Merge branch 'develop' of https://github.com/sanger/sequencescape int…

…o depfu/update/group/rails-7.0.8.1

.github/workflows/append_release.yml

@@ -8,7 +8,7 @@ jobs:
   build-and-append-to-release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1

.github/workflows/automated_docker_release.yml

@@ -14,7 +14,7 @@ jobs:
     name: Automated release fo Docker image
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: nelonoel/[email protected]
 

.github/workflows/automated_release.yml

@@ -9,7 +9,7 @@ jobs:
   build-and-release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: nelonoel/[email protected]
 

.github/workflows/check_docker_build.yml

@@ -11,7 +11,7 @@ jobs:
     name: Check docker image building process
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Build image
         run: >-

.github/workflows/generate_pages.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1

.github/workflows/js_test.yml

@@ -9,7 +9,7 @@ jobs:
     name: Test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup node
         uses: actions/setup-node@v3
         with:

.github/workflows/lint_yard_docs.yml

@@ -16,7 +16,7 @@ jobs:
     env:
       BUNDLE_WITHOUT: "cucumber deployment profile development default test"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:

.github/workflows/ruby_test.yml

@@ -46,7 +46,7 @@ jobs:
           MYSQL_ROOT_PASSWORD: "" # Set root PW to nothing
           MYSQL_ALLOW_EMPTY_PASSWORD: yes
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:
@@ -90,7 +90,7 @@ jobs:
         ci_node_total: [3]
         ci_node_index: [0, 1, 2]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:
@@ -168,7 +168,7 @@ jobs:
         ci_node_total: [2]
         ci_node_index: [0, 1]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:

.release-version

@@ -1 +1 @@
-14.48.0
+14.49.0

README.md

@@ -42,6 +42,7 @@ a organisation of 900 people.
       - [Adjusting config](#adjusting-config)
       - [Default setup](#default-setup)
     - [Starting rails](#starting-rails)
+    - [Vite](#vite)
       - [Delayed job](#delayed-job)
     - [Message broker](#message-broker)
   - [Testing](#testing)
@@ -57,6 +58,7 @@ a organisation of 900 people.
     - [NPG - Illumina tracking software](#npg---illumina-tracking-software)
     - [Troubleshooting](#troubleshooting)
       - [MySQL errors when installing](#mysql-errors-when-installing)
+      - [MySQL errors after system updates](#mysql-errors-after-system-updates)
       - [Installing on Apple Silicon (M1)](#installing-on-apple-silicon-m1)
     - [API V2 Authentication](#api-v2-authentication)
     - [Publishing AMQP Messages](#publishing-amqp-messages)
@@ -420,6 +422,14 @@ gem install mysql2 -v '0.5.6' -- \
 --with-mysql-include=/opt/homebrew/Cellar/mysql/9.0.1_1/include
 ```
 
+#### MySQL errors after system updates
+
+If you encounter a LoadError at dlopen call to mysql2 bundle because of a missing dynamic library, try the following command to update the cached gem.
+
+```
+gem pristine mysql2
+```
+
 #### Installing on Apple Silicon (M1)
 
 If installation issues are encountered with Docker on M1 processors, try the fixes below:

app/controllers/api/v2/submission_pools_controller.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API controller for submission templates.
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation.
+    class SubmissionPoolsController < JSONAPI::ResourceController
+      # By default JSONAPI::ResourceController provides most of the standard
+      # behaviour, and in many cases this file may be left empty.
+    end
+  end
+end

app/resources/api/v2/plate_resource.rb

@@ -26,6 +26,7 @@ class PlateResource < BaseResource
 
       # Associations:
       has_many :wells, readonly: true
+      has_many :submission_pools, readonly: true
 
       # Attributes
       attribute :number_of_rows, readonly: true, delegate: :height

app/resources/api/v2/submission_pool_resource.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    class SubmissionPoolResource < BaseResource
+      attribute :plates_in_submission, readonly: true
+      attribute :used_tag2_layout_templates, readonly: true
+      attribute :used_tag_layout_templates, readonly: true
+    end
+  end
+end

app/views/workflows/_cherrypicking_volume_parameters.html.erb

@@ -4,7 +4,7 @@
   <strong>Either</strong>
     <table cellspacing='0' cellpadding='0'>
       <tr>
-        <td><label for="cherrypick_action_nano_grams_per_micro_litre">Pick by ng/&micro;l</label>:</td>
+        <td><label for="cherrypick_action_nano_grams_per_micro_litre">Pick by concentration (ng/&micro;l)</label>:</td>
         <td><%= radio_button("cherrypick", "action", "nano_grams_per_micro_litre", checked: true) %></td>
       </tr>
       <%= fields_for :nano_grams_per_micro_litre do |ff|%>
@@ -18,7 +18,7 @@
         </tr>
         <tr>
           <td><%= ff.label 'robot_minimum_picking_volume', 'Robot Minimum Picking Volume' %> (&micro;l):</td>
-          <td><%= ff.text_field 'robot_minimum_picking_volume', value: 1.0, size: 5, type: 'number', step: 0.1, min: 1, max: 9 %></td>
+          <td><%= ff.text_field 'robot_minimum_picking_volume', value: 5.0, size: 5, type: 'number', step: 0.1, min: 1, max: 9 %></td>
         </tr>
       <% end %>
     </table>
@@ -30,7 +30,7 @@
   <strong>Or</strong>
     <table cellspacing='0' cellpadding='0'>
       <tr>
-        <td><label for="cherrypick_action_nano_grams">Pick by ng</label>:</td>
+        <td><label for="cherrypick_action_nano_grams">Pick by amount (ng)</label></td>
         <td><%= radio_button("cherrypick", "action", "nano_grams") %></td>
       </tr>
       <%= fields_for :nano_grams do |ff|%>
@@ -48,7 +48,7 @@
         </tr>
         <tr>
           <td><%= ff.label 'robot_minimum_picking_volume', 'Robot Minimum Picking Volume' %> (&micro;l):</td>
-          <td><%= ff.text_field 'robot_minimum_picking_volume', value: 1.0, size: 5, type: 'number', step: 0.1, min: 1, max: 9 %></td>
+          <td><%= ff.text_field 'robot_minimum_picking_volume', value: 5.0, size: 5, type: 'number', step: 0.1, min: 1, max: 9 %></td>
         </tr>
       <% end %>
     </table>
@@ -60,7 +60,7 @@
   <strong>Or</strong>
     <table cellspacing='0' cellpadding='0'>
       <tr>
-        <td><label for="cherrypick_action_micro_litre">Pick by &micro;l</label>:</td>
+        <td><label for="cherrypick_action_micro_litre">Pick by volume (&micro;l)</label>:</td>
         <td><%= radio_button("cherrypick", "action", "micro_litre") %></td>
       </tr>
       <%= fields_for :micro_litre do |ff|%>

app/views/workflows/_plate_template_batches.html.erb

@@ -52,10 +52,9 @@
       <%= select_tag "robot_id", options_for_select(@robots.collect {|p| [ p.name, p.id ] }), class: 'select2' %>
     </fieldset>
   <% end %>
-
-  <%= panel(:info,title:"Step 3: Set volumes and concentrations") do %>
-    <%= render partial: 'cherrypicking_volume_parameters' %>
-  <% end %>
+    <%= panel(:info, title: "Step 3: Set volumes and concentrations <a href='https://ssg-confluence.internal.sanger.ac.uk/x/NoHdDQ'><small>Information about cherrypicking options</small></a>".html_safe) do %>
+      <%= render partial: 'cherrypicking_volume_parameters' %>
+    <% end %>
 
   <%= render partial: "next_stage_submit" %>
 <% end %>

config/default_records/plate_purposes/011_scrna_core_cdna_prep_plate_purposes.yml

@@ -2,10 +2,10 @@
 # Most are defined in the Limber config, but the below also need to be defined in Sequencescape.
 # They are in a separate file so it can be 'feature flagged off' until needed.
 ---
-# The 'LRC PBMC Pools Input' purpose is included here so that it's available for
+# The 'LRC GEM-X 5p GEMs Input' purpose is included here so that it's available for
 # sample manifests, and also because it is an acceptable purpose for the scRNA Core cDNA Prep Input
 # submission template.
-LRC PBMC Pools Input:
+LRC GEM-X 5p GEMs Input:
   input_plate: true
   stock_plate: true
   cherrypickable_target: false

config/default_records/request_types/014_limber_scrna_core_cdna_prep_request_types.yml

@@ -16,16 +16,16 @@ limber_scrna_core_cdna_prep_gem_x_5p:
     - LRC Bank Seq
     - LRC Bank Spare
     - LRC Bank Input
-limber_scrna_core_cdna_prep_gem_x_5p_pbmc_pools_input:
-  name: scRNA Core cDNA Prep GEM-X 5p PBMC Pools Input
+limber_scrna_core_cdna_prep_gem_x_5p_gems_input:
+  name: scRNA Core cDNA Prep GEM-X 5p GEMs Input
   asset_type: Well
   order: 1
   request_class_name: CustomerRequest
   for_multiplexing: false
   billable: true
   product_line_name: Short Read
   acceptable_purposes:
-    - LRC PBMC Pools Input
+    - LRC GEM-X 5p GEMs Input
 limber_scrna_core_aggregation:
   name: scRNA Core Aggregation
   asset_type: Well

config/default_records/submission_templates/011_scrna_core_cdna_prep_submission_templates.yml

@@ -16,9 +16,9 @@ Limber-Htp - scRNA Core cDNA Prep GEM-X 5p:
     request_type_keys: ["limber_scrna_core_cdna_prep_gem_x_5p"]
     product_line_name: Short Read
     product_catalogue_name: scRNA Core
-Limber-Htp - scRNA Core cDNA Prep GEM-X 5p PBMC Pools Input:
+Limber-Htp - scRNA Core cDNA Prep GEM-X 5p GEMs Input:
   submission_class_name: "LinearSubmission"
   related_records:
-    request_type_keys: ["limber_scrna_core_cdna_prep_gem_x_5p_pbmc_pools_input"]
+    request_type_keys: ["limber_scrna_core_cdna_prep_gem_x_5p_gems_input"]
     product_line_name: Short Read
     product_catalogue_name: scRNA Core

config/default_records/submission_templates/014_lcm_triomics_submission_templates.wip.yml

@@ -1,7 +1,7 @@
 # Submission templates for LCM Triomics WGS and EMSeq
 ---
 # LCM Triomics EMSeq submission template
-Limber-Htp - LCM Triomics EMSeq:
+Limber-Htp - LCM Triomics:
   submission_class_name: "LinearSubmission"
   related_records:
     request_type_keys: ["limber_lcm_triomics_emseq"]

config/environments/development.rb

@@ -12,9 +12,12 @@
   # In the development environment your application's code is reloaded on
   # every request. This slows down response time but is perfect for development
   # since you don't have to restart the web server when you make code changes.
-  config.cache_classes = ENV.fetch('CACHE_CLASSES', 'true') == 'true'
+  config.cache_classes = ENV.fetch('CACHE_CLASSES', 'false') == 'true'
 
-  # Do not eager load code on boot.
+  # Eager load code on boot. This eager loads most of Rails and
+  # your application in memory, allowing both threaded web servers
+  # and those relying on copy on write to perform better.
+  # Rake tasks automatically ignore this option for performance.
   config.eager_load = true
 
   # Show full error reports.

spec/features/pipelines/cherrypick/cherrypick_pipeline_spec.rb

@@ -102,7 +102,7 @@ def initialize_plates(plates)
 
   describe 'where picking by ng/µl for a tecan robot' do
     let(:concentrations_required) { true }
-    let(:layout_volume_option) { 'Pick by ng/µl' }
+    let(:layout_volume_option) { 'Pick by concentration (ng/µl)' }
     let(:custom_destination_type) { create(:plate_type, name: 'Custom Type') }
     let(:expected_plates_by_destination_plate) do
       { destination_plate_human_barcode => { 1 => { sources: [plates[0], plates[1], plates[2]] } } }
@@ -276,7 +276,7 @@ def initialize_plates(plates)
 
   describe 'where picking by ng for a tecan robot' do
     let(:concentrations_required) { true }
-    let(:layout_volume_option) { 'Pick by ng' }
+    let(:layout_volume_option) { 'Pick by amount (ng)' }
     let(:plate_type) { create(:plate_type, name: 'ABgene_0800', maximum_volume: 800) }
     let(:expected_plates_by_destination_plate) do
       { destination_plate_human_barcode => { 1 => { sources: [plates[0], plates[1], plates[2]] } } }
@@ -321,7 +321,7 @@ def initialize_plates(plates)
   end
 
   describe 'where the number of plates does not exceed the max beds for the robot' do
-    let(:layout_volume_option) { 'Pick by µl' }
+    let(:layout_volume_option) { 'Pick by volume (µl)' }
     let(:expected_plates_by_destination_plate) do
       { destination_plate_human_barcode => { 1 => { sources: [plates[0], plates[1], plates[2]] } } }
     end
@@ -330,7 +330,7 @@ def initialize_plates(plates)
   end
 
   describe 'where the number of plates exceeds the max beds for the robot' do
-    let(:layout_volume_option) { 'Pick by µl' }
+    let(:layout_volume_option) { 'Pick by volume (µl)' }
     let(:max_plates) { 2 }
     let(:expected_plates_by_destination_plate) do
       { destination_plate_human_barcode => { 1 => { sources: [plates[0], plates[1]] }, 2 => { sources: [plates[2]] } } }
@@ -340,7 +340,7 @@ def initialize_plates(plates)
   end
 
   describe 'where there are multiple destination plates and the number of plates exceeds the max beds for the robot' do
-    let(:layout_volume_option) { 'Pick by µl' }
+    let(:layout_volume_option) { 'Pick by volume (µl)' }
     let(:max_plates) { 2 }
     let(:full_plate) { create(:plate_with_untagged_wells_and_custom_name, sample_count: 96) }
     let(:additional_plates) { create_list(:plate_with_untagged_wells_and_custom_name, 3, sample_count: 2) }
@@ -375,7 +375,7 @@ def initialize_plates(plates)
     let(:max_plates) { 25 }
     let(:robot) { create(:hamilton, barcode: '444', max_plates_value: max_plates) }
     let(:concentrations_required) { true }
-    let(:layout_volume_option) { 'Pick by ng/µl' }
+    let(:layout_volume_option) { 'Pick by concentration (ng/µl)' }
     let(:custom_destination_type) { create(:plate_type, name: 'Custom Type') }
     let(:expected_plates_by_destination_plate) do
       { destination_plate_human_barcode => { 1 => { sources: [plates[0], plates[1]], control: control_plate } } }
@@ -413,7 +413,7 @@ def initialize_plates(plates)
     let(:max_plates) { 25 }
     let(:robot) { create(:hamilton, barcode: '444', max_plates_value: max_plates) }
     let(:concentrations_required) { true }
-    let(:layout_volume_option) { 'Pick by ng/µl' }
+    let(:layout_volume_option) { 'Pick by concentration (ng/µl)' }
     let(:custom_destination_type) { create(:plate_type, name: 'Custom Type') }
     let(:expected_plates_by_destination_plate) do
       {

spec/features/shared_examples/cherrypicking.rb

@@ -44,12 +44,12 @@
         choose(layout_volume_option)
 
         case layout_volume_option
-        when 'Pick by µl'
+        when 'Pick by  volume (µl)'
           fill_in('micro_litre_volume_required', with: '13')
-        when 'Pick by ng/µl'
+        when 'Pick by concentration (ng/µl)'
           fill_in('Volume Required', with: '65')
           within('#pick_by_nano_grams_per_micro_litre') { fill_in('Robot Minimum Picking Volume', with: '1.0') }
-        when 'Pick by ng'
+        when 'Pick by amount (ng)'
           within('#pick_by_nano_grams') do
             fill_in('Robot Minimum Picking Volume', with: '2.0')
             fill_in('Quantity to pick', with: 10_000)