import json
from opentrons import protocol_api, types

metadata = {
    "protocolName": "Columns 11 & 12 Pipette Shearing for ONT",
    "author": "ad46",
    "description": "Protocol for pipette shearing 16 DNA extracts in columns 11 & 12 of a KingFisher Apex plate to ~50 kb fragment sizes.",
    "created": "2025-04-28T13:57:56.949Z",
    "lastModified": "2025-10-17T12:50:04.586Z",
    "protocolDesigner": "8.5.6",
    "source": "Protocol Designer",
}

requirements = {"robotType": "OT-2", "apiLevel": "2.24"}

def run(protocol: protocol_api.ProtocolContext) -> None:
    # Load Labware:
    tip_rack_1 = protocol.load_labware(
        "opentrons_96_tiprack_300ul",
        location="2",
        namespace="opentrons",
        version=1,
    )
    well_plate_1 = protocol.load_labware_from_definition(
        CUSTOM_LABWARE["custom_beta/thermofisher_96_wellplate_2000ul/1"],
        location="1",
    )

    # Load Pipettes:
    pipette_right = protocol.load_instrument(
        "p300_multi", "right", tip_racks=[tip_rack_1],
    )

    # Define Liquids:
    liquid_1 = protocol.define_liquid(
        "HMW DNA",
        description="Unsheared HMW DNA",
        display_color="#ff80f5ff",
    )

    # Load Liquids:
    well_plate_1.load_liquid(
        wells=[
            "A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11",
            "A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12"
        ],
        liquid=liquid_1,
        volume=300,
    )

    # PROTOCOL STEPS

    # Step 1:
    pipette_right.pick_up_tip(location=tip_rack_1)
    pipette_right.mix(
        repetitions=800,
        volume=200,
        location=well_plate_1["A11"].bottom(z=4),
        aspirate_flow_rate=769,
        dispense_flow_rate=772,
        final_push_out=0,
    )
    pipette_right.flow_rate.blow_out = 785
    pipette_right.blow_out(well_plate_1["A11"].top(z=-10))
    pipette_right.drop_tip()

    # Step 2:
    pipette_right.pick_up_tip(location=tip_rack_1)
    pipette_right.mix(
        repetitions=800,
        volume=200,
        location=well_plate_1["A12"].bottom(z=4),
        aspirate_flow_rate=769,
        dispense_flow_rate=772,
        final_push_out=0,
    )
    pipette_right.flow_rate.blow_out = 785
    pipette_right.blow_out(well_plate_1["A12"].top(z=-10))
    pipette_right.drop_tip()

CUSTOM_LABWARE = json.loads("""{"custom_beta/thermofisher_96_wellplate_2000ul/1":{"ordering":[["A1","B1","C1","D1","E1","F1","G1","H1"],["A2","B2","C2","D2","E2","F2","G2","H2"],["A3","B3","C3","D3","E3","F3","G3","H3"],["A4","B4","C4","D4","E4","F4","G4","H4"],["A5","B5","C5","D5","E5","F5","G5","H5"],["A6","B6","C6","D6","E6","F6","G6","H6"],["A7","B7","C7","D7","E7","F7","G7","H7"],["A8","B8","C8","D8","E8","F8","G8","H8"],["A9","B9","C9","D9","E9","F9","G9","H9"],["A10","B10","C10","D10","E10","F10","G10","H10"],["A11","B11","C11","D11","E11","F11","G11","H11"],["A12","B12","C12","D12","E12","F12","G12","H12"]],"brand":{"brand":"ThermoFisher","brandId":["95040450"]},"metadata":{"displayName":"ThermoFisher 96 Well Plate 2000 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