def __init__(self, max_od: float, **kwargs) -> None:
super(TrackOD, self).__init__(**kwargs)
assert max_od is not None, "max_od should be set"
self.max_od = max_od
self.white_light = config.get(
"leds", "white_light") # TODO: update to new led config.ini syntax
self.set_led_intensity(self.white_light, 0)
def setup_pwm(self) -> PWM:
hertz = 1
pin = PWM_TO_PIN[HEATER_PWM_TO_PIN]
pin = PWM_TO_PIN[config.get("PWM_reverse", "heating")]
pwm = PWM(pin, hertz)
pwm.start(0)
return pwm
def __init__(self,
duty_cycle: float = 100.0,
hz: float = 150.0,
**kwargs) -> None:
super(ContinuousCycle, self).__init__(**kwargs)
pin = PWM_TO_PIN[config.get("PWM_reverse", "media")]
self.pwm = PWM(pin, hz)
self.duty_cycle = duty_cycle
def stop_ir_led(self):
if self.fake_data:
return
ir_channel = config.get("leds", "ir_led")
led_intensity(ir_channel,
intensity=0,
unit=self.unit,
experiment=self.experiment)
def __init__(
self,
target_rpm: float,
unit: str,
experiment: str,
rpm_calculator: Optional[RpmCalculator],
hertz: float = 150,
) -> None:
super(Stirrer, self).__init__(job_name="stirring",
unit=unit,
experiment=experiment)
self.logger.debug(f"Starting stirring with initial {target_rpm} RPM.")
self.rpm_calculator = rpm_calculator
if not hardware.is_HAT_present():
self.logger.error("Pioreactor HAT must be present.")
self.set_state(self.DISCONNECTED)
raise exc.HardwareNotFoundError("Pioreactor HAT must be present.")
if (self.rpm_calculator
is not None) and not hardware.is_heating_pcb_present():
self.logger.error("Heating PCB must be present to measure RPM.")
self.set_state(self.DISCONNECTED)
raise exc.HardwareNotFoundError(
"Heating PCB must be present to measure RPM.")
pin = hardware.PWM_TO_PIN[config.get("PWM_reverse", "stirring")]
self.pwm = PWM(pin, hertz)
self.pwm.lock()
self.rpm_to_dc_lookup = self.initialize_rpm_to_dc_lookup()
self.target_rpm = target_rpm
self.duty_cycle = self.rpm_to_dc_lookup(self.target_rpm)
# set up PID
self.pid = PID(
Kp=config.getfloat("stirring.pid", "Kp"),
Ki=config.getfloat("stirring.pid", "Ki"),
Kd=config.getfloat("stirring.pid", "Kd"),
setpoint=self.target_rpm,
unit=self.unit,
experiment=self.experiment,
job_name=self.job_name,
target_name="rpm",
output_limits=(-20, 20), # avoid whiplashing
)
# set up thread to periodically check the rpm
self.rpm_check_repeated_thread = RepeatedTimer(
17, # 17 and 5 are coprime
self.poll_and_update_dc,
job_name=self.job_name,
run_immediately=True,
run_after=5,
poll_for_seconds=
4, # technically should be a function of the RPM: lower RPM, longer to get sufficient data.
)
def get_ir_channel_from_configuration(self) -> pt.LedChannel:
try:
return cast(pt.LedChannel, config.get("leds_reverse", IR_keyword))
except Exception:
self.logger.error(
"""`leds` section must contain `IR` value. Ex:
[leds]
A=IR
"""
)
raise KeyError("`IR` value not found in section.")
def backup_database(output):
"""
This action will create a backup of the SQLite3 database into specified output. It then
will try to scp the backup to any available worker Pioreactors as a futher backup.
A cronjob is set up as well to run this action every 12 hours.
"""
import sqlite3
from sh import scp, ErrorReturnCode
def progress(status, remaining, total):
logger.debug(f"Copied {total-remaining} of {total} pages.")
logger.debug(f"Starting backup of database to {output}")
con = sqlite3.connect(config.get("storage", "database"))
bck = sqlite3.connect(output)
with bck:
con.backup(bck, pages=-1, progress=progress)
bck.close()
con.close()
logger.debug(
f"Completed backup of database to {output}. Attempting distributed backup..."
)
n_backups = 2
backups_complete = 0
available_workers = get_active_workers_in_inventory()
while (backups_complete < n_backups) and (len(available_workers) > 0):
backup_unit = available_workers.pop()
if backup_unit == get_unit_name():
continue
try:
scp(output, f"{backup_unit}:{output}")
except ErrorReturnCode:
logger.debug(
f"Unable to backup database to {backup_unit}. Is it online?",
exc_info=True,
)
logger.warning(f"Unable to backup database to {backup_unit}.")
else:
logger.debug(f"Backed up database to {backup_unit}:{output}.")
backups_complete += 1
return
def start_ir_led(self):
ir_channel = config.get("leds", "ir_led")
r = led_intensity(
ir_channel,
intensity=100,
source_of_event=self.job_name,
unit=self.unit,
experiment=self.experiment,
)
if not r:
raise ValueError(
"IR LED could not be started. Stopping OD reading.")
time.sleep(0.25) # give LED a moment to get to max value
return
def __init__(self, **kwargs) -> None:
super(FlashUV, self).__init__(**kwargs)
self.uv_led = config.get("leds_reverse", "uv")
self.set_led_intensity(self.uv_led, 0)
def backup_database(output_file: str) -> None:
"""
This action will create a backup of the SQLite3 database into specified output. It then
will try to copy the backup to any available worker Pioreactors as a further backup.
This job actually consumes _a lot_ of resources, and I've seen the LED output
drop due to this running. See issue #81. For now, we will skip the backup if `od_reading` is running
Elsewhere, a cronjob is set up as well to run this action every N days.
"""
import sqlite3
from sh import ErrorReturnCode, rsync # type: ignore
unit = get_unit_name()
experiment = UNIVERSAL_EXPERIMENT
with publish_ready_to_disconnected_state(unit, experiment,
"backup_database"):
logger = create_logger("backup_database",
experiment=experiment,
unit=unit)
if is_pio_job_running("od_reading"):
logger.warning("Won't run if OD Reading is running. Exiting")
return
def progress(status: int, remaining: int, total: int) -> None:
logger.debug(f"Copied {total-remaining} of {total} SQLite3 pages.")
logger.debug(f"Writing to local backup {output_file}.")
logger.debug(f"Starting backup of database to {output_file}")
sleep(
1
) # pause a second so the log entry above gets recorded into the DB.
con = sqlite3.connect(config.get("storage", "database"))
bck = sqlite3.connect(output_file)
with bck:
con.backup(bck, pages=-1, progress=progress)
bck.close()
con.close()
with local_persistant_storage("database_backups") as cache:
cache["latest_backup_timestamp"] = current_utc_time()
logger.info("Completed backup of database.")
n_backups = config.getint("number_of_backup_replicates_to_workers",
fallback=2)
backups_complete = 0
available_workers = list(get_active_workers_in_inventory())
while (backups_complete < n_backups) and (len(available_workers) > 0):
backup_unit = available_workers.pop()
if backup_unit == get_unit_name():
continue
try:
rsync(
"-hz",
"--partial",
"--inplace",
output_file,
f"{backup_unit}:{output_file}",
)
except ErrorReturnCode:
logger.debug(
f"Unable to backup database to {backup_unit}. Is it online?",
exc_info=True,
)
logger.warning(
f"Unable to backup database to {backup_unit}. Is it online?"
)
else:
logger.debug(
f"Backed up database to {backup_unit}:{output_file}.")
backups_complete += 1
return
return ODReader(
channel_angle_map,
interval=sampling_rate,
unit=unit,
experiment=experiment,
adc_reader=ADCReader(
channels=channels, fake_data=fake_data, interval=sampling_rate
),
ir_led_reference_tracker=ir_led_reference_tracker,
)
@click.command(name="od_reading")
@click.option(
"--od-angle-channel1",
default=config.get("od_config.photodiode_channel", "1", fallback=None),
type=click.STRING,
show_default=True,
help="specify the angle(s) between the IR LED(s) and the PD in channel 1, separated by commas. Don't specify if channel is empty.",
)
@click.option(
"--od-angle-channel2",
default=config.get("od_config.photodiode_channel", "2", fallback=None),
type=click.STRING,
show_default=True,
help="specify the angle(s) between the IR LED(s) and the PD in channel 2, separated by commas. Don't specify if channel is empty.",
)
@click.option("--fake-data", is_flag=True, help="produce fake data (for testing)")
def click_od_reading(
od_angle_channel1: pt.PdAngle, od_angle_channel2: pt.PdAngle, fake_data: bool
):
ODReader(
channel_label_map,
sampling_rate=sampling_rate,
unit=unit,
experiment=experiment,
fake_data=fake_data,
)
signal.pause()
@click.command(name="od_reading")
@click.option(
"--od-angle-channel",
multiple=True,
default=config.get("od_config.photodiode_channel",
"od_angle_channel").split("|"),
type=click.STRING,
show_default=True,
help="""
pair of angle,channel for optical density reading. Can be invoked multiple times. Ex:
--od-angle-channel 135,0 --od-angle-channel 90,1 --od-angle-channel 45,3
""",
)
@click.option("--fake-data",
is_flag=True,
help="produce fake data (for testing)")
def click_od_reading(od_angle_channel, fake_data):
"""
Start the optical density reading job
def __init__(self, **kwargs):
super(FlashUV, self).__init__(**kwargs)
self.uv_led = config.get("leds", "uv380")
self.set_led_intensity(self.uv_led, 0)
def __init__(self, **kwargs):
super(TrackOD, self).__init__(**kwargs)
self.white_light = config.get("leds", "white_light")
# set luminosity to 10% initially
self.set_led_intensity(self.white_light, 0.1)
def pump(
unit: str,
experiment: str,
pump_name: str,
ml: Optional[float] = None,
duration: Optional[float] = None,
source_of_event: Optional[str] = None,
calibration: Optional[dict] = None,
continuously: bool = False,
):
"""
Parameters
------------
pump_name: one of "media", "alt_media", "waste"
calibration:
specify a calibration for the dosing. Should be a dict
with fields "duration_", "hz", "dc", and "bias_"
Returns
-----------
Amount of volume passed (approximate in some cases)
"""
action_name = {
"media": "add_media",
"alt_media": "add_alt_media",
"waste": "remove_waste",
}[pump_name]
logger = create_logger(action_name)
with utils.publish_ready_to_disconnected_state(
unit, experiment, action_name
) as exit_event:
assert (
(ml is not None) or (duration is not None) or continuously
), "either ml or duration must be set"
assert not (
(ml is not None) and (duration is not None)
), "Only select ml or duration"
if calibration is None:
with utils.local_persistant_storage("pump_calibration") as cache:
try:
calibration = loads(cache[f"{pump_name}_ml_calibration"])
except KeyError:
logger.error("Calibration not defined. Run pump calibration first.")
return 0.0
try:
GPIO_PIN = PWM_TO_PIN[config.get("PWM_reverse", pump_name)]
except NoOptionError:
logger.error(f"Add `{pump_name}` to `PWM` section to config_{unit}.ini.")
return 0.0
if ml is not None:
assert ml >= 0, "ml should be greater than 0"
duration = utils.pump_ml_to_duration(
ml, calibration["duration_"], calibration["bias_"]
)
logger.info(f"{round(ml, 2)}mL")
elif duration is not None:
ml = utils.pump_duration_to_ml(
duration, calibration["duration_"], calibration["bias_"]
)
logger.info(f"{round(duration, 2)}s")
elif continuously:
duration = 600
ml = utils.pump_duration_to_ml(
duration, calibration["duration_"], calibration["bias_"]
)
logger.info("Running pump continuously.")
assert isinstance(ml, (float, int))
assert isinstance(duration, (float, int))
assert duration >= 0, "duration should be greater than 0"
if duration == 0:
return 0.0
# publish this first, as downstream jobs need to know about it.
json_output = dumps(
{
"volume_change": ml,
"event": action_name,
"source_of_event": source_of_event,
"timestamp": current_utc_time(),
}
)
publish(
f"pioreactor/{unit}/{experiment}/dosing_events",
json_output,
qos=QOS.EXACTLY_ONCE,
)
try:
pwm = PWM(GPIO_PIN, calibration["hz"])
pwm.lock()
with catchtime() as delta_time:
pwm.start(calibration["dc"])
pump_start_time = time.time()
exit_event.wait(max(0, duration - delta_time()))
if continuously:
while not exit_event.wait(duration):
publish(
f"pioreactor/{unit}/{experiment}/dosing_events",
json_output,
qos=QOS.EXACTLY_ONCE,
)
except SystemExit:
# a SigInt, SigKill occurred
pass
except Exception as e:
# some other unexpected error
logger.debug(e, exc_info=True)
logger.error(e)
finally:
pwm.stop()
pwm.cleanup()
if continuously:
logger.info(f"Stopping {pump_name} pump.")
if exit_event.is_set():
# ended early for some reason
shortened_duration = time.time() - pump_start_time
ml = utils.pump_duration_to_ml(
shortened_duration, calibration["duration_"], calibration["bias_"]
)
return ml