feat(protocol-designer, step-generation, app): introduce pythonName to each entity #17463

jerader · 2025-02-07T14:01:46Z

Overview

For python/pd interop, we want to add a pythonName to liquidEntity, labwareEntity, moduleEntity, and pipetteEntity. This PR does that by adding them in redux, that way, the pythonName is not polluting the JSON structure. For Quick Transfer, the pythonName is generated in generateQuickTransferArgs.

The python name patterning is as follows:

modules: moduleType minus Type in snake case plus the number so heater_shaker_module_1 and then heater_shaker_module_2 for 2 heater-shaker modules
pipettes: pipette_left or pipette_right
labware: the labware displayCategory in snake case plus the number. So 2 well plates and 1 reservoir would be well_plate_1, well_plate_2, reservoir_1
liquids: just liquid with the number so liquid_1, liquid_2, etc.

Test Plan and Hands on Testing

Since the python names are not included in the JSON structure and not actually held in the redux tree, you'll have to console.log invariant context. I guess an easy one to check is:

add console.log('invariantContext', invariantContext) to delay.ts in step-generation

upload this attached protocol with labware, pipettes, liquids, and modules and go to the step timeline. check console and look at invariant context. test deleting different things and making sure the numbers update correctly

pythonNames.json

there should be 5 well plates, 3 tipracks, 2 adapters, 1 reservoir, 3 liquids, 2 heater-shakers, 2 magnetic blocks, 1 thermocycler, 2 pipettes

Changelog

modify redux reducers to add python names
make some utils for getting the python name
refactor liquids so python name is not in the json file
fix affected tests
fix quick transfer

Review requests

Review my redux changes in particular. The files to look at for that are:

protocol-designer/src/labware-ingred/actions/thunks.ts for editing subsequent labware numbering -> so if you have 2 well plates and delete 1, it ensures the number of that 1 remaining is well_plate_1

protocol-designer/src/modules/thunks.ts for editing subsequent module numbering -> so if you have 2 h-s and delete 1, it ensures the number of that 1 remaining is heater_shaker_1

protocol-designer/src/step-forms/reducers/index.ts has the redux reducer logic for adding the python name to modules and labware

protocol-designer/src/step-forms/selectors/index.ts has the pipette selector logic for adding the python name

Risk assessment

med-ish but its contained in redux and only adding stuff on instead of changing how the entities are generated

…h entity closes AUTH-1383

codecov · 2025-02-07T14:09:21Z

Codecov Report

Attention: Patch coverage is 28.49162% with 256 lines in your changes missing coverage. Please review.

Project coverage is 20.06%. Comparing base (f16f6a0) to head (4818287).
Report is 15 commits behind head on edge.

Files with missing lines	Patch %	Lines
protocol-designer/src/step-forms/reducers/index.ts	33.33%	74 Missing ⚠️
...ocol-designer/src/labware-ingred/actions/thunks.ts	7.27%	51 Missing ⚠️
protocol-designer/src/modules/thunks.ts	5.00%	38 Missing ⚠️
...ol-designer/src/file-data/selectors/fileCreator.ts	33.33%	16 Missing ⚠️
...ickTransferFlow/utils/generateQuickTransferArgs.ts	0.00%	14 Missing ⚠️
...ocol-designer/src/labware-ingred/reducers/index.ts	0.00%	13 Missing ⚠️
protocol-designer/src/utils/index.ts	18.75%	13 Missing ⚠️
...rotocol-designer/src/step-forms/selectors/index.ts	26.66%	11 Missing ⚠️
...col-designer/src/labware-ingred/actions/actions.ts	0.00%	6 Missing ⚠️
protocol-designer/src/ui/modules/utils.ts	0.00%	5 Missing ⚠️
... and 7 more

Additional details and impacted files

@@            Coverage Diff             @@
##             edge   #17463      +/-   ##
==========================================
+ Coverage   18.19%   20.06%   +1.86%     
==========================================
  Files        3175     3194      +19     
  Lines      229678   230611     +933     
  Branches     6907     8217    +1310     
==========================================
+ Hits        41787    46266    +4479     
+ Misses     187891   184345    -3546

Flag	Coverage Δ
protocol-designer	`17.39% <28.49%> (+0.01%)`	⬆️
step-generation	`4.08% <4.21%> (?)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
.../file-data/__fixtures__/createFile/commonFields.ts	`100.00% <100.00%> (ø)`
protocol-designer/src/file-types.ts	`75.00% <ø> (+3.57%)`	⬆️
protocol-designer/src/labware-ingred/types.ts	`100.00% <ø> (ø)`
...src/organisms/EditInstrumentsModal/editPipettes.ts	`1.92% <ø> (ø)`
...signer/src/pages/CreateNewProtocolWizard/index.tsx	`0.00% <ø> (ø)`
...er/src/pages/Designer/DeckSetup/DeckSetupTools.tsx	`67.82% <100.00%> (ø)`
.../src/pages/Designer/DeckSetup/SlotOverflowMenu.tsx	`79.58% <100.00%> (ø)`
...rotocol-designer/src/step-forms/actions/modules.ts	`23.07% <ø> (+2.02%)`	⬆️
...ocol-designer/src/step-forms/test/reducers.test.ts	`100.00% <100.00%> (ø)`
protocol-designer/src/step-forms/types.ts	`100.00% <ø> (ø)`
... and 21 more

... and 190 files with indirect coverage changes

smb2268

The quick transfer changes make sense - just left one comment. Thanks for adding that version bump!

app/src/organisms/ODD/QuickTransferFlow/utils/generateQuickTransferArgs.ts

ddcc4 · 2025-02-07T19:58:32Z

app/src/organisms/ODD/QuickTransferFlow/utils/createQuickTransferFile.ts

@@ -204,7 +204,7 @@ export function createQuickTransferFile(
    },
    designerApplication: {
      name: 'opentrons/quick-transfer',
-      version: '1.0.0',
+      version: '1.1.0',


How does Quick Transfer versioning work? Like, what cares about this version number?

@ddcc4 Right now, nothing cares about this version number since once these files are created the designerApplicationData isn't read. However, we may want to read it and add migration functionality in the future. I'm working on a doc to keep track of this - you can see my draft here: https://github.com/Opentrons/opentrons/blob/e9a77696e65022c480ae704edecb22c794c45111/app/src/organisms/ODD/QuickTransferFlow/README.md

ddcc4 · 2025-02-07T20:00:17Z

app/src/organisms/ODD/QuickTransferFlow/utils/generateQuickTransferArgs.ts

@@ -96,18 +98,28 @@ function getInvariantContextAndRobotState(
      },
    }
  }
+  const sourceDisplayCategory =
+    quickTransferState.source.metadata.displayCategory


What's a sourceDisplayCategory?

it is the source labware in quick transfer (aka where you are aspirating from). quick transfer is limited to only a source and destination labware

ddcc4 · 2025-02-07T20:07:30Z

protocol-designer/src/labware-ingred/actions/thunks.ts

+interface DeleteContainerArgs {
+  labwareId: string
+}
+export const deleteContainer: (


Hey, what is the container that this is referring to?

deleteContainer is our redux action for deleting a labware. idk why we called it container (definitely from before my time working on PD) but i made a new one in the thunk since the old deleteContainer was a singular action. This way in the future when devs need to delete a container, they can just refer to an intuitive fn name like deleteContainer instead of something more in depth like deleteContainerAndRenamePythonName

ddcc4 · 2025-02-07T20:08:30Z

protocol-designer/src/labware-ingred/actions/thunks.ts

+    },
+  })
+
+  if (typeCount > 1) {


Why is this limited to typeCount > 1? What happens if it's 1?

oh if its equal to 1, you won't need to call the action that renames the rest of the pythonNames. like if you have 1 wellPlate and you delete it, no sense calling the action to rename the rest of the pythonNames in labware because they don't exist

protocol-designer/src/step-forms/reducers/index.ts

ddcc4 · 2025-02-07T20:17:39Z

protocol-designer/src/step-forms/reducers/index.ts

            model: moduleLoadInfo.model,
+            pythonName: getModulePythonName(moduleType, typeCount + 1),


Ohhh! ... I figured out what this is doing :) I was confused at first because I thought "Isn't typeCount a constant? Won't this give all the modules the same pythonName when you LOAD_FILE?"

But you're recomputing typeCount for each module in the loop, so this works.

ddcc4 · 2025-02-07T20:20:33Z

step-generation/src/types.ts

+export type Ingredient = Omit<LiquidEntity, 'pythonName'>
+export interface Ingredients {
+  [liquidId: string]: Ingredient
+}


Trying to keep all the types straight in my head: when do we use LiquidEntities and when do we use Ingredients?

Ingredients refers to the json structure type for the ingredients key, it is just like liquidEntities but does not include pythonName. It's similar to how we have a labwareLoadInfo, moduleLoadInfo, etc for the labware and modules keys in designerApplication

…o each entity (#17463) closes AUTH-1383 For python/pd interop, we want to add a `pythonName` to `liquidEntity`, `labwareEntity`, `moduleEntity`, and `pipetteEntity`. This PR does that by adding them in redux, that way, the `pythonName` is not polluting the JSON structure. For Quick Transfer, the `pythonName` is generated in `generateQuickTransferArgs`. The python name patterning is as follows: - modules: moduleType minus `Type` in snake case plus the number so `heater_shaker_module_1` and then `heater_shaker_module_2` for 2 heater-shaker modules - pipettes: `pipette_left` or `pipette_right` - labware: the labware displayCategory in snake case plus the number. So 2 well plates and 1 reservoir would be `well_plate_1`, `well_plate_2`, `reservoir_1` - liquids: just liquid with the number so `liquid_1`, `liquid_2`, etc.

jerader added 6 commits February 6, 2025 12:15

add module pythonNames

5e40cad

pythonName for pipettes

6de8a52

keep liquid pythonName in redux

f1efc5c

add labware pythonName

1094048

feat(protocol-designer, step-generation): introduce pythonName to eac…

26f7185

…h entity closes AUTH-1383

fix test

d1af586

jerader marked this pull request as ready for review February 7, 2025 14:10

jerader requested review from a team as code owners February 7, 2025 14:10

jerader requested review from smb2268 and ddcc4 and removed request for a team February 7, 2025 14:10

jerader added 2 commits February 7, 2025 10:41

fix prettier

5e80d58

update qt version to 1.1.0

96029b0

smb2268 reviewed Feb 7, 2025

View reviewed changes

app/src/organisms/ODD/QuickTransferFlow/utils/generateQuickTransferArgs.ts Outdated Show resolved Hide resolved

ddcc4 reviewed Feb 7, 2025

View reviewed changes

address feedback

4818287

ddcc4 approved these changes Feb 7, 2025

View reviewed changes

jerader merged commit f687a3a into edge Feb 7, 2025
41 checks passed

jerader deleted the pd_pythonNames-to-entities branch February 7, 2025 21:21

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feat(protocol-designer, step-generation, app): introduce pythonName to each entity #17463

feat(protocol-designer, step-generation, app): introduce pythonName to each entity #17463

jerader commented Feb 7, 2025 •

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jerader Feb 7, 2025

		model: moduleLoadInfo.model,
		pythonName: getModulePythonName(moduleType, typeCount + 1),

feat(protocol-designer, step-generation, app): introduce pythonName to each entity #17463

feat(protocol-designer, step-generation, app): introduce pythonName to each entity #17463

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jerader commented Feb 7, 2025 • edited Loading

Overview

Test Plan and Hands on Testing

Changelog

Review requests

Risk assessment

codecov bot commented Feb 7, 2025 • edited Loading

Codecov Report

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jerader commented Feb 7, 2025 •

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