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Heater shaker test forpr #4124

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0c96a6b
files for custom python protocol for heater shaker beta testing
Oct 24, 2022
5b15cc7
makefile and parseOT2v2 changes
Oct 24, 2022
607c09d
api version change 2.0 to 2.3
Oct 24, 2022
cab8678
updated 1-tip pickup function to use ctx._hw_manager.hardware
Oct 24, 2022
57349b0
changed api version from 2.0 to 2.3
Oct 24, 2022
1940e8e
changed api version from 2.0 to 2.3
Oct 24, 2022
534e5d6
updated tip pickup current change code to use ctx._hw_manager.hardware
Oct 24, 2022
0dc5fe5
line 98 updated to avoid error - can not aspirate or dispense to tiprack
Oct 24, 2022
cbd214f
updated ctx._implementation._hw_manager.hardware to ctx._hw_manager.h…
Oct 24, 2022
7b31c40
changed api version from 2.0 to 2.3
Oct 24, 2022
ef62e10
updated ctx._implementation._hw_manager.hardware to ctx._hw_manager.h…
Oct 24, 2022
92261b8
temporarily removed parseREADME code for heater shaker protocol
Oct 24, 2022
d2cf1d6
updated to ctx._hw_manager.hardware
Oct 24, 2022
b261f8e
updated api version 2.0 to 2.3
Oct 24, 2022
74ec764
updated to ctx._hw_manager.hardware
Oct 24, 2022
c0639b5
updated to ctx._hw_manager.hardware
Oct 24, 2022
5fe2e4d
build files for custom python protocol for beta testing of heater shaker
Oct 24, 2022
f1f85bb
build files for protocol library update to 6.1.0
Oct 24, 2022
3fe328e
build files for upgrade to 6.1.0
Oct 25, 2022
0ead77b
include heater shaker module in parseREADME.py process
Oct 25, 2022
d8213e3
build files for changed protocols during update to 6.1.0
Oct 25, 2022
86f0663
fixed linting error in parseOT2v2.py
Oct 26, 2022
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2 changes: 1 addition & 1 deletion Makefile
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
SHELL := /bin/bash

MONOREPO_URI := https://github.com/Opentrons/opentrons.git
OT2_VERSION_TAG := v4.3.0
OT2_VERSION_TAG := v6.1.0
OT2_MONOREPO_DIR := ot2monorepoClone

# Parsers output to here
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2 changes: 1 addition & 1 deletion protoBuilds/118e8c/118e8c.ot2.apiv2.py.json

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2 changes: 1 addition & 1 deletion protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json

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2 changes: 1 addition & 1 deletion protoBuilds/1bcd67/normalization.ot2.apiv2.py.json
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Normalization',\n 'author': 'Nick <[email protected]>',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n ] = get_values( # noqa: F821\n 'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n 'final_vol')\n\n # labware\n dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n 'deepwell plate')\n final_dilution_plates = [\n ctx.load_labware('nunc_96_wellplate_500ul', slot,\n f'final dilution plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n '9', 'diluent').wells()[0]\n tipracks1000 = [\n ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n for slot in ['10']]\n tipracks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['7']]\n\n # pipettes\n if p1000_mount == m300_mount:\n raise Exception('Pipette mounts cannot match.')\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tipracks1000)\n p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for rack in tipracks300[::-1]\n for col in rack.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n def extract_well_name(well_obj):\n return well_obj.display_name.split(' ')[0]\n\n def custom_transfer(vol, source, dest, pip=p300):\n num_trans = math.ceil(vol/pip.max_volume)\n vol_per_trans = vol/num_trans\n for n in range(num_trans):\n pip.aspirate(vol_per_trans, source)\n pip.dispense(vol_per_trans, dest)\n\n def determine_dil(col):\n rows = 'ABCDEFGH'\n col = dw_plate.rows()[0].index(col)\n dict = [dict1, dict2, dict3][col % 3]\n wells_to_check = [row + str(col+1) for row in rows]\n for well in wells_to_check:\n if dict[well]:\n return True\n return False\n\n # pre-parse `None` to `null`\n dil_json_1 = dil_json_1.replace('None', 'null')\n dil_json_2 = dil_json_2.replace('None', 'null')\n dil_json_3 = dil_json_3.replace('None', 'null')\n\n # read .json files as dictionaries\n dict1 = json.loads(dil_json_1)\n dict2 = json.loads(dil_json_2)\n dict3 = json.loads(dil_json_3)\n\n map_dil_wells = {\n well_set[0]: {\n well_set[0]: dict1[extract_well_name(well_set[0])],\n well_set[1]: dict2[extract_well_name(well_set[1])],\n well_set[2]: dict3[extract_well_name(well_set[2])]\n }\n for well_set in [\n row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n }\n\n final_locations = []\n for key, dict in map_dil_wells.items():\n final_well = None\n for well, vol in dict.items():\n if vol:\n final_well = well\n final_locations.append(final_well)\n\n # pre-add diluent\n pickup_p300('multi')\n for col in dw_plate.rows()[0]:\n if determine_dil(col):\n for _ in range(4): # 4x 200ul = 800ul\n p300.transfer(200, diluent, col, new_tip='never')\n p300.drop_tip()\n\n # prompt user to transfer neat sample\n display_wells = [\n well for well, vol in dict1.items() if vol]\n display_vols = [\n round(vol, 2) for vol in dict1.values() if vol]\n sample_str = '\\n'.join([\n f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n for display_well, display_vol in zip(display_wells, display_vols)])\n ctx.pause(msg=sample_str)\n\n # perform dilutions\n for set in map_dil_wells.values():\n for i, (well, vol) in enumerate(set.items()):\n if i > 0 and vol: # neat is manually added\n if vol <= 200:\n pip = p300\n pickup_p300('single')\n else:\n pip = p1000\n p1000.pick_up_tip()\n custom_transfer(vol, list(set.keys())[i-1], well, pip)\n pip.mix(5, 200, well)\n pip.drop_tip()\n\n # final transfer\n final_targets = [\n well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n for source, dest in zip(final_locations, final_targets):\n if source:\n col = int(source.display_name.split(' ')[0][1:])\n if col % 3 == 1:\n pip.mix(5, 200, source)\n p1000.transfer(final_vol, source, dest)\n",
"content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Normalization',\n 'author': 'Nick <[email protected]>',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n ] = get_values( # noqa: F821\n 'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n 'final_vol')\n\n # labware\n dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n 'deepwell plate')\n final_dilution_plates = [\n ctx.load_labware('nunc_96_wellplate_500ul', slot,\n f'final dilution plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n '9', 'diluent').wells()[0]\n tipracks1000 = [\n ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n for slot in ['10']]\n tipracks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['7']]\n\n # pipettes\n if p1000_mount == m300_mount:\n raise Exception('Pipette mounts cannot match.')\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tipracks1000)\n p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for rack in tipracks300[::-1]\n for col in rack.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n def extract_well_name(well_obj):\n return well_obj.display_name.split(' ')[0]\n\n def custom_transfer(vol, source, dest, pip=p300):\n num_trans = math.ceil(vol/pip.max_volume)\n vol_per_trans = vol/num_trans\n for n in range(num_trans):\n pip.aspirate(vol_per_trans, source)\n pip.dispense(vol_per_trans, dest)\n\n def determine_dil(col):\n rows = 'ABCDEFGH'\n col = dw_plate.rows()[0].index(col)\n dict = [dict1, dict2, dict3][col % 3]\n wells_to_check = [row + str(col+1) for row in rows]\n for well in wells_to_check:\n if dict[well]:\n return True\n return False\n\n # pre-parse `None` to `null`\n dil_json_1 = dil_json_1.replace('None', 'null')\n dil_json_2 = dil_json_2.replace('None', 'null')\n dil_json_3 = dil_json_3.replace('None', 'null')\n\n # read .json files as dictionaries\n dict1 = json.loads(dil_json_1)\n dict2 = json.loads(dil_json_2)\n dict3 = json.loads(dil_json_3)\n\n map_dil_wells = {\n well_set[0]: {\n well_set[0]: dict1[extract_well_name(well_set[0])],\n well_set[1]: dict2[extract_well_name(well_set[1])],\n well_set[2]: dict3[extract_well_name(well_set[2])]\n }\n for well_set in [\n row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n }\n\n final_locations = []\n for key, dict in map_dil_wells.items():\n final_well = None\n for well, vol in dict.items():\n if vol:\n final_well = well\n final_locations.append(final_well)\n\n # pre-add diluent\n pickup_p300('multi')\n for col in dw_plate.rows()[0]:\n if determine_dil(col):\n for _ in range(4): # 4x 200ul = 800ul\n p300.transfer(200, diluent, col, new_tip='never')\n p300.drop_tip()\n\n # prompt user to transfer neat sample\n display_wells = [\n well for well, vol in dict1.items() if vol]\n display_vols = [\n round(vol, 2) for vol in dict1.values() if vol]\n sample_str = '\\n'.join([\n f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n for display_well, display_vol in zip(display_wells, display_vols)])\n ctx.pause(msg=sample_str)\n\n # perform dilutions\n for set in map_dil_wells.values():\n for i, (well, vol) in enumerate(set.items()):\n if i > 0 and vol: # neat is manually added\n if vol <= 200:\n pip = p300\n pickup_p300('single')\n else:\n pip = p1000\n p1000.pick_up_tip()\n custom_transfer(vol, list(set.keys())[i-1], well, pip)\n pip.mix(5, 200, well)\n pip.drop_tip()\n\n # final transfer\n final_targets = [\n well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n for source, dest in zip(final_locations, final_targets):\n if source:\n col = int(source.display_name.split(' ')[0][1:])\n if col % 3 == 1:\n pip.mix(5, 200, source)\n p1000.transfer(final_vol, source, dest)\n",
"custom_labware_defs": [
{
"brand": {
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