def system_initialize():
ham_int, reader_int, reader_int, shaker, *_ = sys_state.instruments
if mid_run:
print('CONTINUING A PREVIOUSLY INITIALIZED AND PAUSED RUN. WILL SKIP CLEANING. OK? 5 SECONDS TO CANCEL...')
time.sleep(5)
local_log_dir = os.path.join(method_local_dir, 'log')
if not os.path.exists(local_log_dir):
os.mkdir(local_log_dir)
main_logfile = os.path.join(local_log_dir, 'main.log')
logging.basicConfig(filename=main_logfile, level=logging.DEBUG, format='[%(asctime)s] %(name)s %(levelname)s %(message)s')
add_robot_level_log()
add_stderr_logging()
for banner_line in log_banner('Begin execution of ' + __file__):
logging.info(banner_line)
if sys_state.disable_pumps or simulation_on:
pump_int.disable()
if simulation_on:
reader_int.disable()
shaker.disable()
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
if mid_run:
prime_and_clean = None
else:
prime_and_clean = run_async(lambda: (#pump_int.prime(), # important that the shaker is
shaker.start(shake_speed), pump_int.bleach_clean(),
shaker.stop())) # started and stopped at least once
initialize(ham_int)
hepa_on(ham_int, simulate=int(simulation_on))
method_start_time = time.time()
if not sys_state.disable_pumps:
wash_empty_refill(ham_int, refillAfterEmpty=2, chamber2WashLiquid=0) # 2=chamber 1 only; 0=Liquid 1 (bleach)
if prime_and_clean:
prime_and_clean.join()
shaker.start(shake_speed) # TODO: For asynchrony
def system_clean():
ham_int, reader_int, reader_int, shaker, *_ = sys_state.instruments
sys_state.waffle_clean_thread = run_async(pump_int.bleach_clean)
tip_pick_up_96(ham_int, wash_tips)
for i in range(2):
aspirate_96(ham_int, bleach_site, wash_vol)
dispense_96(ham_int, reader_plate, wash_vol)
aspirate_96(ham_int, reader_plate, wash_vol + read_sample_vol, mixVolume=wash_vol, mixCycles=2)
dispense_96(ham_int, bleach_site, wash_vol + read_sample_vol)
tip_eject_96(ham_int, wash_tips)
if not sys_state.disable_pumps:
wash_empty_refill(ham_int, refillAfterEmpty=2, chamber2WashLiquid=0) # 2=chamber 1 only; 0=Liquid 1 (bleach)
def service_lagoons(ham_int, pump_int, reader_int):
logging.info(
'\n\n##### ------------------ Servicing lagoons ------------------'
)
logging.info('\n##### Filling reservoir and adding inducer.')
culture_fill_thread = run_async(
lambda: pump_int.refill(culture_supply_vol))
#while True:
# try:
# tip_pick_up(ham_int, [next(inducer_tip_pos_gen)])
# break
# except pyhamilton.NoTipError:
# continue
#liq_class_300uL = 'StandardVolumeFilter_Water_DispenseJet_Empty_with_transport_vol'
while True:
try:
tip_pick_up(ham_int, next(disp_lagoon_tips_gen))
break
except pyhamilton.NoTipError:
continue
tip_eject(ham_int, disp_tip_poss)
culture_fill_thread.join()
#aspirate(ham_int, [(inducer_site, 0)], [inducer_vol], liquidClass=liq_class_300uL)
#dispense(ham_int, [(culture_reservoir, 93)], [inducer_vol], liquidClass=liq_class_300uL)
#tip_eject(ham_int)
logging.info('\n##### Moving fresh culture into lagoons.')
change_96_tips(ham_int, culture_tips)
aspirate_96(ham_int,
culture_reservoir,
cycle_replace_vol,
mixCycles=6,
mixVolume=100,
liquidHeight=.5,
airTransportRetractDist=30)
waffle_clean_thread = run_async(lambda: (pump_int.empty(
culture_supply_vol), clean_reservoir(pump_int, shaker)))
dispense_96(ham_int,
lagoon_plate,
cycle_replace_vol,
liquidHeight=lagoon_fly_disp_height,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
put_96_tips(ham_int, culture_tips, immediately=True)
logging.info('\n##### Mixing lagoons.')
if sys_state.need_to_read_plate:
logging.info(
'\n##### Sampling liquid from lagoons to reader plates.')
while True:
try:
reader_plate = next(reader_plate_gen)
move_plate(ham_int, reader_plate, reader_plate_site)
break
except pyhamilton.LabwareError:
pass
change_96_tips(ham_int, mixing_tips)
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
reader_plate_site,
read_sample_vol,
liquidHeight=5,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
else:
change_96_tips(ham_int, mixing_tips)
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
lagoon_plate,
read_sample_vol,
liquidHeight=fixed_lagoon_height + 3,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
logging.info('\n##### Draining lagoons to constant height.')
excess_vol = max_transfer_vol * .8
aspirate_96(ham_int,
lagoon_plate,
excess_vol,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
bleach_site,
excess_vol,
liquidHeight=10,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
put_96_tips(ham_int, mixing_corral)
change_96_tips(ham_int, temp_layout)
if sys_state.need_to_read_plate:
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
reader_plate_site,
read_sample_vol,
liquidHeight=5,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
else:
aspirate_96(ham_int,
lagoon_plate,
read_sample_vol,
mixCycles=2,
mixPosition=2,
mixVolume=400,
liquidFollowing=1,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
lagoon_plate,
read_sample_vol,
liquidHeight=fixed_lagoon_height + 3,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
logging.info('\n##### Draining lagoons to constant height.')
aspirate_96(ham_int,
lagoon_plate,
excess_vol,
liquidHeight=fixed_lagoon_height,
airTransportRetractDist=30)
dispense_96(ham_int,
bleach_site,
excess_vol,
liquidHeight=10,
dispenseMode=9,
airTransportRetractDist=30) # mode: blowout
put_96_tips(ham_int, DEFAULT_WASTE, immediately=True)
def bleach():
change_96_tips(ham_int, mixing_corral)
bleach_mounted_tips(ham_int, destination=mixing_tips)
change_96_tips(ham_int, None)
if sys_state.need_to_read_plate:
plate_id = reader_plate_id(reader_plate)
protocols = ['17_8_12_lum', '17_8_12_abs']
data_types = ['lum', 'abs']
platedatas = read_plate(
ham_int,
reader_int,
reader_tray,
reader_plate_site,
protocols,
plate_id,
plate_destination=plate_trash,
async_task=bleach
) # throw out plate when done and asynchronously bleach
if simulation_on:
platedatas = [
PlateData(os.path.join('assets', 'dummy_platedata.csv'))
] * 2 # sim dummies
for platedata, data_type in zip(platedatas, data_types):
platedata.wait_for_file()
db_add_plate_data(platedata, data_type, reader_plate, lagoons,
[
*range(8 * 10),
*range(8 * 11, 8 * 11 + num_disp_lagoons)
])
reader_int.plate_in(block=False)
sys_state.need_to_read_plate = False
else:
bleach()
change_96_tips(ham_int, None)
waffle_clean_thread.join()
logging.info(
'\n##### --------------- Done servicing lagoons ---------------\n')
shaker = Shaker()
with HamiltonInterface(simulate=simulation_on) as ham_int, LBPumps(
) as pump_int, ClarioStar() as reader_int:
if sys_state.disable_pumps or simulation_on:
pump_int.disable()
if simulation_on:
reader_int.disable()
shaker.disable()
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
logging.info('\n##### Priming pump lines and cleaning reservoir.')
if mid_run:
prime_and_clean = None
else:
prime_and_clean = run_async(lambda: (
pump_int.prime(), # important that the shaker is
shaker.start(300),
pump_int.bleach_clean(),
shaker.stop())) # started and stopped at least once
initialize(ham_int)
hepa_on(ham_int, simulate=int(simulation_on))
logging.info(
'\n##### Filling bleach so first waste dispense does not froth up.'
)
if not sys_state.disable_pumps:
wash_empty_refill(
ham_int, refillAfterEmpty=3,
chamber2WashLiquid=0) # 3=chamber 2 only; 0=Liquid 1 (bleach)
if prime_and_clean:
prime_and_clean.join()
try:
errmsg_str = ''
with HamiltonInterface(simulate=simulation_on) as ham_int, LBPumps(
) as pump_int, ClarioStar() as reader_int:
if sys_state.disable_pumps or simulation_on:
pump_int.disable()
if simulation_on:
reader_int.disable()
shaker.disable()
ham_int.set_log_dir(os.path.join(local_log_dir, 'hamilton.log'))
logging.info('\n##### Priming pump lines and cleaning reservoir.')
if mid_run:
prime_and_clean = None
else:
prime_and_clean = run_async(
lambda:
( #pump_int.prime(), # important that the shaker is
shaker.start(300), pump_int.bleach_clean(), shaker.stop()
)) # started and stopped at least once
initialize(ham_int)
hepa_on(ham_int, simulate=int(simulation_on))
method_start_time = time.time()
try:
# make sure we initially have something to dispense frothy waste into
if not sys_state.disable_pumps:
wash_empty_refill(
ham_int,
refillAfterEmpty=
3, # 3=Refill chamber 2 only, which is BLEACH
chamber2WashLiquid=0
) # 0=Liquid 1 (red container) (bleach)