feat(abr-testing): protocol to test disposable lid with any pcr plate type (#16837)

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# Overview

Protocol for testing `opentrons_tough_pcr_auto_sealing_lid` with any pcr
plate

## Test Plan and Hands on Testing

- Simulated profile with each lid type
- Physically tested lid on thermocycler with biorad plate

## Changelog

- added helper function for parameter with pcr plate types
- added evaporation protocol
- fixed abr1 bug where it resets a tip rack twice which causes the
pipette to pick up from an empty slot
- changed abr10 protocol to reflect comments about liquids at top

## Review requests

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- What do you need from reviewers to feel confident this PR is ready to
merge?
- Ask questions.
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## Risk assessment

- lid is currently not compatible with biorad plate or nest plate, but
pr in progress for this.

Author: rclarke0

abr-testing/abr_testing/protocols/active_protocols/10_ZymoBIOMICS_Magbead_DNA_Cells_Flex.py

@@ -94,7 +94,6 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
         bind_time_1 = bind_time_2 = wash_time = 0.25
         drybeads = 0.5
         lysis_rep_1 = lysis_rep_2 = bead_reps_2 = 1
-    PK_vol = 20.0
     bead_vol = 25.0
     starting_vol = lysis_vol + sample_vol
     binding_buffer_vol = bind_vol + bead_vol
@@ -137,7 +136,7 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     """
     lysis_ = res1.wells()[0]
     binding_buffer = res1.wells()[1:4]
-    bind2_res = res1.wells()[4:6]
+    bind2_res = res1.wells()[4:8]
     wash1 = res1.wells()[6:8]
     elution_solution = res1.wells()[-1]
     wash2 = res2.wells()[:6]
@@ -149,16 +148,12 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     samps = sample_plate.wells()[: (8 * num_cols)]
 
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Lysis": [{"well": lysis_, "volume": lysis_vol}],
-        "PK": [{"well": lysis_, "volume": PK_vol}],
-        "Beads": [{"well": binding_buffer, "volume": bead_vol}],
-        "Binding": [{"well": binding_buffer, "volume": bind_vol}],
-        "Binding 2": [{"well": bind2_res, "volume": bind2_vol}],
-        "Wash 1": [{"well": wash1_vol, "volume": wash1}],
-        "Wash 2": [{"well": wash2_vol, "volume": wash2}],
-        "Wash 3": [{"well": wash3_vol, "volume": wash3}],
-        "Final Elution": [{"well": elution_solution, "volume": elution_vol}],
-        "Samples": [{"well": samps, "volume": 0}],
+        "Lysis and PK": [{"well": lysis_, "volume": 12320.0}],
+        "Beads and Binding": [{"well": binding_buffer, "volume": 11875.0}],
+        "Binding 2": [{"well": bind2_res, "volume": 13500.0}],
+        "Final Elution": [{"well": elution_solution, "volume": 52000}],
+        "Samples": [{"well": samps, "volume": 0.0}],
+        "Reagents": [{"well": res2.wells(), "volume": 9000.0}],
     }
     flattened_list_of_wells = helpers.find_liquid_height_of_loaded_liquids(
         ctx, liquid_vols_and_wells, m1000

abr-testing/abr_testing/protocols/active_protocols/1_Simple Normalize Long Right.py

@@ -121,8 +121,6 @@ def run(protocol: ProtocolContext) -> None:
         style=SINGLE, start="H1", tip_racks=[tiprack_x_1, tiprack_x_2, tiprack_x_3]
     )
     helpers.find_liquid_height_of_all_wells(protocol, p1000, wells)
-    tiprack_x_1.reset()
-
     sample_quant_csv = """
     sample_plate_1, Sample_well,DYE,DILUENT
     sample_plate_1,A1,0,100

abr-testing/abr_testing/protocols/helpers.py

@@ -14,7 +14,6 @@
     ThermocyclerContext,
     TemperatureModuleContext,
 )
-
 from typing import List, Union, Dict
 from opentrons.hardware_control.modules.types import ThermocyclerStep
 from opentrons_shared_data.errors.exceptions import PipetteLiquidNotFoundError
@@ -225,6 +224,31 @@ def create_hs_speed_parameter(parameters: ParameterContext) -> None:
     )
 
 
+def create_tc_compatible_labware_parameter(parameters: ParameterContext) -> None:
+    """Create parameter for labware type compatible with thermocycler."""
+    parameters.add_str(
+        variable_name="labware_tc_compatible",
+        display_name="Labware Type for Thermocycler",
+        description="labware compatible with thermocycler.",
+        default="biorad_96_wellplate_200ul_pcr",
+        choices=[
+            {
+                "display_name": "Armadillo_200ul",
+                "value": "armadillo_96_wellplate_200ul_pcr_full_skirt",
+            },
+            {"display_name": "Bio-Rad_200ul", "value": "biorad_96_wellplate_200ul_pcr"},
+            {
+                "display_name": "NEST_100ul",
+                "value": "nest_96_wellplate_100ul_pcr_full_skirt",
+            },
+            {
+                "display_name": "Opentrons_200ul",
+                "value": "opentrons_96_wellplate_200ul_pcr_full_skirt",
+            },
+        ],
+    )
+
+
 # FUNCTIONS FOR COMMON MODULE SEQUENCES
 
 

abr-testing/abr_testing/protocols/liquid_setups/10_ZymoBIOMICS Magbead Liquid Setup.py

@@ -29,23 +29,35 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     res1 = protocol.load_labware("nest_12_reservoir_15ml", "C3", "R1")
     res2 = protocol.load_labware("nest_12_reservoir_15ml", "B3", "R2")
 
-    lysis_and_pk = (3200 + 320) / 8
-    beads_and_binding = (275 + 6600) / 8
-    binding2 = 5500 / 8
-    wash1 = 5500 / 8
-    final_elution = 2100 / 8
+    lysis_and_pk = 12320 / 8
+    beads_and_binding = 11875 / 8
+    binding2 = 13500 / 8
     wash2 = 9000 / 8
-    wash3 = 9000 / 8
+    wash2_list = [wash2] * 12
     # Fill up Plates
     # Res1
     p1000.transfer(
-        volume=[lysis_and_pk, beads_and_binding, binding2, wash1, final_elution],
+        volume=[
+            lysis_and_pk,
+            beads_and_binding,
+            beads_and_binding,
+            beads_and_binding,
+            binding2,
+            binding2,
+            binding2,
+            binding2,
+            binding2,
+        ],
         source=source_reservoir["A1"].bottom(z=0.2),
         dest=[
             res1["A1"].top(),
             res1["A2"].top(),
+            res1["A3"].top(),
+            res1["A4"].top(),
             res1["A5"].top(),
+            res1["A6"].top(),
             res1["A7"].top(),
+            res1["A8"].top(),
             res1["A12"].top(),
         ],
         blow_out=True,
@@ -54,9 +66,9 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     )
     # Res2
     p1000.transfer(
-        volume=[wash2, wash3],
+        volume=wash2_list,
         source=source_reservoir["A1"],
-        dest=[res2["A1"].top(), res2["A7"].top()],
+        dest=res2.wells(),
         blow_out=True,
         blowout_location="source well",
         trash=False,

abr-testing/abr_testing/protocols/test_protocols/tc_biorad_evap_test.py

@@ -0,0 +1,109 @@
+"""Test TC Disposable Lid with BioRad Plate."""
+
+from opentrons.protocol_api import (
+    ProtocolContext,
+    ParameterContext,
+    Well,
+    Labware,
+    InstrumentContext,
+)
+from typing import List
+from abr_testing.protocols import helpers
+from opentrons.protocol_api.module_contexts import ThermocyclerContext
+from opentrons.hardware_control.modules.types import ThermocyclerStep
+
+metadata = {"protocolName": "Tough Auto Seal Lid Evaporation Test"}
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
+
+
+def add_parameters(parameters: ParameterContext) -> None:
+    """Add Parameters."""
+    helpers.create_single_pipette_mount_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
+    helpers.create_tc_compatible_labware_parameter(parameters)
+
+
+def _pcr_cycle(thermocycler: ThermocyclerContext) -> None:
+    """30x cycles of: 70° for 30s 72° for 30s 95° for 10s."""
+    profile_TAG2: List[ThermocyclerStep] = [
+        {"temperature": 70, "hold_time_seconds": 30},
+        {"temperature": 72, "hold_time_seconds": 30},
+        {"temperature": 95, "hold_time_seconds": 10},
+    ]
+    thermocycler.execute_profile(
+        steps=profile_TAG2, repetitions=30, block_max_volume=50
+    )
+
+
+def _fill_with_liquid_and_measure(
+    protocol: ProtocolContext,
+    pipette: InstrumentContext,
+    reservoir: Labware,
+    plate_in_cycler: Labware,
+) -> None:
+    """Fill plate with 10 ul per well."""
+    locations: List[Well] = [
+        plate_in_cycler["A1"],
+        plate_in_cycler["A2"],
+        plate_in_cycler["A3"],
+        plate_in_cycler["A4"],
+        plate_in_cycler["A5"],
+        plate_in_cycler["A6"],
+        plate_in_cycler["A7"],
+        plate_in_cycler["A8"],
+        plate_in_cycler["A9"],
+        plate_in_cycler["A10"],
+        plate_in_cycler["A11"],
+        plate_in_cycler["A12"],
+    ]
+    volumes = [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10]
+    protocol.pause("Weight Armadillo Plate, place on thermocycler")
+    # pipette 10uL into Armadillo wells
+    source_well: Well = reservoir["A1"]
+    pipette.distribute(
+        volume=volumes,
+        source=source_well,
+        dest=locations,
+        return_tips=True,
+        blow_out=False,
+    )
+    protocol.pause("Weight Armadillo Plate, place on thermocycler, put on lid")
+
+
+def run(ctx: ProtocolContext) -> None:
+    """Evaporation Test."""
+    pipette_mount = ctx.params.pipette_mount  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
+    labware_tc_compatible = ctx.params.labware_tc_compatible  # type: ignore[attr-defined]
+    tiprack_50 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "B2")
+    ctx.load_trash_bin("A3")
+    tc_mod: ThermocyclerContext = ctx.load_module(
+        helpers.tc_str
+    )  # type: ignore[assignment]
+    plate_in_cycler = tc_mod.load_labware(labware_tc_compatible)
+    p50 = ctx.load_instrument("flex_8channel_50", pipette_mount, tip_racks=[tiprack_50])
+    unused_lids = helpers.load_disposable_lids(ctx, 5, ["D2"], deck_riser)
+    top_lid = unused_lids[0]
+    reservoir = ctx.load_labware("nest_12_reservoir_15ml", "A2")
+    tc_mod.open_lid()
+    tc_mod.set_block_temperature(4)
+    tc_mod.set_lid_temperature(105)
+
+    # hold at 95° for 3 minutes
+    profile_TAG: List[ThermocyclerStep] = [{"temperature": 95, "hold_time_minutes": 3}]
+    # hold at 72° for 5min
+    profile_TAG3: List[ThermocyclerStep] = [{"temperature": 72, "hold_time_minutes": 5}]
+    tc_mod.open_lid()
+    _fill_with_liquid_and_measure(ctx, p50, reservoir, plate_in_cycler)
+    ctx.move_labware(top_lid, plate_in_cycler, use_gripper=True)
+    tc_mod.close_lid()
+    tc_mod.execute_profile(steps=profile_TAG, repetitions=1, block_max_volume=50)
+    _pcr_cycle(tc_mod)
+    tc_mod.execute_profile(steps=profile_TAG3, repetitions=1, block_max_volume=50)
+    # # # Cool to 4°
+    tc_mod.set_block_temperature(4)
+    tc_mod.set_lid_temperature(105)
+    # Open lid
+    tc_mod.open_lid()
+    ctx.move_labware(top_lid, "C2", use_gripper=True)
+    ctx.move_labware(top_lid, unused_lids[1], use_gripper=True)