From 72b5c9106cca1f9c3c5ffc60555ffb304f67eacb Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Sat, 4 May 2024 00:05:21 +0000
Subject: [PATCH 01/20] Update rubocop-rspec to version 2.29.2

---
 Gemfile.lock | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 43613555..463ad197 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -96,7 +96,7 @@ GEM
       nenv (~> 0.1)
       shellany (~> 0.0)
     parallel (1.24.0)
-    parser (3.3.0.5)
+    parser (3.3.1.0)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
@@ -149,7 +149,7 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.63.0)
+    rubocop (1.63.4)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -160,8 +160,8 @@ GEM
       rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.31.2)
-      parser (>= 3.3.0.4)
+    rubocop-ast (1.31.3)
+      parser (>= 3.3.1.0)
     rubocop-capybara (2.20.0)
       rubocop (~> 1.41)
     rubocop-factory_bot (2.25.1)
@@ -174,12 +174,12 @@ GEM
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (2.29.1)
+    rubocop-rspec (2.29.2)
       rubocop (~> 1.40)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
       rubocop-rspec_rails (~> 2.28)
-    rubocop-rspec_rails (2.28.2)
+    rubocop-rspec_rails (2.28.3)
       rubocop (~> 1.40)
     ruby-progressbar (1.13.0)
     sanger_warren (0.4.1)

From 659f58a86df43d520d3943b34193f8f96fa38d32 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Mon, 13 May 2024 18:55:29 +0000
Subject: [PATCH 02/20] Update nokogiri to version 1.16.5

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

diff --git a/Gemfile.lock b/Gemfile.lock
index 43613555..55f84039 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -83,13 +83,13 @@ GEM
       nokogiri (>= 1.12.0)
     lumberjack (1.2.9)
     method_source (1.0.0)
-    mini_portile2 (2.8.5)
+    mini_portile2 (2.8.6)
     minitest (5.22.3)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
     nenv (0.3.0)
-    nokogiri (1.16.3)
+    nokogiri (1.16.5)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)

From d675b538f9c72b9a8c2145d90f409016b7b1e125 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 13:00:55 +0000
Subject: [PATCH 03/20] Update rubocop to version 1.63.5

---
 Gemfile.lock | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 463ad197..c41f6b67 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -102,7 +102,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    racc (1.7.3)
+    racc (1.8.0)
     rack (2.2.9)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -126,8 +126,9 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rbtree (0.4.4)
-    regexp_parser (2.9.0)
-    rexml (3.2.6)
+    regexp_parser (2.9.2)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
       rspec-expectations (~> 3.13.0)
@@ -149,7 +150,7 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.63.4)
+    rubocop (1.63.5)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -198,6 +199,7 @@ GEM
     sorted_set (1.0.3)
       rbtree
       set (~> 1.0)
+    strscan (3.1.0)
     thor (1.3.1)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)

From cb367c82ad0cee5b61eda7dcb14cd0a584512d8e Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 29 May 2024 08:05:44 +0000
Subject: [PATCH 04/20] Update rubocop-rails to version 2.25.0

---
 Gemfile.lock | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5a999286..7039d87b 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -71,7 +71,7 @@ GEM
       guard-compat (~> 1.1)
       rspec (>= 2.99.0, < 4.0)
     hashie (5.0.0)
-    i18n (1.14.4)
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
     json (2.7.2)
     language_server-protocol (3.17.0.3)
@@ -84,7 +84,7 @@ GEM
     lumberjack (1.2.9)
     method_source (1.0.0)
     mini_portile2 (2.8.6)
-    minitest (5.22.3)
+    minitest (5.23.1)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
@@ -150,7 +150,7 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.63.5)
+    rubocop (1.64.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -170,7 +170,7 @@ GEM
     rubocop-performance (1.21.0)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rails (2.24.1)
+    rubocop-rails (2.25.0)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)

From ae4d9ad52d2c07d23537fcf7d27172e3d9507b16 Mon Sep 17 00:00:00 2001
From: Shiv <44001656+SHIV5T3R@users.noreply.github.com>
Date: Thu, 30 May 2024 11:48:30 +0100
Subject: [PATCH 05/20] Create assign_issue_number.yml

---
 .github/workflows/assign_issue_number.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 .github/workflows/assign_issue_number.yml

diff --git a/.github/workflows/assign_issue_number.yml b/.github/workflows/assign_issue_number.yml
new file mode 100644
index 00000000..ef05cbc5
--- /dev/null
+++ b/.github/workflows/assign_issue_number.yml
@@ -0,0 +1,12 @@
+name: Assign Issue Number
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  call-add-to-project:
+    uses: sanger/.github/.github/workflows/generate-issue-number.yml@master
+    secrets:
+      app_id: ${{ secrets.ISSUE_GEN_APP_ID }}
+      app_key: ${{ secrets.ISSUE_GEN_APP_KEY }}

From 0942c70a5a96462f693717fdd89c099949f5154d Mon Sep 17 00:00:00 2001
From: Shiv <44001656+SHIV5T3R@users.noreply.github.com>
Date: Thu, 30 May 2024 11:56:46 +0100
Subject: [PATCH 06/20] Update assign_issue_number.yml

---
 .github/workflows/assign_issue_number.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/assign_issue_number.yml b/.github/workflows/assign_issue_number.yml
index ef05cbc5..90630b1e 100644
--- a/.github/workflows/assign_issue_number.yml
+++ b/.github/workflows/assign_issue_number.yml
@@ -6,7 +6,7 @@ on:
 
 jobs:
   call-add-to-project:
-    uses: sanger/.github/.github/workflows/generate-issue-number.yml@master
+    uses: sanger/.github/.github/workflows/generate_issue_number.yml@master
     secrets:
       app_id: ${{ secrets.ISSUE_GEN_APP_ID }}
       app_key: ${{ secrets.ISSUE_GEN_APP_KEY }}

From f595e3dfc782c91b5e2e3f80dc1490360fd8f306 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Sat, 1 Jun 2024 19:05:28 +0000
Subject: [PATCH 07/20] Update rubocop to version 1.64.1

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

diff --git a/Gemfile.lock b/Gemfile.lock
index 7039d87b..f4ad2087 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -96,7 +96,7 @@ GEM
       nenv (~> 0.1)
       shellany (~> 0.0)
     parallel (1.24.0)
-    parser (3.3.1.0)
+    parser (3.3.2.0)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
@@ -150,7 +150,7 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.64.0)
+    rubocop (1.64.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)

From 9611963911205017983fc2de6be5fd0bce8e41b5 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 5 Jun 2024 00:30:42 +0000
Subject: [PATCH 08/20] Update all of rails to version 7.0.8.4

---
 Gemfile.lock | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 7039d87b..a65db2c4 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -7,25 +7,25 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actionpack (7.0.8.1)
-      actionview (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionpack (7.0.8.4)
+      actionview (= 7.0.8.4)
+      activesupport (= 7.0.8.4)
       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 (7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionview (7.0.8.4)
+      activesupport (= 7.0.8.4)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activemodel (7.0.8.1)
-      activesupport (= 7.0.8.1)
-    activerecord (7.0.8.1)
-      activemodel (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
-    activesupport (7.0.8.1)
+    activemodel (7.0.8.4)
+      activesupport (= 7.0.8.4)
+    activerecord (7.0.8.4)
+      activemodel (= 7.0.8.4)
+      activesupport (= 7.0.8.4)
+    activesupport (7.0.8.4)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -39,7 +39,7 @@ GEM
       amq-protocol (~> 2.3, >= 2.3.1)
       sorted_set (~> 1, >= 1.0.2)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.1)
     connection_pool (2.2.5)
     crass (1.0.6)
     diff-lcs (1.5.1)
@@ -82,8 +82,8 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lumberjack (1.2.9)
-    method_source (1.0.0)
-    mini_portile2 (2.8.6)
+    method_source (1.1.0)
+    mini_portile2 (2.8.7)
     minitest (5.23.1)
     msgpack (1.7.2)
     multi_json (1.15.0)
@@ -113,15 +113,15 @@ GEM
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    railties (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    railties (7.0.8.4)
+      actionpack (= 7.0.8.4)
+      activesupport (= 7.0.8.4)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
       zeitwerk (~> 2.5)
     rainbow (3.1.1)
-    rake (13.1.0)
+    rake (13.2.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
@@ -204,7 +204,7 @@ GEM
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.5.0)
-    zeitwerk (2.6.13)
+    zeitwerk (2.6.15)
 
 PLATFORMS
   ruby

From 8693327178367fddc703aa83d00df81100d036a9 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 14 Jun 2024 14:54:04 +0100
Subject: [PATCH 09/20] Remove created from aliquots table.

---
 .../20240614135209_remove_create_from_aliquots.rb     | 11 +++++++++++
 db/schema.rb                                          |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)
 create mode 100644 db/migrate/20240614135209_remove_create_from_aliquots.rb

diff --git a/db/migrate/20240614135209_remove_create_from_aliquots.rb b/db/migrate/20240614135209_remove_create_from_aliquots.rb
new file mode 100644
index 00000000..705dbe44
--- /dev/null
+++ b/db/migrate/20240614135209_remove_create_from_aliquots.rb
@@ -0,0 +1,11 @@
+class RemoveCreateFromAliquots < ActiveRecord::Migration[7.0]
+  def change
+    def up
+      remove_column :aliquots, :create, :string
+    end
+
+    def down
+      add_column :aliquots, :create, :string
+    end
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 759f4c1a..7cdfb52e 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: 2024_04_04_142248) do
+ActiveRecord::Schema[7.0].define(version: 2024_06_14_135209) do
   create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
     t.string "lims_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"

From b7be65ebbb7f9bde2a92b6107a6876b48273b557 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 14 Jun 2024 15:01:57 +0100
Subject: [PATCH 10/20] Remove created column from aliquots table

---
 .../20240614135209_remove_create_from_aliquots.rb     | 11 -----------
 .../20240614135209_remove_created_from_aliquots.rb    | 11 +++++++++++
 2 files changed, 11 insertions(+), 11 deletions(-)
 delete mode 100644 db/migrate/20240614135209_remove_create_from_aliquots.rb
 create mode 100644 db/migrate/20240614135209_remove_created_from_aliquots.rb

diff --git a/db/migrate/20240614135209_remove_create_from_aliquots.rb b/db/migrate/20240614135209_remove_create_from_aliquots.rb
deleted file mode 100644
index 705dbe44..00000000
--- a/db/migrate/20240614135209_remove_create_from_aliquots.rb
+++ /dev/null
@@ -1,11 +0,0 @@
-class RemoveCreateFromAliquots < ActiveRecord::Migration[7.0]
-  def change
-    def up
-      remove_column :aliquots, :create, :string
-    end
-
-    def down
-      add_column :aliquots, :create, :string
-    end
-  end
-end
diff --git a/db/migrate/20240614135209_remove_created_from_aliquots.rb b/db/migrate/20240614135209_remove_created_from_aliquots.rb
new file mode 100644
index 00000000..76c81dc9
--- /dev/null
+++ b/db/migrate/20240614135209_remove_created_from_aliquots.rb
@@ -0,0 +1,11 @@
+class RemoveCreatedFromAliquots < ActiveRecord::Migration[7.0]
+  def change
+    def up
+      remove_column :aliquots, :created, :datetime
+    end
+
+    def down
+      add_column :aliquots, :created, :datetime
+    end
+  end
+end

From 671efe8b7eda20330b649c65ab01aab44e21de59 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Fri, 14 Jun 2024 15:51:19 +0100
Subject: [PATCH 11/20] Remove 'created' column from Aliquot model and database
 table.

---
 app/models/aliquot.rb                                |  2 ++
 .../20240614135209_remove_created_from_aliquots.rb   | 12 +++++-------
 db/schema.rb                                         |  1 -
 spec/factories.rb                                    |  1 -
 spec/models/aliquots_spec.rb                         |  3 +--
 5 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/app/models/aliquot.rb b/app/models/aliquot.rb
index 6f7f9255..ce402cab 100644
--- a/app/models/aliquot.rb
+++ b/app/models/aliquot.rb
@@ -14,5 +14,7 @@ def self.base_resource_key
     translate(
       uuid: :lims_uuid
     )
+
+    ignore :created
   end
 end
diff --git a/db/migrate/20240614135209_remove_created_from_aliquots.rb b/db/migrate/20240614135209_remove_created_from_aliquots.rb
index 76c81dc9..7541f67d 100644
--- a/db/migrate/20240614135209_remove_created_from_aliquots.rb
+++ b/db/migrate/20240614135209_remove_created_from_aliquots.rb
@@ -1,11 +1,9 @@
 class RemoveCreatedFromAliquots < ActiveRecord::Migration[7.0]
-  def change
-    def up
-      remove_column :aliquots, :created, :datetime
-    end
+  def up
+    remove_column :aliquot, :created, :datetime
+  end
 
-    def down
-      add_column :aliquots, :created, :datetime
-    end
+  def down
+    add_column :aliquot, :created, :datetime
   end
 end
diff --git a/db/schema.rb b/db/schema.rb
index 7cdfb52e..56409ac3 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -22,7 +22,6 @@
     t.string "used_by_barcode", null: false, comment: "The barcode of the entity that the aliquot is used by"
     t.decimal "volume", precision: 10, scale: 2, null: false, comment: "The volume of the aliquot (uL)"
     t.decimal "concentration", precision: 10, scale: 2, comment: "The concentration of the aliquot (ng/ul)"
-    t.datetime "created", null: false, comment: "The date and time that the aliquot was created"
     t.datetime "last_updated", null: false, comment: "The date and time that the aliquot was last updated"
     t.datetime "deleted_at", comment: "The date and time that the aliquot was deleted"
     t.datetime "recorded_at", comment: "The date and time that the aliquot was recorded"
diff --git a/spec/factories.rb b/spec/factories.rb
index 3174162c..a06bc826 100644
--- a/spec/factories.rb
+++ b/spec/factories.rb
@@ -95,7 +95,6 @@
     used_by_barcode { 'pool-barcode' }
     volume { 24.98589115 }
     concentration { 12.46979445 }
-    created { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
     last_updated { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
   end
 end
diff --git a/spec/models/aliquots_spec.rb b/spec/models/aliquots_spec.rb
index 35d50c10..3a671c7b 100644
--- a/spec/models/aliquots_spec.rb
+++ b/spec/models/aliquots_spec.rb
@@ -15,8 +15,7 @@
         'sample_name' => 'aliquot-sample',
         'used_by_type' => 'pool',
         'used_by_barcode' => 'pool-barcode',
-        'last_updated' => '2012-03-11 10:20:08',
-        'created' => '2012-03-11 10:20:08' }
+        'last_updated' => '2012-03-11 10:20:08' }
     end
     it_behaves_like 'a singular resource'
   end

From 0de8dc8040623fa2bc775eb34549af212beeac70 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Tue, 18 Jun 2024 19:00:31 +0000
Subject: [PATCH 12/20] Update rubocop-rspec to version 2.31.0

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

diff --git a/Gemfile.lock b/Gemfile.lock
index f4ad2087..69bbc989 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -95,8 +95,8 @@ GEM
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.24.0)
-    parser (3.3.2.0)
+    parallel (1.25.1)
+    parser (3.3.3.0)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
@@ -127,8 +127,8 @@ GEM
       ffi (~> 1.0)
     rbtree (0.4.4)
     regexp_parser (2.9.2)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.0)
+      strscan
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
       rspec-expectations (~> 3.13.0)
@@ -163,10 +163,10 @@ GEM
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.31.3)
       parser (>= 3.3.1.0)
-    rubocop-capybara (2.20.0)
-      rubocop (~> 1.41)
-    rubocop-factory_bot (2.25.1)
+    rubocop-capybara (2.21.0)
       rubocop (~> 1.41)
+    rubocop-factory_bot (2.26.1)
+      rubocop (~> 1.61)
     rubocop-performance (1.21.0)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
@@ -175,13 +175,13 @@ GEM
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (2.29.2)
+    rubocop-rspec (2.31.0)
       rubocop (~> 1.40)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
       rubocop-rspec_rails (~> 2.28)
-    rubocop-rspec_rails (2.28.3)
-      rubocop (~> 1.40)
+    rubocop-rspec_rails (2.29.1)
+      rubocop (~> 1.61)
     ruby-progressbar (1.13.0)
     sanger_warren (0.4.1)
       bunny (~> 2.17)

From 493a2402de9bc44ddeb8ac4bb0131ba0bf06090f Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 21 Jun 2024 19:05:31 +0000
Subject: [PATCH 13/20] Update rubocop-rspec to version 3.0.1

---
 Gemfile.lock | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 9cc36f33..b83ca843 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -163,10 +163,6 @@ GEM
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.31.3)
       parser (>= 3.3.1.0)
-    rubocop-capybara (2.21.0)
-      rubocop (~> 1.41)
-    rubocop-factory_bot (2.26.1)
-      rubocop (~> 1.61)
     rubocop-performance (1.21.0)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
@@ -175,12 +171,7 @@ GEM
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (2.31.0)
-      rubocop (~> 1.40)
-      rubocop-capybara (~> 2.17)
-      rubocop-factory_bot (~> 2.22)
-      rubocop-rspec_rails (~> 2.28)
-    rubocop-rspec_rails (2.29.1)
+    rubocop-rspec (3.0.1)
       rubocop (~> 1.61)
     ruby-progressbar (1.13.0)
     sanger_warren (0.4.1)

From 69964033f06ee51e2f104a41db0c6ed2884c2b0f Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 21 Jun 2024 19:15:25 +0000
Subject: [PATCH 14/20] Update rspec-rails to version 6.1.3

---
 Gemfile.lock | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 9cc36f33..f550bf5f 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -34,17 +34,17 @@ GEM
     ast (2.4.2)
     bootsnap (1.18.3)
       msgpack (~> 1.2)
-    builder (3.2.4)
+    builder (3.3.0)
     bunny (2.19.0)
       amq-protocol (~> 2.3, >= 2.3.1)
       sorted_set (~> 1, >= 1.0.2)
     coderay (1.1.3)
-    concurrent-ruby (1.3.1)
+    concurrent-ruby (1.3.3)
     connection_pool (2.2.5)
     crass (1.0.6)
     diff-lcs (1.5.1)
     docile (1.4.0)
-    erubi (1.12.0)
+    erubi (1.13.0)
     factory_bot (6.4.5)
       activesupport (>= 5.0.0)
     factory_bot_rails (6.4.3)
@@ -84,12 +84,12 @@ GEM
     lumberjack (1.2.9)
     method_source (1.1.0)
     mini_portile2 (2.8.7)
-    minitest (5.23.1)
+    minitest (5.24.0)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
     nenv (0.3.0)
-    nokogiri (1.16.5)
+    nokogiri (1.16.6)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -135,13 +135,13 @@ GEM
       rspec-mocks (~> 3.13.0)
     rspec-core (3.13.0)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.0)
+    rspec-expectations (3.13.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-mocks (3.13.0)
+    rspec-mocks (3.13.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (6.1.2)
+    rspec-rails (6.1.3)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
@@ -204,7 +204,7 @@ GEM
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.5.0)
-    zeitwerk (2.6.15)
+    zeitwerk (2.6.16)
 
 PLATFORMS
   ruby

From a206960b6b4199dce6191266616f5cfc489aec05 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Mon, 1 Jul 2024 10:45:08 +0100
Subject: [PATCH 15/20] Remove 'created' column from Aliquot model and database
 table.

Also removed deleted_at and made recorded_at required.

Added comments.
---
 .../20240614135209_remove_created_from_aliquots.rb    |  7 +++++++
 db/schema.rb                                          |  4 ++--
 spec/models/aliquots_spec.rb                          | 11 +++++++++--
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/db/migrate/20240614135209_remove_created_from_aliquots.rb b/db/migrate/20240614135209_remove_created_from_aliquots.rb
index 7541f67d..2347fd01 100644
--- a/db/migrate/20240614135209_remove_created_from_aliquots.rb
+++ b/db/migrate/20240614135209_remove_created_from_aliquots.rb
@@ -1,9 +1,16 @@
 class RemoveCreatedFromAliquots < ActiveRecord::Migration[7.0]
   def up
     remove_column :aliquot, :created, :datetime
+    # we will never need this column again, so we can remove it
+    remove_column :aliquot, :deleted_at, :datetime
+    add_column :aliquot, :created_at, :datetime, null: false, comment: 'The date and time that this record was created'
+    change_column_null :aliquot, :recorded_at, false
   end
 
   def down
     add_column :aliquot, :created, :datetime
+    add_column :aliquot, :deleted_at, :datetime
+    remove_column :aliquot, :created_at, :datetime
+    change_column_null :aliquot, :recorded_at, true
   end
 end
diff --git a/db/schema.rb b/db/schema.rb
index 56409ac3..6514896a 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -23,8 +23,8 @@
     t.decimal "volume", precision: 10, scale: 2, null: false, comment: "The volume of the aliquot (uL)"
     t.decimal "concentration", precision: 10, scale: 2, comment: "The concentration of the aliquot (ng/ul)"
     t.datetime "last_updated", null: false, comment: "The date and time that the aliquot was last updated"
-    t.datetime "deleted_at", comment: "The date and time that the aliquot was deleted"
-    t.datetime "recorded_at", comment: "The date and time that the aliquot was recorded"
+    t.datetime "recorded_at", null: false, comment: "The date and time that the aliquot was recorded"
+    t.datetime "created_at", null: false, comment: "The date and time that this record was created"
   end
 
   create_table "bmap_flowcell", primary_key: "id_bmap_flowcell_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
diff --git a/spec/models/aliquots_spec.rb b/spec/models/aliquots_spec.rb
index 3a671c7b..19ff5b2c 100644
--- a/spec/models/aliquots_spec.rb
+++ b/spec/models/aliquots_spec.rb
@@ -4,6 +4,8 @@
 
 describe Aliquot do
   context 'aliquots' do
+    let(:example_lims) { 'example' }
+
     let(:json) do
       { 'id_lims' => 'example',
         'aliquot_type' => 'DNA',
@@ -15,8 +17,13 @@
         'sample_name' => 'aliquot-sample',
         'used_by_type' => 'pool',
         'used_by_barcode' => 'pool-barcode',
-        'last_updated' => '2012-03-11 10:20:08' }
+        'last_updated' => '2012-03-11 10:20:08',
+        'recorded_at' => '2012-03-11 10:20:08',
+        'created_at' => '2012-03-11 10:20:08' }
+    end
+
+    it 'saves the correct resource' do
+      expect(described_class.create_or_update_from_json(json, example_lims)).to be_truthy
     end
-    it_behaves_like 'a singular resource'
   end
 end

From a126cb7a1ad049ce3029e10fb303e7ee62fc0ce0 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Mon, 1 Jul 2024 10:55:24 +0100
Subject: [PATCH 16/20] Modified aliquots factory.

---
 spec/factories.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/spec/factories.rb b/spec/factories.rb
index a06bc826..4fd0f24d 100644
--- a/spec/factories.rb
+++ b/spec/factories.rb
@@ -96,5 +96,7 @@
     volume { 24.98589115 }
     concentration { 12.46979445 }
     last_updated { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
+    created_at { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
+    recorded_at { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
   end
 end

From 1849c7d3bc0e9b138d3be6d4faf1a77f06fc5d67 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Mon, 1 Jul 2024 10:51:11 +0000
Subject: [PATCH 17/20] Update rubocop-performance to version 1.21.1

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

diff --git a/Gemfile.lock b/Gemfile.lock
index b83ca843..02c81e0a 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -127,7 +127,7 @@ GEM
       ffi (~> 1.0)
     rbtree (0.4.4)
     regexp_parser (2.9.2)
-    rexml (3.3.0)
+    rexml (3.3.1)
       strscan
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
@@ -163,7 +163,7 @@ GEM
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.31.3)
       parser (>= 3.3.1.0)
-    rubocop-performance (1.21.0)
+    rubocop-performance (1.21.1)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
     rubocop-rails (2.25.0)

From 2208dccac222f4ca8b3ec8064039212c0eb71c39 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Mon, 1 Jul 2024 19:25:33 +0000
Subject: [PATCH 18/20] Update rubocop-rails to version 2.25.1

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

diff --git a/Gemfile.lock b/Gemfile.lock
index 3ac84c85..1cefce65 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -84,7 +84,7 @@ GEM
     lumberjack (1.2.9)
     method_source (1.1.0)
     mini_portile2 (2.8.7)
-    minitest (5.24.0)
+    minitest (5.24.1)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
@@ -166,7 +166,7 @@ GEM
     rubocop-performance (1.21.1)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rails (2.25.0)
+    rubocop-rails (2.25.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)

From 7c812b497dc23f9c1b0c38175525e2411cbf2484 Mon Sep 17 00:00:00 2001
From: Stephen <519327+stevieing@users.noreply.github.com>
Date: Mon, 8 Jul 2024 09:15:14 +0100
Subject: [PATCH 19/20] Added insert size to aliquot table.

---
 db/migrate/20240708081135_add_insert_size_to_aliquots.rb | 9 +++++++++
 db/schema.rb                                             | 3 ++-
 spec/models/{aliquots_spec.rb => aliquot_spec.rb}        | 3 ++-
 3 files changed, 13 insertions(+), 2 deletions(-)
 create mode 100644 db/migrate/20240708081135_add_insert_size_to_aliquots.rb
 rename spec/models/{aliquots_spec.rb => aliquot_spec.rb} (93%)

diff --git a/db/migrate/20240708081135_add_insert_size_to_aliquots.rb b/db/migrate/20240708081135_add_insert_size_to_aliquots.rb
new file mode 100644
index 00000000..990197cf
--- /dev/null
+++ b/db/migrate/20240708081135_add_insert_size_to_aliquots.rb
@@ -0,0 +1,9 @@
+class AddInsertSizeToAliquots < ActiveRecord::Migration[7.0]
+  def up
+    add_column :aliquot, :insert_size, :integer, comment: 'The size of the insert in base pairs'
+  end
+
+  def down
+    remove_column :aliquot, :insert_size, :integer
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 6514896a..ee5ee844 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: 2024_06_14_135209) do
+ActiveRecord::Schema[7.0].define(version: 2024_07_08_081135) do
   create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
     t.string "lims_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
@@ -25,6 +25,7 @@
     t.datetime "last_updated", null: false, comment: "The date and time that the aliquot was last updated"
     t.datetime "recorded_at", null: false, comment: "The date and time that the aliquot was recorded"
     t.datetime "created_at", null: false, comment: "The date and time that this record was created"
+    t.integer "insert_size", comment: "The size of the insert in base pairs"
   end
 
   create_table "bmap_flowcell", primary_key: "id_bmap_flowcell_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
diff --git a/spec/models/aliquots_spec.rb b/spec/models/aliquot_spec.rb
similarity index 93%
rename from spec/models/aliquots_spec.rb
rename to spec/models/aliquot_spec.rb
index 19ff5b2c..297f44d2 100644
--- a/spec/models/aliquots_spec.rb
+++ b/spec/models/aliquot_spec.rb
@@ -3,7 +3,7 @@
 require 'spec_helper'
 
 describe Aliquot do
-  context 'aliquots' do
+  context 'aliquot' do
     let(:example_lims) { 'example' }
 
     let(:json) do
@@ -11,6 +11,7 @@
         'aliquot_type' => 'DNA',
         'volume' => 5.43,
         'concentration' => 2.34,
+        'insert_size' => 100,
         'lims_uuid' => '000000-0000-0000-0000-0000000002',
         'source_type' => 'library',
         'source_barcode' => 'PR-rna-00000001_H12',

From 839db9584cc68d8e37577423a147e41bf9b7038f Mon Sep 17 00:00:00 2001
From: Stephen Inglis <519327+stevieing@users.noreply.github.com>
Date: Wed, 10 Jul 2024 08:27:31 +0100
Subject: [PATCH 20/20] Update .release-version

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

diff --git a/.release-version b/.release-version
index 622f042f..84cc5294 100644
--- a/.release-version
+++ b/.release-version
@@ -1 +1 @@
-1.17.6
+1.18.0