def test_changing_algo_over_mqtt_with_wrong_type_is_okay() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = "0.0"
algo = DosingController(
"pid_turbidostat",
volume=1.0,
target_od=0.4,
duration=2 / 60,
unit=unit,
experiment=experiment,
)
assert algo.automation["automation_name"] == "pid_turbidostat"
assert algo.automation_name == "pid_turbidostat"
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/automation/set",
'{"automation_name": "pid_turbidostat", "duration": "60", "target_od": "1.0", "volume": "1.0"}',
)
time.sleep(
7
) # need to wait for all jobs to disconnect correctly and threads to join.
assert isinstance(algo.automation_job, PIDTurbidostat)
assert algo.automation_job.target_od == 1.0
algo.set_state(algo.DISCONNECTED)
def test_custom_class_will_register_and_run() -> None:
class NaiveTurbidostat(DosingAutomation):
automation_name = "naive_turbidostat"
published_settings = {
"target_od": {
"datatype": "float",
"settable": True,
"unit": "AU"
},
"duration": {
"datatype": "float",
"settable": True,
"unit": "min"
},
}
def __init__(self, target_od: float, **kwargs: Any) -> None:
super(NaiveTurbidostat, self).__init__(**kwargs)
self.target_od = target_od
def execute(self) -> None:
if self.latest_od > self.target_od:
self.execute_io_action(media_ml=1.0, waste_ml=1.0)
algo = DosingController(
"naive_turbidostat",
target_od=2.0,
duration=10,
unit=get_unit_name(),
experiment=get_latest_experiment_name(),
)
algo.set_state(algo.DISCONNECTED)
def test_changing_algo_over_mqtt_will_not_produce_two_dosing_jobs() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_fraction") as c:
c[experiment] = "0.0"
algo = DosingController(
"pid_turbidostat",
volume=1.0,
target_od=0.4,
duration=60,
unit=unit,
experiment=experiment,
)
assert algo.automation["automation_name"] == "pid_turbidostat"
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/automation/set",
'{"automation_name": "turbidostat", "duration": 60, "target_od": 1.0, "volume": 1.0, "skip_first_run": 1}',
)
time.sleep(
10
) # need to wait for all jobs to disconnect correctly and threads to join.
assert isinstance(algo.automation_job, Turbidostat)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/growth_rate",
'{"growth_rate": 1.0}',
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/od_filtered",
'{"od_filtered": 1.0}',
)
pause()
# note that we manually run, as we have skipped the first run in the json
algo.automation_job.run()
time.sleep(5)
assert algo.automation_job.media_throughput == 1.0
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_automation/target_od/set", 1.5)
pause()
pause()
assert algo.automation_job.target_od == 1.5
algo.set_state(algo.DISCONNECTED)
def test_execute_io_action() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = "0.0"
with DosingController("silent", unit=unit, experiment=experiment) as ca:
ca.automation_job.execute_io_action(media_ml=0.65,
alt_media_ml=0.35,
waste_ml=0.65 + 0.35)
pause()
assert ca.automation_job.media_throughput == 0.65
assert ca.automation_job.alt_media_throughput == 0.35
ca.automation_job.execute_io_action(media_ml=0.15,
alt_media_ml=0.15,
waste_ml=0.3)
pause()
assert ca.automation_job.media_throughput == 0.80
assert ca.automation_job.alt_media_throughput == 0.50
ca.automation_job.execute_io_action(media_ml=1.0,
alt_media_ml=0,
waste_ml=1)
pause()
assert ca.automation_job.media_throughput == 1.80
assert ca.automation_job.alt_media_throughput == 0.50
ca.automation_job.execute_io_action(media_ml=0.0,
alt_media_ml=1.0,
waste_ml=1)
pause()
assert ca.automation_job.media_throughput == 1.80
assert ca.automation_job.alt_media_throughput == 1.50
def test_changing_algo_over_mqtt_with_wrong_type_is_okay():
pubsub.publish(
f"pioreactor/{unit}/{experiment}/throughput_calculating/media_throughput",
None,
retain=True,
)
algo = DosingController(
"pid_turbidostat",
volume=1.0,
target_od=0.4,
duration=2 / 60,
unit=unit,
experiment=experiment,
)
assert algo.dosing_automation == "pid_turbidostat"
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/dosing_automation/set",
'{"dosing_automation": "pid_turbidostat", "duration": "60", "target_od": "1.0", "volume": "1.0"}',
)
time.sleep(
7
) # need to wait for all jobs to disconnect correctly and threads to join.
assert isinstance(algo.dosing_automation_job, PIDTurbidostat)
assert algo.dosing_automation_job.target_od == 1.0
def test_throughput_calculator_manual_set() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = str(1.0)
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = str(1.5)
with DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
pause()
assert algo.automation_job.media_throughput == 1.0
assert algo.automation_job.alt_media_throughput == 1.5
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_automation/alt_media_throughput/set",
0,
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_automation/media_throughput/set",
0)
pause()
pause()
assert algo.automation_job.media_throughput == 0
assert algo.automation_job.alt_media_throughput == 0
def test_changing_algo_over_mqtt_when_it_fails_will_rollback():
algo = DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
)
assert algo.dosing_automation == "turbidostat"
assert isinstance(algo.dosing_automation_job, Turbidostat)
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/dosing_automation/set",
'{"dosing_automation": "pid_morbidostat", "duration": 60}',
)
time.sleep(8)
assert algo.dosing_automation == "turbidostat"
assert isinstance(algo.dosing_automation_job, Turbidostat)
assert algo.dosing_automation_job.target_od == 1.0
algo.set_state("disconnected")
def test_changing_algo_over_mqtt_solo():
algo = DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
)
assert algo.dosing_automation == "turbidostat"
assert isinstance(algo.dosing_automation_job, Turbidostat)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/dosing_automation/set",
'{"dosing_automation": "pid_morbidostat", "duration": 60, "target_od": 1.0, "target_growth_rate": 0.07}',
)
time.sleep(8)
assert algo.dosing_automation == "pid_morbidostat"
assert isinstance(algo.dosing_automation_job, PIDMorbidostat)
assert algo.dosing_automation_job.target_growth_rate == 0.07
algo.set_state("disconnected")
def test_pause_in_dosing_control_also_pauses_automation() -> None:
algo = DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
)
pause()
pubsub.publish(f"pioreactor/{unit}/{experiment}/dosing_control/$state/set",
"sleeping")
pause()
assert algo.state == "sleeping"
assert algo.automation_job.state == "sleeping"
pubsub.publish(f"pioreactor/{unit}/{experiment}/dosing_control/$state/set",
"ready")
pause()
assert algo.state == "ready"
assert algo.automation_job.state == "ready"
algo.set_state(algo.DISCONNECTED)
def test_changing_algo_over_mqtt_will_not_produce_two_dosing_jobs():
pubsub.publish(
f"pioreactor/{unit}/{experiment}/throughput_calculating/media_throughput",
None,
retain=True,
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/throughput_calculating/alt_media_throughput",
None,
retain=True,
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/alt_media_calculating/alt_media_fraction",
None,
retain=True,
)
algo = DosingController(
"pid_turbidostat",
volume=1.0,
target_od=0.4,
duration=60,
unit=unit,
experiment=experiment,
)
assert algo.dosing_automation == "pid_turbidostat"
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/dosing_automation/set",
'{"dosing_automation": "turbidostat", "duration": 60, "target_od": 1.0, "volume": 1.0, "skip_first_run": 1}',
)
time.sleep(
10
) # need to wait for all jobs to disconnect correctly and threads to join.
assert isinstance(algo.dosing_automation_job, Turbidostat)
pubsub.publish(f"pioreactor/{unit}/{experiment}/growth_rate", 0.15)
pubsub.publish(f"pioreactor/{unit}/{experiment}/od_filtered/135/0", 1.5)
pause()
# note that we manually run, as we have skipped the first run in the json
algo.dosing_automation_job.run()
time.sleep(5)
assert algo.dosing_automation_job.throughput_calculator.media_throughput == 1.0
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_automation/target_od/set", 1.5)
pause()
pause()
assert algo.dosing_automation_job.target_od == 1.5
def test_disconnect_cleanly():
algo = DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
unit=unit,
volume=1.0,
experiment=experiment,
)
assert algo.dosing_automation == "turbidostat"
assert isinstance(algo.dosing_automation_job, Turbidostat)
pubsub.publish(f"pioreactor/{unit}/{experiment}/dosing_control/$state/set",
"disconnected")
time.sleep(10)
def test_execute_io_action2() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_fraction") as c:
c[experiment] = "0.0"
with DosingController("silent", unit=unit, experiment=experiment) as ca:
ca.automation_job.execute_io_action(media_ml=1.25,
alt_media_ml=0.01,
waste_ml=1.26)
pause()
assert ca.automation_job.media_throughput == 1.25
assert ca.automation_job.alt_media_throughput == 0.01
assert abs(ca.automation_job.alt_media_fraction - 0.0007142) < 0.000001
def test_throughput_calculator_restart() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = str(1.0)
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = str(1.5)
with DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
pause()
assert algo.automation_job.media_throughput == 1.0
assert algo.automation_job.alt_media_throughput == 1.5
def test_changing_algo_over_mqtt_when_it_fails_will_rollback() -> None:
with DosingController(
"turbidostat",
target_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
assert algo.automation["automation_name"] == "turbidostat"
assert isinstance(algo.automation_job, Turbidostat)
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/dosing_control/automation/set",
'{"automation_name": "pid_morbidostat", "duration": 60}',
)
time.sleep(10)
assert algo.automation["automation_name"] == "turbidostat"
assert isinstance(algo.automation_job, Turbidostat)
assert algo.automation_job.target_od == 1.0
pause()
pause()
pause()
def test_throughput_calculator() -> None:
with local_persistant_storage("media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = "0.0"
with local_persistant_storage("alt_media_fraction") as c:
c[experiment] = "0.0"
algo = DosingController(
"pid_morbidostat",
target_growth_rate=0.05,
target_od=1.0,
duration=60,
unit=unit,
experiment=experiment,
)
assert algo.automation_job.media_throughput == 0
pause()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/growth_rate",
'{"growth_rate": 0.08}',
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/od_filtered",
'{"od_filtered": 1.0}',
)
pause()
algo.automation_job.run()
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/growth_rate",
'{"growth_rate": 0.08}',
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/od_filtered",
'{"od_filtered": 0.95}',
)
pause()
algo.automation_job.run()
assert algo.automation_job.media_throughput > 0
assert algo.automation_job.alt_media_throughput > 0
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/growth_rate",
'{"growth_rate": 0.07}',
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/od_filtered",
'{"od_filtered": 0.95}',
)
pause()
algo.automation_job.run()
assert algo.automation_job.media_throughput > 0
assert algo.automation_job.alt_media_throughput > 0
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/growth_rate",
'{"growth_rate": 0.065}',
)
pubsub.publish(
f"pioreactor/{unit}/{experiment}/growth_rate_calculating/od_filtered",
'{"od_filtered": 0.95}',
)
pause()
algo.automation_job.run()
assert algo.automation_job.media_throughput > 0
assert algo.automation_job.alt_media_throughput > 0
algo.set_state(algo.DISCONNECTED)