From e7bf7b3fa43d32bdf87a4a5912d44e893bba4d41 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Sun, 10 Sep 2023 21:50:23 +0000
Subject: [PATCH 01/27] Update all of rails to version 7.0.8

---
 Gemfile.lock | 40 ++++++++++++++++++++--------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 9015145a..5af3b6fd 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -7,25 +7,25 @@ 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)
@@ -83,13 +83,13 @@ GEM
       nokogiri (>= 1.12.0)
     lumberjack (1.2.8)
     method_source (1.0.0)
-    mini_portile2 (2.8.2)
-    minitest (5.18.1)
+    mini_portile2 (2.8.4)
+    minitest (5.20.0)
     msgpack (1.5.2)
     multi_json (1.15.0)
     mysql2 (0.5.5)
     nenv (0.3.0)
-    nokogiri (1.15.2)
+    nokogiri (1.15.4)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -103,19 +103,19 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     racc (1.7.1)
-    rack (2.2.7)
+    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)
@@ -198,7 +198,7 @@ GEM
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.4.2)
-    zeitwerk (2.6.8)
+    zeitwerk (2.6.11)
 
 PLATFORMS
   ruby

From d61b91f468d7fd23f8432605d993eba198d84c52 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 19:00:21 +0000
Subject: [PATCH 02/27] Update guard to version 2.18.1

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 9015145a..1cb3b9d8 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -52,7 +52,7 @@ GEM
       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)
@@ -81,7 +81,7 @@ GEM
     loofah (2.21.3)
       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)

From 615004d96d9720003a2d1f87a4454c8d830e8532 Mon Sep 17 00:00:00 2001
From: Javid Ahmed <ja33@sanger.ac.uk>
Date: Fri, 8 Dec 2023 10:11:09 +0000
Subject: [PATCH 03/27] Add location_name column to labware_location table

---
 .../20231207143456_add_location_name_to_labware_location.rb  | 5 +++++
 db/schema.rb                                                 | 3 ++-
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100644 db/migrate/20231207143456_add_location_name_to_labware_location.rb

diff --git a/db/migrate/20231207143456_add_location_name_to_labware_location.rb b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
new file mode 100644
index 00000000..959d1dd3
--- /dev/null
+++ b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
@@ -0,0 +1,5 @@
+class AddLocationNameToLabwareLocation < ActiveRecord::Migration[7.0]
+  def change
+    add_column :labware_location, :location_name, :string, null: false, comment: 'Name of location where labware is stored', after: :full_location_address
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index e960553a..5ce766f3 100644
--- a/db/schema.rb
+++ b/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

From ecc8bc4982244b1db249273d72491ec533e7057e Mon Sep 17 00:00:00 2001
From: Javid Ahmed <ja33@sanger.ac.uk>
Date: Fri, 8 Dec 2023 10:19:58 +0000
Subject: [PATCH 04/27] Add default value

---
 .../20231207143456_add_location_name_to_labware_location.rb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/db/migrate/20231207143456_add_location_name_to_labware_location.rb b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
index 959d1dd3..6c38f677 100644
--- a/db/migrate/20231207143456_add_location_name_to_labware_location.rb
+++ b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
@@ -1,5 +1,5 @@
 class AddLocationNameToLabwareLocation < ActiveRecord::Migration[7.0]
   def change
-    add_column :labware_location, :location_name, :string, null: false, comment: 'Name of location where labware is stored', after: :full_location_address
+    add_column :labware_location, :location_name, :string, null: false, default: "", comment: 'Name of location where labware is stored', after: :full_location_address
   end
 end

From 4f518eef346469184b86aebc51f9bafb02e571b9 Mon Sep 17 00:00:00 2001
From: Javid Ahmed <ja33@sanger.ac.uk>
Date: Fri, 8 Dec 2023 10:21:50 +0000
Subject: [PATCH 05/27] Revert "Add default value"

This reverts commit ecc8bc4982244b1db249273d72491ec533e7057e.
---
 .../20231207143456_add_location_name_to_labware_location.rb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/db/migrate/20231207143456_add_location_name_to_labware_location.rb b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
index 6c38f677..959d1dd3 100644
--- a/db/migrate/20231207143456_add_location_name_to_labware_location.rb
+++ b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
@@ -1,5 +1,5 @@
 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
+    add_column :labware_location, :location_name, :string, null: false, comment: 'Name of location where labware is stored', after: :full_location_address
   end
 end

From a6a94216a9a7cb588ab76a0f46adbbe4f7518073 Mon Sep 17 00:00:00 2001
From: Javid Ahmed <ja33@sanger.ac.uk>
Date: Fri, 8 Dec 2023 10:22:08 +0000
Subject: [PATCH 06/27] Add default value

---
 .../20231207143456_add_location_name_to_labware_location.rb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/db/migrate/20231207143456_add_location_name_to_labware_location.rb b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
index 959d1dd3..aba54041 100644
--- a/db/migrate/20231207143456_add_location_name_to_labware_location.rb
+++ b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
@@ -1,5 +1,5 @@
 class AddLocationNameToLabwareLocation < ActiveRecord::Migration[7.0]
   def change
-    add_column :labware_location, :location_name, :string, null: false, comment: 'Name of location where labware is stored', after: :full_location_address
+    add_column :labware_location, :location_name, :string, null: false, default: '', comment: 'Name of location where labware is stored', after: :full_location_address
   end
 end

From a98d15355f4394869c9126116cd6c534c7437602 Mon Sep 17 00:00:00 2001
From: Javid Ahmed <ja33@sanger.ac.uk>
Date: Fri, 8 Dec 2023 10:24:18 +0000
Subject: [PATCH 07/27] Fix linting

---
 .../20231207143456_add_location_name_to_labware_location.rb    | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/db/migrate/20231207143456_add_location_name_to_labware_location.rb b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
index aba54041..a10136da 100644
--- a/db/migrate/20231207143456_add_location_name_to_labware_location.rb
+++ b/db/migrate/20231207143456_add_location_name_to_labware_location.rb
@@ -1,3 +1,6 @@
+# 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

From 840a1fa63d1b435b83ef1cad8fc9d34554b4bacd Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 01:20:26 +0000
Subject: [PATCH 08/27] Update rubocop-rails to version 2.23.1

---
 Gemfile.lock | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5af3b6fd..986712ba 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -73,7 +73,7 @@ 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)
@@ -95,14 +95,14 @@ GEM
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.23.0)
-    parser (3.2.2.3)
+    parallel (1.24.0)
+    parser (3.2.2.4)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    racc (1.7.1)
+    racc (1.7.3)
     rack (2.2.8)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -126,7 +126,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rbtree (0.4.4)
-    regexp_parser (2.8.1)
+    regexp_parser (2.8.3)
     rexml (3.2.6)
     rspec (3.12.0)
       rspec-core (~> 3.12.0)
@@ -149,18 +149,18 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.0)
-    rubocop (1.55.1)
+    rubocop (1.59.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.2.2.4)
       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 (~> 1.41)
@@ -169,10 +169,11 @@ GEM
     rubocop-performance (1.18.0)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
-    rubocop-rails (2.20.2)
+    rubocop-rails (2.23.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
     rubocop-rspec (2.23.0)
       rubocop (~> 1.33)
       rubocop-capybara (~> 2.17)
@@ -197,7 +198,7 @@ GEM
     thor (1.2.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     zeitwerk (2.6.11)
 
 PLATFORMS

From 6ec193f4797f0fca46b8080a9ee6380cb7df2b30 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 01:25:16 +0000
Subject: [PATCH 09/27] Update rspec-rails to version 6.1.0

---
 Gemfile.lock | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5af3b6fd..70c14c8d 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -78,18 +78,18 @@ GEM
     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)
     method_source (1.0.0)
-    mini_portile2 (2.8.4)
+    mini_portile2 (2.8.5)
     minitest (5.20.0)
     msgpack (1.5.2)
     multi_json (1.15.0)
     mysql2 (0.5.5)
     nenv (0.3.0)
-    nokogiri (1.15.4)
+    nokogiri (1.16.0)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -102,7 +102,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    racc (1.7.1)
+    racc (1.7.3)
     rack (2.2.8)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -121,7 +121,7 @@ GEM
       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)
@@ -137,10 +137,10 @@ 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 (6.1.0)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
@@ -148,7 +148,7 @@ GEM
       rspec-expectations (~> 3.12)
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
-    rspec-support (3.12.0)
+    rspec-support (3.12.1)
     rubocop (1.55.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
@@ -194,11 +194,11 @@ 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 (2.6.11)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   ruby

From 733117e5216820738e27824e2b2260b9f4918f2e Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Wed, 3 Jan 2024 01:44:49 +0000
Subject: [PATCH 10/27] bump tj-actions/changed-files from 23 to 41 in
 /.github/workflows

Bumps tj-actions/changed-files from 23 to 41.
---
 .github/workflows/check_release_version.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check_release_version.yml b/.github/workflows/check_release_version.yml
index e5db52d7..3f441c5f 100644
--- a/.github/workflows/check_release_version.yml
+++ b/.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

From 99817309e802b49d908f7b14a0bc3125aec19ace Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Wed, 3 Jan 2024 01:53:34 +0000
Subject: [PATCH 11/27] Use the latest supported bundler version 2.4.22 for
 Ruby 2.7

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index d4fa9bcf..ec8efe12 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 FROM ruby:2.7
 
-RUN gem install bundler
+RUN gem install bundler -v 2.4.22
 
 # throw errors if Gemfile has been modified since Gemfile.lock
 RUN bundle config --global frozen 1

From d1141e9b4008e4296cc81723cc37599aa3206e9b Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Sat, 6 Jan 2024 19:05:18 +0000
Subject: [PATCH 12/27] Update rubocop-rspec to version 2.26.1

---
 Gemfile.lock | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5af3b6fd..193b78b6 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -73,7 +73,7 @@ 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)
@@ -95,14 +95,14 @@ GEM
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.23.0)
-    parser (3.2.2.3)
+    parallel (1.24.0)
+    parser (3.3.0.0)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    racc (1.7.1)
+    racc (1.7.3)
     rack (2.2.8)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -126,7 +126,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rbtree (0.4.4)
-    regexp_parser (2.8.1)
+    regexp_parser (2.8.3)
     rexml (3.2.6)
     rspec (3.12.0)
       rspec-core (~> 3.12.0)
@@ -149,22 +149,22 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.0)
-    rubocop (1.55.1)
+    rubocop (1.59.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.2.2.4)
       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)
@@ -173,8 +173,8 @@ GEM
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
-    rubocop-rspec (2.23.0)
-      rubocop (~> 1.33)
+    rubocop-rspec (2.26.1)
+      rubocop (~> 1.40)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
     ruby-progressbar (1.13.0)
@@ -197,7 +197,7 @@ GEM
     thor (1.2.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     zeitwerk (2.6.11)
 
 PLATFORMS

From e3c5e3ba801dd7400f37eddf2f71de4eedfda092 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Tue, 9 Jan 2024 19:35:32 +0000
Subject: [PATCH 13/27] Update rubocop-performance to version 1.20.2

---
 Gemfile.lock | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5af3b6fd..72ea920e 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -73,7 +73,7 @@ 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)
@@ -95,14 +95,14 @@ GEM
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.23.0)
-    parser (3.2.2.3)
+    parallel (1.24.0)
+    parser (3.3.0.2)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    racc (1.7.1)
+    racc (1.7.3)
     rack (2.2.8)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -126,7 +126,7 @@ GEM
     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)
@@ -149,26 +149,26 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.0)
-    rubocop (1.55.1)
+    rubocop (1.59.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.2.2.4)
       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 (~> 1.41)
     rubocop-factory_bot (2.23.1)
       rubocop (~> 1.33)
-    rubocop-performance (1.18.0)
-      rubocop (>= 1.7.0, < 2.0)
-      rubocop-ast (>= 0.4.0)
+    rubocop-performance (1.20.2)
+      rubocop (>= 1.48.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
     rubocop-rails (2.20.2)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
@@ -197,7 +197,7 @@ GEM
     thor (1.2.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     zeitwerk (2.6.11)
 
 PLATFORMS

From 7d50ed4647f7f87d4aba5724929d0de285bfba6c Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Sat, 13 Jan 2024 19:05:31 +0000
Subject: [PATCH 14/27] Update bootsnap to version 1.17.1

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5af3b6fd..28f5992a 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -32,7 +32,7 @@ GEM
       tzinfo (~> 2.0)
     amq-protocol (2.3.2)
     ast (2.4.2)
-    bootsnap (1.16.0)
+    bootsnap (1.17.1)
       msgpack (~> 1.2)
     builder (3.2.4)
     bunny (2.19.0)
@@ -85,7 +85,7 @@ GEM
     method_source (1.0.0)
     mini_portile2 (2.8.4)
     minitest (5.20.0)
-    msgpack (1.5.2)
+    msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.5)
     nenv (0.3.0)

From 9ee7694030157cc76c2c17f681f9fe264e8f04d3 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Thu, 25 Jan 2024 15:29:54 +0000
Subject: [PATCH 15/27] Updated ruby and rubocopped.

---
 .ruby-version                                               | 2 +-
 app/models/associated_with_roles.rb                         | 2 +-
 ...20230522131908_add_library_tube_barcode_to_pacbio_run.rb | 2 +-
 lib/resource_tools/json.rb                                  | 6 +++---
 lib/tasks/remove_duplicate_pac_bio_runs.rake                | 2 +-
 lib/tasks/update_pac_bio_run_name.rake                      | 2 +-
 .../update_pac_bio_run_sequencescape_plate_numbers.rake     | 2 +-
 spec/models/flowcell_spec.rb                                | 4 ++--
 spec/support/it_behaves_like_a_nested_resource.rb           | 4 ++--
 spec/support/it_behaves_like_associated_with_roles.rb       | 2 +-
 10 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/.ruby-version b/.ruby-version
index 75a22a26..ef538c28 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-3.0.3
+3.1.2
diff --git a/app/models/associated_with_roles.rb b/app/models/associated_with_roles.rb
index fe5c8a50..e1d0704e 100644
--- a/app/models/associated_with_roles.rb
+++ b/app/models/associated_with_roles.rb
@@ -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
       )
diff --git a/db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb b/db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb
index c69887a9..d9077f5f 100644
--- a/db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb
+++ b/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
diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 28f19040..33e3a7e4 100644
--- a/lib/resource_tools/json.rb
+++ b/lib/resource_tools/json.rb
@@ -146,11 +146,11 @@ def custom_value(name, &block)
       end
     end
 
-    def initialize(*args, &block)
+    def initialize(...)
       super
       if self.class.custom_values.present?
-        self.class.custom_values.each do |k, block|
-          self[k] = instance_eval(&block)
+        self.class.custom_values.each_key do |k|
+          self[k] = instance_eval(...)
         end
       end
       convert_booleans
diff --git a/lib/tasks/remove_duplicate_pac_bio_runs.rake b/lib/tasks/remove_duplicate_pac_bio_runs.rake
index 25de3039..79c91293 100644
--- a/lib/tasks/remove_duplicate_pac_bio_runs.rake
+++ b/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
diff --git a/lib/tasks/update_pac_bio_run_name.rake b/lib/tasks/update_pac_bio_run_name.rake
index b4df5f2c..f5db66f5 100644
--- a/lib/tasks/update_pac_bio_run_name.rake
+++ b/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
diff --git a/lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake b/lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake
index 4c85d1dc..87c23bec 100644
--- a/lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake
+++ b/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
diff --git a/spec/models/flowcell_spec.rb b/spec/models/flowcell_spec.rb
index 3e8c9eab..6eb0c3c0 100644
--- a/spec/models/flowcell_spec.rb
+++ b/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
 
diff --git a/spec/support/it_behaves_like_a_nested_resource.rb b/spec/support/it_behaves_like_a_nested_resource.rb
index ade0a271..cb15471d 100644
--- a/spec/support/it_behaves_like_a_nested_resource.rb
+++ b/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
diff --git a/spec/support/it_behaves_like_associated_with_roles.rb b/spec/support/it_behaves_like_associated_with_roles.rb
index 81cabcb2..e2dfb8f8 100644
--- a/spec/support/it_behaves_like_associated_with_roles.rb
+++ b/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
 

From b8f8cb446c009ef37a41a61cb5feb667d3ad0958 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Thu, 25 Jan 2024 15:48:02 +0000
Subject: [PATCH 16/27] Reverted rubocop for failing tests.

---
 .ruby-version                                                 | 2 +-
 app/models/associated_with_roles.rb                           | 2 +-
 .../20230522131908_add_library_tube_barcode_to_pacbio_run.rb  | 2 +-
 lib/resource_tools/json.rb                                    | 2 ++
 lib/tasks/remove_duplicate_pac_bio_runs.rake                  | 2 +-
 lib/tasks/update_pac_bio_run_name.rake                        | 2 +-
 lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake | 2 +-
 spec/models/flowcell_spec.rb                                  | 4 ++--
 spec/support/it_behaves_like_a_nested_resource.rb             | 4 ++--
 spec/support/it_behaves_like_associated_with_roles.rb         | 2 +-
 10 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/.ruby-version b/.ruby-version
index 75a22a26..ef538c28 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-3.0.3
+3.1.2
diff --git a/app/models/associated_with_roles.rb b/app/models/associated_with_roles.rb
index fe5c8a50..e1d0704e 100644
--- a/app/models/associated_with_roles.rb
+++ b/app/models/associated_with_roles.rb
@@ -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
       )
diff --git a/db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb b/db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb
index c69887a9..d9077f5f 100644
--- a/db/migrate/20230522131908_add_library_tube_barcode_to_pacbio_run.rb
+++ b/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
diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 28f19040..87d980dc 100644
--- a/lib/resource_tools/json.rb
+++ b/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|
diff --git a/lib/tasks/remove_duplicate_pac_bio_runs.rake b/lib/tasks/remove_duplicate_pac_bio_runs.rake
index 25de3039..79c91293 100644
--- a/lib/tasks/remove_duplicate_pac_bio_runs.rake
+++ b/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
diff --git a/lib/tasks/update_pac_bio_run_name.rake b/lib/tasks/update_pac_bio_run_name.rake
index b4df5f2c..f5db66f5 100644
--- a/lib/tasks/update_pac_bio_run_name.rake
+++ b/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
diff --git a/lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake b/lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake
index 4c85d1dc..87c23bec 100644
--- a/lib/tasks/update_pac_bio_run_sequencescape_plate_numbers.rake
+++ b/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
diff --git a/spec/models/flowcell_spec.rb b/spec/models/flowcell_spec.rb
index 3e8c9eab..6eb0c3c0 100644
--- a/spec/models/flowcell_spec.rb
+++ b/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
 
diff --git a/spec/support/it_behaves_like_a_nested_resource.rb b/spec/support/it_behaves_like_a_nested_resource.rb
index ade0a271..cb15471d 100644
--- a/spec/support/it_behaves_like_a_nested_resource.rb
+++ b/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
diff --git a/spec/support/it_behaves_like_associated_with_roles.rb b/spec/support/it_behaves_like_associated_with_roles.rb
index 81cabcb2..e2dfb8f8 100644
--- a/spec/support/it_behaves_like_associated_with_roles.rb
+++ b/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
 

From ddbb79191690e7bb8a9d414e5661d78b6041c356 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Thu, 25 Jan 2024 15:50:50 +0000
Subject: [PATCH 17/27] Tried again to revert and fix.

---
 lib/resource_tools/json.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 1671b57c..87d980dc 100644
--- a/lib/resource_tools/json.rb
+++ b/lib/resource_tools/json.rb
@@ -150,8 +150,8 @@ def custom_value(name, &block)
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
-        self.class.custom_values.each_key do |k|
-          self[k] = instance_eval(...)
+        self.class.custom_values.each do |k, block|
+          self[k] = instance_eval(&block)
         end
       end
       convert_booleans

From 50c3b7c929cf92390ef623df3dbc80b4b6dc8f1e Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Thu, 25 Jan 2024 16:01:03 +0000
Subject: [PATCH 18/27] Trying something.

---
 lib/resource_tools/json.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 87d980dc..74a85ac9 100644
--- a/lib/resource_tools/json.rb
+++ b/lib/resource_tools/json.rb
@@ -146,7 +146,7 @@ def custom_value(name, &block)
       end
     end
 
-    # rubocop:disable Style/ArgumentsForwarding
+    # rubocop:disable Naming/BlockForwarding
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
@@ -157,7 +157,7 @@ def initialize(*args, &block)
       convert_booleans
       delete_if { |k, _| ignoreable.include?(k) }
     end
-    # rubocop:enable Style/ArgumentsForwarding
+    # rubocop:enable Naming/BlockForwarding
 
     def convert_booleans
       self.stored_as_boolean.each do |key|

From a07ad8d24a66b3402ed587e9a4a940bf2bfd1ef3 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 26 Jan 2024 11:59:23 +0000
Subject: [PATCH 19/27] Code review comments.

---
 .rubocop.yml | 1 +
 Dockerfile   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.rubocop.yml b/.rubocop.yml
index 8ba9e9da..5a9dd502 100644
--- a/.rubocop.yml
+++ b/.rubocop.yml
@@ -24,6 +24,7 @@ AllCops:
     - 'vendor/**/*'
     - db/schema.rb
     - db/views_schema.rb
+    - db/migrate/*
   SuggestExtensions: false
 
 Style/DocumentDynamicEvalDefinition:
diff --git a/Dockerfile b/Dockerfile
index ec8efe12..ddab96c2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ruby:2.7
+FROM ruby:3.1.2
 
 RUN gem install bundler -v 2.4.22
 

From 12113a4c00036b3a950605dd2cda45e72d3aae8e Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 26 Jan 2024 15:34:43 +0000
Subject: [PATCH 20/27] Update Dockerfile and JSON.rb

---
 Dockerfile                 | 2 +-
 lib/resource_tools/json.rb | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ddab96c2..4a2d6f7f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 FROM ruby:3.1.2
 
-RUN gem install bundler -v 2.4.22
+RUN gem install bundler
 
 # throw errors if Gemfile has been modified since Gemfile.lock
 RUN bundle config --global frozen 1
diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 74a85ac9..87d980dc 100644
--- a/lib/resource_tools/json.rb
+++ b/lib/resource_tools/json.rb
@@ -146,7 +146,7 @@ def custom_value(name, &block)
       end
     end
 
-    # rubocop:disable Naming/BlockForwarding
+    # rubocop:disable Style/ArgumentsForwarding
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
@@ -157,7 +157,7 @@ def initialize(*args, &block)
       convert_booleans
       delete_if { |k, _| ignoreable.include?(k) }
     end
-    # rubocop:enable Naming/BlockForwarding
+    # rubocop:enable Style/ArgumentsForwarding
 
     def convert_booleans
       self.stored_as_boolean.each do |key|

From bfd769891f9f96d79aad9e5e0d10463265981c17 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 26 Jan 2024 15:41:54 +0000
Subject: [PATCH 21/27] Disable block forwarding in JSON module

---
 lib/resource_tools/json.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 87d980dc..74a85ac9 100644
--- a/lib/resource_tools/json.rb
+++ b/lib/resource_tools/json.rb
@@ -146,7 +146,7 @@ def custom_value(name, &block)
       end
     end
 
-    # rubocop:disable Style/ArgumentsForwarding
+    # rubocop:disable Naming/BlockForwarding
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
@@ -157,7 +157,7 @@ def initialize(*args, &block)
       convert_booleans
       delete_if { |k, _| ignoreable.include?(k) }
     end
-    # rubocop:enable Style/ArgumentsForwarding
+    # rubocop:enable Naming/BlockForwarding
 
     def convert_booleans
       self.stored_as_boolean.each do |key|

From 7ed7b8a2cefff17b734b0927d0436874b8a57596 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 26 Jan 2024 16:10:58 +0000
Subject: [PATCH 22/27] Update Gemfile.lock and lib/resource_tools/json.rb

---
 Gemfile.lock               | 14 +++++++-------
 lib/resource_tools/json.rb |  4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 2324b5e8..3294e615 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -39,7 +39,7 @@ GEM
       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)
@@ -84,7 +84,7 @@ GEM
     lumberjack (1.2.9)
     method_source (1.0.0)
     mini_portile2 (2.8.5)
-    minitest (5.20.0)
+    minitest (5.21.2)
     msgpack (1.5.2)
     multi_json (1.15.0)
     mysql2 (0.5.5)
@@ -96,7 +96,7 @@ GEM
       nenv (~> 0.1)
       shellany (~> 0.0)
     parallel (1.24.0)
-    parser (3.3.0.0)
+    parser (3.3.0.5)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
@@ -126,7 +126,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rbtree (0.4.4)
-    regexp_parser (2.8.3)
+    regexp_parser (2.9.0)
     rexml (3.2.6)
     rspec (3.12.0)
       rspec-core (~> 3.12.0)
@@ -149,11 +149,11 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.1)
-    rubocop (1.59.0)
+    rubocop (1.60.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.4)
+      parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
@@ -173,9 +173,9 @@ GEM
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
     rubocop-rspec (2.26.1)
       rubocop (~> 1.40)
-      rubocop-ast (>= 1.30.0, < 2.0)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
     ruby-progressbar (1.13.0)
diff --git a/lib/resource_tools/json.rb b/lib/resource_tools/json.rb
index 74a85ac9..87d980dc 100644
--- a/lib/resource_tools/json.rb
+++ b/lib/resource_tools/json.rb
@@ -146,7 +146,7 @@ def custom_value(name, &block)
       end
     end
 
-    # rubocop:disable Naming/BlockForwarding
+    # rubocop:disable Style/ArgumentsForwarding
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
@@ -157,7 +157,7 @@ def initialize(*args, &block)
       convert_booleans
       delete_if { |k, _| ignoreable.include?(k) }
     end
-    # rubocop:enable Naming/BlockForwarding
+    # rubocop:enable Style/ArgumentsForwarding
 
     def convert_booleans
       self.stored_as_boolean.each do |key|

From 760328df7e2da6fc2a49278f41cec3efb16d5e22 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 26 Jan 2024 16:55:15 +0000
Subject: [PATCH 23/27] Rubocopped.

---
 app/models/associated_with_roles.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/associated_with_roles.rb b/app/models/associated_with_roles.rb
index e1d0704e..5e2f0fc2 100644
--- a/app/models/associated_with_roles.rb
+++ b/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

From b00563d38eee0f9b858fc4f7184a3543c9697804 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 26 Jan 2024 19:00:19 +0000
Subject: [PATCH 24/27] Update factory_bot_rails to version 6.4.3

---
 Gemfile.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index a3433901..e4cbb0c0 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -45,10 +45,10 @@ GEM
     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)

From 079a914a7c3569bb1e3997ca33df45e2b3af6186 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 26 Jan 2024 19:30:41 +0000
Subject: [PATCH 25/27] Update rspec-rails to version 6.1.1

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index a3433901..0c33baeb 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -140,7 +140,7 @@ GEM
     rspec-mocks (3.12.6)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
-    rspec-rails (6.1.0)
+    rspec-rails (6.1.1)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)

From 077a328de445516321406fd89d81625cce7d4cef Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 19:10:25 +0000
Subject: [PATCH 26/27] Update bootsnap to version 1.18.3

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index e4cbb0c0..e0e3f00c 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -32,7 +32,7 @@ GEM
       tzinfo (~> 2.0)
     amq-protocol (2.3.2)
     ast (2.4.2)
-    bootsnap (1.17.1)
+    bootsnap (1.18.3)
       msgpack (~> 1.2)
     builder (3.2.4)
     bunny (2.19.0)

From 71789389dbfca339f4424cae4d45ff84c8611ebd Mon Sep 17 00:00:00 2001
From: Stephen Inglis <519327+stevieing@users.noreply.github.com>
Date: Wed, 7 Feb 2024 10:35:14 +0000
Subject: [PATCH 27/27] Update .release-version

---
 .release-version | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.release-version b/.release-version
index b9a05a6d..b5aaf81f 100644
--- a/.release-version
+++ b/.release-version
@@ -1 +1 @@
-1.17.3
+1.17.4