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.sourceline import cmap
from .matcher import JsonDiffMatcher
+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):
"make_fs_access": make_fs_access,
"tmpdir": "/tmp",
"enable_reuse": enable_reuse,
- "priority": 500})
+ "priority": 500,
+ "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ })
return loadingContext, runtimeContext
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": [],
}
},
'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()
},
},
'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.output_callback.assert_called_with({"out": "stuff"}, "success")
runner.add_intermediate_output.assert_called_with("zzzzz-4zz18-zzzzzzzzzzzzzz2")
+ @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):
+ api = mock.MagicMock()
+ api._rootDesc = copy.deepcopy(get_rootDesc())
+ del api._rootDesc.get('resources')['jobs']['methods']['create']
+
+ # Set up runner with mocked runtime_status_update()
+ self.assertFalse(gcc_mock.called)
+ runtime_status_update = mock.MagicMock()
+ arvados_cwl.ArvCwlExecutor.runtime_status_update = runtime_status_update
+ runner = arvados_cwl.ArvCwlExecutor(api)
+ self.assertEqual(runner.work_api, 'containers')
+
+ # Make sure ArvCwlExecutor thinks it's running inside a container so it
+ # adds the logging handler that will call runtime_status_update() mock
+ gcc_mock.return_value = {"uuid" : "zzzzz-dz642-zzzzzzzzzzzzzzz"}
+ self.assertTrue(gcc_mock.called)
+ root_logger = logging.getLogger('')
+ handlerClasses = [h.__class__ for h in root_logger.handlers]
+ self.assertTrue(arvados_cwl.RuntimeStatusLoggingHandler in handlerClasses)
+
+ 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"
+ })
+
+ runtime_status_update.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")
"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()
"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()
_, kwargs = runner.api.container_requests().create.call_args
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"}
-
- container = arvados_cwl.ArvadosContainer(arvrunner)
-
- info = container._get_intermediate_collection_info()
-
- 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"})
projects / arvados.git / blobdiff