Merge pull request #4824 from Opentrons/feat-5eee17_volume

feat(protocols/5eee17): add field for dilution volume

data/data/fields.csv

@@ -1602,6 +1602,7 @@ vol_deaddeepwell,1
 vol_deadreservoir,1
 vol_dil_to_d,1
 vol_dil_to_e,1
+vol_dilution,1
 vol_dispense,1
 vol_dispensed,1
 vol_dna,2

protoBuilds/5eee17/dilution.ot2.apiv2.py.json

@@ -1,5 +1,5 @@
 {
-    "content": "import math\n\nmetadata = {\n    'protocolName': 'HPLC Dilution',\n    'author': 'Nick Diehl <[email protected]>',\n    'source': 'Custom Protocol Request',\n    'apiLevel': '2.12'\n}\n\n\ndef run(ctx):\n\n    [num_extracts, lw_hplc, mixreps_dilution, height_source,\n     height_intermediate_low, height_intermediate_middle,\n     height_intermediate_high, height_final] = get_values(  # noqa: F821\n        'num_extracts', 'lw_hplc', 'mixreps_dilution', 'height_source',\n        'height_intermediate_low', 'height_intermediate_middle',\n        'height_intermediate_high', 'height_final')\n\n    tuberacks_50 = [\n        ctx.load_labware('bd_24_tuberack_50ml_green', slot, '50ml tubes')\n        for slot in ['1', '2']]\n    tuberack_15 = ctx.load_labware('bd_72_tuberack_15ml_orange', '3')\n    tuberack_hplc = ctx.load_labware(lw_hplc, '11', 'HPLC tuberack')\n    tiprack = [ctx.load_labware('opentrons_96_tiprack_1000ul', '10')]\n    p1000l, p1000r = [\n        ctx.load_instrument('p1000_single_gen2', mount, tip_racks=tiprack)\n        for mount in ['left', 'right']]\n    pips = [p1000l, p1000r]\n\n    tip_max = len([well for rack in tiprack for well in rack.wells()])\n    tip_count = 0\n\n    def pick_up(pipettes):\n        nonlocal tip_count\n        for pip in pipettes:\n            if tip_count == tip_max:\n                ctx.pause('Refill tiprack before resuming.')\n                [rack.reset() for rack in tiprack]\n                tip_count = 0\n            tip_count += 1\n            pip.pick_up_tip()\n\n    mix_height_list = [height_intermediate_low, height_intermediate_middle,\n                       height_intermediate_high]\n\n    def mix(pip, reps, vol, loc):\n        p1000r.flow_rate.aspirate *= 6\n        p1000l.flow_rate.aspirate *= 6\n        p1000r.flow_rate.dispense *= 3\n        p1000l.flow_rate.dispense *= 3\n        for rep_ind in range(reps):\n            asp_ind = (rep_ind*2) % 3\n            disp_ind = (rep_ind*2+1) % 3\n            pip.aspirate(vol, loc.bottom(mix_height_list[asp_ind]))\n            pip.dispense(vol, loc.bottom(mix_height_list[disp_ind]))\n        p1000r.flow_rate.aspirate /= 6\n        p1000l.flow_rate.aspirate /= 6\n        p1000r.flow_rate.dispense /= 3\n        p1000l.flow_rate.dispense /= 3\n\n    refill_map = {\n        'source': len(\n            [well for rack in tuberacks_50 for well in rack.wells()]),\n        'intermediate': len(tuberack_15.wells()),\n        'final': len(tuberack_hplc.wells())\n    }\n\n    def check_refill(index):\n        refill_items = []\n        for key, val in refill_map.items():\n            if index % val == 0 and index > 0:\n                refill_items.append(key)\n        if len(refill_items) > 0:\n            ctx.pause(f'Please refill {\", \".join(refill_items)} tubes before \\\nresuming.')\n\n    def get_set_index(set_index, tubes_set_type):\n        set_index_transform = set_index % \\\n            math.floor(refill_map[tubes_set_type]/2)\n        return set_index_transform\n\n    sources = [\n        well for rack in tuberacks_50\n        for well in rack.wells()]\n    source_sets = [\n        sources[i*2:(i+1)*2] if i < math.ceil(len(sources)/2)\n        else sources[i*2:]\n        for i in range(math.ceil(len(sources)/2))]\n    intermediates = [\n        well for col in tuberack_15.columns()\n        for well in col]\n    intermediate_sets = [\n        intermediates[i*2:(i+1)*2]\n        if i < math.ceil(len(intermediates)/2) - 1\n        else intermediates[i*2:]\n        for i in range(math.ceil(len(intermediates)/2))]\n    finals = [\n        well for row in tuberack_hplc.rows()\n        for well in row]\n    final_sets = [\n        finals[i*2:(i+1)*2] if i < math.ceil(len(finals)/2) - 1\n        else finals[i*2:]\n        for i in range(math.ceil(len(finals)/2))]\n\n    # dilute\n    num_sets = math.ceil(num_extracts/2)\n    for set_ind in range(num_sets):\n        check_refill(set_ind*2)\n        source_set = source_sets[get_set_index(set_ind, 'source')]\n        intermediate_set = intermediate_sets[\n            get_set_index(set_ind, 'intermediate')]\n        final_set = final_sets[get_set_index(set_ind, 'final')]\n        pick_up([p1000l, p1000r][:len(source_set)])\n\n        for pip, tube in zip(pips, source_set):\n            pip.aspirate(500, tube.bottom(height_source))\n            pip.air_gap(100)\n\n        for pip, i_tube, f_tube in zip(pips, intermediate_set, final_set):\n            pip.dispense(100, i_tube.top())\n            pip.dispense(pip.current_volume,\n                         i_tube.bottom(height_intermediate_middle))\n            mix(pip, mixreps_dilution, 1000, i_tube)\n            pip.transfer(800, i_tube.bottom(height_intermediate_low),\n                         f_tube.bottom(height_final),\n                         new_tip='never')\n        [pip.drop_tip() for pip in [p1000l, p1000r] if pip.has_tip]\n",
+    "content": "import math\n\nmetadata = {\n    'protocolName': 'HPLC Dilution',\n    'author': 'Nick Diehl <[email protected]>',\n    'source': 'Custom Protocol Request',\n    'apiLevel': '2.12'\n}\n\n\ndef run(ctx):\n\n    [num_extracts, lw_hplc, vol_dilution, mixreps_dilution, height_source,\n     height_intermediate_low, height_intermediate_middle,\n     height_intermediate_high, height_final] = get_values(  # noqa: F821\n        'num_extracts', 'lw_hplc', 'vol_dilution', 'mixreps_dilution',\n        'height_source', 'height_intermediate_low',\n        'height_intermediate_middle', 'height_intermediate_high',\n        'height_final')\n\n    tuberacks_50 = [\n        ctx.load_labware('bd_24_tuberack_50ml_green', slot, '50ml tubes')\n        for slot in ['1', '2']]\n    tuberack_15 = ctx.load_labware('bd_72_tuberack_15ml_orange', '3')\n    tuberack_hplc = ctx.load_labware(lw_hplc, '11', 'HPLC tuberack')\n    tiprack = [ctx.load_labware('opentrons_96_tiprack_1000ul', '10')]\n    p1000l, p1000r = [\n        ctx.load_instrument('p1000_single_gen2', mount, tip_racks=tiprack)\n        for mount in ['left', 'right']]\n    pips = [p1000l, p1000r]\n\n    tip_max = len([well for rack in tiprack for well in rack.wells()])\n    tip_count = 0\n\n    def pick_up(pipettes):\n        nonlocal tip_count\n        for pip in pipettes:\n            if tip_count == tip_max:\n                ctx.pause('Refill tiprack before resuming.')\n                [rack.reset() for rack in tiprack]\n                tip_count = 0\n            tip_count += 1\n            pip.pick_up_tip()\n\n    mix_height_list = [height_intermediate_low, height_intermediate_middle,\n                       height_intermediate_high]\n\n    def mix(pip, reps, vol, loc):\n        p1000r.flow_rate.aspirate *= 6\n        p1000l.flow_rate.aspirate *= 6\n        p1000r.flow_rate.dispense *= 3\n        p1000l.flow_rate.dispense *= 3\n        for rep_ind in range(reps):\n            asp_ind = (rep_ind*2) % 3\n            disp_ind = (rep_ind*2+1) % 3\n            pip.aspirate(vol, loc.bottom(mix_height_list[asp_ind]))\n            pip.dispense(vol, loc.bottom(mix_height_list[disp_ind]))\n        p1000r.flow_rate.aspirate /= 6\n        p1000l.flow_rate.aspirate /= 6\n        p1000r.flow_rate.dispense /= 3\n        p1000l.flow_rate.dispense /= 3\n\n    refill_map = {\n        'source': len(\n            [well for rack in tuberacks_50 for well in rack.wells()]),\n        'intermediate': len(tuberack_15.wells()),\n        'final': len(tuberack_hplc.wells())\n    }\n\n    def check_refill(index):\n        refill_items = []\n        for key, val in refill_map.items():\n            if index % val == 0 and index > 0:\n                refill_items.append(key)\n        if len(refill_items) > 0:\n            ctx.pause(f'Please refill {\", \".join(refill_items)} tubes before \\\nresuming.')\n\n    def get_set_index(set_index, tubes_set_type):\n        set_index_transform = set_index % \\\n            math.floor(refill_map[tubes_set_type]/2)\n        return set_index_transform\n\n    sources = [\n        well for rack in tuberacks_50\n        for well in rack.wells()]\n    source_sets = [\n        sources[i*2:(i+1)*2] if i < math.ceil(len(sources)/2)\n        else sources[i*2:]\n        for i in range(math.ceil(len(sources)/2))]\n    intermediates = [\n        well for col in tuberack_15.columns()\n        for well in col]\n    intermediate_sets = [\n        intermediates[i*2:(i+1)*2]\n        if i < math.ceil(len(intermediates)/2) - 1\n        else intermediates[i*2:]\n        for i in range(math.ceil(len(intermediates)/2))]\n    finals = [\n        well for row in tuberack_hplc.rows()\n        for well in row]\n    final_sets = [\n        finals[i*2:(i+1)*2] if i < math.ceil(len(finals)/2) - 1\n        else finals[i*2:]\n        for i in range(math.ceil(len(finals)/2))]\n\n    # dilute\n    num_sets = math.ceil(num_extracts/2)\n    for set_ind in range(num_sets):\n        check_refill(set_ind*2)\n        source_set = source_sets[get_set_index(set_ind, 'source')]\n        intermediate_set = intermediate_sets[\n            get_set_index(set_ind, 'intermediate')]\n        final_set = final_sets[get_set_index(set_ind, 'final')]\n        pick_up([p1000l, p1000r][:len(source_set)])\n\n        for pip, tube in zip(pips, source_set):\n            pip.aspirate(500, tube.bottom(height_source))\n            pip.air_gap(100)\n\n        for pip, i_tube, f_tube in zip(pips, intermediate_set, final_set):\n            pip.dispense(100, i_tube.top())\n            pip.dispense(pip.current_volume,\n                         i_tube.bottom(height_intermediate_middle))\n            mix(pip, mixreps_dilution, 1000, i_tube)\n            pip.transfer(800, i_tube.bottom(height_intermediate_low),\n                         f_tube.bottom(height_final),\n                         new_tip='never')\n        [pip.drop_tip() for pip in [p1000l, p1000r] if pip.has_tip]\n",
     "custom_labware_defs": [
         {
             "brand": {
@@ -2458,6 +2458,12 @@
             ],
             "type": "dropDown"
         },
+        {
+            "default": 500.0,
+            "label": "dilution volume (in ul)",
+            "name": "vol_dilution",
+            "type": "float"
+        },
         {
             "default": 5,
             "label": "mix repetitions of dilution",
@@ -2468,31 +2474,31 @@
             "default": 5.0,
             "label": "source 50ml tube aspiration height (in mm above bottom)",
             "name": "height_source",
-            "type": "int"
+            "type": "float"
         },
         {
             "default": 5.0,
             "label": "dilution 15ml tube low mix height (in mm above bottom)",
             "name": "height_intermediate_low",
-            "type": "int"
+            "type": "float"
         },
         {
             "default": 30.0,
             "label": "dilution 15ml tube middle mix height (in mm above bottom)",
             "name": "height_intermediate_middle",
-            "type": "int"
+            "type": "float"
         },
         {
             "default": 60.0,
             "label": "dilution 15ml tube high mix height (in mm above bottom)",
             "name": "height_intermediate_high",
-            "type": "int"
+            "type": "float"
         },
         {
             "default": 5.0,
             "label": "final HPLC tube dispense height (in mm above bottom)",
             "name": "height_final",
-            "type": "int"
+            "type": "float"
         }
     ],
     "instruments": [

protocols/5eee17/dilution.ot2.apiv2.py

@@ -10,12 +10,13 @@
 
 def run(ctx):
 
-    [num_extracts, lw_hplc, mixreps_dilution, height_source,
+    [num_extracts, lw_hplc, vol_dilution, mixreps_dilution, height_source,
      height_intermediate_low, height_intermediate_middle,
      height_intermediate_high, height_final] = get_values(  # noqa: F821
-        'num_extracts', 'lw_hplc', 'mixreps_dilution', 'height_source',
-        'height_intermediate_low', 'height_intermediate_middle',
-        'height_intermediate_high', 'height_final')
+        'num_extracts', 'lw_hplc', 'vol_dilution', 'mixreps_dilution',
+        'height_source', 'height_intermediate_low',
+        'height_intermediate_middle', 'height_intermediate_high',
+        'height_final')
 
     tuberacks_50 = [
         ctx.load_labware('bd_24_tuberack_50ml_green', slot, '50ml tubes')

protocols/5eee17/fields.json

@@ -14,38 +14,44 @@
       {"label": "blue", "value": "bd_48_tuberack_5ml_blue"}
     ]
   },
+  {
+    "type": "float",
+    "label": "dilution volume (in ul)",
+    "name": "vol_dilution",
+    "default": 500.0
+  },
   {
     "type": "int",
     "label": "mix repetitions of dilution",
     "name": "mixreps_dilution",
     "default": 5
   },
   {
-    "type": "int",
+    "type": "float",
     "label": "source 50ml tube aspiration height (in mm above bottom)",
     "name": "height_source",
     "default": 5.0
   },
   {
-    "type": "int",
+    "type": "float",
     "label": "dilution 15ml tube low mix height (in mm above bottom)",
     "name": "height_intermediate_low",
     "default": 5.0
   },
   {
-    "type": "int",
+    "type": "float",
     "label": "dilution 15ml tube middle mix height (in mm above bottom)",
     "name": "height_intermediate_middle",
     "default": 30.0
   },
   {
-    "type": "int",
+    "type": "float",
     "label": "dilution 15ml tube high mix height (in mm above bottom)",
     "name": "height_intermediate_high",
     "default": 60.0
   },
   {
-    "type": "int",
+    "type": "float",
     "label": "final HPLC tube dispense height (in mm above bottom)",
     "name": "height_final",
     "default": 5.0