import functools
import cwltool.process
import cwltool.secrets
+from cwltool.update import INTERNAL_VERSION
from schema_salad.ref_resolver import Loader
from schema_salad.sourceline import cmap
def setUp(self):
cwltool.process._names = set()
+ arv_docker_clear_cache()
def helper(self, runner, enable_reuse=True):
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION)
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
"basedir": "",
"make_fs_access": make_fs_access,
"loader": Loader({}),
- "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}})
+ "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}})
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
"basedir": "",
def setup_and_test_container_executor_and_logging(self, gcc_mock) :
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
- del api._rootDesc.get('resources')['jobs']['methods']['create']
# Make sure ArvCwlExecutor thinks it's running inside a container so it
# adds the logging handler that will call runtime_status_update() mock
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
"id": "#",
- "class": "CommandLineTool"
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner, enable_reuse)
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}))
# The test passes some fields in builder.resources
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
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()
+ runner.api._rootDesc = {"revision": "20210628"}
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
}],
"baseCommand": "ls",
"id": "#",
- "class": "CommandLineTool"
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner)
'partitions': ['blurb']
},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}
call_body = call_kwargs.get('body', None)
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
@mock.patch("arvados.collection.Collection")
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()
+ runner.api._rootDesc = {"revision": "20210628"}
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
}],
"baseCommand": "ls",
"id": "#",
- "class": "CommandLineTool"
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner)
'scheduling_parameters': {
},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}
call_body = call_kwargs.get('body', None)
# Test redirecting stdin/stdout/stderr
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
def test_redirects(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()
+ runner.api._rootDesc = {"revision": "20210628"}
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")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION)
tool = cmap({
"inputs": [],
"stdin": "/keep/99999999999999999999999999999996+99/file.txt",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
"id": "#",
- "class": "CommandLineTool"
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner)
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}))
@mock.patch("arvados.collection.Collection")
except RuntimeError:
self.fail("RuntimeStatusLoggingHandler should not be called recursively")
+
+ # Test to make sure that an exception raised from
+ # get_current_container doesn't cause the logger to raise an
+ # exception
+ @mock.patch("arvados_cwl.util.get_current_container")
+ def test_runtime_status_get_current_container_exception(self, gcc_mock):
+ self.setup_and_test_container_executor_and_logging(gcc_mock)
+ root_logger = logging.getLogger('')
+
+ # get_current_container is invoked when we call
+ # runtime_status_update, it is going to also raise an
+ # exception.
+ gcc_mock.side_effect = Exception("Second Error")
+ try:
+ root_logger.error("First Error")
+ except Exception:
+ self.fail("Exception in logger should not propagate")
+ self.assertTrue(gcc_mock.called)
+
@mock.patch("arvados_cwl.ArvCwlExecutor.runtime_status_update")
@mock.patch("arvados_cwl.util.get_current_container")
@mock.patch("arvados.collection.CollectionReader")
# 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_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()
+ runner.api._rootDesc = {"revision": "20210628"}
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
"id": "#",
- "class": "CommandLineTool"
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner)
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
'properties': {},
- 'secret_mounts': {}
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
}))
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
def test_secrets(self, keepdocker):
- arv_docker_clear_cache()
-
runner = mock.MagicMock()
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
tool = cmap({"arguments": ["md5sum", "example.conf"],
- "class": "CommandLineTool",
+ "class": "org.w3id.cwl.cwl.CommandLineTool",
"hints": [
{
"class": "http://commonwl.org/cwltool#Secrets",
"content": "username: user\npassword: blorp\n",
"kind": "text"
}
- }
+ },
+ 'output_storage_classes': ["default"]
}))
# The test passes no builder.resources
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
def test_timelimit(self, keepdocker):
- arv_docker_clear_cache()
-
runner = mock.MagicMock()
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
runner.api.collections().get().execute.return_value = {
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
"id": "#",
- "class": "CommandLineTool",
+ "class": "org.w3id.cwl.cwl.CommandLineTool",
"hints": [
{
"class": "ToolTimeLimit",
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()
+ runner.api._rootDesc = {"revision": "20210628"}
+
+ 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": "org.w3id.cwl.cwl.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"]
+ }))
+
+
+ # 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_process_properties(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()
+ runner.api._rootDesc = {"revision": "20210628"}
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ runner.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99"}
+
+ tool = cmap({
+ "inputs": [
+ {"id": "x", "type": "string"}],
+ "outputs": [],
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+ "id": "#",
+ "class": "org.w3id.cwl.cwl.CommandLineTool",
+ "hints": [
+ {
+ "class": "http://arvados.org/cwl#ProcessProperties",
+ "processProperties": [
+ {"propertyName": "foo",
+ "propertyValue": "bar"},
+ {"propertyName": "baz",
+ "propertyValue": "$(inputs.x)"},
+ {"propertyName": "quux",
+ "propertyValue": {
+ "q1": 1,
+ "q2": 2
+ }
+ }
+ ],
+ }
+ ]
+ })
+
+ loadingContext, runtimeContext = self.helper(runner, True)
+
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool.formatgraph = None
+
+ for j in arvtool.job({"x": "blorp"}, 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': {
+ "baz": "blorp",
+ "foo": "bar",
+ "quux": {
+ "q1": 1,
+ "q2": 2
+ }
+ },
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
+ }))
+
+
class TestWorkflow(unittest.TestCase):
def setUp(self):
cwltool.process._names = set()
+ arv_docker_clear_cache()
def helper(self, runner, enable_reuse=True):
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
"basedir": "",
"make_fs_access": make_fs_access,
"loader": document_loader,
- "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
+ "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
"construct_tool_object": runner.arv_make_tool})
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
@mock.patch("arvados.collection.Collection")
@mock.patch('arvados.commands.keepdocker.list_images_in_arv')
def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader):
- arv_docker_clear_cache()
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
loadingContext, runtimeContext = self.helper(runner)
runner.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
+ mockcollectionreader().exists.return_value = True
+
tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
"--no-container",
"--move-outputs",
"--preserve-entire-environment",
- "workflow.cwl#main",
+ "workflow.cwl",
"cwl.input.yml"
],
"container_image": "99999999999999999999999999999993+99",
"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(
@mock.patch("arvados.collection.Collection")
@mock.patch('arvados.commands.keepdocker.list_images_in_arv')
def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader):
- arv_docker_clear_cache()
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
u'--no-container',
u'--move-outputs',
u'--preserve-entire-environment',
- u'workflow.cwl#main',
+ u'workflow.cwl',
u'cwl.input.yml'
],
'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):
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
- del api._rootDesc.get('resources')['jobs']['methods']['create']
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
projects / arvados.git / blobdiff