Update 4e4c0c.ot2.apiv2.py.json

Fixed blowout in the protoBuilds

protoBuilds/4e4c0c/4e4c0c.ot2.apiv2.py.json

@@ -1,5 +1,5 @@
 {
-    "content": "import math\n\nmetadata = {\n    'protocolName': 'KingFisher Flex Plate Set Up',\n    'author': 'Steve Plonk <[email protected]>',\n    'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n    # get parameter values from json\n    [num_cols, labware_processing_plate, labware_reservoir_12well,\n     labware_reservoir_1well,\n        m300_mount, m20_mount] = get_values(  # noqa: F821\n      \"num_cols\", \"labware_processing_plate\", \"labware_reservoir_12well\",\n      \"labware_reservoir_1well\", \"m300_mount\", \"m20_mount\")\n\n    ctx.set_rail_lights(True)\n    ctx.delay(seconds=5)\n    if not 1 <= num_cols <= 12:\n        raise Exception('Invalid number of columns (must be 1-12).')\n\n    # tips, p300 and p20 multi\n    tips300 = [ctx.load_labware(\n     \"opentrons_96_filtertiprack_200ul\", str(slot)) for slot in [11]]\n    p300m = ctx.load_instrument(\n        \"p300_multi_gen2\", m300_mount, tip_racks=tips300)\n\n    tips20 = [ctx.load_labware(\n     \"opentrons_96_filtertiprack_20ul\", str(slot)) for slot in [10]]\n    p20m = ctx.load_instrument(\n        \"p20_multi_gen2\", m20_mount, tip_racks=tips20)\n\n    # yield list chunks of size n\n    def create_chunks(list_name, n):\n        for i in range(0, len(list_name), n):\n            yield list_name[i:i+n]\n\n    # return liquid height in a well\n    def liq_height(well, effective_diameter=None):\n        if well.diameter:\n            if effective_diameter:\n                radius = effective_diameter / 2\n            else:\n                radius = well.diameter / 2\n            csa = math.pi*(radius**2)\n        else:\n            csa = well.length*well.width\n        return well.liq_vol / csa\n\n    def slow_tip_withdrawal(pipette, well_location, to_center=False):\n        if pipette.mount == 'right':\n            axis = 'A'\n        else:\n            axis = 'Z'\n\n        ctx.max_speeds[axis] = 10\n        if to_center is False:\n            pipette.move_to(well_location.top())\n        else:\n            pipette.move_to(well_location.center())\n        ctx.max_speeds[axis] = None\n\n    # to extend aspirate\n    def extended1(func):\n        \"\"\"\n        Extend aspirate method.\n\n        For viscous liquids.\n        Half default flow rate.\n        Delay after aspiration.\n        Slow departure of tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs, rate=0.5)\n            ctx.delay(seconds=1)\n            slow_tip_withdrawal(func.__self__, [*args][1].labware.object)\n        return wrapper\n\n    # to extend aspirate\n    def extended2(func):\n        \"\"\"\n        Extend aspirate method.\n\n        For volatile liquids.\n        Post-aspirate air gap.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs)\n            func.__self__.air_gap(20)\n        return wrapper\n\n    # to extend dispense\n    def extended3(func):\n        \"\"\"\n        Extend dispense method.\n\n        For viscous liquids.\n        Half default flow rate.\n        Delay after dispense.\n        Blow out at top of well.\n        Touch tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs, rate=0.5)\n            ctx.delay(seconds=1)\n            func.__self__.blow_out([*args][1].labware.object.top())\n            func.__self__.touch_tip()\n        return wrapper\n\n    # to extend dispense\n    def extended4(func):\n        \"\"\"\n        Extend dispense method.\n\n        For volatile liquids.\n        Delayed blow out at top of well.\n        Touch tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs)\n            func.__self__.move_to([*args][1].labware.object.top())\n            ctx.delay(seconds=0.5)\n            func.__self__.blow_out([*args][1].labware.object.top())\n            func.__self__.touch_tip()\n        return wrapper\n\n    # to extend dispense\n    def extended5(func):\n        \"\"\"\n        Extend dispense method.\n\n        For aqueous liquids.\n        Blow out at top of well.\n        Touch tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs)\n            func.__self__.blow_out([*args][1].labware.object.top())\n            func.__self__.touch_tip()\n        return wrapper\n\n    washreservoir = ctx.load_labware(\n     labware_reservoir_1well, '8', 'Wash Buffer')\n\n    etohreservoir = ctx.load_labware(\n     labware_reservoir_1well, '9', '80 Percent EtOH')\n\n    twelvewellreservoir = ctx.load_labware(\n        labware_reservoir_12well, '7', '12-Well Reservoir')\n\n    source_dict = {\n     'Proteinase K Solution': twelvewellreservoir.wells_by_name()['A1'],\n     'Wash Buffer': washreservoir.wells()[0],\n     '80 Percent EtOH': etohreservoir.wells()[0],\n     'Elution Solution': twelvewellreservoir.wells_by_name()['A12']}\n\n    processingplates = [\n     ctx.load_labware(\n      labware_processing_plate, str(slot+1), name) for name, slot in zip(\n      ['Sample Plate',\n       'Wash Plate 1',\n       'Wash Plate 2',\n       'Wash Plate 3',\n       'Elution Plate 4'],\n      [*range(5)])]\n\n    for source, lc, tfervol in zip(\n     [value for value in source_dict.values()],\n     ['aqueous', 'viscous', 'volatile', 'aqueous'],\n     [10, 1000, 1500, 100]):\n\n        source.liq_class = lc\n        source.liq_vol = 1.1*(tfervol*8*num_cols)\n\n    for source, transfervolume, plate in zip(\n        [source_dict[reagent] for reagent in [\n         'Proteinase K Solution',\n         'Wash Buffer',\n         '80 Percent EtOH',\n         '80 Percent EtOH',\n         'Elution Solution']],\n        [10, 1000, 1000, 500, 100],\n            processingplates):\n\n        pip = p20m if transfervolume <= 20 else p300m\n\n        # python dict to store and dispatch extended aspirate\n        pip_aspirate = {'viscous': extended1(pip.aspirate),\n                        'volatile': extended2(pip.aspirate),\n                        'aqueous': pip.aspirate}\n\n        # python dict to store and dispatch extended dispense\n        pip_dispense = {'viscous': extended3(pip.dispense),\n                        'volatile': extended4(pip.dispense),\n                        'aqueous': extended5(pip.dispense)}\n\n        vol_airgap = 20 if source.liq_class == 'volatile' else 0\n\n        reps = math.ceil(\n         transfervolume / (\n          pip.tip_racks[0].wells()[0].max_volume - vol_airgap))\n\n        v = transfervolume / reps\n\n        pip.pick_up_tip()\n\n        for column in plate.columns()[:num_cols]:\n\n            dest = column[0].top(\n            ) if v > 50 else column[0].bottom(1)\n\n            for rep in range(reps):\n\n                source.liq_vol -= v*pip.channels\n\n                tipheight = liq_height(\n                 source) - 3 if liq_height(source) - 3 > 1 else 1\n\n                pip_aspirate[source.liq_class](v, source.bottom(tipheight))\n\n                pip_dispense[source.liq_class](v+vol_airgap, dest)\n\n        pip.drop_tip()\n\n    ctx.comment(\"Finished set up of five processing plates\")\n",
+    "content": "import math\n\nmetadata = {\n    'protocolName': 'KingFisher Flex Plate Set Up',\n    'author': 'Steve Plonk <[email protected]>',\n    'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n    # get parameter values from json\n    [num_cols, labware_processing_plate, labware_reservoir_12well,\n     labware_reservoir_1well,\n        m300_mount, m20_mount] = get_values(  # noqa: F821\n      \"num_cols\", \"labware_processing_plate\", \"labware_reservoir_12well\",\n      \"labware_reservoir_1well\", \"m300_mount\", \"m20_mount\")\n\n    ctx.set_rail_lights(True)\n    ctx.delay(seconds=5)\n    if not 1 <= num_cols <= 12:\n        raise Exception('Invalid number of columns (must be 1-12).')\n\n    # tips, p300 and p20 multi\n    tips300 = [ctx.load_labware(\n     \"opentrons_96_filtertiprack_200ul\", str(slot)) for slot in [11]]\n    p300m = ctx.load_instrument(\n        \"p300_multi_gen2\", m300_mount, tip_racks=tips300)\n\n    tips20 = [ctx.load_labware(\n     \"opentrons_96_filtertiprack_20ul\", str(slot)) for slot in [10]]\n    p20m = ctx.load_instrument(\n        \"p20_multi_gen2\", m20_mount, tip_racks=tips20)\n\n    # yield list chunks of size n\n    def create_chunks(list_name, n):\n        for i in range(0, len(list_name), n):\n            yield list_name[i:i+n]\n\n    # return liquid height in a well\n    def liq_height(well, effective_diameter=None):\n        if well.diameter:\n            if effective_diameter:\n                radius = effective_diameter / 2\n            else:\n                radius = well.diameter / 2\n            csa = math.pi*(radius**2)\n        else:\n            csa = well.length*well.width\n        return well.liq_vol / csa\n\n    def slow_tip_withdrawal(pipette, well_location, to_center=False):\n        if pipette.mount == 'right':\n            axis = 'A'\n        else:\n            axis = 'Z'\n\n        ctx.max_speeds[axis] = 10\n        if to_center is False:\n            pipette.move_to(well_location.top())\n        else:\n            pipette.move_to(well_location.center())\n        ctx.max_speeds[axis] = None\n\n    # to extend aspirate\n    def extended1(func):\n        \"\"\"\n        Extend aspirate method.\n\n        For viscous liquids.\n        Half default flow rate.\n        Delay after aspiration.\n        Slow departure of tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs, rate=0.5)\n            ctx.delay(seconds=1)\n            slow_tip_withdrawal(func.__self__, [*args][1].labware.object)\n        return wrapper\n\n    # to extend aspirate\n    def extended2(func):\n        \"\"\"\n        Extend aspirate method.\n\n        For volatile liquids.\n        Post-aspirate air gap.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs)\n            func.__self__.air_gap(20)\n        return wrapper\n\n    # to extend dispense\n    def extended3(func):\n        \"\"\"\n        Extend dispense method.\n\n        For viscous liquids.\n        Half default flow rate.\n        Delay after dispense.\n        Blow out at top of well.\n        Touch tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs, rate=0.5)\n            ctx.delay(seconds=1)\n            # func.__self__.blow_out([*args][1].labware.object.top())\n            func.__self__.touch_tip()\n        return wrapper\n\n    # to extend dispense\n    def extended4(func):\n        \"\"\"\n        Extend dispense method.\n\n        For volatile liquids.\n        Delayed blow out at top of well.\n        Touch tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs)\n            func.__self__.move_to([*args][1].labware.object.top())\n            ctx.delay(seconds=0.5)\n            # func.__self__.blow_out([*args][1].labware.object.top())\n            func.__self__.touch_tip()\n        return wrapper\n\n    # to extend dispense\n    def extended5(func):\n        \"\"\"\n        Extend dispense method.\n\n        For aqueous liquids.\n        Blow out at top of well.\n        Touch tip.\n        \"\"\"\n        def wrapper(*args, **kwargs):\n            func(*args, **kwargs)\n            func.__self__.blow_out([*args][1].labware.object.top())\n            func.__self__.touch_tip()\n        return wrapper\n\n    washreservoir = ctx.load_labware(\n     labware_reservoir_1well, '8', 'Wash Buffer')\n\n    etohreservoir = ctx.load_labware(\n     labware_reservoir_1well, '9', '80 Percent EtOH')\n\n    twelvewellreservoir = ctx.load_labware(\n        labware_reservoir_12well, '7', '12-Well Reservoir')\n\n    source_dict = {\n     'Proteinase K Solution': twelvewellreservoir.wells_by_name()['A1'],\n     'Wash Buffer': washreservoir.wells()[0],\n     '80 Percent EtOH': etohreservoir.wells()[0],\n     'Elution Solution': twelvewellreservoir.wells_by_name()['A12']}\n\n    processingplates = [\n     ctx.load_labware(\n      labware_processing_plate, str(slot+1), name) for name, slot in zip(\n      ['Sample Plate',\n       'Wash Plate 1',\n       'Wash Plate 2',\n       'Wash Plate 3',\n       'Elution Plate 4'],\n      [*range(5)])]\n\n    for source, lc, tfervol in zip(\n     [value for value in source_dict.values()],\n     ['aqueous', 'viscous', 'volatile', 'aqueous'],\n     [10, 1000, 1500, 100]):\n\n        source.liq_class = lc\n        source.liq_vol = 1.1*(tfervol*8*num_cols)\n\n    for source, transfervolume, plate in zip(\n        [source_dict[reagent] for reagent in [\n         'Proteinase K Solution',\n         'Wash Buffer',\n         '80 Percent EtOH',\n         '80 Percent EtOH',\n         'Elution Solution']],\n        [10, 1000, 1000, 500, 100],\n            processingplates):\n\n        pip = p20m if transfervolume <= 20 else p300m\n\n        # python dict to store and dispatch extended aspirate\n        pip_aspirate = {'viscous': extended1(pip.aspirate),\n                        'volatile': extended2(pip.aspirate),\n                        'aqueous': pip.aspirate}\n\n        # python dict to store and dispatch extended dispense\n        pip_dispense = {'viscous': extended3(pip.dispense),\n                        'volatile': extended4(pip.dispense),\n                        'aqueous': extended5(pip.dispense)}\n\n        vol_airgap = 20 if source.liq_class == 'volatile' else 0\n\n        reps = math.ceil(\n         transfervolume / (\n          pip.tip_racks[0].wells()[0].max_volume - vol_airgap))\n\n        v = transfervolume / reps\n\n        pip.pick_up_tip()\n\n        for column in plate.columns()[:num_cols]:\n\n            dest = column[0].top(\n            ) if v > 50 else column[0].bottom(1)\n\n            for rep in range(reps):\n\n                source.liq_vol -= v*pip.channels\n\n                tipheight = liq_height(\n                 source) - 3 if liq_height(source) - 3 > 1 else 1\n\n                pip_aspirate[source.liq_class](v, source.bottom(tipheight))\n\n                pip_dispense[source.liq_class](v+vol_airgap, dest)\n\n        pip.drop_tip()\n\n    ctx.comment(\"Finished set up of five processing plates\")\n",
     "custom_labware_defs": [
         {
             "brand": {
@@ -1396,4 +1396,4 @@
         "protocolName": "KingFisher Flex Plate Set Up"
     },
     "modules": []
-}
+}