def find_max_stock_volume_labware(experiment_csv_dict,
custom_labware_dict=None):
"""
Using the stock labware name from the csv, loads the appropiate labware
from both a custom and the native libary and determines the maximum volume
for one stock labware well. Assumes all labware is all identical.
Parameters
-----------
Returns
--------
"""
# Protocol encapsulated as only need an instance to simualte and toss
if custom_labware_dict:
protocol = simulate.get_protocol_api('2.8',
extra_labware=custom_labware_dict)
else:
protocol = simulate.get_protocol_api('2.8')
stock_plate = protocol.load_labware(
experiment_csv_dict['OT2 Stock Labwares'][0],
experiment_csv_dict['OT2 Stock Labware Slots'][0])
stock_plate_rows = [well for row in stock_plate.rows() for well in row]
stock_plate_well_volume = stock_plate.__dict__['_well_definition']['A1'][
'totalLiquidVolume']
return stock_plate_well_volume
def test_add_buffer_fullplate():
protocol = get_protocol_api(apilevel)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
3, 'plate')
reagents = protocol.load_labware('usascientific_12_reservoir_22ml',
9, 'reagents')
pipette = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tips])
remaining, source_wells = add_buffer(pipette,
[reagents['A1'],
reagents['A2']],
plate,
['A1', 'A2', 'A3', 'A4',
'A5', 'A6', 'A7', 'A8',
'A9', 'A10', 'A11', 'A12'],
300,
20000 / 8,
dead_vol=800 / 8)
assert remaining == 1300
assert source_wells == [reagents['A2']]
def test_bead_mix():
protocol = get_protocol_api('2.5')
scraper = CommandScraper(logging.getLogger('opentrons'), '1',
protocol.broker)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 3, 'plate')
pipette = protocol.load_instrument('p300_multi', 'left', tip_racks=[tips])
cols = ['A1']
bead_mix(pipette, plate, cols, tips)
exp = [
'Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Mixing 5 times with a volume of 200.0 ul',
'Aspirating 200.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 200.0 uL into A1 of plate on 3 at 1.0 speed',
'Aspirating 200.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 200.0 uL into A1 of plate on 3 at 1.0 speed',
'Aspirating 200.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 200.0 uL into A1 of plate on 3 at 1.0 speed',
'Aspirating 200.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 200.0 uL into A1 of plate on 3 at 1.0 speed',
'Aspirating 200.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 200.0 uL into A1 of plate on 3 at 1.0 speed',
'Blowing out at A1 of plate on 3', 'Returning tip',
'Dropping tip into A1 of Opentrons 96 Tip Rack 300 µL on 8'
]
obs = [x['payload']['text'] for x in scraper.commands]
assert exp == obs
def test_transfer_elute():
protocol = get_protocol_api('2.5')
scraper = CommandScraper(logging.getLogger('opentrons'), '1',
protocol.broker)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 3, 'plate')
elute = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 7, 'elute')
pipette = protocol.load_instrument('p300_multi', 'left', tip_racks=[tips])
cols = ['A1']
transfer_elute(pipette,
plate,
elute,
cols,
tips,
50,
z_offset=0.5,
x_offset=1,
rate=0.25,
drop_tip=True)
exp = [
'Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Aspirating 50.0 uL from A1 of plate on 3 at 0.25 speed',
'Dispensing 50.0 uL into A1 of elute on 7 at 1.0 speed',
'Dropping tip into A1 of Opentrons Fixed Trash on 12'
]
obs = [x['payload']['text'] for x in scraper.commands]
assert exp == obs
def test_add_buffer():
protocol = get_protocol_api(apilevel)
scraper = CommandScraper(logging.getLogger('opentrons'),
'1',
protocol.broker)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
3, 'plate')
reagents = protocol.load_labware('nest_12_reservoir_15ml',
9, 'reagents')
pipette = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tips])
remaining, source_wells = add_buffer(pipette,
[reagents['A1']],
plate,
['A1', 'A2'],
300,
1000)
assert remaining == 400
assert source_wells == [reagents['A1']]
exp = ['Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A1 of plate on 3 at 1.0 speed',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A1 of plate on 3 at 1.0 speed',
'Blowing out',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A2 of plate on 3 at 1.0 speed',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A2 of plate on 3 at 1.0 speed',
'Blowing out',
'Dropping tip into A1 of Opentrons Fixed Trash on 12']
obs = [x['payload']['text'] for x in scraper.commands]
assert exp == obs
def test_simulate_extra_labware(protocol, protocol_file, monkeypatch):
fixturedir = HERE / '..' / '..' / '..' /\
'shared-data' / 'labware' / 'fixtures' / '2'
# make sure we can load labware explicitly
# make sure we don't have an exception from not finding the labware
runlog, _ = simulate.simulate(protocol.filelike, 'custom_labware.py',
custom_labware_paths=[str(fixturedir)])
assert len(runlog) == 4
protocol.filelike.seek(0)
# make sure we don't get autoload behavior when not on a robot
with pytest.raises(ExceptionInProtocolError,
match='.*FileNotFoundError.*'):
simulate.simulate(protocol.filelike, 'custom_labware.py')
no_lw = simulate.get_protocol_api('2.0')
assert not no_lw._extra_labware
protocol.filelike.seek(0)
monkeypatch.setattr(simulate, 'IS_ROBOT', True)
monkeypatch.setattr(simulate, 'JUPYTER_NOTEBOOK_LABWARE_DIR',
fixturedir)
# make sure we don't have an exception from not finding the labware
runlog, _ = simulate.simulate(protocol.filelike, 'custom_labware.py')
assert len(runlog) == 4
# make sure the extra labware loaded by default is right
ctx = simulate.get_protocol_api('2.0')
assert len(ctx._extra_labware.keys()) == len(os.listdir(fixturedir))
assert ctx.load_labware('fixture_12_trough', 1, namespace='fixture')
# if there is no labware dir, make sure everything still works
monkeypatch.setattr(simulate, 'JUPYTER_NOTEBOOK_LABWARE_DIR',
HERE / 'nosuchdirectory')
ctx = simulate.get_protocol_api('2.0')
with pytest.raises(FileNotFoundError):
ctx.load_labware("fixture_12_trough", 1, namespace='fixture')
def test_add_buffer_runout():
protocol = get_protocol_api(apilevel)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
3, 'plate')
reagents = protocol.load_labware('nest_12_reservoir_15ml',
9, 'reagents')
pipette = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tips])
with pytest.raises(IndexError):
remaining, source_wells = add_buffer(pipette,
[reagents['A1']],
plate,
['A1', 'A2'],
300,
600)
def test_remove_supernatant():
protocol = get_protocol_api('2.5')
scraper = CommandScraper(logging.getLogger('opentrons'), '1',
protocol.broker)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 3, 'plate')
waste = protocol.load_labware('nest_1_reservoir_195ml', 7, 'waste')
pipette = protocol.load_instrument('p300_multi', 'left', tip_racks=[tips])
cols = ['A1']
remove_supernatant(pipette,
plate,
cols,
tips,
waste['A1'],
super_vol=200,
tip_vol=200,
rate=0.25,
bottom_offset=2,
drop_tip=False)
exp = [
'Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Aspirating 190.0 uL from A1 of plate on 3 at 0.25 speed', 'Air gap',
'Aspirating 10.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 200.0 uL into A1 of waste on 7 at 1.0 speed',
'Aspirating 10.0 uL from A1 of plate on 3 at 0.25 speed', 'Air gap',
'Aspirating 10.0 uL from A1 of plate on 3 at 1.0 speed',
'Dispensing 20.0 uL into A1 of waste on 7 at 1.0 speed', 'Blowing out',
'Returning tip',
'Dropping tip into A1 of Opentrons 96 Tip Rack 300 µL on 8'
]
obs = [x['payload']['text'] for x in scraper.commands]
assert exp == obs
_all_values = json.loads(
"""{"pipette_type":"p300_multi_gen2","dilution_factor":3,"num_of_dilutions":11,"total_mixing_volume":150,"tip_use_strategy":"never"}"""
)
return [_all_values[n] for n in names]
metadata = {
'protocolName': 'Customizable Serial Dilution',
'author': 'Opentrons <*****@*****.**>',
'source': 'Protocol Library',
'apiLevel': '2.7'
}
from opentrons import simulate
metadata = {'apiLevel': '2.7'}
protocol = simulate.get_protocol_api('2.7')
[
pipette_type, dilution_factor, num_of_dilutions, total_mixing_volume,
tip_use_strategy
] = get_values( # noqa: F821
'pipette_type', 'dilution_factor', 'num_of_dilutions',
'total_mixing_volume', 'tip_use_strategy')
# labware
trough = protocol.load_labware('usascientific_12_reservoir_22ml', '2')
liquid_trash = trough.wells()[0]
plate = protocol.load_labware('corning_96_wellplate_360ul_flat', '3')
tiprack = [
protocol.load_labware('opentrons_96_tiprack_300ul', slot)
for slot in ['1', '4']
]
# touch tip
if(j < (len(c_target_deck)-1)):
if("384" not in str(labwareCaller[get_LabwareCaller(c_target_deck[-1])])):
c_pipette.touch_tip(labwareCaller[get_LabwareCaller(c_target_deck[-1])].wells_by_name()[c_target_slot[-1]])
else:
c_pipette.touch_tip(labwareCaller[get_LabwareCaller(c_target_deck[-1])].wells_by_name()[c_target_slot[-1]],
radius=0.8, speed=15)
# update target amount list
amtList = update_amtList(amtList, c_target_deck[j], c_target_slot[j], float(c_amt[j]), 'dispense')
# blow out at last target
c_pipette.blow_out(labwareCaller[get_LabwareCaller(c_target_deck[-1])].wells_by_name()[c_target_slot[-1]].bottom(current_dspH+3))
if("384" not in str(labwareCaller[get_LabwareCaller(c_target_deck[-1])])):
c_pipette.touch_tip(labwareCaller[get_LabwareCaller(c_target_deck[-1])].wells_by_name()[c_target_slot[-1]])
else:
c_pipette.touch_tip(labwareCaller[get_LabwareCaller(c_target_deck[-1])].wells_by_name()[c_target_slot[-1]],
radius=0.8, speed=15)
#drop tip decision
if(int(tip_next) != int(current_tip) or (i == len(aspirate_groups2)-1)):
c_pipette.drop_tip(protocol.fixed_trash['A1'].top().move(types.Point(10, 5, 12)))
######### SIMULATION ############
from opentrons import simulate
bep = simulate.get_protocol_api('2.10')
bep.home()
run(bep)
def simulate(self):
from opentrons import simulate
self.run(simulate.get_protocol_api(self.metadata["apiLevel"]))
def to96(self, maxVol: int, filepath: str):
self.protocol = simulate.get_protocol_api(self._api)
self.protocol.home()
tuberack_1 = self.protocol.load_labware(self._tuberack1_name, self._tuberack1_pos)
tuberack_2 = self.protocol.load_labware(self._tuberack2_name, self._tuberack2_pos)
tiprack_1 = self.protocol.load_labware(self._tiprack_name, self._tiprack_pos)
plate = self.protocol.load_labware(self._plate_name, self._plate_pos)
pipette = self.protocol.load_instrument('p300_single', 'right', tip_racks=[tiprack_1])
df = pd.read_csv(filepath, sep='\t')
#[0.0 for df1.loc[i] in [1..12]
#calculate the concentration (total should = 1)
sources = list(df)
sources.remove("wells")
tubes = len(df.columns) - 1
df['sumVol'] = df[sources].sum(axis=1)
#create the output file
df1 = pd.DataFrame(columns = [])
df1.index.name = 'wells'
#initialize the sources column
for i in range (12):
df1['source ' + str(i+1)] = 0
#initialize the values of each cell
for i in range (96):
df1.loc[i] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
#make index start at 1
df1.index=df1.index+1
df1.sort_index()
#check invalid concentration (total not = 1)
#create an ignore array that includes wells with no solution
#determine validWells to constrain the range of inner for loop
ignore=[]
validWells = 0;
for i in df.index:
sum = df['sumVol'][i]
if int(round(sum,3)) != 1 and sum != 0:
print("Invalid vol at well ")
print (i+1)
ignore.append(i)
elif int(round(sum,3)) == 1:
validWells = i+1;
elif sum == 0:
ignore.append(i)
#set tubeRack
#start transfering
curRack = tuberack_1
curTube = -1;
#nested loops to transfer from 1 tube to many wells
#outer loop: accessing tube
for i in range(tubes):
#switch from tuberack_1 to tuberack_2
if i+1 == 7:
curRack = tuberack_2
curTube = -1
curTube += 1
pipette.pick_up_tip()
#inner loop: accessing the wells
for j in range(validWells):
volTip = (df.iat[j,i+1])*maxVol
if j not in ignore:
if volTip != 0:
pipette.aspirate(float(volTip), curRack.wells()[curTube])
pipette.dispense(float(volTip), plate.wells()[j])
pipette.blow_out(curRack.wells()[curTube])
if i+1 < 7:
df1.at[j+1,'source '+str(curTube+1)] = float(volTip)
else:
df1.at[j+1,'source '+str(curTube+7)] = float(volTip)
if j == validWells - 1:
pipette.drop_tip()
df1.to_csv("output.tsv", sep="\t")
for line in self.protocol.commands():
print (line)
def test_bead_wash():
apilevel = '2.5'
protocol = get_protocol_api(apilevel)
scraper = CommandScraper(logging.getLogger('opentrons'), '1',
protocol.broker)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
reagents = protocol.load_labware('nest_12_reservoir_15ml', 9, 'reagents')
waste = protocol.load_labware('nest_1_reservoir_195ml', 7, 'waste')
pipette = protocol.load_instrument('p300_multi', 'left', tip_racks=[tips])
magblock = protocol.load_module('Magnetic Module', 10)
mag_plate = magblock.load_labware('biorad_96_wellplate_200ul_pcr')
cols = ['A1']
remaining, wells = bead_wash( # global arguments
protocol,
magblock,
pipette,
mag_plate,
cols,
# super arguments
waste['A1'],
tips,
# wash buffer arguments
[reagents['A1']],
20000 / 8,
# mix arguments
tips,
# optional arguments
super_vol=150,
rate=0.25,
super_bottom_offset=2,
drop_super_tip=True,
wash_vol=150,
remaining=None,
wash_tip=None,
drop_wash_tip=True,
mix_vol=200,
mix_n=2,
drop_mix_tip=False,
mag_engage_height=None,
pause_s=300)
assert remaining == pytest.approx(2350.0)
assert wells == [reagents['A1']]
exp = [
'Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Aspirating 150.0 uL from A1 of Bio-Rad 96 Well Plate 200 µL PCR on'
' Magnetic Module GEN1 on 10 at 0.25 speed', 'Air gap',
'Aspirating 10.0 uL from A1 of Bio-Rad 96 Well Plate 200 µL PCR on '
'Magnetic Module GEN1 on 10 at 1.0 speed',
'Dispensing 160.0 uL into A1 of waste on 7 at 1.0 speed',
'Blowing out', 'Dropping tip into A1 of Opentrons Fixed Trash on 12',
'Disengaging Magnetic Module',
'Picking up tip from A2 of Opentrons 96 Tip Rack 300 µL on 8',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed', 'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A1 of Bio-Rad 96 Well Plate 200 µL PCR on '
'Magnetic Module GEN1 on 10 at 1.0 speed', 'Blowing out',
'Dropping tip into A1 of Opentrons Fixed Trash on 12',
'Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Mixing 2 times with a volume of 200.0 ul',
'Aspirating 200.0 uL from A1 of Bio-Rad 96 Well Plate 200 µL PCR on '
'Magnetic Module GEN1 on 10 at 1.0 speed',
'Dispensing 200.0 uL into A1 of Bio-Rad 96 Well Plate 200 µL PCR on '
'Magnetic Module GEN1 on 10 at 1.0 speed',
'Aspirating 200.0 uL from A1 of Bio-Rad 96 Well Plate 200 µL PCR on '
'Magnetic Module GEN1 on 10 at 1.0 speed',
'Dispensing 200.0 uL into A1 of Bio-Rad 96 Well Plate 200 µL PCR on '
'Magnetic Module GEN1 on 10 at 1.0 speed',
'Blowing out at A1 of Bio-Rad 96 Well Plate 200 µL PCR on Magnetic '
'Module GEN1 on 10', 'Returning tip',
'Dropping tip into A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Engaging Magnetic Module', 'Delaying for 5 minutes and 0 seconds'
]
obs = [x['payload']['text'] for x in scraper.commands]
assert exp == obs
