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_get_device_info(monkeypatch):
import types
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
command_log = []
model = 'temp-v1'
firmware_version = 'edge-1a2b345'
serial = 'td20180102A01'
def _mock_send_command(self, command, timeout=None, tag=None):
nonlocal command_log
command_log += [command]
return 'model:' + model \
+ ' version:' + firmware_version \
+ ' serial:' + serial
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
res = temp_deck.get_device_info()
assert res == {
'model': model,
'version': firmware_version,
'serial': serial
}
def test_fail_get_temp_deck_temperature():
# Get the curent and target temperatures
# If no target temp has been previously set,
# then the response will set 'T' to 'none'
import types
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
return_string = 'T:none C:90'
def _mock_send_command(self, command, timeout=None):
return return_string
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
temp_deck.update_temperature()
assert temp_deck._temperature == {'current': 90, 'target': None}
return_string = 'Tx:none C:1'
def _mock_send_command(self, command, timeout=None):
return return_string
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
temp_deck.update_temperature()
assert temp_deck._temperature == {'current': 90, 'target': None}
def test_get_temp_deck_temperature():
# Get the curent and target temperatures
# If no target temp has been previously set,
# then the response will set 'T' to 'none'
import types
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
command_log = []
return_string = 'T:none C:90'
def _mock_send_command(self, command, timeout=None, tag=None):
nonlocal command_log, return_string
command_log += [command]
return return_string
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
assert temp_deck.temperature == 25 # driver's initialized value
assert temp_deck.target is None
temp_deck.update_temperature()
assert command_log == ['M105']
assert temp_deck.temperature == 90
assert temp_deck.target is None
command_log = []
return_string = 'T:99 C:90'
temp_deck.update_temperature()
assert command_log == ['M105']
assert temp_deck.temperature == 90
assert temp_deck.target == 99
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 connect(self):
"""
Connect to the 'TempDeck' port
Planned change- will connect to the correct port in case of multiple
TempDecks
"""
if self._port:
self._driver = TempDeckDriver()
self._driver.connect(self._port)
self._device_info = self._driver.get_device_info()
Thread(target=self._poll_temperature).start()
else:
# Sanity check Should never happen, because connect should never
# be called without a port on Module
raise MissingDevicePortError(
"TempDeck couldnt connect to port {}".format(self._port))
def test_fail_get_temp_deck_temperature():
# Get the curent and target temperatures
# If get fails, temp_deck temperature is not updated
import types
from opentrons.drivers.temp_deck import TempDeck
temp_deck = TempDeck()
temp_deck.simulating = False
done = False
def _mock_send_command1(self, command, timeout=None, tag=None):
nonlocal done
done = True
return 'T:none C:90'
temp_deck._send_command = types.MethodType(_mock_send_command1, temp_deck)
temp_deck.update_temperature()
time.sleep(0.25)
while not done:
time.sleep(0.25)
assert temp_deck._temperature == {'current': 90, 'target': None}
def _mock_send_command2(self, command, timeout=None, tag=None):
nonlocal done
done = True
return 'Tx:none C:1' # Failure premise
temp_deck._send_command = types.MethodType(_mock_send_command2, temp_deck)
done = False
temp_deck.update_temperature()
time.sleep(0.25)
while not done:
time.sleep(0.25)
assert temp_deck._temperature == {'current': 90, 'target': None}
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'
def connect(self):
"""
Connect to the 'TempDeck' port
Planned change- will connect to the correct port in case of multiple
TempDecks
"""
if self._port:
if temp_locks.get(self._port):
self._driver = temp_locks[self._port][1]
else:
self._driver = TempDeckDriver()
if not self._driver.is_connected():
self._driver.connect(self._port)
self._device_info = self._driver.get_device_info()
self._poll_stop_event = Event()
Thread(target=self._poll_temperature, daemon=True).start()
else:
# Sanity check Should never happen, because connect should never
# be called without a port on Module
raise MissingDevicePortError(
"TempDeck couldn't connect to port {}".format(self._port))
def test_dfu_command(monkeypatch):
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 ''
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
temp_deck.enter_programming_mode()
assert command_log == ['dfu']
def test_turn_off_temp_deck(monkeypatch):
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 ''
temp_deck._send_command = types.MethodType(_mock_send_command, temp_deck)
temp_deck.deactivate()
assert command_log == ['M18']
class TempDeck(commands.CommandPublisher):
"""
Under development. API subject to change without a version bump
"""
def __init__(self, lw=None, port=None, broker=None):
super().__init__(broker)
self.labware = lw
self._port = port
self._driver = None
self._device_info = None
self._poll_stop_event = None
@commands.publish.both(command=commands.tempdeck_set_temp)
def set_temperature(self, celsius):
"""
Set temperature in degree Celsius
Range: 4 to 95 degree Celsius (QA tested).
The internal temp range is -9 to 99 C, which is limited by the 2-digit
temperature display. Any input outside of this range will be clipped
to the nearest limit
"""
if self._driver and self._driver.is_connected():
self._driver.legacy_set_temperature(celsius)
@commands.publish.both(command=commands.tempdeck_deactivate)
def deactivate(self):
""" Stop heating/cooling and turn off the fan """
if self._driver and self._driver.is_connected():
self._driver.deactivate()
def wait_for_temp(self):
"""
This method exits only if set temperature has reached.Subject to change
"""
if self._driver and self._driver.is_connected():
while self.status != 'holding at target':
pass
@classmethod
def name(cls):
return 'tempdeck'
@classmethod
def display_name(cls):
return 'Temperature Deck'
# TODO: there should be a separate decoupled set of classes that construct
# the http api response entity given the model instance.
def to_dict(self):
return {
'name': self.name(),
'port': self.port,
'serial': self.device_info and self.device_info.get('serial'),
'model': self.device_info and self.device_info.get('model'),
'fwVersion': self.device_info and self.device_info.get('version'),
'displayName': self.display_name(),
**self.live_data
}
@property
def live_data(self):
return {
'status': self.status,
'data': {
'currentTemp': self.temperature,
'targetTemp': self.target
}
}
@property
def port(self):
""" Serial Port """
return self._port
@property
def device_info(self):
"""
Returns a dict:
{ 'serial': 'abc123', 'model': '8675309', 'version': '9001' }
"""
return self._device_info
@property
def temperature(self):
""" Current temperature in degree celsius """
return self._driver.temperature
@property
def target(self):
"""
Target temperature in degree celsius.
Returns None if no target set
"""
return self._driver.target
@property
def status(self):
"""
Returns a string: 'heating'/'cooling'/'holding at target'/'idle'.
NOTE: Depends on _poll_temperature thread to update the temperature to
be used to determine the status
"""
return self._driver and self._driver.status
# Internal Methods
def _poll_temperature(self):
while not self._poll_stop_event.wait(TEMP_POLL_INTERVAL_SECS):
self._driver and self._driver.update_temperature()
def connect(self):
"""
Connect to the 'TempDeck' port
Planned change- will connect to the correct port in case of multiple
TempDecks
"""
if self._port:
if temp_locks.get(self._port):
self._driver = temp_locks[self._port][1]
else:
self._driver = TempDeckDriver()
if not self._driver.is_connected():
self._driver.connect(self._port)
self._device_info = self._driver.get_device_info()
self._poll_stop_event = Event()
Thread(target=self._poll_temperature, daemon=True).start()
else:
# Sanity check Should never happen, because connect should never
# be called without a port on Module
raise MissingDevicePortError(
"TempDeck couldn't connect to port {}".format(self._port))
def disconnect(self):
'''
Disconnect from the serial port
'''
if self._poll_stop_event:
self._poll_stop_event.set()
if self._driver:
if self.status != 'idle':
self.deactivate()
self._driver.disconnect(port=self._port)
def temp_deck():
temp_deck = TempDeck()
temp_deck.simulating = False
temp_deck._lock = Lock()
yield temp_deck
temp_deck._lock = None
# Variables are case sensitive
Plasmid1_wells = [Compcells.cols['B']['2':'11':2] + Compcells.cols['C']['2':'11':2] + Compcells.cols['D']['2':'11':2] # Prevents the use of outside rows and columns, wells to add plasmid 1 to
+ Compcells.cols['D']['2':'11':2] + Compcells.cols['E']['2':'11':2] + Compcells.cols['F']['2':'11':2]] # Specify the target wells that you want to have bacterial aliquots in
# Change Compcells to match whatever the container with the competent cells is called, Line 15
Plasmid2_wells = [] # The letter specifies the column, the numbers specify the range i.e 2 to 11, the third number specifies steps, 2 to 11 in steps of 2
# Additional List can be added, but these list need to be included in the All_wells array
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
'F10'
]
Buffers_positions = Buffers.wells(
'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."
'E9',
'F2',
'F4',
'F6',
'F8',
'F10'
]
Buffers_positions = Buffers.wells('A1', length=25)
target_temperature = 4 # Specified temperatures for cold incubated,
target_temperature1 = 4 # heat shock and recovery incubation
target_temperature2 = 42
target_temperature3 = 37 # first position in reagent_pos list
tempdeck = TempDeck() # Connects the Tempdeck module to OT-2
#########################################################################################
#########################################################################################
robot.home()
#No.1
for counter, reagent in enumerate(reagents1, 0):
# These objects are temporary and will only exist within this loop
source = reagent_pos1[
counter] # Counter is use to index an independent list (e.g. reagent_pos)
P10list = [source] # This is then added to both list
P300list = [source]
P300.pick_up_tip(
) # Picks up pipette tip for both P10 and P300 to allow to alternate
P10.pick_up_tip()