def test_mounts(self, keepdocker):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
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"
}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool = cmap({
"inputs": [{
"id": "p1",
"type": "Directory"
}],
"outputs": [],
"baseCommand": "ls",
"arguments": [{
"valueFrom": "$(runtime.outdir)"
}],
"id": "#",
"class": "CommandLineTool"
})
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="containers",
avsc_names=avsc_names,
basedir="",
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
job_order = {
"p1": {
"class":
"Directory",
"location":
"keep:99999999999999999999999999999994+44",
"listing": [{
"class":
"File",
"location":
"keep:99999999999999999999999999999994+44/file1",
}, {
"class":
"File",
"location":
"keep:99999999999999999999999999999994+44/file2",
}]
}
}
for j in arvtool.job(job_order,
mock.MagicMock(),
basedir="",
name="test_run_mounts",
make_fs_access=make_fs_access,
tmpdir="/tmp"):
j.run(priority=500)
runner.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher({
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'name': 'test_run_mounts',
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': True,
'priority': 500,
'mounts': {
"/keep/99999999999999999999999999999994+44": {
"kind":
"collection",
"portable_data_hash":
"99999999999999999999999999999994+44"
},
'/tmp': {
'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
"capacity": 1073741824
}
},
'state': 'Committed',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': 'arvados/jobs',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
'secret_mounts': {}
}))
def test_secrets(self, keepdocker):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
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"
}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool = cmap({
"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": [],
"requirements": [{
"class":
"InitialWorkDirRequirement",
"listing": [{
"entry": "username: user\npassword: $(inputs.pw)\n",
"entryname": "example.conf"
}]
}]
})
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="containers",
avsc_names=avsc_names,
basedir="",
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
job_order = {"pw": "blorp"}
runner.secret_store.store(["pw"], job_order)
for j in arvtool.job(job_order,
mock.MagicMock(),
basedir="",
name="test_secrets",
make_fs_access=make_fs_access,
tmpdir="/tmp"):
j.run(enable_reuse=True, priority=500)
runner.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher({
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'name': 'test_secrets',
'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',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': 'arvados/jobs',
'command': ['md5sum', 'example.conf'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
"secret_mounts": {
"/var/spool/cwl/example.conf": {
"content": "username: user\npassword: blorp\n",
"kind": "text"
}
}
}))
def test_initial_work_dir(self, collection_mock, keepdocker):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
sourcemock = mock.MagicMock()
def get_collection_mock(p):
if "/" in p:
return (sourcemock, p.split("/", 1)[1])
else:
return (sourcemock, "")
runner.fs_access.get_collection.side_effect = get_collection_mock
vwdmock = mock.MagicMock()
collection_mock.return_value = vwdmock
vwdmock.portable_data_hash.return_value = "99999999999999999999999999999996+99"
tool = cmap({
"inputs": [],
"outputs": [],
"hints": [{
"class":
"InitialWorkDirRequirement",
"listing": [{
"class":
"File",
"basename":
"foo",
"location":
"keep:99999999999999999999999999999995+99/bar"
}, {
"class":
"Directory",
"basename":
"foo2",
"location":
"keep:99999999999999999999999999999995+99"
}, {
"class":
"File",
"basename":
"filename",
"location":
"keep:99999999999999999999999999999995+99/baz/filename"
}, {
"class":
"Directory",
"basename":
"subdir",
"location":
"keep:99999999999999999999999999999995+99/subdir"
}]
}],
"baseCommand":
"ls",
"id":
"#",
"class":
"CommandLineTool"
})
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="containers",
avsc_names=avsc_names,
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({},
mock.MagicMock(),
basedir="",
name="test_initial_work_dir",
make_fs_access=make_fs_access,
tmpdir="/tmp"):
j.run(priority=500)
call_args, call_kwargs = runner.api.container_requests(
).create.call_args
vwdmock.copy.assert_has_calls(
[mock.call('bar', 'foo', source_collection=sourcemock)])
vwdmock.copy.assert_has_calls(
[mock.call('', 'foo2', source_collection=sourcemock)])
vwdmock.copy.assert_has_calls([
mock.call('baz/filename', 'filename', source_collection=sourcemock)
])
vwdmock.copy.assert_has_calls(
[mock.call('subdir', 'subdir', source_collection=sourcemock)])
call_body_expected = {
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'name': 'test_initial_work_dir',
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': True,
'priority': 500,
'mounts': {
'/tmp': {
'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl/foo': {
'kind': 'collection',
'path': 'foo',
'portable_data_hash': '99999999999999999999999999999996+99'
},
'/var/spool/cwl/foo2': {
'kind': 'collection',
'path': 'foo2',
'portable_data_hash': '99999999999999999999999999999996+99'
},
'/var/spool/cwl/filename': {
'kind': 'collection',
'path': 'filename',
'portable_data_hash': '99999999999999999999999999999996+99'
},
'/var/spool/cwl/subdir': {
'kind': 'collection',
'path': 'subdir',
'portable_data_hash': '99999999999999999999999999999996+99'
}
},
'state': 'Committed',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': 'arvados/jobs',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
'secret_mounts': {}
}
call_body = call_kwargs.get('body', None)
self.assertNotEqual(None, call_body)
for key in call_body:
self.assertEqual(call_body_expected.get(key), call_body.get(key))
def test_resource_requirements(self, keepdocker):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 3600
runner.secret_store = cwltool.secrets.SecretStore()
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
tool = cmap({
"inputs": [],
"outputs": [],
"hints": [{
"class": "ResourceRequirement",
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000,
"outdirMin": 5000
}, {
"class": "http://arvados.org/cwl#RuntimeConstraints",
"keep_cache": 512
}, {
"class": "http://arvados.org/cwl#APIRequirement",
}, {
"class": "http://arvados.org/cwl#PartitionRequirement",
"partition": "blurb"
}, {
"class": "http://arvados.org/cwl#IntermediateOutput",
"outputTTL": 7200
}, {
"class": "http://arvados.org/cwl#ReuseRequirement",
"enableReuse": False
}],
"baseCommand":
"ls",
"id":
"#",
"class":
"CommandLineTool"
})
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="containers",
avsc_names=avsc_names,
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({},
mock.MagicMock(),
basedir="",
name="test_resource_requirements",
make_fs_access=make_fs_access,
tmpdir="/tmp"):
j.run(enable_reuse=True, priority=500)
call_args, call_kwargs = runner.api.container_requests(
).create.call_args
call_body_expected = {
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'name': 'test_resource_requirements',
'runtime_constraints': {
'vcpus': 3,
'ram': 3145728000,
'keep_cache_ram': 536870912,
'API': True
},
'use_existing': False,
'priority': 500,
'mounts': {
'/tmp': {
'kind': 'tmp',
"capacity": 4194304000
},
'/var/spool/cwl': {
'kind': 'tmp',
"capacity": 5242880000
}
},
'state': 'Committed',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 7200,
'container_image': 'arvados/jobs',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {
'partitions': ['blurb']
},
'properties': {},
'secret_mounts': {}
}
call_body = call_kwargs.get('body', None)
self.assertNotEqual(None, call_body)
for key in call_body:
self.assertEqual(call_body_expected.get(key), call_body.get(key))
def test_run(self, list_images_in_arv, mockcollection):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection(
).portable_data_hash.return_value = "99999999999999999999999999999999+118"
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosWorkflow(runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
basedir="",
make_fs_access=make_fs_access,
loader=document_loader,
makeTool=runner.arv_make_tool,
metadata=metadata)
arvtool.formatgraph = None
it = arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access)
it.next().run()
it.next().run()
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = f.read()
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher(
{
'minimum_script_version':
'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.vwd': {
'workflow.cwl':
'$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
'cwl.input.yml':
'$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
},
'command': [
u'cwltool', u'--no-container',
u'--move-outputs',
u'--preserve-entire-environment',
u'workflow.cwl#main', u'cwl.input.yml'
],
'task.stdout':
'cwl.output.json'
}]
},
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'
}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'a3f2cb186e437bfce0031b024b2157b73ed2717d'
], ['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
mockcollection().open().__enter__().write.assert_has_calls(
[mock.call(subwf)])
mockcollection().open().__enter__().write.assert_has_calls(
[mock.call('''{
"sleeptime": 5
}''')])
def test_run(self, list_images_in_arv):
for enable_reuse in (True, False):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
tool = cmap({
"inputs": [],
"outputs": [],
"baseCommand": "ls",
"arguments": [{
"valueFrom": "$(runtime.outdir)"
}]
})
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(
runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(
runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
basedir="",
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access):
j.run(enable_reuse=enable_reuse)
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'command': ['ls', '$(task.outdir)']
}],
},
'script_version': 'master',
'minimum_script_version':
'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 1,
'min_ram_mb_per_node': 1024,
'min_scratch_mb_per_node':
2048 # tmpdirSize + outdirSize
}
}),
find_or_create=enable_reuse,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'a3f2cb186e437bfce0031b024b2157b73ed2717d'
],
[
'docker_image_locator', 'in docker',
'arvados/jobs'
]])
def test_resource_requirements(self, list_images_in_arv):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
arvados_cwl.add_arv_hints()
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool = {
"inputs": [],
"outputs": [],
"hints": [{
"class": "ResourceRequirement",
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000
}, {
"class": "http://arvados.org/cwl#RuntimeConstraints",
"keep_cache": 512,
"outputDirType": "keep_output_dir"
}, {
"class": "http://arvados.org/cwl#APIRequirement",
}],
"baseCommand":
"ls"
}
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access):
j.run()
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.keepTmpOutput': True,
'command': ['ls']
}]
},
'script_version': 'master',
'minimum_script_version':
'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3512, # ramMin + keep_cache
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
}),
find_or_create=True,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'a3f2cb186e437bfce0031b024b2157b73ed2717d'
], ['docker_image_locator', 'in docker', 'arvados/jobs']])