#
# SPDX-License-Identifier: Apache-2.0
+from builtins import str
+from builtins import object
+
import arvados_cwl
import arvados_cwl.context
+import arvados_cwl.util
from arvados_cwl.arvdocker import arv_docker_clear_cache
+import copy
+import arvados.config
import logging
import mock
import unittest
import os
-import datetime
import functools
import cwltool.process
import cwltool.secrets
from schema_salad.ref_resolver import Loader
from schema_salad.sourceline import cmap
-from .matcher import JsonDiffMatcher
+from .matcher import JsonDiffMatcher, StripYAMLComments
+from .mock_discovery import get_rootDesc
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
-class MockDateTime(datetime.datetime):
- @classmethod
- def now(cls):
- return datetime.datetime(2018, 1, 1, 0, 0, 0, 0)
+class CollectionMock(object):
+ def __init__(self, vwdmock, *args, **kwargs):
+ self.vwdmock = vwdmock
+ self.count = 0
+
+ def open(self, *args, **kwargs):
+ self.count += 1
+ return self.vwdmock.open(*args, **kwargs)
+
+ def copy(self, *args, **kwargs):
+ self.count += 1
+ self.vwdmock.copy(*args, **kwargs)
+
+ def save_new(self, *args, **kwargs):
+ pass
+
+ def __len__(self):
+ return self.count
+
+ def portable_data_hash(self):
+ if self.count == 0:
+ return arvados.config.EMPTY_BLOCK_LOCATOR
+ else:
+ return "99999999999999999999999999999996+99"
-datetime.datetime = MockDateTime
class TestContainer(unittest.TestCase):
def helper(self, runner, enable_reuse=True):
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
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": "v1.0"}})
+ "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}})
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
"basedir": "",
"make_fs_access": make_fs_access,
"tmpdir": "/tmp",
"enable_reuse": enable_reuse,
- "priority": 500})
+ "priority": 500,
+ "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ })
return loadingContext, runtimeContext
+ # Helper function to set up the ArvCwlExecutor to use the containers api
+ # and test that the RuntimeStatusLoggingHandler is set up correctly
+ 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
+ self.assertFalse(gcc_mock.called)
+ runner = arvados_cwl.ArvCwlExecutor(api)
+ self.assertEqual(runner.work_api, 'containers')
+ root_logger = logging.getLogger('')
+ handlerClasses = [h.__class__ for h in root_logger.handlers]
+ self.assertTrue(arvados_cwl.RuntimeStatusLoggingHandler in handlerClasses)
+ return runner
+
# 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")
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()
"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': 'arvados/jobs',
+ 'container_image': '99999999999999999999999999999993+99',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
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()
"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': 'arvados/jobs',
+ 'container_image': '99999999999999999999999999999993+99',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {
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()
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"
+ collection_mock.side_effect = lambda *args, **kwargs: CollectionMock(vwdmock, *args, **kwargs)
tool = cmap({
"inputs": [],
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('.', '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)])
}
},
'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': 'arvados/jobs',
+ 'container_image': '99999999999999999999999999999993+99',
'command': ['ls'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {
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()
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")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
tool = cmap({
"inputs": [],
},
},
'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',
+ 'container_image': '99999999999999999999999999999993+99',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
runner = mock.MagicMock()
runner.api = api
- runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
col().open.return_value = []
+ loadingContext, runtimeContext = self.helper(runner)
+
arvjob = arvados_cwl.ArvadosContainer(runner,
+ runtimeContext,
mock.MagicMock(),
{},
None,
})
self.assertFalse(api.collections().create.called)
+ self.assertFalse(runner.runtime_status_error.called)
- arvjob.collect_outputs.assert_called_with("keep:abc+123")
+ arvjob.collect_outputs.assert_called_with("keep:abc+123", 0)
arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
runner.add_intermediate_output.assert_called_with("zzzzz-4zz18-zzzzzzzzzzzzzz2")
+ # Test to make sure we dont call runtime_status_update if we already did
+ # some where higher up in the call stack
+ @mock.patch("arvados_cwl.util.get_current_container")
+ def test_recursive_runtime_status_update(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
+ # so try and log again!
+ gcc_mock.side_effect = lambda *args: root_logger.error("Second Error")
+ try:
+ root_logger.error("First Error")
+ except RuntimeError:
+ self.fail("RuntimeStatusLoggingHandler should not be called recursively")
+
+ @mock.patch("arvados_cwl.ArvCwlExecutor.runtime_status_update")
+ @mock.patch("arvados_cwl.util.get_current_container")
+ @mock.patch("arvados.collection.CollectionReader")
+ @mock.patch("arvados.collection.Collection")
+ def test_child_failure(self, col, reader, gcc_mock, rts_mock):
+ runner = self.setup_and_test_container_executor_and_logging(gcc_mock)
+
+ gcc_mock.return_value = {"uuid" : "zzzzz-dz642-zzzzzzzzzzzzzzz"}
+ self.assertTrue(gcc_mock.called)
+
+ runner.num_retries = 0
+ runner.ignore_docker_for_reuse = False
+ runner.intermediate_output_ttl = 0
+ runner.secret_store = cwltool.secrets.SecretStore()
+ runner.label = mock.MagicMock()
+ runner.label.return_value = '[container testjob]'
+
+ runner.api.containers().get().execute.return_value = {
+ "state":"Complete",
+ "output": "abc+123",
+ "exit_code": 1,
+ "log": "def+234"
+ }
+
+ col().open.return_value = []
+
+ loadingContext, runtimeContext = self.helper(runner)
+
+ arvjob = arvados_cwl.ArvadosContainer(runner,
+ runtimeContext,
+ mock.MagicMock(),
+ {},
+ None,
+ [],
+ [],
+ "testjob")
+ arvjob.output_callback = mock.MagicMock()
+ arvjob.collect_outputs = mock.MagicMock()
+ arvjob.successCodes = [0]
+ arvjob.outdir = "/var/spool/cwl"
+ arvjob.output_ttl = 3600
+ arvjob.collect_outputs.return_value = {"out": "stuff"}
+
+ arvjob.done({
+ "state": "Final",
+ "log_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
+ "output_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
+ "uuid": "zzzzz-xvhdp-zzzzzzzzzzzzzzz",
+ "container_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "modified_at": "2017-05-26T12:01:22Z"
+ })
+
+ rts_mock.assert_called_with(
+ 'error',
+ 'arvados.cwl-runner: [container testjob] (zzzzz-xvhdp-zzzzzzzzzzzzzzz) error log:',
+ ' ** log is empty **'
+ )
+ arvjob.output_callback.assert_called_with({"out": "stuff"}, "permanentFail")
+
# 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")
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"}
+ "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")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
tool = cmap({
"inputs": [
"p1": {
"class": "Directory",
"location": "keep:99999999999999999999999999999994+44",
+ "http://arvados.org/cwl#collectionUUID": "zzzzz-4zz18-zzzzzzzzzzzzzzz",
"listing": [
{
"class": "File",
'mounts': {
"/keep/99999999999999999999999999999994+44": {
"kind": "collection",
- "portable_data_hash": "99999999999999999999999999999994+44"
+ "portable_data_hash": "99999999999999999999999999999994+44",
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz"
},
'/tmp': {'kind': 'tmp',
"capacity": 1073741824 },
"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': 'arvados/jobs',
+ 'container_image': '99999999999999999999999999999994+99',
'command': ['ls', '/var/spool/cwl'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
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()
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")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
tool = cmap({"arguments": ["md5sum", "example.conf"],
"class": "CommandLineTool",
"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': 'arvados/jobs',
+ 'container_image': '99999999999999999999999999999993+99',
'command': ['md5sum', 'example.conf'],
'cwd': '/var/spool/cwl',
'scheduling_parameters': {},
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()
"class": "CommandLineTool",
"hints": [
{
- "class": "http://commonwl.org/cwltool#TimeLimit",
+ "class": "ToolTimeLimit",
"timelimit": 42
}
]
self.assertEqual(42, kwargs['body']['scheduling_parameters'].get('max_run_time'))
- def test_get_intermediate_collection_info(self):
- arvrunner = mock.MagicMock()
- arvrunner.intermediate_output_ttl = 60
- arvrunner.api.containers().current().execute.return_value = {"uuid" : "zzzzz-8i9sb-zzzzzzzzzzzzzzz"}
+class TestWorkflow(unittest.TestCase):
+ def helper(self, runner, enable_reuse=True):
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+
+ document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=make_fs_access(""))
+ document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
+ document_loader.fetch_text = document_loader.fetcher.fetch_text
+ document_loader.check_exists = document_loader.fetcher.check_exists
+
+ loadingContext = arvados_cwl.context.ArvLoadingContext(
+ {"avsc_names": avsc_names,
+ "basedir": "",
+ "make_fs_access": make_fs_access,
+ "loader": document_loader,
+ "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
+ "construct_tool_object": runner.arv_make_tool})
+ runtimeContext = arvados_cwl.context.ArvRuntimeContext(
+ {"work_api": "containers",
+ "basedir": "",
+ "name": "test_run_wf_"+str(enable_reuse),
+ "make_fs_access": make_fs_access,
+ "tmpdir": "/tmp",
+ "enable_reuse": enable_reuse,
+ "priority": 500})
+
+ return loadingContext, runtimeContext
+
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.collection.CollectionReader")
+ @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()
+ 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
+}''')])
+
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.collection.CollectionReader")
+ @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()
+ 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")
- container = arvados_cwl.ArvadosContainer(arvrunner)
+ mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mock.MagicMock(), *args, **kwargs)
- info = container._get_intermediate_collection_info()
+ 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_default_work_api(self):
+ arvados_cwl.add_arv_hints()
- self.assertEqual(info["name"], "Intermediate collection")
- self.assertEqual(info["trash_at"], datetime.datetime(2018, 1, 1, 0, 1))
- self.assertEqual(info["properties"], {"type" : "Intermediate", "container" : "zzzzz-8i9sb-zzzzzzzzzzzzzzz"})
+ 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