Merge remote-tracking branch 'origin/develop' into y24-335-barcode-fo…

…r-norm-plate-uat
sanger · Nov 6, 2024 · cb6ba11 · cb6ba11
2 parents d8e9543 + b6cd841
commit cb6ba11
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diff --git a/.github/workflows/check_release_version.yml b/.github/workflows/check_release_version.yml
@@ -5,12 +5,21 @@ on:
   pull_request:
     branches:
       - master
+    types:
+      # defaults
+      - opened
+      - synchronize
+      - reopened
+      # custom
+      - ready_for_review # required for Github-created PRs
 
 jobs:
   check:
     runs-on: ubuntu-latest
+    # only run when PR is not draft
+    if: ${{ !github.event.pull_request.draft }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Get specific changed files
         id: changed-files-specific

diff --git a/.github/workflows/create_release_pr.yml b/.github/workflows/create_release_pr.yml
@@ -0,0 +1,10 @@
+# Create or update merge-to-master pull requests for production releases
+# Note that by design, creating or editing a PR will not trigger a downstream `pull_request` event as this could lead to recursion
+name: Release
+on:
+  push:
+    branches:
+      - develop
+jobs:
+  pull_request:
+    uses: sanger/.github/.github/workflows/create-release-pr.yml@master
diff --git a/.nvmrc b/.nvmrc
@@ -1 +1 @@
-20.15.1
+22.11.0
diff --git a/.release-version b/.release-version
@@ -1 +1 @@
-14.45.0
+14.48.0
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -34,73 +34,73 @@ GEM
   specs:
     aasm (5.5.0)
       concurrent-ruby (~> 1.0)
-    actioncable (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actioncable (6.1.7.10)
+      actionpack (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activestorage (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionmailbox (6.1.7.10)
+      actionpack (= 6.1.7.10)
+      activejob (= 6.1.7.10)
+      activerecord (= 6.1.7.10)
+      activestorage (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       mail (>= 2.7.1)
-    actionmailer (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      actionview (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionmailer (6.1.7.10)
+      actionpack (= 6.1.7.10)
+      actionview (= 6.1.7.10)
+      activejob (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (6.1.7.8)
-      actionview (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionpack (6.1.7.10)
+      actionview (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       rack (~> 2.0, >= 2.0.9)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
     actionpack-xml_parser (2.0.1)
       actionpack (>= 5.0)
       railties (>= 5.0)
-    actiontext (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activestorage (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actiontext (6.1.7.10)
+      actionpack (= 6.1.7.10)
+      activerecord (= 6.1.7.10)
+      activestorage (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       nokogiri (>= 1.8.5)
-    actionview (6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionview (6.1.7.10)
+      activesupport (= 6.1.7.10)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (6.1.7.8)
-      activesupport (= 6.1.7.8)
+    activejob (6.1.7.10)
+      activesupport (= 6.1.7.10)
       globalid (>= 0.3.6)
-    activemodel (6.1.7.8)
-      activesupport (= 6.1.7.8)
+    activemodel (6.1.7.10)
+      activesupport (= 6.1.7.10)
     activemodel-serializers-xml (1.0.2)
       activemodel (> 5.x)
       activesupport (> 5.x)
       builder (~> 3.1)
-    activerecord (6.1.7.8)
-      activemodel (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    activerecord (6.1.7.10)
+      activemodel (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
     activerecord-import (1.7.0)
       activerecord (>= 4.2)
     activeresource (6.1.0)
       activemodel (>= 6.0)
       activemodel-serializers-xml (~> 1.0)
       activesupport (>= 6.0)
-    activestorage (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    activestorage (6.1.7.10)
+      actionpack (= 6.1.7.10)
+      activejob (= 6.1.7.10)
+      activerecord (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (6.1.7.8)
+    activesupport (6.1.7.10)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -198,7 +198,7 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
-    date (3.3.4)
+    date (3.4.0)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
     delayed_job_active_record (4.1.8)
@@ -259,7 +259,7 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     logger (1.6.1)
-    loofah (2.22.0)
+    loofah (2.23.1)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.8.1)
@@ -287,7 +287,7 @@ GEM
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
     mysql2 (0.5.6)
-    net-imap (0.4.14)
+    net-imap (0.5.0)
       date
       net-protocol
     net-ldap (0.19.0)
@@ -298,7 +298,7 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.7.3)
+    nio4r (2.7.4)
     nokogiri (1.16.7-arm64-darwin)
       racc (~> 1.4)
     nokogiri (1.16.7-x86_64-darwin)
@@ -324,7 +324,7 @@ GEM
     puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
-    rack (2.2.9)
+    rack (2.2.10)
     rack-acceptable (0.1.0)
       rack (>= 1.1.0)
     rack-cors (2.0.2)
@@ -338,20 +338,20 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (6.1.7.8)
-      actioncable (= 6.1.7.8)
-      actionmailbox (= 6.1.7.8)
-      actionmailer (= 6.1.7.8)
-      actionpack (= 6.1.7.8)
-      actiontext (= 6.1.7.8)
-      actionview (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activemodel (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activestorage (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    rails (6.1.7.10)
+      actioncable (= 6.1.7.10)
+      actionmailbox (= 6.1.7.10)
+      actionmailer (= 6.1.7.10)
+      actionpack (= 6.1.7.10)
+      actiontext (= 6.1.7.10)
+      actionview (= 6.1.7.10)
+      activejob (= 6.1.7.10)
+      activemodel (= 6.1.7.10)
+      activerecord (= 6.1.7.10)
+      activestorage (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       bundler (>= 1.15.0)
-      railties (= 6.1.7.8)
+      railties (= 6.1.7.10)
       sprockets-rails (>= 2.0.0)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
@@ -370,9 +370,9 @@ GEM
       loofah (~> 2.21)
       nokogiri (~> 1.14)
     rails-perftest (0.0.7)
-    railties (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    railties (6.1.7.10)
+      actionpack (= 6.1.7.10)
+      activesupport (= 6.1.7.10)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -390,7 +390,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.7)
+    rexml (3.3.9)
     roo (2.10.1)
       nokogiri (~> 1)
       rubyzip (>= 1.3.0, < 3.0.0)
@@ -502,7 +502,7 @@ GEM
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
-    sprockets-rails (3.5.1)
+    sprockets-rails (3.5.2)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       sprockets (>= 3.0.0)
@@ -562,7 +562,7 @@ GEM
       ostruct
       rainbow
       yard
-    zeitwerk (2.6.18)
+    zeitwerk (2.7.1)
 
 PLATFORMS
   arm64-darwin

diff --git a/app/controllers/api/v2/bait_library_layouts_controller.rb b/app/controllers/api/v2/bait_library_layouts_controller.rb
@@ -33,7 +33,7 @@ def preview
           respond_with_errors('Validation failed', e.record.errors.full_messages, :unprocessable_entity) and return
         end
 
-        json = { data: { type: 'bait_library_layouts', attributes: { layout: preview.layout } } }
+        json = { data: { type: 'bait_library_layouts', attributes: { well_layout: preview.well_layout } } }
         render json: json, status: :ok
       end
 

diff --git a/app/models/accessionable/base.rb b/app/models/accessionable/base.rb
@@ -95,6 +95,8 @@ class FieldSerializer
       MISSING_DATA_AGGREEMENT_PRE2023 = 'missing: data agreement established pre-2023'
       MISSING_ENDANGERED_SPECIES = 'missing: endangered species'
       MISSING_HUMAN_IDENTIFIABLE = 'missing: human-identifiable'
+      MISSING_CONTROL_SAMPLE = 'missing: control sample'
+      MISSING_SAMPLE_GROUP = 'missing: sample group'
 
       OTHER_DEFAULT_SETTINGS = [
         NOT_COLLECTED,
@@ -107,7 +109,9 @@ class FieldSerializer
         MISING_THIRD_PARTY_DATA,
         MISSING_DATA_AGGREEMENT_PRE2023,
         MISSING_ENDANGERED_SPECIES,
-        MISSING_HUMAN_IDENTIFIABLE
+        MISSING_HUMAN_IDENTIFIABLE,
+        MISSING_CONTROL_SAMPLE,
+        MISSING_SAMPLE_GROUP
       ].freeze
 
       def value_for(value)

diff --git a/app/models/cherrypick_task.rb b/app/models/cherrypick_task.rb
@@ -21,8 +21,16 @@ class CherrypickTask < Task # rubocop:todo Metrics/ClassLength
   #
   # @return [CherrypickTask::ControlLocator] A generator of control locations
   #
-  def new_control_locator(batch_id, total_wells, num_control_wells, wells_to_leave_free: DEFAULT_WELLS_TO_LEAVE_FREE)
-    CherrypickTask::ControlLocator.new(batch_id:, total_wells:, num_control_wells:, wells_to_leave_free:)
+
+  def new_control_locator(params)
+    CherrypickTask::ControlLocator.new(
+      batch_id: params[:batch_id],
+      total_wells: params[:total_wells],
+      num_control_wells: params[:num_control_wells],
+      wells_to_leave_free: params[:wells_to_leave_free] || DEFAULT_WELLS_TO_LEAVE_FREE,
+      control_source_plate: params[:control_source_plate],
+      template: params[:template]
+    )
   end
 
   #
@@ -38,7 +46,7 @@ def can_link_directly?
   # rubocop:todo Metrics/ParameterLists
   def pick_new_plate(requests, template, robot, plate_purpose, control_source_plate = nil, workflow_controller = nil)
     target_type = PickTarget.for(plate_purpose)
-    perform_pick(requests, robot, control_source_plate, workflow_controller) do
+    perform_pick(requests, robot, control_source_plate, workflow_controller, template) do
       target_type.new(template, plate_purpose.try(:asset_shape))
     end
   end
@@ -54,7 +62,7 @@ def pick_onto_partial_plate(
     purpose = partial_plate.plate_purpose
     target_type = PickTarget.for(purpose)
 
-    perform_pick(requests, robot, control_source_plate, workflow_controller) do
+    perform_pick(requests, robot, control_source_plate, workflow_controller, template) do
       target_type
         .new(template, purpose.try(:asset_shape), partial_plate)
         .tap do
@@ -66,7 +74,7 @@ def pick_onto_partial_plate(
   # rubocop:enable Metrics/ParameterLists
 
   # rubocop:todo Metrics/CyclomaticComplexity, Metrics/PerceivedComplexity, Metrics/MethodLength
-  def perform_pick(requests, robot, control_source_plate, workflow_controller) # rubocop:todo Metrics/AbcSize
+  def perform_pick(requests, robot, control_source_plate, workflow_controller, template) # rubocop:todo Metrics/AbcSize
     max_plates = robot.max_beds
     raise StandardError, 'The chosen robot has no beds!' if max_plates.zero?
 
@@ -80,7 +88,22 @@ def perform_pick(requests, robot, control_source_plate, workflow_controller) # r
       num_plate = 0
       batch = requests.first.batch
       control_assets = control_source_plate.wells.joins(:samples)
-      control_locator = new_control_locator(batch.id, current_destination_plate.size, control_assets.count)
+      control_locator =
+        new_control_locator(
+          {
+            batch_id: batch.id,
+            total_wells: current_destination_plate.size,
+            num_control_wells: control_assets.count,
+            template: template,
+            control_source_plate: control_source_plate
+          }
+        )
+
+      if control_locator.handle_incompatible_plates
+        message = 'The control plate and plate template are incompatible'
+        workflow_controller.send(:flash)[:error] = message unless workflow_controller.nil?
+        workflow_controller.redirect_to action: 'stage', batch_id: batch.id, workflow_id: workflow.id
+      end
       control_posns = control_locator.control_positions(num_plate)
 
       # If is an incomplete plate, or a plate with a template applied, copy all the controls missing into the