[release] Merge Develop into Master for 14.93.0

.github/workflows/cucumber_tests.yml

@@ -64,6 +64,12 @@ jobs:
       - name: Setup Node
         uses: sanger/.github/.github/actions/setup/node@master
 
+      - name: Fix apt mirrors + networking
+        run: |
+          sudo sed -i 's|http://azure.archive.ubuntu.com|http://archive.ubuntu.com|g' /etc/apt/apt-mirrors.txt
+          echo 'Acquire::ForceIPv4 "true";' | sudo tee /etc/apt/apt.conf.d/99force-ipv4
+          echo 'Acquire::Retries "1";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
       - name: Setup stable Chrome
         uses: sanger/.github/.github/actions/tests/setup-chrome@master
         with:

.github/workflows/rspec_feature_tests.yml

@@ -64,6 +64,12 @@ jobs:
       - name: Setup Node
         uses: sanger/.github/.github/actions/setup/node@master
 
+      - name: Fix apt mirrors + networking
+        run: |
+          sudo sed -i 's|http://azure.archive.ubuntu.com|http://archive.ubuntu.com|g' /etc/apt/apt-mirrors.txt
+          echo 'Acquire::ForceIPv4 "true";' | sudo tee /etc/apt/apt.conf.d/99force-ipv4
+          echo 'Acquire::Retries "1";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
       - name: Setup stable Chrome
         uses: sanger/.github/.github/actions/tests/setup-chrome@master
         with:

.nvmrc

@@ -1 +1 @@
-24.14.1
+24.15.0

Gemfile

@@ -34,7 +34,7 @@ group :default do
 
   # Provides bulk insert capabilities
   gem 'activerecord-import'
-  gem 'record_loader', git: 'https://github.com/sanger/record_loader'
+  gem 'record_loader', git: 'https://github.com/sanger/record_loader', tag: 'v0.3.0'
 
   gem 'mysql2', platforms: :mri
   gem 'will_paginate'

Gemfile.lock

@@ -16,7 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/sanger/record_loader
-  revision: 9e7481f4d2342f042ab13465962e5d6689863198
+  revision: 238db7fa24fffee5ad413bd9cd4c6b857d1626c9
+  tag: v0.3.0
   specs:
     record_loader (0.3.0)
 
@@ -338,7 +339,7 @@ GEM
       bigdecimal
     net-http (0.9.1)
       uri (>= 0.11.1)
-    net-imap (0.6.3)
+    net-imap (0.6.4)
       date
       net-protocol
     net-ldap (0.20.0)

app/models/sample_manifest/sample_tube_behaviour.rb

@@ -20,7 +20,7 @@ def io_samples
     end
 
     def acceptable_purposes
-      Tube::Purpose.where(target_type: SampleTube)
+      Tube::Purpose.where(target_type: SampleTube, deprecated: false)
     end
 
     def default_purpose

app/models/sample_manifest/tube_rack_behaviour.rb

@@ -20,7 +20,7 @@ def generate
     end
 
     def acceptable_purposes
-      Tube::Purpose.where(target_type: SampleTube)
+      Tube::Purpose.where(target_type: SampleTube, deprecated: false)
     end
 
     def acceptable_rack_purposes

config/default_records/descriptors/002_element_aviti_descriptors.yml

@@ -7,6 +7,7 @@ Quant method used:
   selection:
     Tapestation: Tapestation
     Tapestation & qPCR: Tapestation & qPCR
+    Not applicable: Not applicable
   required: true
   sorter: 0
 Pipette Carousel:

db/migrate/20260429114103_add_deprecated_fields_to_plate_purposes.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+class AddDeprecatedFieldsToPlatePurposes < ActiveRecord::Migration[8.0]
+  def change
+    add_column :plate_purposes, :deprecated, :boolean, default: false, null: false
+    add_column :plate_purposes, :deprecated_at, :datetime
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[8.0].define(version: 2026_04_24_000000) do
+ActiveRecord::Schema[8.0].define(version: 2026_04_29_114103) do
   create_table "accession_sample_statuses", charset: "utf8mb4", collation: "utf8mb4_unicode_ci", force: :cascade do |t|
     t.integer "sample_id", null: false
     t.string "status", null: false
@@ -857,6 +857,8 @@
     t.integer "source_purpose_id"
     t.integer "lifespan"
     t.integer "barcode_prefix_id"
+    t.boolean "deprecated", default: false, null: false
+    t.datetime "deprecated_at"
     t.index ["barcode_prefix_id"], name: "fk_rails_763bed2756"
     t.index ["target_type"], name: "index_plate_purposes_on_target_type"
     t.index ["type"], name: "index_plate_purposes_on_type"

lib/tasks/deprecate_lrc_bank_input_purpose.rake

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+# # One-time task run to deprecate the LRC Bank Input tube purpose.
+# # For reference: Y26-075
+
+namespace :LRC_BANK_INPUT do
+  desc 'Deprecate LRC Bank Input tube purpose'
+  task deprecate_lrc_bank_input_purpose: :environment do
+    lrc_bank_input_purpose = Tube::Purpose.find_by(name: 'LRC Bank Input')
+
+    unless lrc_bank_input_purpose
+      puts "Tube Purpose 'LRC Bank Input' not found. No action taken."
+      next
+    end
+
+    lrc_bank_input_purpose.update!(deprecated: true, deprecated_at: DateTime.now)
+
+    puts 'Done: LRC Bank Input tube purpose is been deprecated.'
+  end
+end

package.json

@@ -7,7 +7,7 @@
     "bootstrap": "^4.6.2",
     "codemirror": "^5.65.18",
     "css-loader": "^6.0.0",
-    "datatables.net-bs4": "^2.3.6",
+    "datatables.net-bs4": "^2.3.8",
     "datatables.net-buttons-bs4": "^3.2.6",
     "datatables.net-fixedcolumns-bs4": "^5.0.5",
     "datatables.net-fixedheader-bs4": "^4.0.5",

yarn.lock

@@ -1855,14 +1855,22 @@ data-urls@^5.0.0:
     whatwg-mimetype "^4.0.0"
     whatwg-url "^14.0.0"
 
-datatables.net-bs4@>=1.11.0, datatables.net-bs4@^2, datatables.net-bs4@^2.3.6:
+datatables.net-bs4@>=1.11.0, datatables.net-bs4@^2:
   version "2.3.7"
   resolved "https://registry.yarnpkg.com/datatables.net-bs4/-/datatables.net-bs4-2.3.7.tgz#c361ff8f439bf63e1ec4862085ec667fb96bfd7f"
   integrity sha512-ZyofK/3Unj0lQdAIsI9gT5oGCwTnx8y2UF6muYkbdO/Rw9h+x2kQwFkuCX5J0j6N2B+YCwzHk2OPu9yU8nk1Kw==
   dependencies:
     datatables.net "2.3.7"
     jquery ">=1.7"
 
+datatables.net-bs4@^2.3.8:
+  version "2.3.8"
+  resolved "https://registry.yarnpkg.com/datatables.net-bs4/-/datatables.net-bs4-2.3.8.tgz#da3660b5981ba062aa59dda1c81c524201111742"
+  integrity sha512-i65jbIw6DPG6KyUXRacCFzbawRYA2UjPg68tPkOns/r9YXQngSMQ/+izdmJk1xnPDRXh3cuTqV8cqOIy1NXH1A==
+  dependencies:
+    datatables.net "2.3.8"
+    jquery ">=1.7"
+
 datatables.net-buttons-bs4@^3.2.6:
   version "3.2.6"
   resolved "https://registry.yarnpkg.com/datatables.net-buttons-bs4/-/datatables.net-buttons-bs4-3.2.6.tgz#a2b11cf21c685b1389ac4d7d9fa362f156732952"
@@ -1972,6 +1980,13 @@ [email protected], datatables.net@>=1.11.0, datatables.net@^2:
   dependencies:
     jquery ">=1.7"
 
+[email protected]:
+  version "2.3.8"
+  resolved "https://registry.yarnpkg.com/datatables.net/-/datatables.net-2.3.8.tgz#55a8dbe3bd2196951c498ab79bf44602a2bf3229"
+  integrity sha512-uhViowhlDlheAuo5a8TrkQqADsjrtGeOyvrigvr4t0+K3MyAWqClORXWAYIcN9VLX6iIX0C8O9gwJNd01hITRg==
+  dependencies:
+    jquery ">=1.7"
+
 debug@4, debug@^4.1.0, debug@^4.3.1, debug@^4.3.2, debug@^4.3.4, debug@^4.4.3:
   version "4.4.3"
   resolved "https://registry.yarnpkg.com/debug/-/debug-4.4.3.tgz#c6ae432d9bd9662582fce08709b038c58e9e3d6a"