def test_parent_children__fail(self):
parent_state = create_state_from_ee2(BATCH_PARENT)
child_states = [create_state_from_ee2(job_id) for job_id in BATCH_CHILDREN]
with self.assertRaisesRegex(
ValueError, "Must supply children when setting children of batch job parent"
):
Job(parent_state)
child_jobs = [Job(child_state) for child_state in child_states]
with self.assertRaisesRegex(ValueError, CHILD_ID_MISMATCH):
Job(
parent_state,
children=child_jobs[1:],
)
with self.assertRaisesRegex(ValueError, CHILD_ID_MISMATCH):
Job(
parent_state,
children=child_jobs * 2,
)
with self.assertRaisesRegex(ValueError, CHILD_ID_MISMATCH):
Job(
parent_state,
children=child_jobs + [create_job_from_ee2(JOB_COMPLETED)],
)
def test_parameters__param_fetch_fail(self):
"""
test failure to retrieve job params data
"""
job_state = get_test_job(JOB_TERMINATED)
del job_state["job_input"]["params"]
job = Job(job_state)
self.assertEqual(job.params, JOB_ATTR_DEFAULTS["params"])
with self.assertRaisesRegex(Exception, "Unable to fetch parameters for job"):
job.parameters()
def test_query_job_state(self):
for job_id in ALL_JOBS:
exp = create_state_from_ee2(
job_id, exclude_fields=JOB_INIT_EXCLUDED_JOB_STATE_FIELDS
)
got = Job.query_ee2_state(job_id, init=True)
self.assertEqual(exp, got)
exp = create_state_from_ee2(
job_id, exclude_fields=EXCLUDED_JOB_STATE_FIELDS
)
got = Job.query_ee2_state(job_id, init=False)
self.assertEqual(exp, got)
def test_parameters(self):
"""
test that a job returns the correct parameters
"""
job_state = get_test_job(JOB_COMPLETED)
job_params = job_state.get("job_input", {}).get("params", None)
self.assertIsNotNone(job_params)
job = Job(job_state)
self.assertIsNotNone(job.params)
with assert_obj_method_called(MockClients, "get_job_params", call_status=False):
params = job.parameters()
self.assertIsNotNone(params)
self.assertEqual(params, job_params)
def test_query_job_states(self):
states = Job.query_ee2_states(ALL_JOBS, init=True)
for job_id, got in states.items():
exp = create_state_from_ee2(
job_id, exclude_fields=JOB_INIT_EXCLUDED_JOB_STATE_FIELDS
)
self.assertEqual(exp, got)
states = Job.query_ee2_states(ALL_JOBS, init=False)
for job_id, got in states.items():
exp = create_state_from_ee2(
job_id, exclude_fields=EXCLUDED_JOB_STATE_FIELDS
)
self.assertEqual(exp, got)
def test_parameters__param_fetch_ok(self):
"""
test that a job can successfully retrieve parameters from ee2
if they do not exist
"""
job_state = get_test_job(JOB_CREATED)
job_params = job_state.get("job_input", {}).get("params", None)
self.assertIsNotNone(job_params)
# delete the job params from the input
del job_state["job_input"]["params"]
job = Job(job_state)
self.assertEqual(job.params, JOB_ATTR_DEFAULTS["params"])
params = job.parameters()
self.assertEqual(params, job_params)
def phony_job():
return Job.from_state('phony_job', {
'params': [],
'service_ver': '0.0.0'
},
'kbasetest',
'NarrativeTest/test_editor',
tag='dev')
def test_job_init__from_job_ids(self):
job_ids = ALL_JOBS.copy()
job_ids.remove(BATCH_PARENT)
with mock.patch(CLIENTS, get_mock_client):
jobs = Job.from_job_ids(job_ids, return_list=False)
for job_id, job in jobs.items():
self.check_job_attrs(job, job_id)
def get_batch_family_jobs(return_list=False):
"""
As invoked in appmanager's run_app_batch, i.e.,
with from_job_id(s)
"""
child_jobs = Job.from_job_ids(BATCH_CHILDREN, return_list=True)
batch_job = Job.from_job_id(BATCH_PARENT, children=child_jobs)
if return_list:
return [batch_job] + child_jobs
else:
return {
BATCH_PARENT: batch_job,
**{
child_id: child_job
for child_id, child_job in zip(BATCH_CHILDREN, child_jobs)
},
}
def test_parent_children__ok(self):
child_jobs = [Job.from_job_id(job_id) for job_id in BATCH_CHILDREN]
parent_job = Job(
create_state_from_ee2(BATCH_PARENT),
children=child_jobs,
)
self.assertFalse(parent_job.was_terminal())
# Make all child jobs completed
with mock.patch.object(
MockClients,
"check_job",
mock.Mock(return_value={"status": COMPLETED_STATUS}),
):
for child_job in child_jobs:
child_job.state(force_refresh=True)
self.assertTrue(parent_job.was_terminal())
def test_job_init__from_job_id(self):
"""
test job initialisation, as is done by run_app
"""
for job_id in ALL_JOBS:
if job_id == BATCH_PARENT:
continue
with mock.patch(CLIENTS, get_mock_client):
job = Job.from_job_id(job_id)
self.check_job_attrs(job, job_id)
def phony_job():
return Job.from_state(
"phony_job",
{
"params": [],
"service_ver": "0.0.0"
},
"kbasetest",
"NarrativeTest/test_editor",
tag="dev",
)
def _mocked_job(self, with_version=True, with_cell_id=True, with_run_id=True, with_token_id=True):
kwargs = dict()
if with_version:
kwargs["app_version"] = self.app_version
if with_cell_id:
kwargs["cell_id"] = self.cell_id
if with_run_id:
kwargs["run_id"] = self.run_id
if with_token_id:
kwargs["token_id"] = self.token_id
job = Job(self.job_id, self.app_id, self.inputs, self.owner, tag=self.app_tag, **kwargs)
return job
def test_job_from_state(self):
job_info = {
"params": self.inputs,
"service_ver": self.app_version
}
job = Job.from_state(self.job_id, job_info, self.owner, self.app_id, tag=self.app_tag,
cell_id=self.cell_id, run_id=self.run_id, token_id=self.token_id)
self.assertEqual(job.job_id, self.job_id)
self.assertEqual(job.app_id, self.app_id)
self.assertEqual(job.inputs, self.inputs)
self.assertEqual(job.owner, self.owner)
self.assertEqual(job.tag, self.app_tag)
self.assertEqual(job.app_version, self.app_version)
self.assertEqual(job.cell_id, self.cell_id)
self.assertEqual(job.run_id, self.run_id)
self.assertEqual(job.token_id, self.token_id)
def test_job_from_state(self):
job_info = {
"params": self.inputs,
"service_ver": self.app_version
}
job = Job.from_state(self.job_id, job_info, self.owner, self.app_id, tag=self.app_tag,
cell_id=self.cell_id, run_id=self.run_id, token_id=self.token_id)
self.assertEqual(job.job_id, self.job_id)
self.assertEqual(job.app_id, self.app_id)
self.assertEqual(job.inputs, self.inputs)
self.assertEqual(job.owner, self.owner)
self.assertEqual(job.tag, self.app_tag)
self.assertEqual(job.app_version, self.app_version)
self.assertEqual(job.cell_id, self.cell_id)
self.assertEqual(job.run_id, self.run_id)
self.assertEqual(job.token_id, self.token_id)
def test_job_init__extra_state(self):
"""
test job initialisation as is done by run_legacy_batch_app
"""
app_id = "kb_BatchApp/run_batch"
extra_data = {
"batch_app": app_id,
"batch_tag": None,
"batch_size": 300,
}
for job_id in ALL_JOBS:
if job_id == BATCH_PARENT:
continue
with mock.patch(CLIENTS, get_mock_client):
batch_job = Job.from_job_id(
job_id,
extra_data=extra_data,
)
self.check_job_attrs(batch_job, job_id, {"extra_data": extra_data})
def test_job_from_state__custom(self):
"""
test job initialisation with defaults being filled in
TODO do a non-default?
"""
params = [
{
"import_type": "FASTQ/FASTA",
"name": "small.forward.fq",
}
]
test_job = {
"user": "******",
"job_input": {
"params": params,
"service_ver": "42",
"app_id": "This/app",
},
"job_id": "0123456789abcdef",
}
expected = {
"app_id": "This/app",
"app_version": "42",
"batch_id": JOB_ATTR_DEFAULTS["batch_id"],
"cell_id": JOB_ATTR_DEFAULTS["cell_id"],
"extra_data": None,
"job_id": "0123456789abcdef",
"params": params,
"run_id": JOB_ATTR_DEFAULTS["run_id"],
"tag": JOB_ATTR_DEFAULTS["tag"],
"user": "******",
}
job = Job(test_job)
self.check_job_attrs_custom(job, expected)
def test_show_output_widget(self, mock_method):
mock_method.return_value = True
job = Job(get_test_job(JOB_COMPLETED))
self.assertTrue(job.show_output_widget())
mock_method.assert_called_once()
def test_job_init__error_no_job_id(self):
with self.assertRaisesRegex(
ValueError, "Cannot create a job without a job ID!"
):
Job({"params": {}, "app_id": "this/that"})
def test_show_output_widget__incomplete_state(self):
job = Job(get_test_job(JOB_CREATED))
self.assertRegex(
job.show_output_widget(), "Job is incomplete! It has status 'created'"
)
def create_job_from_ee2(job_id, extra_data=None, children=None):
state = get_test_job(job_id)
job = Job(state, extra_data=extra_data, children=children)
return job
def phony_job():
return Job.from_state('phony_job',
{'params': [], 'service_ver': '0.0.0'},
'kbasetest',
'NarrativeTest/test_editor',
tag='dev')
