diff --git a/analyses-snapshot-testing/automation/data/protocols_with_overrides.py b/analyses-snapshot-testing/automation/data/protocols_with_overrides.py index e92381e0a59..d03b45f7bf9 100644 --- a/analyses-snapshot-testing/automation/data/protocols_with_overrides.py +++ b/analyses-snapshot-testing/automation/data/protocols_with_overrides.py @@ -5,6 +5,26 @@ class ProtocolsWithOverrides: + Flex_2_25_96_all_module_LC_Stacker_Overrride: ProtocolWithOverrides = ProtocolWithOverrides( + file_stem="Flex_2_25_96_all_module_LC_Stacker_Overrride", + file_extension="py", + robot="Flex", + override_variable_name="key", + overrides=[ + "1 stacker", + "2 stackers", + "3 stackers", + "1 stacker with OT 12 Well 22 mL", + "2 stackers with OT 12 Well 22 mL", + "3 stackers with OT 12 Well 22 mL", + "1 stacker with OT 4 Well 300 mL", + "2 stackers with OT 4 Well 300 mL", + "3 stackers with OT 4 Well 300 mL", + "1 stacker with OT 1 Well 300mL", + ], + folder=GENERATORS_FOLDER, + ) + Flex_X_v2_18_NO_PIPETTES_Overrides_BadTypesInRTP: ProtocolWithOverrides = ProtocolWithOverrides( file_stem="Flex_X_v2_18_NO_PIPETTES_Overrides_BadTypesInRTP", file_extension="py", @@ -19,7 +39,7 @@ class ProtocolsWithOverrides: "wrong_type_in_description", "wrong_type_in_minimum", "wrong_type_in_maximum", - "wrong_type_in_unit", # we going unit or suffix? + "wrong_type_in_unit", ], folder=GENERATORS_FOLDER, ) diff --git a/analyses-snapshot-testing/files/protocols/generators/Flex_2_25_96_all_module_LC_Stacker_Overrride.py b/analyses-snapshot-testing/files/protocols/generators/Flex_2_25_96_all_module_LC_Stacker_Overrride.py new file mode 100644 index 00000000000..b408a72f7b0 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/generators/Flex_2_25_96_all_module_LC_Stacker_Overrride.py @@ -0,0 +1,718 @@ + +# Uncomment to test +# key = "1 stacker" +# key = "2 stackers" +# key = "3 stackers" +# key = "1 stacker with OT 12 Well 22 mL" +# key = "2 stackers with OT 12 Well 22 mL" +# key = "3 stackers with OT 12 Well 22 mL" +# key = "1 stacker with OT 4 Well 300 mL" +# key = "2 stackers with OT 4 Well 300 mL" +# key = "3 stackers with OT 4 Well 300 mL" +# key = "1 stacker with OT 1 Well 300 mL" +# protocol.override_variable_name = key + +############# +# CHANGELOG # +############# + + +# ---- +# 2.25 +# ---- + +# - - Flex Stacker Module v1 is now supported. + +# ---- +# 2.24 +# ---- + +# - - ProtocolContext.get_liquid_class() accesses Opentrons-verified liquid class definitions for aqueous, volatile, and viscous liquids. +# - - New InstrumentContext methods — transfer_with_liquid_class(), distribute_with_liquid_class(), and consolidate_with_liquid_class() — move liquids according to their properties. + +# ---- +# 2.23 +# ---- + +# - - Wells now have a meniscus() location that corresponds to the top of the liquid, either as set in the protocol or measured by probing with a pipette tip. +# - - Load and move labware lids with a new lid parameter of load_labware() and standalone methods. +# - - Updated set_offset() to match new Labware Position Check behavior in Opentrons App v8.4.0. + +# ---- +# 2.22 +# ---- + +# - - Improvements to loading liquids. Use the new Labware.load_liquid(), Labware.load_liquid_by_well(), and Labware.load_empty() methods instead of Well.load_liquid(), which is now deprecated. +# - - Beta evotips (not included in this protocol) + +# ---- +# 2.21 +# ---- + +# - - Run protocols that use the Absorbance Plate Reader and check the status of the module on the robot details screen for your Flex. +# - - Run protocols that use the new Opentrons Tough PCR Auto-Sealing Lid with the Thermocycler Module GEN2. Stacks of these lids appear in a consolidated view when setting up labware. +# - - Error recovery now works in more situations and has more options - Gripper Errors, Drop Tip Errors, additional recovery options for tip errors, disable error recovery entirely (8.2.0) + +# ---- +# 2.20 +# ---- + +# - configure_nozzle_layout() now accepts row, single, and partial column layout constants. See Partial Tip Pickup. +# - You can now call ProtocolContext.define_liquid() without supplying a description or display_color. +# - You can now call ProtocolContext.liquid_presence_detection() or ProtocolContext.require_liquid_presence() to use LLD on instrument context or on well +# - You now have the option to set RTP using CSV files +# - Error Recovery will now initiate for miss tip pick up, overpressure on aspirate and dispense, and if liquid presence isn't detected (8.0.0) + +# ---- +# 2.19 +# ---- + +# - NO FEATURES OR API CHANGES +# - New values for how much a tip overlaps with the pipette nozzle when the pipette picks up tips + +# ---- +# 2.18 +# ---- + +# - labware.set_offset +# - Runtime Parameters added +# - TrashContainer.top() and Well.top() now return objects of the same type +# - pipette.drop_tip() if location argument not specified the tips will be dropped at different locations in the bin +# - pipette.drop_tip() if location is specified, the tips will be dropped in the same place every time + +# ---- +# 2.17 +# ---- + +# NOTHING NEW +# This protocol is exactly the same as 2.16 Smoke Test V3 +# The only difference is the API version in the metadata +# There were no new positive test cases for 2.17 +# The negative test cases are captured in the 2.17 dispense changes protocol + +# ---- +# 2.16 +# ---- + +# - prepare_to_aspirate added +# - fixed_trash property changed +# - instrument_context.trash_container property changed + +# ---- +# 2.15 +# ---- + +# - move_labware added - Manual Deck State Modification +# - ProtocolContext.load_adapter added +# - OFF_DECK location added + +from typing import List +from opentrons import protocol_api, types # type: ignore +from opentrons.protocol_api import Labware # type: ignore +from dataclasses import dataclass + + +metadata = { + "protocolName": "Flex Smoke Test - v2.25", + "author": "QA team", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.25", +} + + +################# +### CONSTANTS ### +################# + +DeckSlots = [ + "A1", + "A2", + "A3", + "A4", + "B1", + "B2", + "B3", + "B4", + "C1", + "C2", + "C3", + "C4", + "D1", + "D2", + "D3", + "D4", +] + +HEATER_SHAKER_ADAPTER_NAME = "opentrons_96_pcr_adapter" +HEATER_SHAKER_NAME = "heaterShakerModuleV1" +MAGNETIC_BLOCK_NAME = "magneticBlockV1" +TEMPERATURE_MODULE_ADAPTER_NAME = "opentrons_96_well_aluminum_block" +TEMPERATURE_MODULE_NAME = "temperature module gen2" +THERMOCYCLER_NAME = "thermocycler module gen2" +ABSORBANCE_READER = "absorbanceReaderV1" +DECK_RISER_NAME = "opentrons_flex_deck_riser" +TC_LID = "opentrons_tough_pcr_auto_sealing_lid" +LID_COUNT = 5 +TIPRACK_96_ADAPTER_NAME = "opentrons_flex_96_tiprack_adapter" +TIPRACK_96_1000 = "opentrons_flex_96_tiprack_1000ul" +TIPRACK_96_200 = "opentrons_flex_96_tiprack_200ul" +TIPRACK_96_50 = "opentrons_flex_96_tiprack_50ul" +PIPETTE_96_CHANNEL_NAME = "flex_96channel_1000" +WELL_PLATE_STARTING_POSITION = "C2" +RESERVOIR_STARTING_POSITION = "D2" +FLEX_STACKER = "flexStackerModuleV1" + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +############################## +# Runtime Parameters Support # +############################## + +# -------------------------- # +# Added in API version: 2.18 # +# -------------------------- # + + + +def log_position(ctx, item): + ctx.comment(f"Item {item.load_name} is at {item.parent}") + + +@dataclass +class Test: + key: str + number_of_stackers: str + test_configuration: str + reservoir_name: str + well_plate_name: str + +Tests = [ + Test(key="1 stacker", + number_of_stackers="1", + test_configuration="full", + reservoir_name="nest_1_reservoir_290ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="2 stackers", + number_of_stackers="2", + test_configuration="full", + reservoir_name="nest_1_reservoir_290ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="3 stackers", + number_of_stackers="3", + test_configuration="full", + reservoir_name="nest_1_reservoir_290ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="1 stacker with OT 12 Well 22 mL", + number_of_stackers="1", + test_configuration="full", + reservoir_name="opentrons_tough_12_reservoir_22ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="2 stackers with OT 12 Well 22 mL", + number_of_stackers="2", + test_configuration="full", + reservoir_name="opentrons_tough_12_reservoir_22ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="3 stackers with OT 12 Well 22 mL", + number_of_stackers="3", + test_configuration="full", + reservoir_name="opentrons_tough_12_reservoir_22ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="1 stacker with OT 4 Well 300 mL", + number_of_stackers="1", + test_configuration="full", + reservoir_name="opentrons_tough_4_reservoir_72ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="2 stackers with OT 4 Well 300 mL", + number_of_stackers="2", + test_configuration="full", + reservoir_name="opentrons_tough_4_reservoir_72ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="3 stackers with OT 4 Well 300 mL", + number_of_stackers="3", + test_configuration="full", + reservoir_name="opentrons_tough_4_reservoir_72ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), + Test(key="1 stacker with OT 1 Well 300 mL", + number_of_stackers="1", + test_configuration="full", + reservoir_name="opentrons_tough_1_reservoir_300ml", + well_plate_name="opentrons_96_wellplate_200ul_pcr_full_skirt"), +] + + +def get_test(key): + matches = [test for test in Tests if test.key == key] + if not matches: + raise ValueError(f"No test found with key: {key}") + if len(matches) > 1: + raise ValueError(f"Multiple tests found with key: {key}") + return matches[0] + + + +def run(ctx: protocol_api.ProtocolContext) -> None: + test = get_test(key) + comment = f"Running Flex Smoke Test with {test.number_of_stackers} stacker(s) and configuration: {test.test_configuration}" + ctx.comment(msg=comment) + + ################ + ### FIXTURES ### + ################ + + waste_chute = ctx.load_waste_chute() + STACKER_PARAMS = test.number_of_stackers + + + + ###################### + ### STACKER SET UP ### + ###################### + + if STACKER_PARAMS == "1": + stacker_D4 = ctx.load_module(FLEX_STACKER, "D4") + stacker_D4.set_stored_labware(TIPRACK_96_1000, count=6, lid="opentrons_flex_tiprack_lid") + elif STACKER_PARAMS == "2": + stacker_C4 = ctx.load_module(FLEX_STACKER, "C4") + stacker_C4.set_stored_labware(TIPRACK_96_1000, count=0) + + stacker_D4 = ctx.load_module(FLEX_STACKER, "D4") + stacker_D4.set_stored_labware(TIPRACK_96_1000, count=6, lid="opentrons_flex_tiprack_lid") + elif STACKER_PARAMS == "3": + stacker_A4 = ctx.load_module(FLEX_STACKER, "A4") + stacker_A4.set_stored_labware(test.well_plate_name, count=2) + + stacker_C4 = ctx.load_module(FLEX_STACKER, "C4") + stacker_C4.set_stored_labware(TIPRACK_96_1000, count=0) + + stacker_D4 = ctx.load_module(FLEX_STACKER, "D4") + stacker_D4.set_stored_labware(TIPRACK_96_1000, count=6, lid="opentrons_flex_tiprack_lid") + + + ############### + ### MODULES ### + ############### + thermocycler = ctx.load_module(THERMOCYCLER_NAME) # A1 & B1 + magnetic_block = ctx.load_module(MAGNETIC_BLOCK_NAME, "A3") + heater_shaker = ctx.load_module(HEATER_SHAKER_NAME, "C1") + temperature_module = ctx.load_module(TEMPERATURE_MODULE_NAME, "D1") + absorbance_module = ctx.load_module(ABSORBANCE_READER, "B3") + lids = ctx.load_lid_stack(load_name = TC_LID, location = "A4", quantity = 5, adapter = DECK_RISER_NAME) + thermocycler.open_lid() + heater_shaker.open_labware_latch() + absorbance_module.close_lid() + absorbance_module.initialize("single", [600], 450) + absorbance_module.open_lid() + + + ####################### + ### MODULE ADAPTERS ### + ####################### + + temperature_module_adapter = temperature_module.load_adapter(TEMPERATURE_MODULE_ADAPTER_NAME) + heater_shaker_adapter = heater_shaker.load_adapter(HEATER_SHAKER_ADAPTER_NAME) + adapters = [temperature_module_adapter, heater_shaker_adapter] + + ############### + ### LABWARE ### + ############### + + # Load these directly with the RTP + if STACKER_PARAMS == "3": + dest_pcr_plate = stacker_A4.retrieve() + ctx.move_labware(dest_pcr_plate, WELL_PLATE_STARTING_POSITION, use_gripper=True) + stacker_A4.empty('Clear stacker of any labware before resuming the protocol') + stacker_A4.set_stored_labware(test.reservoir_name, count=0) + stacker_A4.fill(1,'Fill stacker with reservoir before resuming the protocol') + source_reservoir = stacker_A4.retrieve() + ctx.move_labware(source_reservoir, RESERVOIR_STARTING_POSITION, use_gripper=True) + else: + dest_pcr_plate = ctx.load_labware(test.well_plate_name, WELL_PLATE_STARTING_POSITION) + source_reservoir = ctx.load_labware(test.reservoir_name, RESERVOIR_STARTING_POSITION) + dest_pcr_plate.load_empty(dest_pcr_plate.wells()) + tip_rack_adapter = ctx.load_adapter(TIPRACK_96_ADAPTER_NAME, "A2") + + tip_racks = [] + + + ######################### + ###LOAD LIQUID CLASSES### + ######################### + + + water = ctx.define_liquid(name="water", description="High Quality H₂O", display_color="#42AB2D") + source_reservoir.wells_by_name()["A1"].load_liquid(liquid=water, volume=20000) + + water_class = ctx.get_liquid_class(name = 'water') + glycerol_50 = ctx.get_liquid_class(name = 'glycerol_50') + ethanol_80 = ctx.get_liquid_class(name = 'ethanol_80') + + ########################## + ### PIPETTE DEFINITION ### + ########################## + + pipette_96_channel = ctx.load_instrument(PIPETTE_96_CHANNEL_NAME, mount="left", tip_racks=tip_racks, liquid_presence_detection= True) + + + pipette_96_channel.trash_container = waste_chute + + assert isinstance(pipette_96_channel.trash_container, protocol_api.WasteChute) + + + ################################ + ### GRIPPER LABWARE MOVEMENT ### + ################################ + + + ctx.move_labware(dest_pcr_plate, magnetic_block) + ctx.move_labware(dest_pcr_plate, WELL_PLATE_STARTING_POSITION) + + log_position(ctx, dest_pcr_plate) + ctx.move_labware(dest_pcr_plate, thermocycler, use_gripper=True) + log_position(ctx, dest_pcr_plate) + # Move it back to the deck + ctx.move_labware(dest_pcr_plate, "C2", use_gripper=True) + log_position(ctx, dest_pcr_plate) + + # Other important moves? + + # manual move + log_position(ctx, source_reservoir) + ctx.move_labware(source_reservoir, stacker_D4, use_gripper=False) + log_position(ctx, source_reservoir) + ctx.move_labware(source_reservoir, RESERVOIR_STARTING_POSITION, use_gripper=True) + log_position(ctx, source_reservoir) + + # Other important manual moves? + + tip_rack_1 = stacker_D4.retrieve() + tip_racks.append(tip_rack_1) + ctx.move_lid(tip_rack_1, waste_chute, use_gripper=True) + ctx.move_labware(tip_rack_1, tip_rack_adapter, use_gripper=True) + + tip_rack_2 = stacker_D4.retrieve() + ctx.move_labware(tip_rack_2, "C3", use_gripper=True) + ctx.move_lid(tip_rack_2, waste_chute, use_gripper=True) # This will retrieve the tip rack from the stacker + + # 96 channel column pickup + pipette_96_channel.configure_nozzle_layout(style=protocol_api.COLUMN, start="A12") + + + pipette_96_channel.pick_up_tip(tip_rack_2["A1"]) + comment_tip_rack_status(ctx, tip_rack_2) + pipette_96_channel.aspirate(5, source_reservoir["A1"]) + pipette_96_channel.touch_tip() + pipette_96_channel.dispense(5, dest_pcr_plate[f"A1"]) + pipette_96_channel.drop_tip(waste_chute) + + # 96 channel single pickup + pipette_96_channel.configure_nozzle_layout(style=protocol_api.SINGLE, start="H12") + + pipette_96_channel.pick_up_tip(tip_rack_2) + pipette_96_channel.aspirate(5, source_reservoir["A1"]) + pipette_96_channel.touch_tip() + pipette_96_channel.dispense(5, source_reservoir["A1"]) + pipette_96_channel.aspirate(500, source_reservoir["A1"]) + pipette_96_channel.dispense(500, source_reservoir["A1"]) + pipette_96_channel.drop_tip(waste_chute) + comment_tip_rack_status(ctx, tip_rack_2) + + + + # put the tip rack in the trash + # since it cannot have a row pickup + + if STACKER_PARAMS == "1": + ctx.move_labware(tip_rack_2, waste_chute, use_gripper=True) + else: + ctx.move_labware(tip_rack_2, stacker_C4, use_gripper=True) + stacker_C4.store() + tip_rack_3 = stacker_D4.retrieve() + ctx.move_lid(tip_rack_3, waste_chute, use_gripper=True) + ctx.move_labware(tip_rack_3, "C3", use_gripper=True) + + # 96 channel row pickup + pipette_96_channel.configure_nozzle_layout(style=protocol_api.ROW, start="H1") + pipette_96_channel.pick_up_tip(tip_rack_3) + pipette_96_channel.mix(3, 500, source_reservoir["A1"]) + pipette_96_channel.drop_tip(waste_chute) + comment_tip_rack_status(ctx, tip_rack_3) + + # 96 channel full rack pickup + pipette_96_channel.configure_nozzle_layout(style=protocol_api.ALL, start="A1") + pipette_96_channel.pick_up_tip(tip_rack_1["A1"]) + comment_tip_rack_status(ctx, tip_rack_1) + pipette_96_channel.aspirate(5, source_reservoir["A1"]) + pipette_96_channel.touch_tip() + pipette_96_channel.air_gap(height=30) + pipette_96_channel.blow_out(waste_chute) + pipette_96_channel.prepare_to_aspirate() + pipette_96_channel.aspirate(5, source_reservoir["A1"]) + pipette_96_channel.touch_tip() + pipette_96_channel.air_gap(height=30) + pipette_96_channel.blow_out(waste_chute) + pipette_96_channel.prepare_to_aspirate() + pipette_96_channel.aspirate(10, source_reservoir["A1"]) + pipette_96_channel.touch_tip() + pipette_96_channel.dispense(10, dest_pcr_plate["A1"]) + pipette_96_channel.mix(repetitions=5, volume=15) + pipette_96_channel.return_tip() + comment_tip_rack_status(ctx, tip_rack_1) + pipette_96_channel.pick_up_tip(tip_rack_1["A1"]) + pipette_96_channel.transfer( + volume=10, + source=source_reservoir["A1"], + dest=dest_pcr_plate["A1"], + new_tip="never", + touch_tip=True, + blow_out=True, + blowout_location="trash", + mix_before=(3, 5), + mix_after=(1, 5), + ) + comment_tip_rack_status(ctx, tip_rack_1) + pipette_96_channel.return_tip(home_after=False) + comment_tip_rack_status(ctx, tip_rack_1) + ctx.comment("I think the above should not be empty?") + + + # Thermocycler lid moves + ctx.move_labware(dest_pcr_plate, thermocycler, use_gripper=True) + ctx.move_lid(source_location=lids, new_location=dest_pcr_plate, use_gripper=True) + thermocycler.close_lid() + thermocycler.set_block_temperature(38, hold_time_seconds=5.0) + thermocycler.set_lid_temperature(38) + thermocycler.open_lid() + ctx.move_lid(source_location=dest_pcr_plate, new_location=waste_chute, use_gripper=True) + thermocycler.deactivate() + + heater_shaker.open_labware_latch() + ctx.move_labware(dest_pcr_plate, heater_shaker_adapter, use_gripper=True) + heater_shaker.close_labware_latch() + + heater_shaker.set_target_temperature(38) + heater_shaker.set_and_wait_for_shake_speed(777) + heater_shaker.wait_for_temperature() + + heater_shaker.deactivate_heater() + heater_shaker.deactivate_shaker() + heater_shaker.open_labware_latch() + + ctx.move_labware(dest_pcr_plate, temperature_module_adapter, use_gripper=True) + temperature_module.set_temperature(38) + temperature_module.deactivate() + + ctx.move_labware(dest_pcr_plate, absorbance_module, use_gripper=True) + absorbance_module.close_lid() + + result = absorbance_module.read(export_filename="smoke_APR_data.csv") + msg = f"single: {result}" + ctx.comment(msg=msg) + ctx.pause(msg=msg) + absorbance_module.open_lid() + ctx.move_labware(dest_pcr_plate, "C2", use_gripper=True) + + if STACKER_PARAMS == "1": + ctx.move_labware(tip_rack_3, waste_chute, use_gripper=True) + else: + ctx.move_labware(tip_rack_3, stacker_C4, use_gripper=True) + stacker_C4.store() + + + ######################### + # Liquid Class Transfer # + ######################### + + ''' + We are going to go through each liquid class at 50, 200, and 1000 with the 1000uL tips + This wil take place on two tip racks. One is the tip rack on the adapter. This will be used with the three main transfers. + One will be on the deck used for partial tip pickups. It will go through water with a column pickup and glycerol with a single + These should have identical steps to their friend above in the last line of the for 'LC in classy' for loop + ''' + + + classy = [water_class,glycerol_50, ethanol_80 ] + ''' + for rack in [tip_rack_5, tip_rack_6]: + water = water_class.get_for(pipette_96_channel,tip_rack_6) + glycerol_50 = glycerol_50.get_for(pipette_96_channel,tip_rack_6) + ethanol_80 = ethanol_80.get_for(pipette_96_channel,tip_rack_6) + water.aspirate.aspirate_position.position_reference = "liquid-meniscus" + water.aspirate.aspirate_position.offset = (0, 0, -1.5) + water.aspirate.retract.end_position.position_reference = "liquid-meniscus" + water.aspirate.retract.end_position.offset = (0, 0, 5) + water.dispense.submerge.start_position.position_reference = "liquid-meniscus" + water.dispense.submerge.start_position.offset = (0, 0, 40) + glycerol_50.aspirate.aspirate_position.position_reference = "liquid-meniscus" + glycerol_50.aspirate.aspirate_position.offset = (0, 0, -1.5) + glycerol_50.aspirate.retract.end_position.position_reference = "liquid-meniscus" + glycerol_50.aspirate.retract.end_position.offset = (0, 0, 5) + glycerol_50.dispense.submerge.start_position.position_reference = "liquid-meniscus" + glycerol_50.dispense.submerge.start_position.offset = (0, 0, 40) + ethanol_80.aspirate.aspirate_position.position_reference = "liquid-meniscus" + ethanol_80.aspirate.aspirate_position.offset = (0, 0, -1.5) + ethanol_80.aspirate.retract.end_position.position_reference = "liquid-meniscus" + ethanol_80.aspirate.retract.end_position.offset = (0, 0, 5) + ethanol_80.dispense.submerge.start_position.position_reference = "liquid-meniscus" + ethanol_80.dispense.submerge.start_position.offset = (0, 0, 40) + ''' + + + liquid_classy_iterator = 0 # Initialize outside the loop + ctx.move_labware(tip_rack_1, waste_chute, use_gripper = True) + print('new') + tip_rack_6 = stacker_D4.retrieve() + ctx.move_lid(tip_rack_6, waste_chute, use_gripper = True) + ctx.move_labware(tip_rack_6, tip_rack_adapter, use_gripper = False) + tip_rack_5 = stacker_D4.retrieve() + ctx.move_lid(tip_rack_5, waste_chute, use_gripper = True) + ctx.move_labware(tip_rack_5, 'C3', use_gripper = False) + pipette_96_channel.liquid_presence_detection = False + + class_names = ['water', 'glycerol_50', 'ethanol_80'] + + for i, LC in enumerate(classy): + ctx.comment(f"This is the liquid class: {class_names[i]}") + + # First part - use tip_rack_6 for all liquid classes + pipette_96_channel.configure_nozzle_layout(style=protocol_api.ALL, start="A1") + pipette_96_channel.pick_up_tip(tip_rack_6['A1']) # Use a different well for each iteration + pipette_96_channel.transfer_with_liquid_class( + liquid_class=LC, + volume=50, + source=[source_reservoir["A1"]], + dest=[dest_pcr_plate['A1']], + new_tip='never', + group_wells = False + ) + pipette_96_channel.transfer_with_liquid_class( + liquid_class=LC, + volume=40, + source=[dest_pcr_plate["A1"]], + dest=[source_reservoir['A1']], + new_tip='never', + group_wells=False + ) + pipette_96_channel.transfer_with_liquid_class( + liquid_class=LC, + volume=50, + source=[source_reservoir['A1']], + dest=[source_reservoir["A1"]], + new_tip='never', + group_wells=False + ) + pipette_96_channel.return_tip() + pipette_96_channel.reset_tipracks() + + # Second part - use different configurations based on the iteration + ctx.comment('This is a configuration') + ctx.pause(msg='When you do single vs. column tip pickup, they should be using the same liquid handling steps') + + # Use a different configuration for each liquid class + if i == 0: # First liquid class (water_class) + pipette_96_channel.configure_nozzle_layout(style=protocol_api.COLUMN, start="A12") + pipette_96_channel.pick_up_tip(tip_rack_5['A1']) + pipette_96_channel.transfer_with_liquid_class( + liquid_class=LC, # Use LC instead of water_class + volume=50, + source=[source_reservoir["A1"]], + dest=[dest_pcr_plate['A2']], + new_tip='never', + group_wells = False + ) + pipette_96_channel.drop_tip() + elif i == 1: # Second liquid class (glycerol_50) + pipette_96_channel.configure_nozzle_layout(style=protocol_api.SINGLE, start="A12") + pipette_96_channel.pick_up_tip(tip_rack_5['A1']) + pipette_96_channel.transfer_with_liquid_class( + liquid_class=LC, # Use LC instead of water_class + volume=50, + source=source_reservoir["A1"], + dest=dest_pcr_plate['B1'], + new_tip='never' + ) + pipette_96_channel.drop_tip() + else: # Third liquid class (ethanol_80) + pass + + # Reset to default configuration after each iteration + pipette_96_channel.configure_nozzle_layout(style=protocol_api.ALL) + + + ###################### + # labware.set_offset # + ###################### + + SET_OFFSET_AMOUNT = 10.0 + ctx.move_labware(labware=source_reservoir, new_location=protocol_api.OFF_DECK, use_gripper=False) + pipette_96_channel.pick_up_tip(tip_rack_6["A1"]) + pipette_96_channel.move_to(dest_pcr_plate.wells_by_name()["A1"].top()) + + ctx.pause("Is the pipette tip in the middle of the PCR Plate, well A1, in slot C2? It should be at the LPC calibrated height.") + + dest_pcr_plate.set_offset( + x=0.0, + y=0.0, + z=SET_OFFSET_AMOUNT, + ) + + pipette_96_channel.move_to(dest_pcr_plate.wells_by_name()["A1"].top()) + ctx.pause( + "Is the pipette tip in the middle of the PCR Plate, well A1, in slot C2? It should be 10mm higher than the LPC calibrated height." + ) + ctx.move_labware(labware=dest_pcr_plate, new_location="D2", use_gripper=False) + pipette_96_channel.move_to(dest_pcr_plate.wells_by_name()["A1"].top()) + + ctx.pause("Is the pipette tip in the middle of the PCR Plate, well A1, in slot D2? It should be at the LPC calibrated height.") + + dest_pcr_plate.set_offset( + x=0.0, + y=0.0, + z=SET_OFFSET_AMOUNT, + ) + + pipette_96_channel.move_to(dest_pcr_plate.wells_by_name()["A1"].top()) + ctx.pause( + "Is the pipette tip in the middle of the PCR Plate, well A1, in slot D2? It should be 10mm higher than the LPC calibrated height." + ) + + ctx.move_labware(labware=dest_pcr_plate, new_location="C2", use_gripper=False) + pipette_96_channel.move_to(dest_pcr_plate.wells_by_name()["A1"].top()) + + ctx.pause( + "Is the pipette tip in the middle of the PCR Plate, well A1, in slot C2? It should be 10mm higher than the LPC calibrated height." + ) + + ctx.move_labware(labware=source_reservoir, new_location="D2", use_gripper=False) + pipette_96_channel.move_to(source_reservoir.wells_by_name()["A1"].top()) + + ctx.pause("Is the pipette tip in the middle of the reservoir , well A1, in slot D2? It should be at the LPC calibrated height.") + + pipette_96_channel.return_tip() + + ctx.pause("!!!!!!!!!!YOU NEED TO REDO LPC!!!!!!!!!!") + ctx.comment('This protocol has completed successfully. 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