From 8f3bd4fc19c3975ab4a0ed5f39ab246e5c0ca89c Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Wed, 8 Jan 2025 09:07:36 -0600 Subject: [PATCH 1/2] test(analyses): add refactored 8.2 smoke test --- .../automation/data/protocols.py | 7 + ...S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke.py | 458 ++++++++++++++++++ 2 files changed, 465 insertions(+) create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke.py diff --git a/analyses-snapshot-testing/automation/data/protocols.py b/analyses-snapshot-testing/automation/data/protocols.py index ada74a736e0..4acad3c0702 100644 --- a/analyses-snapshot-testing/automation/data/protocols.py +++ b/analyses-snapshot-testing/automation/data/protocols.py @@ -709,6 +709,13 @@ class Protocols: robot="Flex", ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke.py + Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke: Protocol = Protocol( + file_stem="Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke", + file_extension="py", + robot="Flex", + ) + OT2_X_v2_18_None_None_duplicateRTPVariableName: Protocol = Protocol( file_stem="OT2_X_v2_18_None_None_duplicateRTPVariableName", file_extension="py", diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke.py new file mode 100644 index 00000000000..20d77fd560f --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke.py @@ -0,0 +1,458 @@ +############# +# CHANGELOG # +############# + +# ---- +# 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 +from opentrons.protocol_api import Labware + + +metadata = { + "protocolName": "Flex Smoke Test - v2.21", + "author": "QA team", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.21", +} + + +################# +### 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_NAME = "opentrons_flex_96_tiprack_1000ul" +PIPETTE_96_CHANNEL_NAME = "flex_96channel_1000" +WELL_PLATE_STARTING_POSITION = "C2" +RESERVOIR_STARTING_POSITION = "D2" + + +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 '๐ŸŸข' for present tips and a 'โŒ' 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 = "๐ŸŸข" if has_tip else "โŒ" + 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 add_parameters(parameters: protocol_api.Parameters): + """This is the standard use of parameters""" + + # We are using the defaults for every case. + # Other tests cover regression testing for + # other types of parameters and UI appearance + # there are many tests in Analyses Battery that cover errors and edge cases + + parameters.add_str( + variable_name="test_configuration", + display_name="Test Configuration", + description="Configuration of QA test to perform", + default="full", + choices=[{"display_name": "Full Smoke Test", "value": "full"}], + ) + + parameters.add_str( + variable_name="reservoir_name", + display_name="Reservoir Name", + description="Name of the reservoir", + default="nest_1_reservoir_290ml", + choices=[{"display_name": "Nest 1 Well 290 mL", "value": "nest_1_reservoir_290ml"}], + ) + + parameters.add_str( + variable_name="well_plate_name", + display_name="Well Plate Name", + description="Name of the well plate", + default="opentrons_96_wellplate_200ul_pcr_full_skirt", + choices=[{"display_name": "Opentrons Tough 96 Well 200 ยตL", "value": "opentrons_96_wellplate_200ul_pcr_full_skirt"}], + ) + + +def log_position(ctx, item): + ctx.comment(f"Item {item.load_name} is at {item.parent}") + + +def run(ctx: protocol_api.ProtocolContext) -> None: + + ################ + ### FIXTURES ### + ################ + + waste_chute = ctx.load_waste_chute() + + ############### + ### MODULES ### + ############### + deck_riser_adapter = ctx.load_adapter(DECK_RISER_NAME, "A4") + 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: List[Labware] = [deck_riser_adapter.load_labware(TC_LID)] + for i in range(LID_COUNT - 1): + lids.append(lids[-1].load_labware(TC_LID)) + lids.reverse() + + 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 + source_reservoir = ctx.load_labware(ctx.params.reservoir_name, RESERVOIR_STARTING_POSITION) + dest_pcr_plate = ctx.load_labware(ctx.params.well_plate_name, WELL_PLATE_STARTING_POSITION) + + tip_rack_1 = ctx.load_labware(TIPRACK_96_NAME, "A2", adapter=TIPRACK_96_ADAPTER_NAME) + tip_rack_adapter = tip_rack_1.parent + + tip_rack_2 = ctx.load_labware(TIPRACK_96_NAME, "C3") + tip_rack_3 = ctx.load_labware(TIPRACK_96_NAME, "C4") + tip_rack_5 = ctx.load_labware(TIPRACK_96_NAME, protocol_api.OFF_DECK) + + tip_racks = [tip_rack_1, tip_rack_2, tip_rack_3] + + ########################## + ### 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) + + ######################## + ### LOAD SOME LIQUID ### + ######################## + + water = ctx.define_liquid(name="water", description="High Quality Hโ‚‚O", display_color="#42AB2D") + source_reservoir.wells_by_name()["A1"].load_liquid(liquid=water, volume=29000) + + ################################ + ### GRIPPER LABWARE MOVEMENT ### + ################################ + + 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, "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? + + # 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 + ctx.move_labware(tip_rack_2, 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_labware(lids[0], dest_pcr_plate, use_gripper=True) # we reversed this list earlier + thermocycler.close_lid() + thermocycler.set_block_temperature(38, hold_time_seconds=5.0) + thermocycler.set_lid_temperature(38) + thermocycler.open_lid() + ctx.move_labware(lids[0], 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) + + # ###################### + # # labware.set_offset # + # ###################### + + # # -------------------------- # + # # Added in API version: 2.18 # + # # -------------------------- # + + 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_1["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.move_labware(tip_rack_3, waste_chute, use_gripper=True) + + ctx.pause("!!!!!!!!!!YOU NEED TO REDO LPC!!!!!!!!!!") + + # Test the unique top() methods for TrashBin and WasteChute. + # Well objects should remain the same + + ######################## + # unique top() methods # + ######################## + + # ---------------------------- # + # Changed in API version: 2.18 # + # ---------------------------- # + + assert isinstance(waste_chute.top(), protocol_api.WasteChute) + assert isinstance(source_reservoir.wells_by_name()["A1"].top(), types.Location) From 0d74ba89437793e206b90414ae2fb25ae6668644 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 8 Jan 2025 09:39:04 -0600 Subject: [PATCH 2/2] fix(analyses-snapshot-testing): heal eight-two-smoke snapshots (#17215) --- ...2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke].json | 15120 ++++++++++++++++ 1 file changed, 15120 insertions(+) create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[2b866b03f3][Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke].json diff --git a/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[2b866b03f3][Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke].json b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[2b866b03f3][Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke].json new file mode 100644 index 00000000000..0454e8ec9c9 --- /dev/null +++ b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[2b866b03f3][Flex_S_v2_21_P1000_96_GRIP_HS_MB_TC_TM_Smoke].json @@ -0,0 +1,15120 @@ +{ + "commandAnnotations": [], + "commands": [ + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "50c7ae73a4e3f7129874f39dfb514803", + "notes": [], + "params": {}, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "loadLabware", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "73d9d4d55ae8466f3a793ceb70545fa5", + "notes": [], + "params": { + "loadName": "opentrons_flex_deck_riser", + "location": { + "addressableAreaName": "A4" + }, + "namespace": "opentrons", + "version": 1 + }, + "result": { + "definition": { + "allowedRoles": [ + "adapter" + ], + "brand": { + "brand": "Opentrons", + "brandId": [] + }, + "cornerOffsetFromSlot": { + "x": -6.125, + "y": -6.125, + "z": 0 + }, + "dimensions": { + "xDimension": 140, + "yDimension": 98, + "zDimension": 55 + }, + "gripperOffsets": {}, + "groups": [ + { + "metadata": {}, + "wells": [] + } + ], + "metadata": { + "displayCategory": "adapter", + "displayName": "Opentrons Flex Deck Riser", + "displayVolumeUnits": "ยตL", + "tags": [] + }, + "namespace": "opentrons", + "ordering": [], + "parameters": { 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