async def test_set_temp_deck_temperature(monkeypatch):
# Set target temperature
import types
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
command_log = []
def _mock_send_command(self, command, timeout=None, tag=None):
nonlocal command_log
command_log += [command]
return ''
def _mock_update_temp(self):
return 'holding at target'
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
temp_deck._update_temp = types.MethodType(_mock_send_command, temp_deck)
try:
await asyncio.wait_for(temp_deck.set_temperature(99), timeout=0.2)
except asyncio.TimeoutError:
pass
assert command_log[-1] == 'M104 S99.0'
try:
await asyncio.wait_for(temp_deck.set_temperature(-9), timeout=0.2)
except asyncio.TimeoutError:
pass
assert command_log[-1] == 'M104 S-9.0'
def test_fail_set_temp_deck_temperature(monkeypatch):
import types
from opentrons.drivers import serial_communication
error_msg = 'ERROR: some error here'
def _raise_error(self, command, ack, serial_connection, timeout=None):
nonlocal error_msg
return error_msg
serial_communication.write_and_return = types.MethodType(
_raise_error, serial_communication)
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
res = temp_deck.set_temperature(-9)
assert res == error_msg
error_msg = 'Alarm: something alarming happened here'
def _raise_error(self, command, ack, serial_connection, timeout=None):
nonlocal error_msg
return error_msg
serial_communication.write_and_return = types.MethodType(
_raise_error, serial_communication)
res = temp_deck.set_temperature(-9)
assert res == error_msg
def test_set_temp_deck_temperature(monkeypatch):
# Set target temperature
import types
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
command_log = []
def _mock_send_command(self, command, timeout=None):
nonlocal command_log
command_log += [command]
return ''
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
temp_deck.set_temperature(99)
assert command_log[-1] == 'M104 S99.0'
temp_deck.set_temperature(-9)
assert command_log[-1] == 'M104 S-9.0'
All_wells = [Plasmid1_wells, Plasmid2_wells] # Creates an array from the lists of wells. More lists can be declared and added to this array
# By adding in another variable to this section a second list for cells requiring a different plasmid can be used
# A third variable would be needed to house both lists and could be used to iterate through the loops with each smaller list being for each plasmid, biglist = [list1,list2], biglist[0]
#All_Wells = Randomizer(All_wells) # Randomizes the wells, delete the hashtag to allow this randomizer to run. Imported from OT2_Functions
#########################################################################################
#########################################################################################
tempdeck = TempDeck() # Saves the temperature deck into a variable,
temperature = {"temp1": 4, "temp2": 42, "temp3": 37} # Saves the temperatures for the protocol into a dictionary. Dictionaries have keys and values
# The value can be called by the key i.e temperature["temp1"] = 4
if not robot.is_simulating(): # If the robot is inactive and the temperature deck isn't processing a command
tempdeck.connect('/dev/ttyACM0') # Connects to and begins cooling the temperature deck
tempdeck.set_temperature(temperature["temp1"]) # Initialization temperature for cooling
tempdeck.wait_for_temp() # Pauses the protocol until the temperature deck reaches the set temperature
target = All_wells # Adds the array of wells into a variable for easier readability during manipulation
SOB_wells = [well.top(1) for well in target] # well.top moves the pipette to the top of the well, the number specifies the distance in mm
robot.pause() # Opentron command that pauses whatever the robot is doing. The user can remove and centrifuge at this point, if the need is there. resumed via the OT app
# The code below handles distributing plasmid DNA
for i in range(NumberofPlasmids): # Transfers plasmid DNA into competent cell aliquots. The variable NumberofPlasmids controls how many times the loop is carried out, once for each plasmid
P10.distribute( # Presumes same plasmid for all cells, adds all doses to the pipette, wells specified later in the block
PlasmidVolume, # Specifies the volume in ul
DNA(i), # Selects which plasmid to pipette based on it's position on the container declared DNA. I increases with each loop, meaning the next plasmid is selected
target, # Target is the specified wells where the plasmid is then distributed (this will not work if multiple plasmids are being used)
blow_out=True, # Empties the pipette with an extra gust of air to ensure it is fluid free
new_tip='always' # Changes the pipette after every dispense to avoid contamination
)
'A1', length=25
) # Specify the buffer positions, change length=25 to whatever the number
# of buffers you have, eg if 15 buffers length=15
#########################################################################################
#########################################################################################
# BELOW IS CODE FOR THE PROTOCOL
# IF WORKING WITH E. COLI, BELOW IS A OPTIMAL PROTOCOL THAT ONLY REQUIRES 1 WASH STEP
# IF INVESTINGATING DIFFERENT INCUBATION TIMES, ALTER P300 DELAYS
# IF WANTING TO CHANGE TEMPDECK ON CONSTANTLY, REMOVE ALL tempdeck.disengage() AND PLACE BEFORE
# FINAL ROBOT COMMENT
tempdeck = TempDeck() # Connects the Tempdeck module to OT-2
if not robot.is_simulating(): # Cannot use while simulating,
tempdeck.connect('/dev/ttyACM0')
tempdeck.set_temperature(
target_temperature) # Sets the temperature to whats specified above
target1 = Compcells1(Even_wells) # Where your cells are going
robot.home() # turbulent airflow within the OT-2
robot.pause()
robot.comment(
"Make sure that centrifuge has been chilled down to 4*C and all buffers are on ice."
)
robot.comment(
"All plates should be chilled at the beginning and culture should be incubated on ice for 15 minutes before start."
)
robot.comment(
"Once at set temperature, insert culture into slot 6 and plate onto TempDeck, then resume!"
)
blow_out=True,
rate=0.5,
new_tip='never')
P300.touch_tip(Buffers(well_counter))
P300.blow_out(Buffers(well_counter))
P300.drop_tip(
) # Drops tips at end of single reagent run to prevent contamination
P10.drop_tip()
#########################################################################################
#########################################################################################
# COMPETENT CELLS
if not robot.is_simulating(): # Cannot use while simulating,
tempdeck.connect('/dev/ttyACM0')
tempdeck.set_temperature(
target_temperature) # Sets the temperature to whats specified above
target1 = Compcells1(Even_wells) # Where your cells are going
robot.home() # turbulent airflow within the OT-2
robot.pause()
robot.comment(
"Make sure that centrifuge has been chilled down to 4*C and all buffers are on ice."
)
robot.comment(
"All plates should be chilled at the beginning and culture should be incubated on ice for 15 minutes before start."
)
robot.comment(
"Once at set temperature, insert culture into slot 6 and plate onto TempDeck, then resume!"
)