feat(shared-data): Add more new labware definitions to shared-data

[Laura-Danielle]

overview

Using the new generator functions, create and test more labware definitions according to issue #2614

changelog

• Add: all modular tuberack defs, all fixed trash defs
• Change definition names in shared-data/definitions to match with shared-data/definitions2 names for easier transition (change corresponding occurrence in PD)

Known Issues

• 15_50 is backwards (oops) I think this is a irregular labware definition issue so I think it might be out of scope for this PR
• 12 row Trough issuing a move_to causes the pipette to move to bottom of the well instead of center -- should this be baked into def or do we handle in code?

Labware Definition Data

1.5ml tuberack eppendorf

brand = {brand: "Opentrons", brandId: ["022363221", "022363247", "022363263", "022363280", "022363301", "022363328"]}
metadata = {tags: ["1.5", "mL", "eppendorf", "snapcap", "tuberack"], displayName: "Opentrons snapcap 1.5mL tuberack", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "tuberack"}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 79.85}
parameters = {format: "irregular", isTiprack: false,isMagneticModuleCompatible: false}
grid = {row: 4, column: 6}
spacing = {row: 19.28, column: 19.89}
offset = {x: 18.21, y: 17.59, z: 79.85}
well = {depth: 37.8, diameter: 8.7, shape: "circular", totalLiquidVolume: 1.5}

2ml Tuberack eppendorf

brand = {brand: "Opentrons", brandId: ["022363344", "022363352", "022363379", "022363476"]}
metadata = {tags: ["2", "mL", "eppendorf", "snapcap", "tuberack"], displayName: "Opentrons snapcap 2mL tuberack", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "tuberack"}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 79.85}
parameters = {format: "irregular", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row: 4, column: 6}
spacing = {row: 19.28, column: 19.89}
offset = {x: 18.21, y: 17.59, z: 79.85}
well = {depth: 38.58, diameter: 9.9, shape: "circular", totalLiquidVolume: 2}

2ml Tuberack screwcap

brand = {brand: "Opentrons", brandId: ["649020"]}
metadata = {tags: ["2", "mL", "E&K Scientific", "screwcap", "tuberack"], displayName: "Opentrons screwcap 2mL tuberack", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "tuberack"}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 79.85}
parameters = {format: "irregular", isTiprack: false,isMagneticModuleCompatible: false}
grid = {row: 4, column: 6}
spacing = {row: 19.28, column 19.89}
offset = {x: 18.21, y: 17.59, z: 79.85}
well = {depth: 42, diameter: 8.5, shape: "circular", totalLiquidVolume: 2}

Opentrons Tuberack 15mL

brand = {brand: "Opentrons", "brandId": ["352096"]}
metadata = {tags: ["15", "mL", "falcon", "tuberack"], displayName: "Opentrons 15 mL tuberack", displayCategory: "tuberack", displayVolumeUnits: "mL", displayLengthUnits: "mm"}
dimensions = {overallLength: 121, overallWidth: 78.75, overallHeight: 123.76}
parameters = {format: "irregular", isTiprack: false}
grid = {row: 3, column: 5}
spacing = {row: 25, column: 25}
offset = {x: 10.5, y: 14.375, z: 123.76}
well = {depth: 117.98, diameter: 14.5, shape: "circular", totalLiquidVolume: 15}

Opentrons 50 mL tuberack

brand = {brand: "Opentrons", "brandId": ["352070"]}
metadata = {tags: ["50", "mL", "falcon", "tuberack"], displayName: "Opentrons 50 mL tuberack", displayCategory: "tuberack", displayVolumeUnits: "mL", displayLengthUnits: "mm"}
dimensions = {overallLength: 121, overallWidth: 78.75, overallHeight: 123.76}
parameters = {format: "irregular", isTiprack: false}
grid = {row: 2, column: 3}
spacing = {row: 35, column: 35}
offset = {x: 33.0, y: 21.875, z: 119.89}
well = {depth: 113.85, diameter: 26.45, shape: "circular", totalLiquidVolume: 50}

Aluminum 2ml block

metadata = {displayName: "Aluminum 2mL block", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "tuberack"}
brand = {brand: "Opentrons", brandId: ["649020"]}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 42}
parameters = {format: "irregular", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row:4, column: 6}
spacing = {row: 17.25, column: 17.25}
offset = {x: 20.75, y: 16.88, z: 48.7}
well = {shape: "circular", depth: 42, diameter: 8.5, totalLiquidVolume: 2}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

Aluminum 96 Block

metadata = {displayName: "Aluminum PCR block 200uL", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "tuberack"}
brand = {brand: "Opentrons", brandId: ["4ti-0785/M"]}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 19.5}
parameters = {format: "96Standard", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row:8, column: 12}
spacing = {row: 9, column: 9}
offset = {x: 14.375, y: 11.250, z: 25.61}
well = {shape: "circular", depth: 20.3, diameter: 5.46, totalLiquidVolume: 200}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

12 Channel Trough

metadata = {displayName: "12 Channel Trough", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "trough"}
brand = {brand: "USA Scientific", brandId: ["1061-8150"]}
dimensions = {overallLength: 127.76, overallWidth: 85.8, overallHeight: 44.45}
parameters = {format: "trough", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row:1, column: 12}
spacing = {row: 0, column: 9.09}
offset = {x: 13.94, y: 42.9, z: 44.45}
well = {shape: "rectangular", depth: 42.16, length: 8.33, width= 71.88, totalLiquidVolume: 22}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

Aluminum 96 PCR Plate Biorad

metadata = {displayName: "Aluminum biorad PCR plate 200uL", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "tuberack"}
brand = {brand: "Opentrons", brandId: ["HSP9601"]}
dimensions = {overallLength: 127.76, overallWidth: 85.48, overallHeight: 18.81}
parameters = {format: "96Standard", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row:8, column: 12}
spacing = {row: 9, column: 9}
offset = {x: 14.38, y: 11.24, z: 18.81}
well = {shape: "circular", depth: 14.81, diameter: 5.46, totalLiquidVolume: 200}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

Eppendorf 10ul Tips

metadata = {displayName: "epT.I.P.S. 0.1-10 uL tiprack", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "tiprack", tags=["SBS", "tips", "10", "uL"]}
brand = {brand: "eppendorf", brandId: ["HSP9601"]}
dimensions = {overallLength: 127.76, overallWidth: 85.48, overallHeight: 65.4}
parameters = {format: "96Standard", isTiprack: true, isMagneticModuleCompatible: false, tipLength: 34}
grid = {row: 8, column: 12}
spacing = {row: 9, column: 9}
offset = {x: 14.38, y: 11.24, z: 65.4}
well = {shape: "circular", depth: 0, diameter: 6, totalLiquidVolume: 10}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

Eppendorf 1000ul Tips

metadata = {displayName: "epT.I.P.S. 50-1000 uL tiprack", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "tiprack", tags=["SBS", "tips", "1000", "uL"]}
brand = {brand: "eppendorf", brandId: ["022491105"]}
dimensions = {overallLength: 127.76, overallWidth: 85.48, overallHeight: 121.9}
parameters = {format: "96Standard", isTiprack: true, isMagneticModuleCompatible: false, tipLength: 70.7}
grid = {row: 8, column: 12}
spacing = {row: 9, column: 9}
offset = {x: 14.38, y: 11.24, z: 121.9}
well = {shape: "circular", depth: 0, diameter: 6, totalLiquidVolume: 1000}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

6 Well Plate Corning

metadata = {displayName: "Corning 6 Well Plate", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "wellPlate", tags=["SBS", "microplate", "16.8", "mL", "6 wells"]}
brand = {brand: "corning", brandId: ["3335", "3506", "3516", "3471"]}
dimensions = {overallLength: 127.76, overallWidth: 85.47, overallHeight: 20.27}
parameters = {format: "irregular", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row: 2, column: 3}
spacing = {row: 39.12, column: 39.12}
offset = {x: 24.76, y: 23.16, z: 20.27}
well = {shape: "circular", depth: 17.4, diameter: 35.43, totalLiquidVolume: 16.8}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

12 Well Plate Corning

metadata = {displayName: "Corning 6 Well Plate", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "wellPlate", tags=["SBS", "microplate", "6.9", "mL", "12 wells"]}
brand = {brand: "corning", brandId: ["3336", "3512", "3513"]}
dimensions = {overallLength: 127.89, overallWidth: 85.6, overallHeight: 20.02}
parameters = {format: "irregular", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row: 3, column: 4}
spacing = {row: 26.01, column: 36.01}
offset = {x: 24.94, y: 16.79, z: 20.02}
well = {shape: "circular", depth: 17.53, diameter: 22.73, totalLiquidVolume: 6.9}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

24 Well Plate Corning

metadata = {displayName: "Corning 24 Well Plate", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "wellPlate", tags=["SBS", "microplate", "3.4", "mL", "24 wells"]}
brand = {brand: "corning", brandId: ["3337", "3524", "3526", "3527", "3473", "3738", "3987"]}
dimensions = {overallLength: 127.76, overallWidth: 85.47, overallHeight: 20.27}
parameters = {format: "irregular", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row: 4, column: 6}
spacing = {row: 19.3, column: 19.3}
offset = {x: 17.48, y: 19.3, z: 20.27}
well = {shape: "circular", depth: 17.40, diameter: 16.26, totalLiquidVolume: 3.4}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

48 Well Plate Corning

metadata = {displayName: "Corning 48 Well Plate", displayVolumeUnits: "mL", displayLengthUnits: "mm", displayCategory: "wellPlate", tags=["SBS", "microplate", "1.6", "mL", "48 wells"]}
brand = {brand: "corning", brandId: ["3548"]}
dimensions = {overallLength: 127.76, overallWidth: 85.47, overallHeight: 20.02}
parameters = {format: "irregular", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row: 6, column: 8}
spacing = {row: 13.08, column: 13.08}
offset = {x: 18.16, y: 10.08, z: 20.02}
well = {shape: "circular", depth: 17.40, diameter: 11.56, totalLiquidVolume: 1.6}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

384 Well Plate Corning

metadata = {displayName: "Corning 384 Well Plate", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "wellPlate", tags=["SBS", "microplate", "112", "uL", "384 wells"]}
brand = {brand: "corning", brandId: ["3640", "3662","3680", "3700", "3701", "3702"]}
dimensions = {overallLength: 127.76, overallWidth: 85.47, overallHeight: 14.22}
parameters = {format: "384Standard", isTiprack: false, isMagneticModuleCompatible: false}
grid = {row: 16, column: 24}
spacing = {row: 4.5, column: 4.5}
offset = {x: 12.12, y: 8.99, z: 14.22}
well = {shape: "circular", depth: 11.43, diameter: 3.63, totalLiquidVolume: 112}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

GEB tiprack 10ul (Opentrons)

metadata = {displayName: "Opentrons GEB 10uL Tiprack", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "tiprack", tags: ["GEB", "tiprack", "10uL", "Opentrons"]}
brand = {brand: "Opentrons"}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 52.25}
parameters = {format: "96Standard", isTiprack: true, isMagneticModuleCompatible: false, tipLength: 39.2}
grid = {row:8, column: 12}
spacing = {row: 9, column: 9}
offset = {x: 14.375, y: 11.250, z: 56.25}
well = {shape: "circular", depth: 0, diameter: 3.46, totalLiquidVolume: 10}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

GEB tiprack 1000ul (Opentrons)

metadata = {displayName: "Opentrons GEB 1000uL Tiprack", displayVolumeUnits: "uL", displayLengthUnits: "mm", displayCategory: "tiprack", tags: ["GEB", "tiprack", "1000uL", "Opentrons"]}
brand = {brand: "Opentrons"}
dimensions = {overallLength: 127.75, overallWidth: 85.5, overallHeight: 100.25}
parameters = {format: "96Standard", isTiprack: true, isMagneticModuleCompatible: false, tipLength: 87.9}
grid = {row:8, column: 12}
spacing = {row: 9, column: 9}
offset = {x: 14.2, y: 11.2, z: 100.25}
well = {shape: "circular", depth: 0, diameter: 7.46, totalLiquidVolume: 1000}
input = {brand, dimensions, well, metadata, spacing, grid, offset, parameters}
def = sharedData.createRegularLabware(input)

review requests

Pls test on a robot if you can by the following:

1. Kill main server

from opentrons import protocol_api, hardware_control, types
import asyncio
ctx = protocol_api.ProtocolContext()
l = asyncio.get_event_loop()
api = l.run_until_complete(hardware_control.API.build_hardware_controller(force=True))
ad = hardware_control.adapters.SynchronousAdapter(api)
ctx.connect(ad)
labware = ctx.load_labware_by_name(LABWARE NAME, SLOT)
pip = ctx.load_instrument(’p300_single’, types.Mount.LEFT (or right) )
pip.move_to(labware.wells()[0].top())

[btmorr]

@IanLondon could you look into what ramifications the rename would have on PD? Specifically, would it make it so a protocol made in a previous version will no longer load correctly? No longer run correctly? Any other weirdness?

[btmorr]

Left a few questions about the data, but they're comparatively minor. Could you attach or link the documents where the measurements came from (machine drawings or the like), and include the arguments you passed to the generator functions for record-sake?

[codecov]

Codecov Report

Merging #2703 into edge will decrease coverage by 0.16%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##             edge    #2703      +/-   ##
==========================================
- Coverage   51.29%   51.13%   -0.17%     
==========================================
  Files         653      671      +18     
  Lines       17874    18793     +919     
==========================================
+ Hits         9169     9609     +440     
- Misses       8705     9184     +479

Impacted Files	Coverage Δ
shared-data/js/labwareTools/index.js	92.59% <100%> (+0.13%)	⬆️
...r/src/step-generation/aspirateUpdateLiquidState.js	72.72% <0%> (-27.28%)	⬇️
...ol-designer/src/file-data/selectors/fileCreator.js	28.12% <0%> (-1.29%)	⬇️
...steplist/formLevel/stepFormToArgs/mixFormToArgs.js	4.34% <0%> (-0.92%)	⬇️
...formLevel/stepFormToArgs/transferLikeFormToArgs.js	3.37% <0%> (-0.02%)	⬇️
...tocol-designer/src/components/steplist/StepItem.js	0% <0%> (ø)	⬆️
...r/src/steplist/formLevel/getDefaultsForStepType.js	0% <0%> (ø)	⬆️
...designer/src/components/StepEditForm/formFields.js	0% <0%> (ø)	⬆️
...signer/src/components/modals/NewFileModal/index.js	0% <0%> (ø)	⬆️
...omponents/RobotSettings/UpdateRobot/VersionList.js	0% <0%> (ø)	⬆️
... and 42 more

---

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[IanLondon]

the labware rename breaks tube racks in old PD protocols and would not allow new PD protocols (this PR) to run on the robot if they use tube racks (see my rambling comment)

[IanLondon]

doing this name change will break existing protocols that our beta users have made in an ugly way (if the protocol uses any of these tuberacks),

it also makes it so protocols using tube racks won't run on the robot because these names don't work with labware.load in Python - as it is now, I think you'd get "ValueError: container not found in default-containers.json" on upload

If we wanted to support these new names now, we could do a migration so that while loading a file, PD swaps the old names to the new names. And we'd also have to make PD translate back to 'opentrons-tuberack-15ml' style name when it saves the file, so that the JSON executor in Python can put that into labware.load

But it seems messy. I think I'd rather do the name change all at once when we move to definitions2/ and have the JSON definitions embedded in the protocols. Once we get to that point, the labware names in JSON protocols no longer need to reference a key in default-containers.json, so it's easier to change the names (they might only have nicknames and no "load name" in the commands part, and in the PD-specific data they would have a "load name" referencing the definitions2/ file name? maybe)

[Laura-Danielle]

That sounds fine to me, Ben had wanted to maybe change the names to make transitioning easier. But it seems like that might cause us to have to do more upfront work and thus defeat the purpose of attempting to change the names earlier

[btmorr]

I agree with doing this in a way that is less painful to PD users

[IanLondon]

LGTM! Did not test on robot

[btmorr]

📻

[sfoster1]

I hate to do it to you but can we take the opportunity now to lowercase the filenames and load names? @IanLondon is right, it's kind of inconsistent and the names are so long that getting the capitalization right is annoying even for us now doing testing.

[sfoster1]

Names are better now but IMO we should still think about changing the python load labware functions to lowercase everything