@ -835,6 +841,79 @@ class TestContainer(unittest.TestCase):
self.assertEqual(42, kwargs['body']['scheduling_parameters'].get('max_run_time'))
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ def test_setting_storage_class(self, keepdocker):
+ arv_docker_clear_cache()
+
+ runner = mock.MagicMock()
+ runner.ignore_docker_for_reuse = False
+ runner.intermediate_output_ttl = 0
+ runner.secret_store = cwltool.secrets.SecretStore()
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ runner.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99"}
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+ "id": "#",
+ "class": "CommandLineTool",
+ "hints": [
+ {
+ "class": "http://arvados.org/cwl#OutputStorageClass",
+ "finalStorageClass": ["baz_sc", "qux_sc"],
+ "intermediateStorageClass": ["foo_sc", "bar_sc"]
+ }
+ ]
+ })
+
+ loadingContext, runtimeContext = self.helper(runner, True)
+
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool.formatgraph = None
+
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': 'test_run_True',
+ 'runtime_constraints': {
+ 'vcpus': 1,
+ 'ram': 1073741824
+ },
+ 'use_existing': True,
+ 'priority': 500,
+ 'mounts': {
+ '/tmp': {'kind': 'tmp',
+ "capacity": 1073741824
+ },
+ '/var/spool/cwl': {'kind': 'tmp',
+ "capacity": 1073741824 }
+ },
+ 'state': 'Committed',
+ 'output_name': 'Output for step test_run_True',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'output_path': '/var/spool/cwl',
+ 'output_ttl': 0,
+ 'container_image': '99999999999999999999999999999993+99',
+ 'command': ['ls', '/var/spool/cwl'],
+ 'cwd': '/var/spool/cwl',
+ 'scheduling_parameters': {},
+ 'properties': {},
+ 'secret_mounts': {},
+ 'output_storage_classes': ["foo_sc", "bar_sc"]
+ }))
+
+
class TestWorkflow(unittest.TestCase):
def setUp(self):
cwltool.process._names = set()
@@ -972,7 +1051,8 @@ class TestWorkflow(unittest.TestCase):
"scheduling_parameters": {},
"secret_mounts": {},
"state": "Committed",
- "use_existing": True
+ "use_existing": True,
+ 'output_storage_classes': ["default"]
}))
mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
mockc.open().__enter__().write.assert_has_calls([mock.call(
@@ -1074,7 +1154,8 @@ class TestWorkflow(unittest.TestCase):
],
'use_existing': True,
'output_name': u'Output for step echo-subwf',
- 'cwd': '/var/spool/cwl'
+ 'cwd': '/var/spool/cwl',
+ 'output_storage_classes': ["default"]
}))
def test_default_work_api(self):
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 12daf6b67..4c96af6b3 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -95,6 +95,11 @@ def stubs(func):
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):
@@ -342,14 +347,6 @@ class TestSubmit(unittest.TestCase):
cwltool.process._names = set()
arvados_cwl.arvdocker.arv_docker_clear_cache()
- @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
@@ -526,6 +523,27 @@ class TestSubmit(unittest.TestCase):
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
+ @stubs
+ def test_submit_multiple_storage_classes(self, stubs):
+ exited = arvados_cwl.main(
+ ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ 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",
+ "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
@@ -568,6 +586,27 @@ class TestSubmit(unittest.TestCase):
make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
self.assertEqual(exited, 0)
+ @mock.patch("cwltool.task_queue.TaskQueue")
+ @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
+ @stubs
+ def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
+ final_output_c = arvados.collection.Collection()
+ make_output.return_value = ({},final_output_c)
+
+ def set_final_output(job_order, output_callback, runtimeContext):
+ output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ return []
+ job.side_effect = set_final_output
+
+ exited = arvados_cwl.main(
+ ["--debug", "--local",
+ "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')
+ self.assertEqual(exited, 0)
+
@stubs
def test_submit_container_output_ttl(self, stubs):
exited = arvados_cwl.main(
diff --git a/sdk/cwl/tests/wf/submit_storage_class_wf.cwl b/sdk/cwl/tests/wf/submit_storage_class_wf.cwl
new file mode 100644
index 000000000..c365d9648
--- /dev/null
+++ b/sdk/cwl/tests/wf/submit_storage_class_wf.cwl
@@ -0,0 +1,30 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# Test case for arvados-cwl-runner
+#
+# Used to test whether scanning a workflow file for dependencies
+# (e.g. submit_tool.cwl) and uploading to Keep works as intended.
+
+class: Workflow
+cwlVersion: v1.0
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+hints:
+ arv:OutputStorageClass:
+ finalStorageClass: [foo, bar]
+inputs:
+ - id: x
+ type: File
+ - id: y
+ type: Directory
+ - id: z
+ type: Directory
+outputs: []
+steps:
+ - id: step1
+ in:
+ - { id: x, source: "#x" }
+ out: []
+ run: ../tool/submit_tool.cwl
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