fix(api, shared-data): Flex Stacker engine command optional fields

[ahiuchingau]

Overview

This fixes a bug where downloading a Flex Stacker protocol run log always fails because of pydantic validation errors. We need to make sure the optional params in our pydantic models are properly annotated with SkipJsonSchem?

Review Request

I've only updated schema 12, since this is targeting the release branch. I will need to make the same changes to schema 13 eventually for edge.

{
    "errors": [
        {
            "id": "UnexpectedError",
            "title": "Unexpected Internal Error",
            "detail": "pydantic_core._pydantic_core.ValidationError: 1 validation error for tagged-union[AirGapInPlace,Aspirate,AspirateInPlace,AspirateWhileTracking,Comment,Custom,Dispense,DispenseInPlace,DispenseWhileTracking,BlowOut,BlowOutInPlace,ConfigureForVolume,ConfigureNozzleLayout,DropTip,DropTipInPlace,Home,RetractAxis,LoadLabware,ReloadLabware,LoadLiquid,LoadLiquidClass,LoadModule,LoadPipette,LoadLidStack,LoadLid,MoveLabware,MoveRelative,MoveToCoordinates,MoveToWell,MoveToAddressableArea,MoveToAddressableAreaForDropTip,PrepareToAspirate,WaitForResume,WaitForResume,WaitForDuration,PickUpTip,SavePosition,SetRailLights,TouchTip,SetStatusBar,VerifyTipPresence,GetTipPresence,GetNextTip,LiquidProbe,TryLiquidProbe,EvotipSealPipette,EvotipDispense,EvotipUnsealPipette,WaitForTemperature,SetTargetTemperature,DeactivateHeater,SetAndWaitForShakeSpeed,DeactivateShaker,OpenLabwareLatch,CloseLabwareLatch,Disengage,Engage,SetTargetTemperature,WaitForTemperature,DeactivateTemperature,SetTargetBlockTemperature,WaitForBlockTemperature,SetTargetLidTemperature,WaitForLidTemperature,DeactivateBlock,DeactivateLid,OpenLid,CloseLid,RunProfile,RunExtendedProfile,CloseLid,OpenLid,Initialize,ReadAbsorbance,Retrieve,Store,SetStoredLabware,Fill,Empty,CloseLatch,OpenLatch,PrepareShuttle,CalibrateGripper,CalibratePipette,CalibrateModule,MoveToMaintenancePosition,UnsafeBlowOutInPlace,UnsafeDropTipInPlace,UpdatePositionEstimators,UnsafeEngageAxes,UnsafeUngripLabware,UnsafePlaceLabware,UnsafeManualRetrieve,MoveTo,MoveAxesRelative,MoveAxesTo,openGripperJaw,closeGripperJaw]\nflexStacker/setStoredLabware.result.adapterLabwareDefinition\n  Field required [type=missing, input_value={'primaryLabwareDefinitio...k_1000ul']}, 'count': 1}, input_type=dict]\n    For further information visit https://errors.pydantic.dev/2.9/v/missing",
            "meta": {
                "type": "ValidationError",
                "code": "4000",
                "message": "pydantic_core._pydantic_core.ValidationError: 1 validation error for tagged-union[AirGapInPlace,Aspirate,AspirateInPlace,AspirateWhileTracking,Comment,Custom,Dispense,DispenseInPlace,DispenseWhileTracking,BlowOut,BlowOutInPlace,ConfigureForVolume,ConfigureNozzleLayout,DropTip,DropTipInPlace,Home,RetractAxis,LoadLabware,ReloadLabware,LoadLiquid,LoadLiquidClass,LoadModule,LoadPipette,LoadLidStack,LoadLid,MoveLabware,MoveRelative,MoveToCoordinates,MoveToWell,MoveToAddressableArea,MoveToAddressableAreaForDropTip,PrepareToAspirate,WaitForResume,WaitForResume,WaitForDuration,PickUpTip,SavePosition,SetRailLights,TouchTip,SetStatusBar,VerifyTipPresence,GetTipPresence,GetNextTip,LiquidProbe,TryLiquidProbe,EvotipSealPipette,EvotipDispense,EvotipUnsealPipette,WaitForTemperature,SetTargetTemperature,DeactivateHeater,SetAndWaitForShakeSpeed,DeactivateShaker,OpenLabwareLatch,CloseLabwareLatch,Disengage,Engage,SetTargetTemperature,WaitForTemperature,DeactivateTemperature,SetTargetBlockTemperature,WaitForBlockTemperature,SetTargetLidTemperature,WaitForLidTemperature,DeactivateBlock,DeactivateLid,OpenLid,CloseLid,RunProfile,RunExtendedProfile,CloseLid,OpenLid,Initialize,ReadAbsorbance,Retrieve,Store,SetStoredLabware,Fill,Empty,CloseLatch,OpenLatch,PrepareShuttle,CalibrateGripper,CalibratePipette,CalibrateModule,MoveToMaintenancePosition,UnsafeBlowOutInPlace,UnsafeDropTipInPlace,UpdatePositionEstimators,UnsafeEngageAxes,UnsafeUngripLabware,UnsafePlaceLabware,UnsafeManualRetrieve,MoveTo,MoveAxesRelative,MoveAxesTo,openGripperJaw,closeGripperJaw]\nflexStacker/setStoredLabware.result.adapterLabwareDefinition\n  Field required [type=missing, input_value={'primaryLabwareDefinitio...k_1000ul']}, 'count': 1}, input_type=dict]\n    For further information visit https://errors.pydantic.dev/2.9/v/missing",
                "detail": {
                    "args": "()",
                    "title": "tagged-union[AirGapInPlace,Aspirate,AspirateInPlace,AspirateWhileTracking,Comment,Custom,Dispense,DispenseInPlace,DispenseWhileTracking,BlowOut,BlowOutInPlace,ConfigureForVolume,ConfigureNozzleLayout,DropTip,DropTipInPlace,Home,RetractAxis,LoadLabware,ReloadLabware,LoadLiquid,LoadLiquidClass,LoadModule,LoadPipette,LoadLidStack,LoadLid,MoveLabware,MoveRelative,MoveToCoordinates,MoveToWell,MoveToAddressableArea,MoveToAddressableAreaForDropTip,PrepareToAspirate,WaitForResume,WaitForResume,WaitForDuration,PickUpTip,SavePosition,SetRailLights,TouchTip,SetStatusBar,VerifyTipPresence,GetTipPresence,GetNextTip,LiquidProbe,TryLiquidProbe,EvotipSealPipette,EvotipDispense,EvotipUnsealPipette,WaitForTemperature,SetTargetTemperature,DeactivateHeater,SetAndWaitForShakeSpeed,DeactivateShaker,OpenLabwareLatch,CloseLabwareLatch,Disengage,Engage,SetTargetTemperature,WaitForTemperature,DeactivateTemperature,SetTargetBlockTemperature,WaitForBlockTemperature,SetTargetLidTemperature,WaitForLidTemperature,DeactivateBlock,DeactivateLid,OpenLid,CloseLid,RunProfile,RunExtendedProfile,CloseLid,OpenLid,Initialize,ReadAbsorbance,Retrieve,Store,SetStoredLabware,Fill,Empty,CloseLatch,OpenLatch,PrepareShuttle,CalibrateGripper,CalibratePipette,CalibrateModule,MoveToMaintenancePosition,UnsafeBlowOutInPlace,UnsafeDropTipInPlace,UpdatePositionEstimators,UnsafeEngageAxes,UnsafeUngripLabware,UnsafePlaceLabware,UnsafeManualRetrieve,MoveTo,MoveAxesRelative,MoveAxesTo,openGripperJaw,closeGripperJaw]",
                    "traceback": "  File \"/opt/opentrons-robot-server/starlette/middleware/errors.py\", line 162, in __call__\n    await self.app(scope, receive, _send)\n\n  File \"/opt/opentrons-robot-server/starlette/middleware/cors.py\", line 83, in __call__\n    await self.app(scope, receive, send)\n\n  File \"/opt/opentrons-robot-server/starlette/middleware/exceptions.py\", line 79, in __call__\n    raise exc\n\n  File \"/opt/opentrons-robot-server/starlette/middleware/exceptions.py\", line 68, in __call__\n    await self.app(scope, receive, sender)\n\n  File \"/opt/opentrons-robot-server/fastapi/middleware/asyncexitstack.py\", line 20, in __call__\n    raise e\n\n  File \"/opt/opentrons-robot-server/fastapi/middleware/asyncexitstack.py\", line 17, in __call__\n    await self.app(scope, receive, send)\n\n  File \"/opt/opentrons-robot-server/starlette/routing.py\", line 718, in __call__\n    await route.handle(scope, receive, send)\n\n  File \"/opt/opentrons-robot-server/starlette/routing.py\", line 276, in handle\n    await self.app(scope, receive, send)\n\n  File \"/opt/opentrons-robot-server/starlette/routing.py\", line 66, in app\n    response = await func(request)\n\n  File \"/opt/opentrons-robot-server/fastapi/routing.py\", line 273, in app\n    raw_response = await run_endpoint_function(\n\n  File \"/opt/opentrons-robot-server/fastapi/routing.py\", line 190, in run_endpoint_function\n    return await dependant.call(**values)\n\n  File \"/opt/opentrons-robot-server/robot_server/runs/router/commands_router.py\", line 306, in get_run_commands\n    command_slice = run_data_manager.get_commands_slice(\n\n  File \"/opt/opentrons-robot-server/robot_server/runs/run_data_manager.py\", line 431, in get_commands_slice\n    return self._run_store.get_commands_slice(\n\n  File \"/opt/opentrons-robot-server/robot_server/runs/run_store.py\", line 519, in get_commands_slice\n    sliced_commands: List[Command] = [\n\n  File \"/opt/opentrons-robot-server/robot_server/runs/run_store.py\", line 520, in <listcomp>\n    _parse_command(row.command) for row in slice_result\n\n  File \"/opt/opentrons-robot-server/robot_server/runs/run_store.py\", line 835, in _parse_command\n    return json_to_pydantic(CommandAdapter, json_str)\n\n  File \"/opt/opentrons-robot-server/robot_server/persistence/pydantic.py\", line 46, in json_to_pydantic\n    return model.validate_json(json_str)\n\n  File \"/opt/opentrons-robot-server/pydantic/type_adapter.py\", line 144, in wrapped\n    return func(self, *args, **kwargs)\n\n  File \"/opt/opentrons-robot-server/pydantic/type_adapter.py\", line 393, in validate_json\n    return self.validator.validate_json(data, strict=strict, context=context)\n",
                    "class": "ValidationError"
                },
                "wrapping": []
            },
            "errorCode": "4000"
        }
    ]
}

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 27.33%. Comparing base (ca3d6af) to head (904a7d0).
Report is 2 commits behind head on chore_release-8.4.0.

Additional details and impacted files

@@                   Coverage Diff                   @@
##           chore_release-8.4.0   #17989      +/-   ##
=======================================================
- Coverage                27.81%   27.33%   -0.48%     
=======================================================
  Files                     3101     3101              
  Lines                   235468   235468              
  Branches                 19127    19131       +4     
=======================================================
- Hits                     65484    64369    -1115     
- Misses                  169966   171083    +1117     
+ Partials                    18       16       -2     

Flag	Coverage Δ
protocol-designer	18.80% <ø> (ø)
step-generation	4.35% <ø> (ø)

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see 29 files with indirect coverage changes

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[sfoster1]

Looks good to me!