Merge pull request #1990 from sanger/develop

[automated] Merge Develop into Master

.pryrc

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+if defined?(PryByebug)
+  Pry.commands.alias_command 's', 'step'
+  Pry.commands.alias_command 'n', 'next'
+  Pry.commands.alias_command 'f', 'finish'
+  Pry.commands.alias_command 'c', 'continue'
+end

.release-version

@@ -1 +1 @@
-3.61.1
+3.62.0

Gemfile.lock

@@ -136,7 +136,7 @@ GEM
     diff-lcs (1.5.1)
     docile (1.4.0)
     drb (2.2.1)
-    dry-cli (1.1.0)
+    dry-cli (1.2.0)
     erubi (1.13.0)
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
@@ -192,10 +192,10 @@ GEM
       tilt
     hashdiff (1.1.0)
     hashie (5.0.0)
-    i18n (1.14.5)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
     io-console (0.7.2)
-    irb (1.14.0)
+    irb (1.14.1)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     json (2.7.2)
@@ -264,7 +264,7 @@ GEM
     puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
-    rack (3.1.7)
+    rack (3.1.8)
     rack-mini-profiler (3.3.1)
       rack (>= 1.2.0)
     rack-proxy (0.7.7)
@@ -319,7 +319,7 @@ GEM
     rdoc (6.7.0)
       psych (>= 4.0.0)
     regexp_parser (2.9.2)
-    reline (0.5.9)
+    reline (0.5.10)
       io-console (~> 0.5)
     rexml (3.3.6)
       strscan
@@ -404,7 +404,7 @@ GEM
       rbs
       syntax_tree (>= 2.0.1)
     temple (0.10.3)
-    thor (1.3.1)
+    thor (1.3.2)
     tilt (2.4.0)
     timeout (0.4.1)
     tzinfo (2.0.6)
@@ -413,8 +413,9 @@ GEM
     vite_rails (3.0.17)
       railties (>= 5.1, < 8)
       vite_ruby (~> 3.0, >= 3.2.2)
-    vite_ruby (3.6.0)
+    vite_ruby (3.9.0)
       dry-cli (>= 0.7, < 2)
+      logger (~> 1.6)
       rack-proxy (~> 0.6, >= 0.6.1)
       zeitwerk (~> 2.2)
     web-console (4.2.1)
@@ -434,7 +435,7 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.36)
-    zeitwerk (2.6.17)
+    zeitwerk (2.6.18)
 
 PLATFORMS
   ruby

app/frontend/entrypoints/application.js

@@ -29,6 +29,15 @@ console.log('Visit the guide for more information: ', 'https://vite-ruby.netlify
 
 // ^^^ Template from Vite. Below is custom code for Limber ^^^
 
+// Import Rails UJS as in Sequencescape
+import Rails from '@rails/ujs'
+
+try {
+  Rails.start()
+} catch {
+  // Nothing
+}
+
 // Import Libraries
 import 'bootstrap'
 import 'popper.js'

app/frontend/javascript/custom-tagged-plate/components/CustomTaggedPlate.spec.js

@@ -833,8 +833,8 @@ describe('CustomTaggedPlate', () => {
           purpose_uuid: 'purpose-uuid',
           parent_uuid: 'parent-plate-uuid',
           tag_layout: {
-            tag_group: 'tag-1-group-uuid',
-            tag2_group: 'tag-2-group-uuid',
+            tag_group_uuid: 'tag-1-group-uuid',
+            tag2_group_uuid: 'tag-2-group-uuid',
             direction: 'column',
             walking_by: 'manual by plate',
             initial_tag: 1,

app/frontend/javascript/custom-tagged-plate/components/CustomTaggedPlate.vue

@@ -619,8 +619,8 @@ export default {
           purpose_uuid: this.purposeUuid,
           parent_uuid: this.parentUuid,
           tag_layout: {
-            tag_group: this.tag1GroupUuid,
-            tag2_group: this.tag2GroupUuid,
+            tag_group_uuid: this.tag1GroupUuid,
+            tag2_group_uuid: this.tag2GroupUuid,
             direction: this.direction,
             walking_by: this.walkingBy,
             initial_tag: initialTag,

app/frontend/javascript/legacy_scripts_a.js

@@ -59,9 +59,12 @@ let limberPlateView = function (defaultTab) {
   control.find('a[href="' + defaultTab + '"]').tab('show')
 
   plateElement.on('click', '.aliquot', function (event) {
+    control.find('a[data-plate-view="pools-view"]').tab('show')
+
     let pool = $(event.currentTarget).data('pool')
 
-    control.find('a[data-plate-view="pools-view"]').tab('show')
+    // Handle cases where pool is not defined to prevent errors
+    if (pool === undefined || pool === '') return
 
     plateElement
       .find('.aliquot[data-pool!=' + pool + ']')

app/frontend/javascript/pipeline-graph/index.js

@@ -226,6 +226,8 @@ const applyMouseEvents = function () {
   // when an edge is clicked, filter the graph to show only that pipeline
   core.on('click', 'edge', (event) => {
     const pipeline = event.target.data('pipeline')
-    applyFilter(pipeline)
+    const group = event.target.data('group')
+    const pipelineOrGroup = pipeline || group
+    applyFilter(pipelineOrGroup)
   })
 }

app/helpers/page_helper.rb

@@ -52,8 +52,8 @@ def jumbotron(jumbotron_id = nil, options = {}, &)
 
   # eg. state_badge('pending')
   # <span class="state-badge-pending">Pending</span>
-  def state_badge(state)
-    tag.span(state.titleize, class: "state-badge #{state}", title: 'Labware State', data: { toggle: 'tooltip' })
+  def state_badge(state, title: 'Labware State')
+    tag.span(state.titleize, class: "state-badge #{state}", title: title, data: { toggle: 'tooltip' })
   end
 
   # eg. count_badge(0)

app/models/labware_creators/baited_plate.rb

@@ -25,12 +25,13 @@ def plate
     end
 
     def bait_library_layout_preview
-      @bait_library_layout_preview ||= api.bait_library_layout.preview!(plate: parent_uuid, user: user_uuid).layout
+      @bait_library_layout_preview ||=
+        Sequencescape::Api::V2::BaitLibraryLayout.preview(plate_uuid: parent_uuid, user_uuid: user_uuid).first.layout
     end
 
     def create_labware!
       create_plate_with_standard_transfer! do |child|
-        api.bait_library_layout.create!(plate: child.uuid, user: user_uuid)
+        Sequencescape::Api::V2::BaitLibraryLayout.create!(plate_uuid: child.uuid, user_uuid: user_uuid)
       end
     end
 

app/models/labware_creators/custom_tagged_plate.rb

@@ -18,10 +18,10 @@ class CustomTaggedPlate < Base
       {
         tag_plate: %i[asset_uuid template_uuid state],
         tag_layout: [
-          :user,
-          :plate,
-          :tag_group,
-          :tag2_group,
+          :user_uuid,
+          :plate_uuid,
+          :tag_group_uuid,
+          :tag2_group_uuid,
           :direction,
           :walking_by,
           :initial_tag,
@@ -47,14 +47,11 @@ def initialize(*args, &)
 
     def create_plate! # rubocop:todo Metrics/AbcSize
       @child =
-        api
-          .pooled_plate_creation
-          .create!(
-            child_purpose: purpose_uuid,
-            user: user_uuid,
-            parents: [parent_uuid, tag_plate.asset_uuid].compact_blank
-          )
-          .child
+        Sequencescape::Api::V2::PooledPlateCreation.create!(
+          child_purpose_uuid: purpose_uuid,
+          parent_uuids: [parent_uuid, tag_plate.asset_uuid].compact_blank,
+          user_uuid: user_uuid
+        ).child
 
       transfer_material_from_parent!(@child.uuid)
 
@@ -107,7 +104,7 @@ def tag_layout_attributes
 
     def create_labware!
       create_plate! do |plate_uuid|
-        api.tag_layout.create!(tag_layout_attributes.merge(plate: plate_uuid, user: user_uuid))
+        Sequencescape::Api::V2::TagLayout.create!(tag_layout_attributes.merge(plate_uuid:, user_uuid:))
       end
     end
   end

app/models/labware_creators/merged_plate.rb

@@ -51,10 +51,10 @@ def barcodes=(barcodes)
     private
 
     def create_plate_from_parent!
-      api.pooled_plate_creation.create!(
-        child_purpose: purpose_uuid,
-        user: user_uuid,
-        parents: source_plates.map(&:uuid)
+      Sequencescape::Api::V2::PooledPlateCreation.create!(
+        child_purpose_uuid: purpose_uuid,
+        parent_uuids: source_plates.map(&:uuid),
+        user_uuid: user_uuid
       )
     end
 

app/models/labware_creators/multi_plate_pool.rb

@@ -17,10 +17,12 @@ class MultiPlatePool < Base
     private
 
     def create_labware!
-      plate_creation =
-        api.pooled_plate_creation.create!(parents: transfers.keys, child_purpose: purpose_uuid, user: user_uuid)
-
-      @child = plate_creation.child
+      @child =
+        Sequencescape::Api::V2::PooledPlateCreation.create!(
+          child_purpose_uuid: purpose_uuid,
+          parent_uuids: transfers.keys,
+          user_uuid: user_uuid
+        ).child
 
       api.bulk_transfer.create!(user: user_uuid, well_transfers: well_transfers)
 

app/models/labware_creators/multi_stamp.rb

@@ -30,10 +30,12 @@ class MultiStamp < Base # rubocop:todo Style/Documentation
     private
 
     def create_labware!
-      plate_creation =
-        api.pooled_plate_creation.create!(parents: parent_uuids, child_purpose: purpose_uuid, user: user_uuid)
-
-      @child = plate_creation.child
+      @child =
+        Sequencescape::Api::V2::PooledPlateCreation.create!(
+          child_purpose_uuid: purpose_uuid,
+          parent_uuids: parent_uuids,
+          user_uuid: user_uuid
+        ).child
 
       transfer_material_from_parent!(@child.uuid)
 

app/models/labware_creators/multi_stamp_tubes.rb

@@ -41,13 +41,14 @@ def create_labware!
       create_and_build_submission
       return if errors.size.positive?
 
-      plate_creation =
-        api.pooled_plate_creation.create!(parents: parent_uuids, child_purpose: purpose_uuid, user: user_uuid)
+      @child =
+        Sequencescape::Api::V2::PooledPlateCreation.create!(
+          child_purpose_uuid: purpose_uuid,
+          parent_uuids: parent_uuids,
+          user_uuid: user_uuid
+        ).child
 
-      @child = plate_creation.child
-      child_v2 = Sequencescape::Api::V2.plate_with_wells(@child.uuid)
-
-      transfer_material_from_parent!(child_v2)
+      transfer_material_from_parent!
 
       yield(@child) if block_given?
       true
@@ -87,15 +88,12 @@ def parent_tubes
       Sequencescape::Api::V2::Tube.find_all(uuid: parent_uuids, includes: 'receptacle,aliquots,aliquots.study')
     end
 
-    def transfer_material_from_parent!(child_plate)
-      api.transfer_request_collection.create!(
-        user: user_uuid,
-        transfer_requests: transfer_request_attributes(child_plate)
-      )
+    def transfer_material_from_parent!
+      api.transfer_request_collection.create!(user: user_uuid, transfer_requests: transfer_request_attributes)
     end
 
-    def transfer_request_attributes(child_plate)
-      transfers.map { |transfer| request_hash(transfer, child_plate) }
+    def transfer_request_attributes
+      transfers.map { |transfer| request_hash(transfer) }
     end
 
     def source_tube_outer_request_uuid(tube)
@@ -108,13 +106,13 @@ def source_tube_outer_request_uuid(tube)
       pending_reqs.first.uuid || nil
     end
 
-    def request_hash(transfer, child_plate)
+    def request_hash(transfer)
       tube = Sequencescape::Api::V2::Tube.find_by(uuid: transfer[:source_tube])
 
       {
         'source_asset' => transfer[:source_asset],
         'target_asset' =>
-          child_plate.wells.detect { |child_well| child_well.location == transfer.dig(:new_target, :location) }&.uuid,
+          @child.wells.detect { |child_well| child_well.location == transfer.dig(:new_target, :location) }&.uuid,
         'outer_request' => source_tube_outer_request_uuid(tube)
       }
     end

app/models/labware_creators/multi_stamp_tubes_using_tube_rack_scan.rb

@@ -65,13 +65,14 @@ def save
     #
     # @return [Boolean] true if the child plate was created successfully.
     def create_labware!
-      plate_creation =
-        api.pooled_plate_creation.create!(parents: parent_tube_uuids, child_purpose: purpose_uuid, user: user_uuid)
+      @child =
+        Sequencescape::Api::V2::PooledPlateCreation.create!(
+          child_purpose_uuid: purpose_uuid,
+          parent_uuids: parent_tube_uuids,
+          user_uuid: user_uuid
+        ).child
 
-      @child = plate_creation.child
-      child_v2 = Sequencescape::Api::V2.plate_with_wells(@child.uuid)
-
-      transfer_material_from_parent!(child_v2)
+      transfer_material_from_parent!
 
       yield(@child) if block_given?
       true
@@ -232,23 +233,18 @@ def tube_has_expected_active_request?(tube_in_db)
     end
 
     # Transfers material from the parent tubes to the given child plate.
-    # @param child_plate [Sequencescape::Api::V2::Plate] The plate to transfer material to.
-    def transfer_material_from_parent!(child_plate)
-      api.transfer_request_collection.create!(
-        user: user_uuid,
-        transfer_requests: transfer_request_attributes(child_plate)
-      )
+    def transfer_material_from_parent!
+      api.transfer_request_collection.create!(user: user_uuid, transfer_requests: transfer_request_attributes)
     end
 
     # Returns an array of hashes representing the transfer requests for the given child plate.
     # Each hash includes the UUIDs of the parent tube and child well, and the UUID of the outer request.
-    # @param child_plate [Sequencescape::Api::V2::Plate] The plate to get the transfer requests for.
     # @return [Array<Hash>] An array of hashes representing the transfer requests.
-    def transfer_request_attributes(child_plate)
+    def transfer_request_attributes
       parent_tubes.each_with_object([]) do |(foreign_barcode, parent_tube), tube_transfers|
         tube_transfers << request_hash(
           parent_tube.uuid,
-          child_plate
+          @child
             .wells
             .detect { |child_well| child_well.location == csv_file.location_by_barcode_details[foreign_barcode] }
             &.uuid,

app/models/labware_creators/plate_split_to_tube_racks.rb

@@ -408,13 +408,12 @@ def parent_wells_for_contingency
     # @param tube_attributes [Hash] A hash of attributes to use for the created tubes.
     # @return [Hash<String, Tube>] A hash of the created tubes indexed by name.
     def create_tubes(tube_purpose_uuid, number_of_tubes, tube_attributes)
-      api
-        .specific_tube_creation
+      Sequencescape::Api::V2::SpecificTubeCreation
         .create!(
-          user: user_uuid,
-          parent: parent_uuid,
-          child_purposes: [tube_purpose_uuid] * number_of_tubes,
-          tube_attributes: tube_attributes
+          child_purpose_uuids: [tube_purpose_uuid] * number_of_tubes,
+          parent_uuids: [parent_uuid],
+          tube_attributes: tube_attributes,
+          user_uuid: user_uuid
         )
         .children
         .index_by(&:name)