Y25-623 scRNA - added a version of tenstamp creator and refactored multistamp JS

app/frontend/javascript/multi-stamp/components/MultiStamp.vue

@@ -59,10 +59,15 @@ import {
 } from '@/javascript/shared/components/plateScanValidators.js'
 import devourApi from '@/javascript/shared/devourApi.js'
 import buildPlateObjs from '@/javascript/shared/plateHelpers.js'
-import { handleFailedRequest, requestIsActive, requestsFromPlates } from '@/javascript/shared/requestHelpers.js'
+import {
+  allWellsFromPlates,
+  handleFailedRequest,
+  requestIsActive,
+  requestsFromPlates,
+} from '@/javascript/shared/requestHelpers.js'
 import resources from '@/javascript/shared/resources.js'
 import { transferPlatesToPlatesCreator } from '@/javascript/shared/transfersCreators.js'
-import { transfersFromRequests } from '@/javascript/shared/transfersLayouts.js'
+import { transfersFromRequests, transfersFromAllWells } from '@/javascript/shared/transfersLayouts.js'
 import MultiStampTransfers from './MultiStampTransfers.vue'
 import NullFilter from './NullFilter.vue'
 import PlateSummary from './PlateSummary.vue'
@@ -150,6 +155,11 @@ export default {
       required: false,
       default: 'false',
     },
+
+    // Flag to transfer all wells with aliquots, regardless of whether they have requests.
+    // Defaults to false.
+    // Also referenced as transfer-all-wells and transfer_all_wells
+    transferAllWells: { type: String, required: false, default: 'false' },
   },
   data() {
     return {
@@ -226,7 +236,13 @@ export default {
       }
       return requestsWithPlatesArray
     },
+    allWellsWithAliquots() {
+      return allWellsFromPlates(this.validPlates)
+    },
     transfers() {
+      if (this.transferAllWells === 'true') {
+        return transfersFromAllWells(this.allWellsWithAliquots, this.transfersLayout)
+      }
       return transfersFromRequests(this.requestsWithPlatesFiltered, this.transfersLayout)
     },
     validTransfers() {

app/frontend/javascript/shared/requestHelpers.js

@@ -29,6 +29,27 @@ const requestsFromPlates = function (plateObjs) {
   return requestsArray
 }
 
+// Gets all wells with aliquots from an array of plateObjs, regardless of whether they have requests.
+// Returns one object per occupied well, with request set to undefined.
+const allWellsFromPlates = function (plateObjs) {
+  const wellsArray = []
+  for (let p = 0; p < plateObjs.length; p++) {
+    const plateObj = plateObjs[p]
+    const wells = plateObj.plate.wells
+    for (let w = 0; w < wells.length; w++) {
+      const well = wells[w]
+      if (well.aliquots.length > 0) {
+        wellsArray.push({
+          request: undefined,
+          well: well,
+          plateObj: plateObj,
+        })
+      }
+    }
+  }
+  return wellsArray
+}
+
 const handleFailedRequest = function (request) {
   // generate an alert on the page
   let title = 'Unexpected error'
@@ -50,4 +71,4 @@ const handleFailedRequest = function (request) {
   })
 }
 
-export { handleFailedRequest, requestIsActive, requestIsLibraryCreation, requestsFromPlates }
+export { allWellsFromPlates, handleFailedRequest, requestIsActive, requestIsLibraryCreation, requestsFromPlates }

app/frontend/javascript/shared/requestHelpers.spec.js

@@ -1,6 +1,69 @@
-import { handleFailedRequest } from '@/javascript/shared/requestHelpers.js'
+import { allWellsFromPlates, handleFailedRequest } from '@/javascript/shared/requestHelpers.js'
 import eventBus from '@/javascript/shared/eventBus.js'
 
+describe('allWellsFromPlates', () => {
+  const buildPlateObj = (index, wells) => ({
+    index,
+    state: 'valid',
+    plate: { uuid: `plate-uuid-${index}`, wells },
+  })
+
+  const buildWell = (position, aliquotCount = 0) => ({
+    uuid: `well-uuid-${position}`,
+    position: { name: position },
+    aliquots: Array.from({ length: aliquotCount }, (_, i) => ({ uuid: `aliquot-${position}-${i}` })),
+  })
+
+  it('returns an empty array when given no plates', () => {
+    expect(allWellsFromPlates([])).toEqual([])
+  })
+
+  it('returns an empty array when all wells are empty', () => {
+    const plateObj = buildPlateObj(0, [buildWell('A1'), buildWell('B1')])
+    expect(allWellsFromPlates([plateObj])).toEqual([])
+  })
+
+  it('returns only wells that have aliquots', () => {
+    const emptyWell = buildWell('A1', 0)
+    const occupiedWell = buildWell('B1', 1)
+    const plateObj = buildPlateObj(0, [emptyWell, occupiedWell])
+
+    const result = allWellsFromPlates([plateObj])
+
+    expect(result).toHaveLength(1)
+    expect(result[0].well).toBe(occupiedWell)
+  })
+
+  it('sets request to undefined for each returned entry', () => {
+    const plateObj = buildPlateObj(0, [buildWell('A1', 2)])
+
+    const result = allWellsFromPlates([plateObj])
+
+    expect(result[0].request).toBeUndefined()
+  })
+
+  it('includes the correct plateObj reference on each entry', () => {
+    const plateObj = buildPlateObj(0, [buildWell('A1', 1)])
+
+    const result = allWellsFromPlates([plateObj])
+
+    expect(result[0].plateObj).toBe(plateObj)
+  })
+
+  it('returns entries for all occupied wells across multiple plates', () => {
+    const plate0 = buildPlateObj(0, [buildWell('A1', 1), buildWell('B1', 0)])
+    const plate1 = buildPlateObj(1, [buildWell('A1', 0), buildWell('C1', 3)])
+
+    const result = allWellsFromPlates([plate0, plate1])
+
+    expect(result).toHaveLength(2)
+    expect(result[0].well.position.name).toBe('A1')
+    expect(result[0].plateObj).toBe(plate0)
+    expect(result[1].well.position.name).toBe('C1')
+    expect(result[1].plateObj).toBe(plate1)
+  })
+})
+
 describe('handleFailedRequest', () => {
   it('emits a danger alert with a formatted message when response contains an array', () => {
     const mockEmit = vi.spyOn(eventBus, '$emit')

app/frontend/javascript/shared/transfersCreators.js

@@ -6,7 +6,7 @@ const transferPlatesToPlatesCreator = function (transfers, extraParams = (_) =>
       source_plate: transfers[i].plateObj.plate.uuid,
       pool_index: transfers[i].plateObj.index + 1,
       source_asset: transfers[i].well.uuid,
-      outer_request: transfers[i].request.uuid,
+      outer_request: transfers[i].request?.uuid ?? null,
       new_target: { location: transfers[i].targetWell },
       ...extraParams(transfers[i]),
     }

app/frontend/javascript/shared/transfersLayouts.js

@@ -93,12 +93,12 @@ const quadrantTransfers = function (requestsWithPlates) {
 // duplicatedRequests array.
 //
 // Note: Indexes are calculated for 96 wells plates only.
-const buildPlatesMatrix = function (requestsWithPlates, maxPlates, maxWellsPerPlate) {
+const buildPlatesMatrix = function (requestsWithPlates, maxPlates, maxWellsPerPlate, transferAllWells = false) {
   const platesMatrix = buildArray(maxPlates, () => new Array(maxWellsPerPlate))
   const duplicatedRequests = []
   for (let i = 0; i < requestsWithPlates.length; i++) {
     const { request, well, plateObj } = requestsWithPlates[i]
-    if (request === undefined) {
+    if (request === undefined && !transferAllWells) {
       continue
     }
     const wellIndex = nameToIndex(well.position.name, 8)
@@ -167,11 +167,12 @@ const buildSequentialTransfersArray = function (transferRequests) {
   const transfers = new Array(transferRequests.length)
   for (let i = 0; i < transferRequests.length; i++) {
     const requestWithPlate = transferRequests[i]
+    const targetWell = indexToName(i, 8)
     transfers[i] = {
       request: requestWithPlate.request,
       well: requestWithPlate.well,
       plateObj: requestWithPlate.plateObj,
-      targetWell: indexToName(i, 8),
+      targetWell: targetWell,
     }
   }
   return transfers
@@ -273,8 +274,8 @@ const buildSequentialTubesTransfersArray = function (transferRequests) {
 // |C1|C2|        |  |  |         |P1D1|P2A1|P2D3
 // +--+--+--~     +--+--+--~      +----+----+----~
 // |D1|  |D3      |  |D2|D3       |P1C2|P2B2|
-const sequentialTransfers = function (requestsWithPlates) {
-  const { platesMatrix, duplicatedRequests } = buildPlatesMatrix(requestsWithPlates, 10, 96)
+const sequentialTransfers = function (requestsWithPlates, transferAllWells = false) {
+  const { platesMatrix, duplicatedRequests } = buildPlatesMatrix(requestsWithPlates, 10, 96, transferAllWells)
   const transferRequests = platesMatrix.flat()
   const validTransfers = buildSequentialTransfersArray(transferRequests)
   const duplicatedTransfers = buildSequentialTransfersArray(duplicatedRequests)
@@ -337,6 +338,21 @@ const transfersFromRequests = function (requestsWithPlates, transfersLayout) {
   return { valid: validTransfers, duplicated: duplicatedTransfers }
 }
 
+// Receives an array of allWellsWithAliquots and a transfer layout name (developed
+// for 'sequential' only).
+// Returns an object containing an array of valid transfers and an array of
+// duplicated transfers.
+// Throws an error if the transfers layout string is not mapped to a transfer
+// function.
+const transfersFromAllWells = function (allWellsWithAliquots, transfersLayout) {
+  const transferFunction = transferFunctions[transfersLayout]
+  if (transferFunction === undefined) {
+    throw `Invalid transfers layout name: ${transfersLayout}`
+  }
+  const { validTransfers, duplicatedTransfers } = transferFunction(allWellsWithAliquots, true)
+  return { valid: validTransfers, duplicated: duplicatedTransfers }
+}
+
 // Receives an array of potential transfers and a transfer layout name
 // (valid options: 'sequentialtubes').
 // Returns an object containing an array of valid transfers
@@ -367,6 +383,7 @@ const transfersForTubes = function (validTubes) {
 
 export {
   transfersFromRequests,
+  transfersFromAllWells,
   transfersForTubes,
   buildPlatesMatrix,
   buildLibrarySplitPlatesMatrix,

app/frontend/javascript/shared/transfersLayouts.spec.js

@@ -1,5 +1,6 @@
 import {
   transfersFromRequests,
+  transfersFromAllWells,
   buildPlatesMatrix,
   buildLibrarySplitPlatesMatrix,
   buildSequentialLibrarySplitTransfersArray,
@@ -281,4 +282,36 @@ describe('transfersLayouts.js', () => {
       ])
     })
   })
+
+  describe('#transfersFromAllWells', () => {
+    const allWells = [
+      { request: undefined, well: well1, plateObj: plateObj1 },
+      { request: undefined, well: well2, plateObj: plateObj2 },
+    ]
+
+    it('throws an error if invalid layout is provided', () => {
+      expect(() => transfersFromAllWells(allWells, 'invalid')).toThrow('Invalid transfers layout name: invalid')
+    })
+
+    it('creates the correct transfers with sequential layout', () => {
+      const transfersResults = transfersFromAllWells(allWells, 'sequential')
+
+      expect(transfersResults.valid).toEqual([
+        {
+          request: undefined,
+          well: well1,
+          plateObj: plateObj1,
+          targetWell: 'A1',
+        },
+        {
+          request: undefined,
+          well: well2,
+          plateObj: plateObj2,
+          targetWell: 'B1',
+        },
+      ])
+
+      expect(transfersResults.duplicated).toEqual([])
+    })
+  })
 })

app/models/concerns/presenters/state_input_no_submission.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Presenters
+  # Include in presenters that suppress state changes under all circumstances
+  module StateInputNoSubmission
+    def control_state_change
+      # You cannot change the state
+    end
+
+    def default_state_change
+      # You cannot change the state
+    end
+  end
+end

app/models/concerns/presenters/stock_no_submission_behaviour.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+# Include in a presenter which handles stock plates that don't require submissions
+module Presenters::StockNoSubmissionBehaviour
+  extend ActiveSupport::Concern
+
+  include Presenters::StateInputNoSubmission
+
+  included { validates_with Validators::StockNoSubmissionStateValidator, if: :pending? }
+
+  def input_barcode
+    barcode
+  end
+end

app/models/labware_creators/multi_stamp.rb

@@ -31,6 +31,10 @@ def require_active_library_requests?
       params&.fetch('require_active_library_requests', false)
     end
 
+    def transfer_all_wells?
+      false
+    end
+
     private
 
     def create_labware!

app/models/labware_creators/ten_stamp_all_wells.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+module LabwareCreators
+  # A variant of TenStamp that transfers all wells containing aliquots,
+  # regardless of whether they have active requests.
+  # Developed for scRNA aggregation, where the XP and Input plates will not have an active submission
+  # at the time of transfer. Instead the submission will be made on the child Cherrypick plate.
+  class TenStampAllWells < TenStamp
+    # Flag to indicate that all wells with aliquots should be transferred, regardless of active requests.
+    # Defaulted to false in MultiStamp (super class of TenStamp), but overriden to true here.
+    # Passed through to the javascript for multi-stamping where it determines the behavior.
+    def transfer_all_wells?
+      true
+    end
+  end
+end

app/models/presenters/stock_plate_with_no_submission_presenter.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module Presenters
+  #
+  # Presenters::StockPlateWithNoSubmissionPresenter is used for stock plates
+  # which do not need a submission to continue.
+  # This is used for the scRNA Core pipeline, specifically for LRC GEM-X 5p CITE SUP Input plates.
+  #
+  class StockPlateWithNoSubmissionPresenter < PlatePresenter
+    include Presenters::StockNoSubmissionBehaviour
+    include Presenters::Statemachine::Permissive
+
+    validates_with Validators::SuboptimalValidator
+
+    def allow_new_submission?
+      true
+    end
+
+    def state
+      'passed'
+    end
+  end
+end

app/models/validators/stock_no_submission_state_validator.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+module Validators
+  # Validator for stock plates that don't require submissions
+  # Same as StockStateValidator but skips checks for submissions
+  class StockNoSubmissionStateValidator < StockStateValidator
+    # rubocop:disable Metrics/MethodLength
+    def validate(presenter)
+      analyzer = Analyzer.new(presenter.labware)
+      if analyzer.no_samples?
+        presenter.errors.add(:plate, 'has no samples. Did the cherry-pick complete successfully?')
+      else
+        if analyzer.duplicates?
+          presenter.errors.add(:plate, "has multiple submissions on: #{analyzer.duplicates.to_sentence}")
+        end
+        if analyzer.empty_wells_with_requests?
+          presenter.errors.add(:plate, "has requests on empty wells: #{analyzer.empty_wells_with_requests.to_sentence}")
+        end
+      end
+    end
+
+    # rubocop:enable Metrics/MethodLength
+  end
+end

app/views/plate_creation/multi_stamp.html.erb

@@ -10,6 +10,7 @@
      data-target-columns="<%= @labware_creator.target_columns %>"
      data-source-plates="<%= @labware_creator.source_plates %>"
      data-acceptable-purposes="<%= @labware_creator.acceptable_purposes %>"
-     data-require-active-library-requests="<%= @labware_creator.require_active_library_requests? %>">
+     data-require-active-library-requests="<%= @labware_creator.require_active_library_requests? %>"
+     data-transfer-all-wells="<%= @labware_creator.transfer_all_wells? %>">
   <div class="spinner-dark">Loading...</div>
 </div>