def test_run(self, keepdocker):
for enable_reuse in (True, False):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
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": [],
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}]
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_"+str(enable_reuse),
make_fs_access=make_fs_access, tmpdir="/tmp"):
j.run(enable_reuse=enable_reuse)
runner.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher({
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'name': 'test_run_'+str(enable_reuse),
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': enable_reuse,
'priority': 1,
'mounts': {
'/tmp': {'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {'kind': 'tmp',
"capacity": 1073741824 }
},
'state': 'Committed',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': 'arvados/jobs',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
}))
def test_run(self, keepdocker):
for enable_reuse in (True, False):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
tool = cmap({
"inputs": [],
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(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="containers", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_"+str(enable_reuse),
make_fs_access=make_fs_access, tmpdir="/tmp"):
j.run(enable_reuse=enable_reuse)
runner.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher({
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'name': 'test_run_'+str(enable_reuse),
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': enable_reuse,
'priority': 1,
'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',
'container_image': 'arvados/jobs',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
}))
def test_timelimit(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"
}
tool = cmap({
"inputs": [],
"outputs": [],
"baseCommand":
"ls",
"arguments": [{
"valueFrom": "$(runtime.outdir)"
}],
"id":
"#",
"class":
"CommandLineTool",
"hints": [{
"class": "http://commonwl.org/cwltool#TimeLimit",
"timelimit": 42
}]
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_timelimit"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
_, kwargs = runner.api.container_requests().create.call_args
self.assertEqual(
42, kwargs['body']['scheduling_parameters'].get('max_run_time'))
def test_timelimit(self, keepdocker):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"}
tool = cmap({
"inputs": [],
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
"id": "#",
"class": "CommandLineTool",
"hints": [
{
"class": "http://commonwl.org/cwltool#TimeLimit",
"timelimit": 42
}
]
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_timelimit"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
_, kwargs = runner.api.container_requests().create.call_args
self.assertEqual(42, kwargs['body']['scheduling_parameters'].get('max_run_time'))
def test_overall_resource_singlecontainer(self, list_images_in_arv,
mockcollection,
mockcollectionreader):
arv_docker_clear_cache()
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_value = {
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.api.collections().list().execute.return_value = {
"items": [{
"uuid":
"zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash":
"99999999999999999999999999999993+99"
}]
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
runner.secret_store = cwltool.secrets.SecretStore()
loadingContext, runtimeContext = self.helper(runner)
runner.fs_access = runtimeContext.make_fs_access(
runtimeContext.basedir)
loadingContext.do_update = True
tool, metadata = loadingContext.loader.resolve_ref(
"tests/wf/echo-wf.cwl")
mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(
mock.MagicMock(), *args, **kwargs)
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
next(it).run(runtimeContext)
next(it).run(runtimeContext)
with open("tests/wf/echo-subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
runner.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher({
'output_ttl':
0,
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'scheduling_parameters': {},
'name':
u'echo-subwf',
'secret_mounts': {},
'runtime_constraints': {
'API': True,
'vcpus': 3,
'ram': 1073741824
},
'properties': {},
'priority':
500,
'mounts': {
'/var/spool/cwl/cwl.input.yml': {
'portable_data_hash':
'99999999999999999999999999999996+99',
'kind': 'collection',
'path': 'cwl.input.yml'
},
'/var/spool/cwl/workflow.cwl': {
'portable_data_hash':
'99999999999999999999999999999996+99',
'kind': 'collection',
'path': 'workflow.cwl'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
'/tmp': {
'kind': 'tmp',
'capacity': 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
'capacity': 3221225472
}
},
'state':
'Committed',
'output_path':
'/var/spool/cwl',
'container_image':
'99999999999999999999999999999993+99',
'command': [
u'cwltool', u'--no-container', u'--move-outputs',
u'--preserve-entire-environment', u'workflow.cwl#main',
u'cwl.input.yml'
],
'use_existing':
True,
'output_name':
u'Output for step echo-subwf',
'cwd':
'/var/spool/cwl'
}))
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
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"
}],
"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="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()
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': True,
'priority': 1,
'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',
'container_image': 'arvados/jobs',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {
'partitions': ['blurb']
},
'properties': {}
}
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_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
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"
})
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()
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': 1,
'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',
'container_image': 'arvados/jobs',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {
},
'properties': {}
}
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_secrets(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"
}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.1")
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"
}]
}]
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_secrets"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
job_order = {"pw": "blorp"}
runner.secret_store.store(["pw"], job_order)
for j in arvtool.job(job_order, 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_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',
'output_name': 'Output for step test_secrets',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': '99999999999999999999999999999993+99',
'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.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"
}
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.side_effect = lambda *args, **kwargs: CollectionMock(
vwdmock, *args, **kwargs)
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"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_initial_work_dir"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
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',
'output_name': 'Output for step test_initial_work_dir',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': '99999999999999999999999999999993+99',
'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_initial_work_dir(self, collection_mock, 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"}
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.side_effect = lambda *args, **kwargs: CollectionMock(vwdmock, *args, **kwargs)
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"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_initial_work_dir"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
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',
'output_name': 'Output for step test_initial_work_dir',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': '99999999999999999999999999999993+99',
'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.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 3600
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": [],
"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"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_resource_requirements"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
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',
'output_name': 'Output for step test_resource_requirements',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 7200,
'container_image': '99999999999999999999999999999993+99',
'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_redirects(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": [],
"outputs": [],
"baseCommand": "ls",
"stdout": "stdout.txt",
"stderr": "stderr.txt",
"stdin": "/keep/99999999999999999999999999999996+99/file.txt",
"arguments": [{
"valueFrom": "$(runtime.outdir)"
}],
"id": "#",
"class": "CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_run_redirect"
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_redirect',
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': True,
'priority': 500,
'mounts': {
'/tmp': {
'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
"capacity": 1073741824
},
"stderr": {
"kind": "file",
"path": "/var/spool/cwl/stderr.txt"
},
"stdin": {
"kind":
"collection",
"path":
"file.txt",
"portable_data_hash":
"99999999999999999999999999999996+99"
},
"stdout": {
"kind": "file",
"path": "/var/spool/cwl/stdout.txt"
},
},
'state': 'Committed',
"output_name": "Output for step test_run_redirect",
'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_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
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"
})
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()
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': 1,
'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',
'container_image': 'arvados/jobs',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {}
}
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
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"
}],
"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="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()
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': True,
'priority': 1,
'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',
'container_image': 'arvados/jobs',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {
'partitions': ['blurb']
},
'properties': {}
}
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 setUp(self):
cwltool.process._names = set()
arv_docker_clear_cache()
def test_run(self, keepdocker):
for enable_reuse in (True, False):
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"
})
loadingContext, runtimeContext = self.helper(runner, enable_reuse)
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_' + str(enable_reuse),
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing':
enable_reuse,
'priority':
500,
'mounts': {
'/tmp': {
'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
"capacity": 1073741824
}
},
'state':
'Committed',
'output_name':
'Output for step test_run_' + str(enable_reuse),
'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': {}
}))
def test_resource_requirements(self, keepdocker):
arv_docker_clear_cache()
runner = mock.MagicMock()
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 3600
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": [],
"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"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_resource_requirements"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
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',
'output_name': 'Output for step test_resource_requirements',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 7200,
'container_image': '99999999999999999999999999999993+99',
'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_mounts(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": "99999999999999999999999999999994+99",
"manifest_text": ". 99999999999999999999999999999994+99 0:0:file1 0:0:file2"}
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"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_run_mounts"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
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(), runtimeContext):
j.run(runtimeContext)
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',
'output_name': 'Output for step test_run_mounts',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': '99999999999999999999999999999994+99',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
'secret_mounts': {}
}))
def test_mounts(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":
"99999999999999999999999999999994+99",
"manifest_text":
". 99999999999999999999999999999994+99 0:0:file1 0:0:file2"
}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.1")
tool = cmap({
"inputs": [{
"id": "p1",
"type": "Directory"
}],
"outputs": [],
"baseCommand": "ls",
"arguments": [{
"valueFrom": "$(runtime.outdir)"
}],
"id": "#",
"class": "CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_run_mounts"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
job_order = {
"p1": {
"class":
"Directory",
"location":
"keep:99999999999999999999999999999994+44",
"http://arvados.org/cwl#collectionUUID":
"zzzzz-4zz18-zzzzzzzzzzzzzzz",
"listing": [{
"class":
"File",
"location":
"keep:99999999999999999999999999999994+44/file1",
}, {
"class":
"File",
"location":
"keep:99999999999999999999999999999994+44/file2",
}]
}
}
for j in arvtool.job(job_order, 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_mounts',
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': True,
'priority': 500,
'mounts': {
"/keep/99999999999999999999999999999994+44": {
"kind": "collection",
"portable_data_hash":
"99999999999999999999999999999994+44",
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz"
},
'/tmp': {
'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
"capacity": 1073741824
}
},
'state': 'Committed',
'output_name': 'Output for step test_run_mounts',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': '99999999999999999999999999999994+99',
'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.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"
}
]
}
]})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_secrets"
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
job_order = {"pw": "blorp"}
runner.secret_store.store(["pw"], job_order)
for j in arvtool.job(job_order, 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_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',
'output_name': 'Output for step test_secrets',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'output_path': '/var/spool/cwl',
'output_ttl': 0,
'container_image': '99999999999999999999999999999993+99',
'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_run(self, list_images_in_arv, mockcollection,
mockcollectionreader):
arv_docker_clear_cache()
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.api.collections().list().execute.return_value = {
"items": [{
"uuid":
"zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash":
"99999999999999999999999999999993+99"
}]
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
runner.secret_store = cwltool.secrets.SecretStore()
loadingContext, runtimeContext = self.helper(runner)
runner.fs_access = runtimeContext.make_fs_access(
runtimeContext.basedir)
tool, metadata = loadingContext.loader.resolve_ref(
"tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockc = mock.MagicMock()
mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(
mockc, *args, **kwargs)
mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(
mock.MagicMock(), "token.txt")
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
next(it).run(runtimeContext)
next(it).run(runtimeContext)
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = StripYAMLComments(f.read()).rstrip()
runner.api.container_requests(
).create.assert_called_with(body=JsonDiffMatcher({
"command": [
"cwltool", "--no-container", "--move-outputs",
"--preserve-entire-environment", "workflow.cwl#main",
"cwl.input.yml"
],
"container_image":
"99999999999999999999999999999993+99",
"cwd":
"/var/spool/cwl",
"environment": {
"HOME": "/var/spool/cwl",
"TMPDIR": "/tmp"
},
"mounts": {
"/keep/99999999999999999999999999999999+118": {
"kind": "collection",
"portable_data_hash":
"99999999999999999999999999999999+118"
},
"/tmp": {
"capacity": 1073741824,
"kind": "tmp"
},
"/var/spool/cwl": {
"capacity": 1073741824,
"kind": "tmp"
},
"/var/spool/cwl/cwl.input.yml": {
"kind": "collection",
"path": "cwl.input.yml",
"portable_data_hash": "99999999999999999999999999999996+99"
},
"/var/spool/cwl/workflow.cwl": {
"kind": "collection",
"path": "workflow.cwl",
"portable_data_hash": "99999999999999999999999999999996+99"
},
"stdout": {
"kind": "file",
"path": "/var/spool/cwl/cwl.output.json"
}
},
"name":
"scatterstep",
"output_name":
"Output for step scatterstep",
"output_path":
"/var/spool/cwl",
"output_ttl":
0,
"priority":
500,
"properties": {},
"runtime_constraints": {
"ram": 1073741824,
"vcpus": 1
},
"scheduling_parameters": {},
"secret_mounts": {},
"state":
"Committed",
"use_existing":
True
}))
mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
mockc.open().__enter__().write.assert_has_calls([
mock.call('''{
"fileblub": {
"basename": "token.txt",
"class": "File",
"location": "/keep/99999999999999999999999999999999+118/token.txt",
"size": 0
},
"sleeptime": 5
}''')
])
def test_run(self, keepdocker):
for enable_reuse in (True, False):
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"
})
loadingContext, runtimeContext = self.helper(runner, enable_reuse)
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_'+str(enable_reuse),
'runtime_constraints': {
'vcpus': 1,
'ram': 1073741824
},
'use_existing': enable_reuse,
'priority': 500,
'mounts': {
'/tmp': {'kind': 'tmp',
"capacity": 1073741824
},
'/var/spool/cwl': {'kind': 'tmp',
"capacity": 1073741824 }
},
'state': 'Committed',
'output_name': 'Output for step test_run_'+str(enable_reuse),
'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': {}
}))
