Merge branch 'develop' into develop-Y24-190

.eslintrc.js

@@ -12,6 +12,7 @@ module.exports = {
     parser: '@babel/eslint-parser',
     sourceType: 'module',
     requireConfigFile: false,
+    ecmaVersion: 2018,
   },
   rules: {
     'linebreak-style': ['error', 'unix'],

.release-version

@@ -1 +1 @@
-3.56.0
+3.56.1

README.md

@@ -7,7 +7,13 @@
 
 ## Description
 
-A flexible front end to plate bases pipelines in Sequencescape.
+A flexible front end to pipelines in Sequencescape.
+
+## User Requirements
+
+- Used on laboratory instrument machines often running older browser versions due to vendor and network limitations.
+  The user-agent strings extracted from the nginx access logs of August 2024 indicate that the the oldest browser suspected of using Limber is Chrome 65. This means that the minified code served to browsers should be compatible with [ECMAScript 2018](https://www.w3schools.com/js/js_2018.asp).
+  Please see the [Limber page on Confluence](https://ssg-confluence.internal.sanger.ac.uk/display/PSDPUB/LIMBer) for more information.
 
 ## Initial Setup (using Docker)
 

app/frontend/javascript/.eslintrc.js

@@ -17,6 +17,7 @@ module.exports = {
     parser: '@babel/eslint-parser',
     sourceType: 'module',
     requireConfigFile: false,
+    ecmaVersion: 2018,
   },
   rules: {
     'linebreak-style': ['error', 'unix'],

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

@@ -51,7 +51,11 @@
 import LabwareScan from '@/javascript/shared/components/LabwareScan.vue'
 import LoadingModal from '@/javascript/shared/components/LoadingModal.vue'
 import Plate from '@/javascript/shared/components/Plate.vue'
-import { checkDuplicates, checkSize } from '@/javascript/shared/components/plateScanValidators.js'
+import {
+  checkDuplicates,
+  checkSize,
+  checkForUnacceptablePlatePurpose,
+} 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'
@@ -127,6 +131,15 @@ export default {
 
     // Default volume to define in the UI for the volume control
     defaultVolume: { type: String, required: false, default: null },
+
+    // Acceptable plate purpose names that can be used as source plates.
+    // Defines a prop `acceptablePurposes` that accepts a string. It is optional and
+    // defaults to a string representation of an array '[]' if not provided.
+    // e.g. "['PurposeA', 'PurposeB']"
+    // See computed method acceptablePurposesArray for conversion to array.
+    // If present is used in scanValidation to check if the user has scanned an
+    // a plate of the correct type.
+    acceptablePurposes: { type: String, required: false, default: '[]' },
   },
   data() {
     return {
@@ -175,6 +188,9 @@ export default {
     targetColumnsNumber() {
       return Number.parseInt(this.targetColumns)
     },
+    acceptablePurposesArray() {
+      return JSON.parse(this.acceptablePurposes)
+    },
     valid() {
       return (
         this.unsuitablePlates.length === 0 && // None of the plates are invalid
@@ -257,7 +273,7 @@ export default {
       return [
         checkSize(12, 8),
         checkDuplicates(currPlates),
-        // checkExcess(this.excessTransfers)
+        checkForUnacceptablePlatePurpose(this.acceptablePurposesArray),
       ]
     },
   },

app/frontend/javascript/multi-stamp/components/filterProps.js

@@ -23,12 +23,12 @@ const filterProps = {
   },
   null: {
     plateFields: {
-      plates: 'labware_barcode,wells,uuid,number_of_rows,number_of_columns',
+      plates: 'labware_barcode,purpose,wells,uuid,number_of_rows,number_of_columns',
       requests: 'uuid,state',
       wells: 'position,requests_as_source,aliquots,uuid',
       aliquots: 'request',
     },
-    plateIncludes: 'wells,wells.requests_as_source,wells.aliquots.request',
+    plateIncludes: 'purpose,wells,wells.requests_as_source,wells.aliquots.request',
     requestsFilter: 'lb-null-filter',
   },
 }

app/frontend/javascript/shared/components/LabwareScan.vue

@@ -134,7 +134,7 @@ export default {
     uid += 1
     return {
       labwareBarcode: '', // The scanned barcode
-      labware: null, // The tube object
+      labware: null, // The labware object
       uid: `labware-scan-${uid}`, // Unique id to ensure label identifies the correct field
       apiActivity: { state: null, message: '' }, // API status
     }

app/frontend/javascript/shared/components/plateScanValidators.js

@@ -84,31 +84,6 @@ const checkDuplicates = (plateList) => {
   }
 }
 
-// Returns a validator that checks if there are wells in the scanned plate that
-// are in excess (i.e. the sum of valid transfers across scanned
-// plates is greater than the number of wells in the target plate).
-// It also returns the excess wells' position.
-// excessTransfers: An array of transfers that cannot be included in the
-//                     target plate as all the wells are already occupied.
-const checkExcess = (excessTransfers) => {
-  return (plate) => {
-    const excessWells = []
-    for (let i = 0; i < excessTransfers.length; i++) {
-      if (plate && excessTransfers[i].plateObj.plate.uuid === plate.uuid) {
-        excessWells.push(excessTransfers[i].well.position.name)
-      }
-    }
-    if (excessWells.length > 0) {
-      return {
-        valid: false,
-        message: 'Wells in excess: ' + excessWells.join(', '),
-      }
-    } else {
-      return validScanMessage()
-    }
-  }
-}
-
 // Returns a validator that ensures the plate has a state that matches to the
 // supplied list of states. e.g. to check a plate has a state of 'available'
 // or 'exhausted':
@@ -375,10 +350,41 @@ const checkPlateWithSameReadyLibrarySubmissions = (cached_submission_ids) => {
   }
 }
 
+// Checks that the scanned plate's purpose matches one of those in the provided list.
+// Args:
+//   acceptable_purposes - An array of acceptable plate purpose name strings e.g. ['Purpose1', 'Purpose2']
+//   plate - Plate object that contains the plate purpose
+// Returns:
+//   Validation object indicating if the plate has passed the condition
+const checkForUnacceptablePlatePurpose = (acceptable_purposes) => {
+  return (plate) => {
+    if (!acceptable_purposes || acceptable_purposes.length == 0) {
+      // return valid if no acceptable purposes are provided
+      return validScanMessage()
+    } else if (!plate.purpose) {
+      // guard for plate not having a purpose (should not happen)
+      return {
+        valid: false,
+        message: 'The scanned plate does not have a plate purpose',
+      }
+    } else if (acceptable_purposes.includes(plate.purpose.name)) {
+      // if we find a matching purpose, return valid
+      return validScanMessage()
+    } else {
+      return {
+        valid: false,
+        message:
+          'The scanned plate has an unacceptable plate purpose type (should be ' +
+          acceptable_purposes.join(' or ') +
+          ')',
+      }
+    }
+  }
+}
+
 export {
   checkSize,
   checkDuplicates,
-  checkExcess,
   checkLibraryTypesInAllWells,
   getAllLibrarySubmissionsWithMatchingStateForPlate,
   checkAllLibraryRequestsWithSameReadySubmissions,
@@ -389,4 +395,5 @@ export {
   checkMaxCountRequests,
   checkMinCountRequests,
   checkAllSamplesInColumnsList,
+  checkForUnacceptablePlatePurpose,
 }

app/frontend/javascript/shared/components/plateScanValidators.spec.js

@@ -9,9 +9,9 @@ import {
   checkLibraryTypesInAllWells,
   checkSize,
   checkDuplicates,
-  checkExcess,
   checkState,
   checkQCableWalkingBy,
+  checkForUnacceptablePlatePurpose,
 } from '@/javascript/shared/components/plateScanValidators'
 
 describe('checkSize', () => {
@@ -65,39 +65,6 @@ describe('checkDuplicates', () => {
   })
 })
 
-describe('checkExcess', () => {
-  it('passes when the plate is not the source of excess transfers', () => {
-    const plate = { uuid: 'plate-uuid-1' }
-    const other_plate = { uuid: 'plate-uuid-2' }
-    const excessTransfers = [
-      {
-        plateObj: { plate: other_plate },
-      },
-    ]
-
-    expect(checkExcess(excessTransfers)(plate)).toEqual({ valid: true })
-  })
-
-  it('fails when the plate is the source of excess transfers', () => {
-    const plate = { uuid: 'plate-uuid-1' }
-    const excessTransfers = [
-      {
-        plateObj: { plate: plate },
-        well: { position: { name: 'D11' } },
-      },
-      {
-        plateObj: { plate: plate },
-        well: { position: { name: 'D12' } },
-      },
-    ]
-
-    expect(checkExcess(excessTransfers)(plate)).toEqual({
-      valid: false,
-      message: 'Wells in excess: D11, D12',
-    })
-  })
-})
-
 describe('checkState', () => {
   it('passes if the state is in the allowed list', () => {
     const plate = { state: 'available' }
@@ -686,3 +653,45 @@ describe('checkPlateWithSameReadyLibrarySubmissions', () => {
     })
   })
 })
+
+describe('checkForUnacceptablePlatePurpose', () => {
+  const plate1 = {
+    purpose: { name: 'PurposeA' },
+  }
+
+  const plate2 = {
+    purpose: { name: 'PurposeB' },
+  }
+
+  const plate3 = {}
+
+  describe('when there is not a list of acceptable purposes', () => {
+    const validator = checkForUnacceptablePlatePurpose([])
+
+    it('validates when there is no list of acceptable purposes', () => {
+      expect(validator(plate1)).toEqual({ valid: true })
+    })
+  })
+
+  describe('when there is a list of acceptable purposes', () => {
+    const validator = checkForUnacceptablePlatePurpose(['PurposeA', 'PurposeC'])
+
+    it('validates when the plate has an acceptable purpose', () => {
+      expect(validator(plate1)).toEqual({ valid: true })
+    })
+
+    it('fails when the plate has an unacceptable purpose', () => {
+      expect(validator(plate2)).toEqual({
+        valid: false,
+        message: 'The scanned plate has an unacceptable plate purpose type (should be PurposeA or PurposeC)',
+      })
+    })
+
+    it('fails when the plate does not have a purpose', () => {
+      expect(validator(plate3)).toEqual({
+        valid: false,
+        message: 'The scanned plate does not have a plate purpose',
+      })
+    })
+  })
+})

app/frontend/javascript/validate-paired-tubes/components/ValidatePairedTubes.spec.js

@@ -105,7 +105,6 @@ describe('TransferVolumes', () => {
       wrapper.vm.destinationTubeValidators // Refresh the evaluation to cause more calls to checkId
 
       // After setting a source tube
-      console.log(checkId.mock.calls)
       expect(checkId.mock.calls[1][0]).toEqual(['test1', 'test2'])
       expect(checkId.mock.calls[1][1]).toEqual('Does not match the source tube')
     })

app/models/labware_creators/multi_stamp.rb

@@ -12,7 +12,8 @@ class MultiStamp < Base # rubocop:todo Style/Documentation
                     :transfers_creator,
                     :target_rows,
                     :target_columns,
-                    :source_plates
+                    :source_plates,
+                    :acceptable_purposes
 
     self.page = 'multi_stamp'
     self.aliquot_partial = 'standard_aliquot'
@@ -22,6 +23,7 @@ class MultiStamp < Base # rubocop:todo Style/Documentation
     self.target_rows = 0
     self.target_columns = 0
     self.source_plates = 0
+    self.acceptable_purposes = []
 
     validates :transfers, presence: true
 

app/models/labware_creators/ten_stamp.rb

@@ -33,6 +33,15 @@ class TenStamp < MultiStamp # rubocop:todo Style/Documentation
     self.target_columns = 12
     self.source_plates = 10
 
+    def acceptable_purposes
+      # catch for older uses of tenstamp in purpose_config where creator_class is a string
+      if purpose_config[:creator_class].is_a?(Hash) && purpose_config.dig(:creator_class, :args, :acceptable_purposes)
+        Array(purpose_config.dig(:creator_class, :args, :acceptable_purposes))
+      else
+        []
+      end
+    end
+
     private
 
     def request_hash(transfer, *args)

app/models/presenters/minimal_pcr_plate_presenter.rb

@@ -6,8 +6,8 @@ class MinimalPcrPlatePresenter < MinimalPlatePresenter # rubocop:todo Style/Docu
     self.summary_partial = 'labware/plates/pcr_summary'
     self.state_transition_name_scope = :pcr
 
-    # summary_items is a hash of a label label, and a symbol representing the
-    # method to call to get the value
+    # Initializes `summary_items` with a hash mapping display names to their corresponding plate attributes.
+    # Used by the summary panel to display information about the plate in the GUI.
     self.summary_items = {
       'Barcode' => :barcode,
       'Number of wells' => :number_of_wells,

app/models/presenters/pcr_with_primer_panel_plate_presenter.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module Presenters
+  # This Presenter shows the PCR primer panel on the left along with the standard plate layout
+  # view and summary information. This version allows you to fail wells on the plate.
+  #
+  # This was specifically requested by the lab team for the GBS pipleine PCR1 plate so they
+  # could fail wells. If well failing functionality was allowed on stock plates in future, that would be a
+  # preferable option for them and they could fail the wells on the parent plate, and the PCR1 plate could
+  # be returned to using the MinimalPcrPlatePresenter.
+  class PcrWithPrimerPanelPlatePresenter < StandardPresenter
+    include HasPrimerPanel
+    self.summary_partial = 'labware/plates/pcr_with_primer_panel_summary'
+    self.state_transition_name_scope = :pcr
+
+    # Initializes `summary_items` with a hash mapping display names to their corresponding plate attributes.
+    # Used by the summary panel to display information about the plate in the GUI.
+    self.summary_items = {
+      'Barcode' => :barcode,
+      'Number of wells' => :number_of_wells,
+      'Plate type' => :purpose_name,
+      'Primer panel' => :panel_name,
+      'Current plate state' => :state,
+      'Input plate barcode' => :input_barcode,
+      'PCR Cycles' => :requested_pcr_cycles,
+      'Created on' => :created_on
+    }
+  end
+end

app/models/presenters/plate_presenter.rb

@@ -20,8 +20,8 @@ class PlatePresenter
     self.pooling_tab = 'plates/pooling_tab'
     self.samples_partial = 'plates/samples_tab'
 
-    # summary_items is a hash of a label label, and a symbol representing the
-    # method to call to get the value
+    # Initializes `summary_items` with a hash mapping display names to their corresponding plate attributes.
+    # Used by the summary panel to display information about the plate in the GUI.
     self.summary_items = {
       'Barcode' => :barcode,
       'Number of wells' => :number_of_wells,

app/views/labware/plates/_pcr_with_primer_panel_summary.html.erb

@@ -0,0 +1,9 @@
+<div id="labware-summary-div" class="card-body text-white bg-info">
+  <dl>
+    <dt>Primer Panel</dt><dd><%= presenter.panel_name %></dd>
+    <dt>PCR Program</dt><dd><%= presenter.pcr_program %></dd>
+    <dt>PCR Duration</dt><dd><%= presenter.pcr_duration %></dd>
+  </dl>
+</div>
+
+<%= render partial: 'labware/plates/standard_summary', locals: { presenter: presenter } %>

app/views/plate_creation/multi_stamp.html.erb

@@ -9,6 +9,7 @@
      data-target-rows="<%= @labware_creator.target_rows %>"
      data-target-columns="<%= @labware_creator.target_columns %>"
      data-source-plates="<%= @labware_creator.source_plates %>"
+     data-acceptable-purposes="<%= @labware_creator.acceptable_purposes %>"
      >
   <div class="spinner-dark">Loading...</div>
 </div>