def test_done(self, col):
api = mock.MagicMock()
runner = mock.MagicMock()
runner.api = api
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
col().open.return_value = []
api.collections().list().execute.side_effect = ({
"items": []
}, {
"items": [{
"manifest_text": "XYZ"
}]
})
arvjob = arvados_cwl.ArvadosContainer(runner)
arvjob.name = "testjob"
arvjob.builder = mock.MagicMock()
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
arvjob.successCodes = [0]
arvjob.outdir = "/var/spool/cwl"
arvjob.done({
"state": "Complete",
"output": "99999999999999999999999999999993+99",
"log": "99999999999999999999999999999994+99",
"uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
"exit_code": 0
})
api.collections().list.assert_has_calls([
mock.call(),
mock.call(
filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
[
'portable_data_hash', '=',
'99999999999999999999999999999993+99'
], ['name', '=', 'Output 9999999 of testjob']]),
mock.call().execute(num_retries=0),
mock.call(limit=1,
filters=[[
'portable_data_hash', '=',
'99999999999999999999999999999993+99'
]],
select=['manifest_text']),
mock.call().execute(num_retries=0)
])
api.collections().create.assert_called_with(
ensure_unique_name=True,
body={
'portable_data_hash': '99999999999999999999999999999993+99',
'manifest_text': 'XYZ',
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'name': 'Output 9999999 of testjob'
})
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")
def test_done(self, col):
api = mock.MagicMock()
runner = mock.MagicMock()
runner.api = api
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
runner.api.containers().get().execute.return_value = {"state":"Complete",
"output": "abc+123",
"exit_code": 0}
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"
})
self.assertFalse(api.collections().create.called)
self.assertFalse(runner.runtime_status_error.called)
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")
def test_done(self, col):
api = mock.MagicMock()
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
runner.api.containers().get().execute.return_value = {
"state": "Complete",
"output": "abc+123",
"exit_code": 0
}
col().open.return_value = []
arvjob = arvados_cwl.ArvadosContainer(runner)
arvjob.name = "testjob"
arvjob.builder = mock.MagicMock()
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"
})
self.assertFalse(api.collections().create.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")
def test_done_use_existing_collection(self, col):
api = mock.MagicMock()
runner = mock.MagicMock()
runner.api = api
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
col().open.return_value = []
api.collections().list().execute.side_effect = ({
"items": [{
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"
}]
}, )
arvjob = arvados_cwl.ArvadosContainer(runner)
arvjob.name = "testjob"
arvjob.builder = mock.MagicMock()
arvjob.output_callback = mock.MagicMock()
arvjob.collect_outputs = mock.MagicMock()
arvjob.successCodes = [0]
arvjob.outdir = "/var/spool/cwl"
arvjob.done({
"state": "Complete",
"output": "99999999999999999999999999999993+99",
"log": "99999999999999999999999999999994+99",
"uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
"exit_code": 0
})
api.collections().list.assert_has_calls([
mock.call(),
mock.call(
filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
[
'portable_data_hash', '=',
'99999999999999999999999999999993+99'
], ['name', '=', 'Output 9999999 of testjob']]),
mock.call().execute(num_retries=0)
])
self.assertFalse(api.collections().create.called)
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")
