feat(app): Plate reader in LPC and CommandText, filter out plate read…

…er lid as labware (#16489)

fix PLAT-483, PLAT-525, PLAT-526, PLAT-547, RQA-3310

app/src/assets/localization/en/protocol_command_text.json

@@ -1,4 +1,8 @@
 {
+  "absorbance_reader_open_lid": "Opening Absorbance Reader lid",
+  "absorbance_reader_close_lid": "Closing Absorbance Reader lid",
+  "absorbance_reader_initialize": "Initializing Absorbance Reader to perform {{mode}} measurement at {{wavelengths}}",
+  "absorbance_reader_read": "Reading plate in Absorbance Reader",
   "adapter_in_mod_in_slot": "{{adapter}} on {{module}} in {{slot}}",
   "adapter_in_slot": "{{adapter}} in {{slot}}",
   "aspirate": "Aspirating {{volume}} µL from well {{well_name}} of {{labware}} in {{labware_location}} at {{flow_rate}} µL/sec",
@@ -49,6 +53,7 @@
   "move_to_coordinates": "Moving to (X: {{x}}, Y: {{y}}, Z: {{z}})",
   "move_to_slot": "Moving to Slot {{slot_name}}",
   "move_to_well": "Moving to well {{well_name}} of {{labware}} in {{labware_location}}",
+  "multiple": "multiple",
   "notes": "notes",
   "off_deck": "off deck",
   "offdeck": "offdeck",
@@ -66,9 +71,10 @@
   "setting_temperature_module_temp": "Setting Temperature Module to {{temp}} (rounded to nearest integer)",
   "setting_thermocycler_block_temp": "Setting Thermocycler block temperature to {{temp}} with hold time of {{hold_time_seconds}} seconds after target reached",
   "setting_thermocycler_lid_temp": "Setting Thermocycler lid temperature to {{temp}}",
+  "single": "single",
+  "slot": "Slot {{slot_name}}",
   "turning_rail_lights_off": "Turning rail lights off",
   "turning_rail_lights_on": "Turning rail lights on",
-  "slot": "Slot {{slot_name}}",
   "target_temperature": "target temperature",
   "tc_awaiting_for_duration": "Waiting for Thermocycler profile to complete",
   "tc_run_profile_steps": "Temperature: {{celsius}}°C, hold time: {{duration}}",
@@ -84,5 +90,6 @@
   "waiting_for_tc_block_to_reach": "Waiting for Thermocycler block to reach target temperature and holding for specified time",
   "waiting_for_tc_lid_to_reach": "Waiting for Thermocycler lid to reach target temperature",
   "waiting_to_reach_temp_module": "Waiting for Temperature Module to reach {{temp}}",
-  "waste_chute": "Waste Chute"
+  "waste_chute": "Waste Chute",
+  "with_reference_of": "with reference of {{wavelength}} nm"
 }

app/src/molecules/Command/hooks/useCommandTextString/index.tsx

@@ -127,7 +127,17 @@ export function useCommandTextString(
           command,
         }),
       }
-
+    case 'absorbanceReader/openLid':
+    case 'absorbanceReader/closeLid':
+    case 'absorbanceReader/initialize':
+    case 'absorbanceReader/read':
+      return {
+        kind: 'generic',
+        commandText: utils.getAbsorbanceReaderCommandText({
+          ...fullParams,
+          command,
+        }),
+      }
     case 'thermocycler/runProfile':
       return utils.getTCRunProfileCommandText({ ...fullParams, command })
 

app/src/molecules/Command/hooks/useCommandTextString/utils/getAbsorbanceReaderCommandText.ts

@@ -0,0 +1,53 @@
+import type {
+  AbsorbanceReaderOpenLidRunTimeCommand,
+  AbsorbanceReaderCloseLidRunTimeCommand,
+  AbsorbanceReaderInitializeRunTimeCommand,
+  AbsorbanceReaderReadRunTimeCommand,
+  RunTimeCommand,
+} from '@opentrons/shared-data'
+import type { HandlesCommands } from './types'
+
+export type AbsorbanceCreateCommand =
+  | AbsorbanceReaderOpenLidRunTimeCommand
+  | AbsorbanceReaderCloseLidRunTimeCommand
+  | AbsorbanceReaderInitializeRunTimeCommand
+  | AbsorbanceReaderReadRunTimeCommand
+
+const KEYS_BY_COMMAND_TYPE: {
+  [commandType in AbsorbanceCreateCommand['commandType']]: string
+} = {
+  'absorbanceReader/openLid': 'absorbance_reader_open_lid',
+  'absorbanceReader/closeLid': 'absorbance_reader_close_lid',
+  'absorbanceReader/initialize': 'absorbance_reader_initialize',
+  'absorbanceReader/read': 'absorbance_reader_read',
+}
+
+type HandledCommands = Extract<
+  RunTimeCommand,
+  { commandType: keyof typeof KEYS_BY_COMMAND_TYPE }
+>
+
+type GetAbsorbanceReaderCommandText = HandlesCommands<HandledCommands>
+
+export const getAbsorbanceReaderCommandText = ({
+  command,
+  t,
+}: GetAbsorbanceReaderCommandText): string => {
+  if (command.commandType === 'absorbanceReader/initialize') {
+    const wavelengths = command.params.sampleWavelengths.join(' nm, ') + ` nm`
+    const mode =
+      command.params.measureMode === 'multi' ? t('multiple') : t('single')
+
+    return `${t('absorbance_reader_initialize', {
+      mode,
+      wavelengths,
+    })} ${
+      command.params.referenceWavelength != null
+        ? t('with_reference_of', {
+            wavelength: command.params.referenceWavelength,
+          })
+        : ''
+    }`
+  }
+  return t(KEYS_BY_COMMAND_TYPE[command.commandType])
+}

app/src/molecules/Command/hooks/useCommandTextString/utils/index.ts

@@ -23,3 +23,4 @@ export { getUnknownCommandText } from './getUnknownCommandText'
 export { getPipettingCommandText } from './getPipettingCommandText'
 export { getLiquidProbeCommandText } from './getLiquidProbeCommandText'
 export { getRailLightsCommandText } from './getRailLightsCommandText'
+export { getAbsorbanceReaderCommandText } from './getAbsorbanceReaderCommandText'

app/src/organisms/Desktop/ProtocolDetails/index.tsx

@@ -47,6 +47,7 @@ import {
   parseInitialLoadedLabwareBySlot,
   parseInitialLoadedModulesBySlot,
   parseInitialPipetteNamesByMount,
+  NON_USER_ADDRESSABLE_LABWARE,
 } from '@opentrons/shared-data'
 
 import { getTopPortalEl } from '/app/App/portal'
@@ -284,7 +285,9 @@ export function ProtocolDetails(
               : []
           ),
         }).filter(
-          labware => labware.result?.definition?.parameters?.format !== 'trash'
+          labware =>
+            labware.result?.definition?.parameters?.format !== 'trash' &&
+            !NON_USER_ADDRESSABLE_LABWARE.includes(labware?.params?.loadName)
         )
       : []
 

app/src/organisms/LabwarePositionCheck/IntroScreen/getPrepCommands.ts

@@ -2,6 +2,8 @@ import {
   getModuleType,
   HEATERSHAKER_MODULE_TYPE,
   THERMOCYCLER_MODULE_TYPE,
+  ABSORBANCE_READER_TYPE,
+  NON_USER_ADDRESSABLE_LABWARE,
 } from '@opentrons/shared-data'
 
 import type {
@@ -13,6 +15,7 @@ import type {
   RunTimeCommand,
   SetupRunTimeCommand,
   TCOpenLidCreateCommand,
+  AbsorbanceReaderOpenLidCreateCommand,
 } from '@opentrons/shared-data'
 
 type LPCPrepCommand =
@@ -21,6 +24,7 @@ type LPCPrepCommand =
   | TCOpenLidCreateCommand
   | HeaterShakerDeactivateShakerCreateCommand
   | HeaterShakerCloseLatchCreateCommand
+  | AbsorbanceReaderOpenLidCreateCommand
 
 export function getPrepCommands(
   protocolData: CompletedProtocolAnalysis
@@ -45,7 +49,8 @@ export function getPrepCommands(
           return [...acc, loadWithPipetteId]
         } else if (
           command.commandType === 'loadLabware' &&
-          command.result?.labwareId != null
+          command.result?.labwareId != null &&
+          !NON_USER_ADDRESSABLE_LABWARE.includes(command.params.loadName)
         ) {
           // load all labware off-deck so that LPC can move them on individually later
           return [
@@ -97,6 +102,26 @@ export function getPrepCommands(
     []
   )
 
+  const AbsorbanceCommands = protocolData.modules.reduce<LPCPrepCommand[]>(
+    (acc, module) => {
+      if (getModuleType(module.model) === ABSORBANCE_READER_TYPE) {
+        return [
+          ...acc,
+          {
+            commandType: 'home',
+            params: {},
+          },
+          {
+            commandType: 'absorbanceReader/openLid',
+            params: { moduleId: module.id },
+          },
+        ]
+      }
+      return acc
+    },
+    []
+  )
+
   const HSCommands = protocolData.modules.reduce<
     HeaterShakerCloseLatchCreateCommand[]
   >((acc, module) => {
@@ -116,7 +141,13 @@ export function getPrepCommands(
     params: {},
   }
   // prepCommands will be run when a user starts LPC
-  return [...loadCommands, ...TCCommands, ...HSCommands, homeCommand]
+  return [
+    ...loadCommands,
+    ...TCCommands,
+    ...AbsorbanceCommands,
+    ...HSCommands,
+    homeCommand,
+  ]
 }
 
 function isLoadCommand(

app/src/organisms/LabwarePositionCheck/useLaunchLPC.tsx

@@ -15,11 +15,6 @@ import { getLabwareDefinitionsFromCommands } from '/app/molecules/Command/utils/
 
 import type { RobotType } from '@opentrons/shared-data'
 
-const filteredLabware = [
-  'opentrons_tough_pcr_auto_sealing_lid',
-  'opentrons_flex_lid_absorbance_plate_reader_module',
-]
-
 export function useLaunchLPC(
   runId: string,
   robotType: RobotType,
@@ -67,11 +62,10 @@ export function useLaunchLPC(
           getLabwareDefinitionsFromCommands(
             mostRecentAnalysis?.commands ?? []
           ).map(def => {
-            if (!filteredLabware.includes(def.parameters.loadName))
-              createLabwareDefinition({
-                maintenanceRunId: maintenanceRun?.data?.id,
-                labwareDef: def,
-              })
+            createLabwareDefinition({
+              maintenanceRunId: maintenanceRun?.data?.id,
+              labwareDef: def,
+            })
           })
         ).then(() => {
           setMaintenanceRunId(maintenanceRun.data.id)

app/src/organisms/LabwarePositionCheck/utils/getProbeBasedLPCSteps.ts

@@ -58,7 +58,10 @@ function getAllCheckSectionSteps(
       const labwareDef = labwareDefinitions.find(
         def => getLabwareDefURI(def) === labwareLocationCombo.definitionUri
       )
-      if ((labwareDef?.allowedRoles ?? []).includes('adapter')) {
+      if (
+        (labwareDef?.allowedRoles ?? []).includes('adapter') ||
+        (labwareDef?.allowedRoles ?? []).includes('lid')
+      ) {
         return acc
       }
       // remove duplicate definitionUri in same location
@@ -73,12 +76,7 @@ function getAllCheckSectionSteps(
     []
   )
 
-  // HACK: Remove LPC for plate reader to unblock science.
-  const filteredLabwareLocations = labwareLocations.filter(labware => {
-    return labware.location?.moduleModel !== 'absorbanceReaderV1'
-  })
-
-  return filteredLabwareLocations.map(
+  return labwareLocations.map(
     ({ location, labwareId, moduleId, adapterId, definitionUri }) => ({
       section: SECTIONS.CHECK_POSITIONS,
       labwareId: labwareId,

app/src/organisms/ModuleCard/AbsorbanceReaderData.tsx

@@ -46,7 +46,7 @@ export const AbsorbanceReaderData = (
         data-testid="abs_module_data"
       >
         {t('abs_reader_lid_status', {
-          status: moduleData.lidStatus === 'on' ? 'open' : 'closed',
+          status: moduleData.lidStatus === 'on' ? 'closed' : 'open',
         })}
       </StyledText>
     </>

app/src/transformations/analysis/getProtocolModulesInfo.ts

@@ -3,6 +3,7 @@ import {
   getModuleDef2,
   getLoadedLabwareDefinitionsByUri,
   getPositionFromSlotId,
+  NON_USER_ADDRESSABLE_LABWARE,
 } from '@opentrons/shared-data'
 import { getModuleInitialLoadInfo } from '../commands'
 import type {
@@ -38,7 +39,8 @@ export const getProtocolModulesInfo = (
         protocolData.commands
           .filter(
             (command): command is LoadLabwareRunTimeCommand =>
-              command.commandType === 'loadLabware'
+              command.commandType === 'loadLabware' &&
+              !NON_USER_ADDRESSABLE_LABWARE.includes(command.params.loadName)
           )
           .find(
             (command: LoadLabwareRunTimeCommand) =>

app/src/transformations/commands/transformations/getLabwareSetupItemGroups.ts

@@ -1,5 +1,8 @@
 import partition from 'lodash/partition'
-import { getLabwareDisplayName } from '@opentrons/shared-data'
+import {
+  getLabwareDisplayName,
+  NON_USER_ADDRESSABLE_LABWARE,
+} from '@opentrons/shared-data'
 
 import type {
   LabwareDefinition2,
@@ -43,7 +46,8 @@ export function getLabwareSetupItemGroups(
     commands.reduce<LabwareSetupItem[]>((acc, c) => {
       if (
         c.commandType === 'loadLabware' &&
-        c.result?.definition?.metadata?.displayCategory !== 'trash'
+        c.result?.definition?.metadata?.displayCategory !== 'trash' &&
+        !NON_USER_ADDRESSABLE_LABWARE.includes(c.params?.loadName)
       ) {
         const { location, displayName } = c.params
         const { definition } = c.result ?? {}

components/src/hardware-sim/BaseDeck/BaseDeck.tsx

@@ -168,7 +168,10 @@ export function BaseDeck(props: BaseDeckProps): JSX.Element {
               color={COLORS.black90}
               show4thColumn={
                 stagingAreaFixtures.length > 0 ||
-                wasteChuteStagingAreaFixtures.length > 0
+                wasteChuteStagingAreaFixtures.length > 0 ||
+                modulesOnDeck.findIndex(
+                  module => module.moduleModel === 'absorbanceReaderV1'
+                ) >= 0
               }
             />
           ) : null}

components/src/hardware-sim/DeckConfigurator/AbsorbanceReaderFixture.tsx

@@ -30,7 +30,7 @@ interface AbsorbanceReaderFixtureProps {
   selected?: boolean
 }
 
-const ABSORBANCE_READER_FIXTURE_DISPLAY_NAME = 'Absorbance Reader'
+const ABSORBANCE_READER_FIXTURE_DISPLAY_NAME = 'Absorbance'
 
 export function AbsorbanceReaderFixture(
   props: AbsorbanceReaderFixtureProps

components/src/hardware-sim/DeckConfigurator/index.tsx

@@ -275,7 +275,8 @@ export function DeckConfigurator(props: DeckConfiguratorProps): JSX.Element {
         show4thColumn={
           stagingAreaFixtures.length > 0 ||
           wasteChuteStagingAreaFixtures.length > 0 ||
-          magneticBlockStagingAreaFixtures.length > 0
+          magneticBlockStagingAreaFixtures.length > 0 ||
+          absorbanceReaderFixtures.length > 0
         }
       />
       {children}

components/src/hardware-sim/ProtocolDeck/utils/getModulesInSlots.ts

@@ -2,6 +2,7 @@ import {
   SPAN7_8_10_11_SLOT,
   getModuleDef2,
   getLoadedLabwareDefinitionsByUri,
+  NON_USER_ADDRESSABLE_LABWARE,
 } from '@opentrons/shared-data'
 import type {
   CompletedProtocolAnalysis,
@@ -36,7 +37,8 @@ export const getModulesInSlots = (
         commands
           .filter(
             (command): command is LoadLabwareRunTimeCommand =>
-              command.commandType === 'loadLabware'
+              command.commandType === 'loadLabware' &&
+              !NON_USER_ADDRESSABLE_LABWARE.includes(command.params.loadName)
           )
           .find(
             (command: LoadLabwareRunTimeCommand) =>