Merge pull request #592 from sanger/develop

Develop into Master

.github/workflows/check_release_version.yml

@@ -14,7 +14,7 @@ jobs:
 
       - name: Get specific changed files
         id: changed-files-specific
-        uses: tj-actions/changed-files@v23
+        uses: tj-actions/changed-files@v41
         with:
           files: |
             .release-version

.release-version

@@ -1 +1 @@
-1.17.3
+1.17.4

.rubocop.yml

@@ -24,6 +24,7 @@ AllCops:
     - 'vendor/**/*'
     - db/schema.rb
     - db/views_schema.rb
+    - db/migrate/*
   SuggestExtensions: false
 
 Style/DocumentDynamicEvalDefinition:

.ruby-version

@@ -1 +1 @@
-3.0.3
+3.1.2

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:2.7
+FROM ruby:3.1.2
 
 RUN gem install bundler
 

Gemfile.lock

@@ -7,52 +7,52 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actionpack (7.0.6)
-      actionview (= 7.0.6)
-      activesupport (= 7.0.6)
+    actionpack (7.0.8)
+      actionview (= 7.0.8)
+      activesupport (= 7.0.8)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actionview (7.0.6)
-      activesupport (= 7.0.6)
+    actionview (7.0.8)
+      activesupport (= 7.0.8)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activemodel (7.0.6)
-      activesupport (= 7.0.6)
-    activerecord (7.0.6)
-      activemodel (= 7.0.6)
-      activesupport (= 7.0.6)
-    activesupport (7.0.6)
+    activemodel (7.0.8)
+      activesupport (= 7.0.8)
+    activerecord (7.0.8)
+      activemodel (= 7.0.8)
+      activesupport (= 7.0.8)
+    activesupport (7.0.8)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
       tzinfo (~> 2.0)
     amq-protocol (2.3.2)
     ast (2.4.2)
-    bootsnap (1.16.0)
+    bootsnap (1.18.3)
       msgpack (~> 1.2)
     builder (3.2.4)
     bunny (2.19.0)
       amq-protocol (~> 2.3, >= 2.3.1)
       sorted_set (~> 1, >= 1.0.2)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     connection_pool (2.2.5)
     crass (1.0.6)
     diff-lcs (1.5.0)
     docile (1.4.0)
     erubi (1.12.0)
-    factory_bot (6.2.0)
+    factory_bot (6.4.5)
       activesupport (>= 5.0.0)
-    factory_bot_rails (6.2.0)
-      factory_bot (~> 6.2.0)
+    factory_bot_rails (6.4.3)
+      factory_bot (~> 6.4)
       railties (>= 5.0.0)
     ffi (1.15.5)
     formatador (1.1.0)
-    guard (2.18.0)
+    guard (2.18.1)
       formatador (>= 0.2.4)
       listen (>= 2.7, < 4.0)
       lumberjack (>= 1.0.12, < 2.0)
@@ -73,60 +73,60 @@ GEM
     hashie (5.0.0)
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
+    json (2.7.1)
     language_server-protocol (3.17.0.3)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.21.3)
+    loofah (2.22.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
-    lumberjack (1.2.8)
+    lumberjack (1.2.9)
     method_source (1.0.0)
-    mini_portile2 (2.8.2)
-    minitest (5.18.1)
-    msgpack (1.5.2)
+    mini_portile2 (2.8.5)
+    minitest (5.21.2)
+    msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.5)
     nenv (0.3.0)
-    nokogiri (1.15.2)
+    nokogiri (1.16.0)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.23.0)
-    parser (3.2.2.3)
+    parallel (1.24.0)
+    parser (3.3.0.5)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    racc (1.7.1)
-    rack (2.2.7)
+    racc (1.7.3)
+    rack (2.2.8)
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails-dom-testing (2.1.1)
+    rails-dom-testing (2.2.0)
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    railties (7.0.6)
-      actionpack (= 7.0.6)
-      activesupport (= 7.0.6)
+    railties (7.0.8)
+      actionpack (= 7.0.8)
+      activesupport (= 7.0.8)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
       zeitwerk (~> 2.5)
     rainbow (3.1.1)
-    rake (13.0.6)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rbtree (0.4.4)
-    regexp_parser (2.8.1)
+    regexp_parser (2.9.0)
     rexml (3.2.6)
     rspec (3.12.0)
       rspec-core (~> 3.12.0)
@@ -137,44 +137,45 @@ GEM
     rspec-expectations (3.12.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
-    rspec-mocks (3.12.5)
+    rspec-mocks (3.12.6)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
-    rspec-rails (6.0.3)
+    rspec-rails (6.1.1)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
       rspec-core (~> 3.12)
       rspec-expectations (~> 3.12)
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
-    rspec-support (3.12.0)
-    rubocop (1.55.1)
+    rspec-support (3.12.1)
+    rubocop (1.60.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.29.0)
+    rubocop-ast (1.30.0)
       parser (>= 3.2.1.0)
-    rubocop-capybara (2.18.0)
+    rubocop-capybara (2.20.0)
       rubocop (~> 1.41)
-    rubocop-factory_bot (2.23.1)
+    rubocop-factory_bot (2.25.0)
       rubocop (~> 1.33)
-    rubocop-performance (1.18.0)
-      rubocop (>= 1.7.0, < 2.0)
-      rubocop-ast (>= 0.4.0)
-    rubocop-rails (2.20.2)
+    rubocop-performance (1.20.2)
+      rubocop (>= 1.48.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
+    rubocop-rails (2.23.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
-    rubocop-rspec (2.23.0)
-      rubocop (~> 1.33)
+      rubocop-ast (>= 1.30.0, < 2.0)
+    rubocop-rspec (2.26.1)
+      rubocop (~> 1.40)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
     ruby-progressbar (1.13.0)
@@ -194,11 +195,11 @@ GEM
     sorted_set (1.0.3)
       rbtree
       set (~> 1.0)
-    thor (1.2.2)
+    thor (1.3.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.4.2)
-    zeitwerk (2.6.8)
+    unicode-display_width (2.5.0)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   ruby

app/models/associated_with_roles.rb

@@ -19,7 +19,7 @@ def self.extended(base)
   end
 
   def has_role(name)
-    define_method("#{name}=") { |users| set_users(name, users) }
+    define_method(:"#{name}=") { |users| set_users(name, users) }
   end
 
   module InstanceMethods
@@ -43,7 +43,7 @@ def maintain_users
       users.create!(
         users_to_maintain.map do |role, user_details|
           user_details.map do |details|
-            details.reverse_merge(role: role.to_s, associated_id: id, last_updated: last_updated)
+            details.reverse_merge(role: role.to_s, associated_id: id, last_updated:)
           end
         end
       )

db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb

@@ -14,7 +14,7 @@ def down
       t.remove :pac_bio_library_tube_barcode
     end
     # Here we add a placeholder value in case any plate barcodes were added as null since the migration
-    PacBioRun.where(plate_barcode: nil).each do |run|
+    PacBioRun.where(plate_barcode: nil).find_each do |run|
       run.plate_barcode = 'plate_barcode placeholder'
       run.save
     end

db/migrate/20231207143456_add_location_name_to_labware_location.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+# New column for name of location where plates are stored
+class AddLocationNameToLabwareLocation < ActiveRecord::Migration[7.0]
+  def change
+    add_column :labware_location, :location_name, :string, null: false, default: '', comment: 'Name of location where labware is stored', after: :full_location_address
+  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[7.0].define(version: 2023_08_21_100520) do
+ActiveRecord::Schema[7.0].define(version: 2023_12_07_143456) do
   create_table "bmap_flowcell", primary_key: "id_bmap_flowcell_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.datetime "last_updated", precision: nil, null: false, comment: "Timestamp of last update"
     t.datetime "recorded_at", precision: nil, null: false, comment: "Timestamp of warehouse update"
@@ -119,6 +119,7 @@
     t.datetime "stored_at", null: false, comment: "Datetime the item was stored at this location"
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
+    t.string "location_name", null: false, comment: "Name of location where labware is stored"
     t.index ["labware_barcode"], name: "index_labware_location_on_labware_barcode", unique: true
     t.index ["location_barcode"], name: "index_labware_location_on_location_barcode"
   end

lib/resource_tools/json.rb

@@ -146,6 +146,7 @@ def custom_value(name, &block)
       end
     end
 
+    # rubocop:disable Style/ArgumentsForwarding
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
@@ -156,6 +157,7 @@ def initialize(*args, &block)
       convert_booleans
       delete_if { |k, _| ignoreable.include?(k) }
     end
+    # rubocop:enable Style/ArgumentsForwarding
 
     def convert_booleans
       self.stored_as_boolean.each do |key|

lib/tasks/remove_duplicate_pac_bio_runs.rake

@@ -186,7 +186,7 @@ namespace :pac_bio_run_table do
     9993
   ]
   task remove_duplicate_pac_bio_runs: :environment do
-    PacBioRun.where(id_pac_bio_run_lims: list_of_runs).each do |pac_bio_run|
+    PacBioRun.where(id_pac_bio_run_lims: list_of_runs).find_each do |pac_bio_run|
       puts "Going to remove #{pac_bio_run.id_pac_bio_run_lims}"
       puts pac_bio_run.attributes
       pac_bio_run.delete

lib/tasks/update_pac_bio_run_name.rake

@@ -4,7 +4,7 @@ namespace :pac_bio_run_table do
   desc 'Update pac_bio_run_name column with the values from id_pac_bio_run_lims'
 
   task update_pac_bio_run_name: :environment do
-    PacBioRun.all.each do |run|
+    PacBioRun.find_each do |run|
       next if run.pac_bio_run_name.present?
 
       run.pac_bio_run_name = run.id_pac_bio_run_lims

lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake

@@ -6,7 +6,7 @@ namespace :pac_bio_run_table do
   desc 'Update pac_bio_run plate_number column with the value 1 for sequencescape plates'
 
   task update_pac_bio_run_sequencescape_plate_numbers: :environment do
-    PacBioRun.where(id_lims: 'SQSCP').each do |run|
+    PacBioRun.where(id_lims: 'SQSCP').find_each do |run|
       run.plate_number = 1
       run.save!
     end

spec/models/flowcell_spec.rb

@@ -39,7 +39,7 @@
     include_examples 'full flowcell json'
 
     it 'flags all entries as spiked' do
-      Flowcell.all.each { |fc| expect(fc.spiked).to be_true }
+      Flowcell.find_each { |fc| expect(fc.spiked).to be_true }
     end
 
     context 'when update with identical tag indexes' do
@@ -130,7 +130,7 @@
     end
 
     it 'flags all entries as not-spiked' do
-      Flowcell.all.each { |fc| expect(fc.spiked).to be_false }
+      Flowcell.find_each { |fc| expect(fc.spiked).to be_false }
     end
   end
 

spec/support/it_behaves_like_a_nested_resource.rb

@@ -6,13 +6,13 @@
   end
 
   it 'ensures that the all rows are current' do
-    described_class.all.each do |row|
+    described_class.find_each do |row|
       expect(row.last_updated).to eq(most_recent_time)
     end
   end
 
   it 'ensures the row is marked with recorded time' do
-    described_class.all.each do |row|
+    described_class.find_each do |row|
       expect(row.recorded_at).to eq(recorded_time)
     end
   end

spec/support/it_behaves_like_associated_with_roles.rb

@@ -2,7 +2,7 @@
 
 shared_examples_for 'maintains roles correctly' do
   after(:each) do
-    described_class.create_or_update_from_json(timestamped_json.merge(updated_roles).merge(updated_at: updated_at), 'example')
+    described_class.create_or_update_from_json(timestamped_json.merge(updated_roles).merge(updated_at:), 'example')
     users_fit_exactly(expected_roles)
   end