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rename funcs/params
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@n1mus
n1mus committed May 19, 2022
1 parent fcf4be8 commit 9020680
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Showing 3 changed files with 33 additions and 33 deletions.
36 changes: 18 additions & 18 deletions src/biokbase/narrative/jobs/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ def __init__(self, ee2_state, extra_data=None, children=None):
if ee2_state.get("job_id") is None:
raise ValueError("Cannot create a job without a job ID!")

self._update_state(ee2_state)
self.update_state(ee2_state)
self.extra_data = extra_data

# verify parent-children relationship
Expand All @@ -130,9 +130,9 @@ def from_job_ids(cls, job_ids, return_list=True):
return jobs

@staticmethod
def _trim_ee2_state(state: dict, exclude: list) -> None:
if exclude:
for field in exclude:
def _trim_ee2_state(state: dict, exclude_fields: list) -> None:
if exclude_fields:
for field in exclude_fields:
if field in state:
del state[field]

Expand Down Expand Up @@ -241,7 +241,7 @@ def __getattr__(self, name):

def __setattr__(self, name, value):
if name in STATE_ATTRS: # TODO are/should these assignments be used?
self._update_state({name: value})
self.update_state({name: value})
else:
object.__setattr__(self, name, value)

Expand Down Expand Up @@ -308,7 +308,7 @@ def parameters(self):
f"Unable to fetch parameters for job {self.job_id} - {e}"
)

def _update_state(self, state: dict, ts: int = None) -> None:
def update_state(self, state: dict, ts: int = None) -> None:
"""
Given a state data structure (as emitted by ee2), update the stored state in the job object
All updates to the job state should go through here to keep the last_updated field accurate
Expand All @@ -320,7 +320,7 @@ def _update_state(self, state: dict, ts: int = None) -> None:
if self._acc_state:
if "job_id" in state and state["job_id"] != self.job_id:
raise ValueError(
f"Job ID mismatch in _update_state: job ID: {self.job_id}; state ID: {state['job_id']}"
f"Job ID mismatch in update_state: job ID: {self.job_id}; state ID: {state['job_id']}"
)

# Check if there would be no change in updating
Expand All @@ -337,28 +337,28 @@ def _update_state(self, state: dict, ts: int = None) -> None:

self.last_updated = time_ns() if ts is None else ts

def refresh_state(self, force_refresh=False, exclude=JOB_INIT_EXCLUDED_JOB_STATE_FIELDS):
def refresh_state(self, force_refresh=False, exclude_fields=JOB_INIT_EXCLUDED_JOB_STATE_FIELDS):
"""
Queries the job service to see the state of the current job.
"""

if force_refresh or not self.was_terminal():
state = self.query_ee2_state(self.job_id, init=False)
self._update_state(state)
self.update_state(state)

return self.current_state(exclude)
return self.cached_state(exclude_fields)

def current_state(self, exclude=None):
def cached_state(self, exclude_fields=None):
"""Wrapper for self._acc_state"""
state = copy.deepcopy(self._acc_state)
self._trim_ee2_state(state, exclude)
self._trim_ee2_state(state, exclude_fields)
return state

def output_state(self, state=None, no_refresh=False) -> dict:
"""
:param state: Supplied when the state is queried beforehand from EE2 in bulk,
or when it is retrieved from a cache. If not supplied, must be
queried with self.refresh_state() or self.current_state()
queried with self.refresh_state() or self.cached_state()
:return: dict, with structure
{
Expand Down Expand Up @@ -411,10 +411,10 @@ def output_state(self, state=None, no_refresh=False) -> dict:
:rtype: dict
"""
if not state:
state = self.current_state() if no_refresh else self.refresh_state()
state = self.cached_state() if no_refresh else self.refresh_state()
else:
self._update_state(state)
state = self.current_state()
self.update_state(state)
state = self.cached_state()

if state is None:
return self._create_error_state(
Expand Down Expand Up @@ -464,8 +464,8 @@ def show_output_widget(self, state=None):
if not state:
state = self.refresh_state()
else:
self._update_state(state)
state = self.current_state()
self.update_state(state)
state = self.cached_state()

if state["status"] == COMPLETED_STATUS and "job_output" in state:
(output_widget, widget_params) = self._get_output_info(state)
Expand Down
2 changes: 1 addition & 1 deletion src/biokbase/narrative/jobs/jobmanager.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -318,7 +318,7 @@ def _construct_job_output_state_set(
# pre-emptively try a job state update
# so can mark the set of fetched (but also changed) states
# with a simultaneous timestamp
job._update_state(fetched_state, now)
job.update_state(fetched_state, now)
output_states[job_id] = job.output_state(fetched_state)
else:
# fetch the current state without updating it
Expand Down
28 changes: 14 additions & 14 deletions src/biokbase/narrative/tests/test_job.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -389,10 +389,10 @@ def test_job_update__no_state(self):

# should fail with error 'state must be a dict'
with self.assertRaisesRegex(TypeError, "state must be a dict"):
job._update_state(None)
job.update_state(None)
self.assertFalse(job.was_terminal())

job._update_state({})
job.update_state({})
self.assertFalse(job.was_terminal())

@mock.patch(CLIENTS, get_mock_client)
Expand All @@ -405,8 +405,8 @@ def test_job_update__invalid_job_id(self):
self.assertEqual(job.refresh_state(), expected)

# try to update it with the job state from a different job
with self.assertRaisesRegex(ValueError, "Job ID mismatch in _update_state"):
job._update_state(get_test_job(JOB_COMPLETED))
with self.assertRaisesRegex(ValueError, "Job ID mismatch in update_state"):
job.update_state(get_test_job(JOB_COMPLETED))

@mock.patch(CLIENTS, get_mock_client)
def test_job_update__last_updated__no_change(self):
Expand All @@ -418,22 +418,22 @@ def test_job_update__last_updated__no_change(self):
ee2_state = get_test_job(job_id)
job._acc_state = get_test_job(job_id)

job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

trim_ee2_state(ee2_state, JOB_INIT_EXCLUDED_JOB_STATE_FIELDS)
job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

trim_ee2_state(ee2_state, EXCLUDED_JOB_STATE_FIELDS)
job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

trim_ee2_state(ee2_state, OUTPUT_STATE_EXCLUDED_JOB_STATE_FIELDS)
job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

job._update_state({})
job.update_state({})
self.assertEqual(last_updated, job.last_updated)

# job has init ee2 state
Expand All @@ -442,18 +442,18 @@ def test_job_update__last_updated__no_change(self):
trim_ee2_state(ee2_state, JOB_INIT_EXCLUDED_JOB_STATE_FIELDS)
trim_ee2_state(job._acc_state, JOB_INIT_EXCLUDED_JOB_STATE_FIELDS)

job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

trim_ee2_state(ee2_state, EXCLUDED_JOB_STATE_FIELDS)
job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

trim_ee2_state(ee2_state, OUTPUT_STATE_EXCLUDED_JOB_STATE_FIELDS)
job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertEqual(last_updated, job.last_updated)

job._update_state({})
job.update_state({})
self.assertEqual(last_updated, job.last_updated)

@mock.patch(CLIENTS, get_mock_client)
Expand All @@ -467,7 +467,7 @@ def test_job_update__last_updated__change(self):
trim_ee2_state(job._acc_state, JOB_INIT_EXCLUDED_JOB_STATE_FIELDS)

ee2_state = get_test_job(job_id)
job._update_state(ee2_state)
job.update_state(ee2_state)
self.assertTrue(last_updated < job.last_updated)

@mock.patch(CLIENTS, get_mock_client)
Expand Down

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