From b54f2c52e294360c50df5110add64ec8e773cd77 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 14 Jan 2026 09:12:55 +0000
Subject: [PATCH 01/57] add orange color

---
 config/sample_manifest_excel/columns.yml                 | 5 +++--
 config/sample_manifest_excel/conditional_formattings.yml | 9 +++++++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/config/sample_manifest_excel/columns.yml b/config/sample_manifest_excel/columns.yml
index 58be3e02e2..e71a2d0f50 100644
--- a/config/sample_manifest_excel/columns.yml
+++ b/config/sample_manifest_excel/columns.yml
@@ -39,7 +39,7 @@ i7:
       promptTitle: "i7"
       prompt: "Input i7."
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
 i5:
   heading: i5 TAG SEQUENCE
   unlocked: true
@@ -50,10 +50,11 @@ i5:
       formula1: "255"
       allowBlank: false
       showInputMessage: true
+      errorStyle: :warning
       promptTitle: "i5"
       prompt: "Input i5."
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
 tag_group:
   heading: TAG GROUP
   unlocked: true
diff --git a/config/sample_manifest_excel/conditional_formattings.yml b/config/sample_manifest_excel/conditional_formattings.yml
index 1554673165..5dc77ad9d6 100644
--- a/config/sample_manifest_excel/conditional_formattings.yml
+++ b/config/sample_manifest_excel/conditional_formattings.yml
@@ -16,6 +16,15 @@ empty_mandatory_cell:
     formula: "FALSE"
     operator: :equal
     priority: 1
+empty_mandatory_cell_2:
+  style:
+    bg_color: "FF991C"
+    type: :dxf
+  options:
+    type: :cellIs
+    formula: "FALSE"
+    operator: :equal
+    priority: 1
 len:
   style:
     bg_color: "FF0000"

From 86cbf2eeea80b54691977c1f94a91cede5e7548a Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Jan 2026 10:53:32 +0000
Subject: [PATCH 02/57] add validation of i7, i5 column

---
 .../sample_manifest_excel/upload/row.rb          | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
index ccce068b63..f608f8ca4b 100644
--- a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
+++ b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
@@ -22,6 +22,22 @@ class Row # rubocop:todo Metrics/ClassLength
       validate :country_of_origin_has_correct_case,
                if: -> { data.present? && columns.present? && columns.names.include?('country_of_origin') }
 
+      validate :i7_present
+      # Ensure i7 column is not blank if it exists in the manifest
+      def i7_present
+        return unless columns.names.include?('i7') && value('i7').blank?
+
+        errors.add(:base, "#{row_title} i7 can't be blank")
+      end
+
+      validate :i5_present
+      # Ensure i5 column is not blank if it exists in the manifest
+      def i5_present
+        return unless columns.names.include?('i5') && value('i5').blank?
+
+        errors.add(:base, "#{row_title} i5 can't be blank, putting “n/a” in i5 if only needs one set of tags")
+      end
+
       delegate :present?, to: :sample, prefix: true
       delegate :aliquots, :asset, to: :manifest_asset
 

From cc016ff531eb9df6743bccb56084bc33321febf4 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Jan 2026 15:04:04 +0000
Subject: [PATCH 03/57] add unit test

---
 .../sample_manifest_excel/upload/row.rb       |  4 +-
 spec/sample_manifest_excel/upload/row_spec.rb | 49 ++++++++++++++++++-
 2 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
index f608f8ca4b..c466503b6d 100644
--- a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
+++ b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
@@ -25,7 +25,7 @@ class Row # rubocop:todo Metrics/ClassLength
       validate :i7_present
       # Ensure i7 column is not blank if it exists in the manifest
       def i7_present
-        return unless columns.names.include?('i7') && value('i7').blank?
+        return unless columns.present? && data.present? && columns.names.include?('i7') && value('i7').blank?
 
         errors.add(:base, "#{row_title} i7 can't be blank")
       end
@@ -33,7 +33,7 @@ def i7_present
       validate :i5_present
       # Ensure i5 column is not blank if it exists in the manifest
       def i5_present
-        return unless columns.names.include?('i5') && value('i5').blank?
+        return unless columns.present? && data.present? && columns.names.include?('i5') && value('i5').blank?
 
         errors.add(:base, "#{row_title} i5 can't be blank, putting “n/a” in i5 if only needs one set of tags")
       end
diff --git a/spec/sample_manifest_excel/upload/row_spec.rb b/spec/sample_manifest_excel/upload/row_spec.rb
index 96a1b7299c..24b464653e 100644
--- a/spec/sample_manifest_excel/upload/row_spec.rb
+++ b/spec/sample_manifest_excel/upload/row_spec.rb
@@ -24,7 +24,7 @@
       tube.human_barcode,
       sample_manifest.sample_manifest_assets.first.sanger_sample_id,
       'AA',
-      '',
+      'CC',
       'My reference genome',
       'My New Library Type',
       200,
@@ -101,6 +101,47 @@
       'Unknown'
     ]
   end
+  let(:data_without_i7_i5) do
+    [
+      tube.human_barcode,
+      sample_manifest.sample_manifest_assets.first.sanger_sample_id,
+      '',
+      '',
+      'My reference genome',
+      'My New Library Type',
+      200,
+      1500,
+      'SCG--1222_A01',
+      '',
+      1,
+      1,
+      'Unknown',
+      '',
+      '',
+      '',
+      'Cell Line',
+      'Nov-16',
+      'Nov-16',
+      '',
+      'No',
+      '',
+      'OTHER',
+      '',
+      '',
+      '',
+      '',
+      '',
+      'SCG--1222_A01',
+      9606,
+      'Homo sapiens',
+      '',
+      '',
+      '',
+      '',
+      11,
+      'Unknown'
+    ]
+  end
 
   it 'is not valid without row number' do
     expect(described_class.new(number: 'one', data: data, columns: columns)).not_to be_valid
@@ -115,6 +156,10 @@
     expect(described_class.new(number: 1, data: data)).not_to be_valid
   end
 
+  it 'is not valid without i7/i5 if i7/i5 column exists' do
+    expect(described_class.new(number: 1, data: data_without_i7_i5, columns: columns)).not_to be_valid
+  end
+
   it '#value returns value for specified key' do
     expect(described_class.new(number: 1, data: data, columns: columns).value(:sanger_sample_id)).to eq(
       sample_manifest.labware.first.sample_manifest_assets.first.sanger_sample_id
@@ -184,7 +229,7 @@
     aliquot = row.aliquots.first
     expect(Sample.count - sample_count).to eq(1)
     expect(aliquot.tag.oligo).to eq('AA')
-    expect(aliquot.tag2).to be_nil
+    expect(aliquot.tag2.oligo).to eq('CC')
     expect(aliquot.insert_size_from).to eq(200)
     expect(aliquot.insert_size_to).to eq(1500)
   end

From 6092baa98063fd52221ba2af5e0d60960fa60282 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Jan 2026 20:26:14 +0000
Subject: [PATCH 04/57] add i7/i5 to the test fiile

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

diff --git a/spec/factories/sample_manifest_excel/test_download_tubes.rb b/spec/factories/sample_manifest_excel/test_download_tubes.rb
index 3241bd7f3b..da95f58694 100644
--- a/spec/factories/sample_manifest_excel/test_download_tubes.rb
+++ b/spec/factories/sample_manifest_excel/test_download_tubes.rb
@@ -31,6 +31,8 @@
         sample_taxon_id: 9606,
         sample_common_name: 'Homo sapiens',
         donor_id: 'id',
+        'i7' => 'ATTACTCG',
+        'i5' => 'CC',
         phenotype: 'Unknown'
       }.with_indifferent_access
     end

From 772bc944e7126daf2b8cab2323e10f6c5bff455c Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Jan 2026 11:27:45 +0000
Subject: [PATCH 05/57] update the test

---
 spec/factories/sample_manifest_excel/test_download_tubes.rb | 2 --
 spec/sample_manifest_excel/upload/rows_spec.rb              | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/spec/factories/sample_manifest_excel/test_download_tubes.rb b/spec/factories/sample_manifest_excel/test_download_tubes.rb
index da95f58694..3241bd7f3b 100644
--- a/spec/factories/sample_manifest_excel/test_download_tubes.rb
+++ b/spec/factories/sample_manifest_excel/test_download_tubes.rb
@@ -31,8 +31,6 @@
         sample_taxon_id: 9606,
         sample_common_name: 'Homo sapiens',
         donor_id: 'id',
-        'i7' => 'ATTACTCG',
-        'i5' => 'CC',
         phenotype: 'Unknown'
       }.with_indifferent_access
     end
diff --git a/spec/sample_manifest_excel/upload/rows_spec.rb b/spec/sample_manifest_excel/upload/rows_spec.rb
index 19ecff54b4..d5e1ff63c6 100644
--- a/spec/sample_manifest_excel/upload/rows_spec.rb
+++ b/spec/sample_manifest_excel/upload/rows_spec.rb
@@ -39,7 +39,7 @@
   end
 
   it 'is valid if some rows are empty' do
-    download = build(:test_download_tubes_partial, columns:)
+    download = build(:test_download_tubes_partial, columns:, manifest_type: 'tube_library_with_tag_sequences')
     download.save(test_file_name)
     expect(described_class.new(SampleManifestExcel::Upload::Data.new(test_file), columns)).to be_valid
   end

From 3a4574eaa63f465c7984b0c1dd58514ff6fc0d8f Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Jan 2026 11:33:13 +0000
Subject: [PATCH 06/57] fix linting

---
 spec/sample_manifest_excel/upload/rows_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spec/sample_manifest_excel/upload/rows_spec.rb b/spec/sample_manifest_excel/upload/rows_spec.rb
index d5e1ff63c6..8efd3e9186 100644
--- a/spec/sample_manifest_excel/upload/rows_spec.rb
+++ b/spec/sample_manifest_excel/upload/rows_spec.rb
@@ -39,7 +39,7 @@
   end
 
   it 'is valid if some rows are empty' do
-    download = build(:test_download_tubes_partial, columns:, manifest_type: 'tube_library_with_tag_sequences')
+    download = build(:test_download_tubes_partial, columns: columns, manifest_type: 'tube_library_with_tag_sequences')
     download.save(test_file_name)
     expect(described_class.new(SampleManifestExcel::Upload::Data.new(test_file), columns)).to be_valid
   end

From d6489dc6d07dc943af11c4e14801a093ad64da1a Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Jan 2026 12:03:33 +0000
Subject: [PATCH 07/57] fix the test

---
 .../uploader_for_manifests_with_tag_sequences_spec.rb        | 5 +++--
 spec/sample_manifest_excel/upload/upload_spec.rb             | 3 ++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb b/spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb
index a62990cec1..4000cb56b4 100644
--- a/spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb
+++ b/spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb
@@ -26,6 +26,7 @@
     let!(:user) { create(:admin) }
     let(:columns) { SampleManifestExcel.configuration.columns.tube_library_with_tag_sequences.dup }
     let(:test_file) { 'test_file.xlsx' }
+    let(:manifest_type) { 'tube_library_with_tag_sequences' }
 
     before do
       download.save(test_file)
@@ -33,7 +34,7 @@
 
     context 'valid' do
       context 'standard' do
-        let(:download) { build(:test_download_tubes, columns:) }
+        let(:download) { build(:test_download_tubes, columns:, manifest_type:) }
 
         it 'upload' do
           login_user(user)
@@ -81,7 +82,7 @@
       end
 
       context 'cgap foreign barcodes' do
-        let(:download) { build(:test_download_tubes_cgap, columns:) }
+        let(:download) { build(:test_download_tubes_cgap, columns:, manifest_type:) }
 
         it 'upload' do
           login_user(user)
diff --git a/spec/sample_manifest_excel/upload/upload_spec.rb b/spec/sample_manifest_excel/upload/upload_spec.rb
index e45611d999..fb7456dae6 100644
--- a/spec/sample_manifest_excel/upload/upload_spec.rb
+++ b/spec/sample_manifest_excel/upload/upload_spec.rb
@@ -28,7 +28,8 @@
     download =
       build(
         :test_download_tubes,
-        columns: SampleManifestExcel.configuration.columns.tube_library_with_tag_sequences.dup
+        columns: SampleManifestExcel.configuration.columns.tube_library_with_tag_sequences.dup,
+        manifest_type: 'tube_library_with_tag_sequences'
       )
     download.save(test_file_name)
     upload = SampleManifestExcel::Upload::Base.new(file: test_file, column_list: columns, start_row: 9)

From 177f438d9df155319eb66791d696b98ec51b2399 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 4 Feb 2026 16:28:20 +0000
Subject: [PATCH 08/57] add more columns to be orange

---
 .../sample_manifest_excel/upload/row.rb       | 32 +++++++++++++++++++
 config/sample_manifest_excel/columns.yml      | 25 ++++++++++-----
 spec/data/sample_manifest_excel/columns.yml   |  8 ++---
 3 files changed, 53 insertions(+), 12 deletions(-)

diff --git a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
index c466503b6d..34aa49c03b 100644
--- a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
+++ b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
@@ -38,6 +38,38 @@ def i5_present
         errors.add(:base, "#{row_title} i5 can't be blank, putting “n/a” in i5 if only needs one set of tags")
       end
 
+      validate :chromium_tag_group
+      # Ensure chromium_tag_group column is not blank if it exists in the manifest
+      def chromium_tag_group
+        return unless columns.present? && data.present? && columns.names.include?('chromium_tag_group') && value('chromium_tag_group').blank?
+
+        errors.add(:base, "#{row_title} chromium_tag_group can't be blank")
+      end
+
+      validate :chromium_tag_well
+      # Ensure chromium_tag_well column is not blank if it exists in the manifest
+      def chromium_tag_well
+        return unless columns.present? && data.present? && columns.names.include?('chromium_tag_well') && value('chromium_tag_well').blank?
+
+        errors.add(:base, "#{row_title} chromium_tag_well can't be blank")
+      end
+
+      validate :dual_index_tag_set
+      # Ensure dual_index_tag_set column is not blank if it exists in the manifest
+      def dual_index_tag_set
+        return unless columns.present? && data.present? && columns.names.include?('dual_index_tag_set') && value('dual_index_tag_set').blank?
+
+        errors.add(:base, "#{row_title} dual_index_tag_set can't be blank")
+      end
+
+      validate :dual_index_tag_well
+      # Ensure dual_index_tag_well column is not blank if it exists in the manifest
+      def dual_index_tag_well
+        return unless columns.present? && data.present? && columns.names.include?('dual_index_tag_well') && value('dual_index_tag_well').blank?
+
+        errors.add(:base, "#{row_title} dual_index_tag_well can't be blank")
+      end
+
       delegate :present?, to: :sample, prefix: true
       delegate :aliquots, :asset, to: :manifest_asset
 
diff --git a/config/sample_manifest_excel/columns.yml b/config/sample_manifest_excel/columns.yml
index e71a2d0f50..9096fd1dca 100644
--- a/config/sample_manifest_excel/columns.yml
+++ b/config/sample_manifest_excel/columns.yml
@@ -32,12 +32,17 @@ i7:
   validation:
     options:
       type: :textLength
-      operator: :lessThanOrEqual
-      formula1: "255"
+      operator: :between
+      formula1: "1"
+      formula2: "255"
       allowBlank: false
       showInputMessage: true
+      showErrorMessage: true
       promptTitle: "i7"
       prompt: "Input i7."
+      errorStyle: :warning
+      errorTitle: "i7"
+      error: "i7 cannot be blank"
   conditional_formattings:
     empty_mandatory_cell_2:
 i5:
@@ -46,11 +51,15 @@ i5:
   validation:
     options:
       type: :textLength
-      operator: :lessThanOrEqual
-      formula1: "255"
+      operator: :between
+      formula1: "1"
+      formula2: "255"
       allowBlank: false
       showInputMessage: true
+      showErrorMessage: true
       errorStyle: :warning
+      errorTitle: "i5"
+      error: "i5 cannot be blank"
       promptTitle: "i5"
       prompt: "Input i5."
   conditional_formattings:
@@ -138,7 +147,7 @@ chromium_tag_group:
       prompt: "Input the name of a valid tag set. All samples in a library need to be tagged with the same tag set."
     range_name: :chromium_tag_groups
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
 chromium_tag_well:
   heading: CHROMIUM TAG WELL
   unlocked: true
@@ -156,7 +165,7 @@ chromium_tag_well:
       errorTitle: "Tag well"
       error: "Tag Index must be a well."
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
     is_number:
     len:
       formula:
@@ -236,7 +245,7 @@ dual_index_tag_set:
       prompt: "Input the name of a valid dual index tag plate."
     range_name: :dual_index_tag_sets
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
 dual_index_tag_well:
   heading: DUAL INDEX TAG WELL
   unlocked: true
@@ -254,7 +263,7 @@ dual_index_tag_well:
       errorTitle: "Dual index tag well"
       error: "Dual Index Tag must be a well."
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
     is_number:
     len:
       formula:
diff --git a/spec/data/sample_manifest_excel/columns.yml b/spec/data/sample_manifest_excel/columns.yml
index 48a29008c3..f6727872f4 100644
--- a/spec/data/sample_manifest_excel/columns.yml
+++ b/spec/data/sample_manifest_excel/columns.yml
@@ -127,7 +127,7 @@ chromium_tag_group:
       prompt: "Input the name of a valid tag set. All samples in a library need to be tagged with the same tag set."
     range_name: :chromium_tag_groups
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
 chromium_tag_well:
   heading: CHROMIUM TAG WELL
   unlocked: true
@@ -145,7 +145,7 @@ chromium_tag_well:
       errorTitle: "Tag well"
       error: "Tag Index must be a well."
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
     is_number:
     len:
       formula:
@@ -184,7 +184,7 @@ dual_index_tag_set:
       prompt: "Input the name of a valid dual index tag plate."
     range_name: :dual_index_tag_sets
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
 dual_index_tag_well:
   heading: DUAL INDEX TAG WELL
   unlocked: true
@@ -202,7 +202,7 @@ dual_index_tag_well:
       errorTitle: "Dual index tag well"
       error: "Dual Index Tag must be a well."
   conditional_formattings:
-    empty_cell:
+    empty_mandatory_cell_2:
     is_number:
     len:
       formula:

From 9493c6f94b2ef5c1c74b155957e1880c1fcbd6af Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Fri, 6 Feb 2026 11:28:43 +0000
Subject: [PATCH 09/57] wip: adds scrna core cdna pooling plan download link to
 submission show page

---
 app/controllers/submissions_controller.rb | 6 ++++++
 app/views/submissions/show.html.erb       | 5 ++++-
 config/routes.rb                          | 1 +
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 3f04313817..82e79674ca 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -115,6 +115,12 @@ def study
     @submissions = @study.submissions
   end
 
+  def download_scrna_core_cdna_pooling_plan
+    csv_string = ''
+    send_data csv_string, type: 'text/plain', filename: "#{params[:id]}_scrna_core_cdna_pooling_plan.csv",
+                          disposition: 'attachment'
+  end
+
   ###################################################               AJAX ROUTES
   # TODO[sd9]: These AJAX routes could be re-factored
 
diff --git a/app/views/submissions/show.html.erb b/app/views/submissions/show.html.erb
index ebd72980d9..80dc9263dd 100644
--- a/app/views/submissions/show.html.erb
+++ b/app/views/submissions/show.html.erb
@@ -4,6 +4,10 @@
   add :menu, "Print labels for #{order.asset_group.name}" => print_study_asset_group_path(order.study,order.asset_group) unless order.asset_group.nil?
 end %>
 <%- add :menu, "Submissions Inbox" => submissions_path if can? :read, Submission -%>
+<%- add :menu, "Download scRNA Core cDNA pooling plan" => download_scrna_core_cdna_pooling_plan_submission_path(@presenter.submission.id) if
+    # TODO - Move this to a helper method
+    @presenter.submission.orders.first.template_name == 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p' 
+-%>
 
 
 <%= page_title("Submission", "#{@presenter.submission.id} - #{@presenter.template_name}") %>
@@ -70,5 +74,4 @@ end %>
 <% end %>
 <% end %>
 
-
 <%= vite_javascript_tag 'submissions' %>
diff --git a/config/routes.rb b/config/routes.rb
index c9c46204c2..8cecf2973c 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -322,6 +322,7 @@
     member do
       post :change_priority
       post :cancel
+      get :download_scrna_core_cdna_pooling_plan
     end
   end
 

From 58f2ee84135f5ff66110a7c368577b3cc20a3ab4 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Fri, 6 Feb 2026 14:54:29 +0000
Subject: [PATCH 10/57] wip: initial attempt at fleshing out pooling plan logic

---
 app/controllers/submissions_controller.rb | 28 +++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 82e79674ca..1e10d6e3dc 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -115,8 +115,32 @@ def study
     @submissions = @study.submissions
   end
 
-  def download_scrna_core_cdna_pooling_plan
-    csv_string = ''
+  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity
+    submission = Submission.find(params[:id])
+
+    # Group requests by study/project/donor and cells_per_chip_well
+    grouped_labware = submission.requests.group_by do |request|
+      aliquot = request.asset.aliquots.first
+      study = aliquot.study.name
+      project = aliquot&.project&.name
+      donor_id = aliquot.sample.sample_metadata.donor_id
+      "#{study} / #{project} / #{donor_id}"
+    end
+
+    # Then group by cells_per_chip_well within those groups
+    grouped_labware = grouped_labware.flat_map do |key, group|
+      group.group_by { |request| request.request_metadata.cells_per_chip_well }
+        .map { |cells, subgroup| [key, cells, subgroup] }
+    end
+
+    csv_string = CSV.generate(row_sep: "\r\n") do |csv|
+      csv << ['Study / Project / Donor ID', 'Pools (num samples)', 'Cells per chip well']
+      grouped_labware.each do |study_project_donor, cells_per_chip_well, subgroup|
+        number_of_samples_in_pool, = subgroup.size.divmod(subgroup.first.request_metadata.number_of_pools)
+        csv << [study_project_donor, number_of_samples_in_pool, cells_per_chip_well]
+      end
+    end
+
     send_data csv_string, type: 'text/plain', filename: "#{params[:id]}_scrna_core_cdna_pooling_plan.csv",
                           disposition: 'attachment'
   end

From 91d3780ba5d6f1b69cef008a56eb79b41e336978 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Mon, 9 Feb 2026 13:13:45 +0000
Subject: [PATCH 11/57] tests: adds pooling download tests

---
 app/controllers/submissions_controller.rb     | 13 ++---
 app/models/ability/base_user.rb               |  2 +-
 config/routes.rb                              |  2 +-
 .../submissions_controller_spec.rb            | 21 +++++++-
 .../submissions/submission_show_spec.rb       | 50 +++++++++++++++++++
 5 files changed, 76 insertions(+), 12 deletions(-)
 create mode 100644 spec/features/submissions/submission_show_spec.rb

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 1e10d6e3dc..95274c5d92 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -115,10 +115,10 @@ def study
     @submissions = @study.submissions
   end
 
-  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity
+  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
     submission = Submission.find(params[:id])
 
-    # Group requests by study/project/donor and cells_per_chip_well
+    # Group requests by study/project/donor
     grouped_labware = submission.requests.group_by do |request|
       aliquot = request.asset.aliquots.first
       study = aliquot.study.name
@@ -127,16 +127,11 @@ def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metr
       "#{study} / #{project} / #{donor_id}"
     end
 
-    # Then group by cells_per_chip_well within those groups
-    grouped_labware = grouped_labware.flat_map do |key, group|
-      group.group_by { |request| request.request_metadata.cells_per_chip_well }
-        .map { |cells, subgroup| [key, cells, subgroup] }
-    end
-
     csv_string = CSV.generate(row_sep: "\r\n") do |csv|
       csv << ['Study / Project / Donor ID', 'Pools (num samples)', 'Cells per chip well']
-      grouped_labware.each do |study_project_donor, cells_per_chip_well, subgroup|
+      grouped_labware.each do |study_project_donor, subgroup|
         number_of_samples_in_pool, = subgroup.size.divmod(subgroup.first.request_metadata.number_of_pools)
+        cells_per_chip_well = subgroup.first.request_metadata.cells_per_chip_well
         csv << [study_project_donor, number_of_samples_in_pool, cells_per_chip_well]
       end
     end
diff --git a/app/models/ability/base_user.rb b/app/models/ability/base_user.rb
index 5cec001764..eb3a2347fe 100644
--- a/app/models/ability/base_user.rb
+++ b/app/models/ability/base_user.rb
@@ -32,7 +32,7 @@ def grant_privileges # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
     can %i[read create], Study
     can :print_asset_group_labels, Study, owners: { id: user.id }
     can :print_asset_group_labels, Study, managers: { id: user.id }
-    can %i[read create update edit], Submission
+    can %i[read create update edit download_scrna_core_cdna_pooling_plan], Submission
     can :read, [TagGroup, TagLayoutTemplate, TagSet]
     can %i[read update print_swipecard], User, { id: user.id }
     can %i[projects study_reports], User
diff --git a/config/routes.rb b/config/routes.rb
index 8cecf2973c..34cc42a627 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -320,9 +320,9 @@
       get :study
     end
     member do
+      get :download_scrna_core_cdna_pooling_plan
       post :change_priority
       post :cancel
-      get :download_scrna_core_cdna_pooling_plan
     end
   end
 
diff --git a/spec/controllers/submissions_controller_spec.rb b/spec/controllers/submissions_controller_spec.rb
index 4d15730d21..1d11ad1ae3 100644
--- a/spec/controllers/submissions_controller_spec.rb
+++ b/spec/controllers/submissions_controller_spec.rb
@@ -2,7 +2,7 @@
 
 require 'rails_helper'
 
-RSpec.describe SubmissionsController do
+RSpec.describe SubmissionsController, type: :controller do
   render_views
 
   let(:request_type) { create(:well_request_type) }
@@ -356,6 +356,25 @@
         assert_select 'div.alert-danger', 0
       end
     end
+
+    describe '#download_scrna_core_cdna_pooling_plan' do
+      before do
+        @template = create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p')
+        @study = create(:study, user: @user)
+        @project = create(:project)
+        submission_order = create(:order_with_submission, template_name: @template.name, study: @study,
+                                                          project: @project,
+                                                          user: @user,
+                                                          asset_group: create(:asset_group, study: @study))
+        @submission = submission_order.submission
+      end
+
+      it 'downloads a pooling plan' do
+        get :download_scrna_core_cdna_pooling_plan, params: { id: @submission.id }
+
+        expect(response.headers['Content-Disposition']).to include("#{@submission.id}_scrna_core_cdna_pooling_plan.csv")
+      end
+    end
   end
 
   def plate_submission(text)
diff --git a/spec/features/submissions/submission_show_spec.rb b/spec/features/submissions/submission_show_spec.rb
new file mode 100644
index 0000000000..73fce64c9b
--- /dev/null
+++ b/spec/features/submissions/submission_show_spec.rb
@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+describe 'Submission show' do
+  let(:user) { create(:admin, login: 'user') }
+  let(:template) { create(:submission_template) }
+  let(:study) { create(:study, name: 'abc123_study') }
+  let(:project) { create(:project, name: 'Test project') }
+  let(:submission) do
+    order = create(:order_with_submission, template_name: template.name, study: study, project: project,
+                                           asset_group: create(:asset_group, study:))
+    order.submission
+  end
+
+  before do
+    login_user user
+    visit submission_path(id: submission.id)
+  end
+
+  describe 'has the correct content' do
+    it 'shows the submission information' do
+      expect(page).to have_content("Submission #{submission.id} - #{template.name}")
+      expect(page).to have_content("Project #{project.name}")
+      expect(page).to have_content("Study #{study.name}")
+    end
+
+    it 'shows the correct sidebar links' do
+      expect(page).to have_link('Print labels for')
+      expect(page).to have_link('Submissions Inbox')
+      # This should only be visible for submissions with the correct scRNA template
+      expect(page).to have_no_link('Download scRNA Core cDNA pooling plan')
+    end
+  end
+
+  describe 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p submissions' do
+    let(:template) { create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p') }
+
+    it 'shows the correct sidebar links' do
+      expect(page).to have_link('Download scRNA Core cDNA pooling plan')
+    end
+
+    it 'downloads the correct pooling plan' do
+      click_link 'Download scRNA Core cDNA pooling plan'
+      expect(page.response_headers['Content-Disposition']).to include(
+        "#{submission.id}_scrna_core_cdna_pooling_plan.csv"
+      )
+    end
+  end
+end

From 1dd45b26371cb495660d113dacd343efec5f7cb8 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Mon, 9 Feb 2026 13:26:45 +0000
Subject: [PATCH 12/57] feat(submission): adds submission helper method to
 identify scrna core pooling submissions

---
 app/controllers/submissions_controller.rb     | 15 +++++++++++++-
 app/models/submission.rb                      |  5 +++++
 app/views/submissions/show.html.erb           |  3 +--
 .../submissions_controller_spec.rb            | 18 +++++++++++++++++
 spec/models/submission_spec.rb                | 20 +++++++++++++++++++
 5 files changed, 58 insertions(+), 3 deletions(-)

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 95274c5d92..274e268333 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -116,7 +116,20 @@ def study
   end
 
   def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
-    submission = Submission.find(params[:id])
+    begin
+      submission = Submission.find(params[:id])
+    rescue ActiveRecord::RecordNotFound
+      flash[:error] = "Submission not found with id #{params[:id]}"
+      redirect_to submissions_path
+      return
+    end
+
+    unless submission.scrna_core_cdna_prep_gem_x_5p_submission?
+      flash[:error] =
+        'This submission does not have the correct template for downloading a scRNA Core cDNA pooling plan'
+      redirect_to submission
+      return
+    end
 
     # Group requests by study/project/donor
     grouped_labware = submission.requests.group_by do |request|
diff --git a/app/models/submission.rb b/app/models/submission.rb
index 7d3b6e4e2c..5688c9f945 100644
--- a/app/models/submission.rb
+++ b/app/models/submission.rb
@@ -22,6 +22,7 @@ class Submission < ApplicationRecord # rubocop:todo Metrics/ClassLength
   include Submission::Priorities
 
   PER_ORDER_REQUEST_OPTIONS = %w[pre_capture_plex_level gigabases_expected].freeze
+  SCRNA_CORE_CDNA_PREP_GEM_X_5P = 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p'
 
   self.per_page = 500
 
@@ -125,6 +126,10 @@ def multiplexed?
     orders.any?(&:multiplexed?)
   end
 
+  def scrna_core_cdna_prep_gem_x_5p_submission?
+    orders.first.template_name == SCRNA_CORE_CDNA_PREP_GEM_X_5P
+  end
+
   # Attempts to find the multiplexed asset (usually a multiplexed library tube) associated
   # with the submission. Useful when trying to pool requests into a pre-existing tube at the
   # end of the process.
diff --git a/app/views/submissions/show.html.erb b/app/views/submissions/show.html.erb
index 80dc9263dd..d61e652014 100644
--- a/app/views/submissions/show.html.erb
+++ b/app/views/submissions/show.html.erb
@@ -5,8 +5,7 @@
 end %>
 <%- add :menu, "Submissions Inbox" => submissions_path if can? :read, Submission -%>
 <%- add :menu, "Download scRNA Core cDNA pooling plan" => download_scrna_core_cdna_pooling_plan_submission_path(@presenter.submission.id) if
-    # TODO - Move this to a helper method
-    @presenter.submission.orders.first.template_name == 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p' 
+    @presenter.submission.scrna_core_cdna_prep_gem_x_5p_submission?
 -%>
 
 
diff --git a/spec/controllers/submissions_controller_spec.rb b/spec/controllers/submissions_controller_spec.rb
index 1d11ad1ae3..77d89cedf0 100644
--- a/spec/controllers/submissions_controller_spec.rb
+++ b/spec/controllers/submissions_controller_spec.rb
@@ -374,6 +374,24 @@
 
         expect(response.headers['Content-Disposition']).to include("#{@submission.id}_scrna_core_cdna_pooling_plan.csv")
       end
+
+      it 'redirects with an error if the submission is not found' do
+        get :download_scrna_core_cdna_pooling_plan, params: { id: 'nonexistent' }
+
+        expect(flash[:error]).to eq('Submission not found with id nonexistent')
+        expect(response).to redirect_to(submissions_path)
+      end
+
+      it 'redirects with an error if the submission does not have the correct template' do
+        @submission.orders.first.update(template_name: 'Some other template')
+
+        get :download_scrna_core_cdna_pooling_plan, params: { id: @submission.id }
+
+        expect(flash[:error]).to eq(
+          'This submission does not have the correct template for downloading a scRNA Core cDNA pooling plan'
+        )
+        expect(response).to redirect_to(submission_path(@submission))
+      end
     end
   end
 
diff --git a/spec/models/submission_spec.rb b/spec/models/submission_spec.rb
index 844f660113..53dfad4d86 100644
--- a/spec/models/submission_spec.rb
+++ b/spec/models/submission_spec.rb
@@ -132,4 +132,24 @@
       expect(submission.used_tags).to eq([[tag_a.oligo, tag2_a.oligo], [tag_b.oligo, tag2_b.oligo]])
     end
   end
+
+  describe '#scrna_core_cdna_prep_gem_x_5p_submission?' do
+    let(:submission) { build(:submission, orders: [order]) }
+
+    context 'when the submission has an order with the Limber-Htp - scRNA Core cDNA Prep GEM-X 5p template' do
+      let(:order) { build(:order, template_name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p') }
+
+      it 'returns true' do
+        expect(submission.scrna_core_cdna_prep_gem_x_5p_submission?).to be true
+      end
+    end
+
+    context 'when the submission does not have an order with the Limber-Htp - scRNA Core cDNA Prep GEM-X 5p template' do
+      let(:order) { build(:order, template_name: 'Some other template') }
+
+      it 'returns false' do
+        expect(submission.scrna_core_cdna_prep_gem_x_5p_submission?).to be false
+      end
+    end
+  end
 end

From 0f8b90a49d830062861f6217991a761e66b3234a Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Mon, 9 Feb 2026 15:03:18 +0000
Subject: [PATCH 13/57] feat(submission): correct scrna core pooling plan pool
 distribution logic

---
 app/controllers/submissions_controller.rb | 26 +++++++++++++++--------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 274e268333..99f1450a15 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -5,7 +5,7 @@
 # such as the fields that get displayed when a submission template is selected, and
 # the creation of each independent order.
 # Most the actual heavy lifting occurs in {Submission::SubmissionCreator}
-class SubmissionsController < ApplicationController
+class SubmissionsController < ApplicationController # rubocop:disable Metrics/ClassLength
   # WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behviour.
   # It should be removed wherever possible and the correct Strong  Parameter options applied in its place.
   before_action :evil_parameter_hack!
@@ -115,7 +115,7 @@ def study
     @submissions = @study.submissions
   end
 
-  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
+  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
     begin
       submission = Submission.find(params[:id])
     rescue ActiveRecord::RecordNotFound
@@ -131,21 +131,29 @@ def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metr
       return
     end
 
-    # Group requests by study/project/donor
+    # Group requests by study/project
     grouped_labware = submission.requests.group_by do |request|
       aliquot = request.asset.aliquots.first
       study = aliquot.study.name
       project = aliquot&.project&.name
-      donor_id = aliquot.sample.sample_metadata.donor_id
-      "#{study} / #{project} / #{donor_id}"
+      "#{study} / #{project}"
     end
 
     csv_string = CSV.generate(row_sep: "\r\n") do |csv|
-      csv << ['Study / Project / Donor ID', 'Pools (num samples)', 'Cells per chip well']
-      grouped_labware.each do |study_project_donor, subgroup|
-        number_of_samples_in_pool, = subgroup.size.divmod(subgroup.first.request_metadata.number_of_pools)
+      csv << ['Study / Project', 'Pools (num samples)', 'Cells per chip well']
+      # It would be nice to refactor the scRNA Validator logic here to pull out the pooling plan logic
+      grouped_labware.each do |study_project, subgroup|
+        number_of_pools = subgroup.first.request_metadata.number_of_pools
+        number_of_samples_in_pool, remainder = subgroup.size.divmod(number_of_pools)
+        samples_in_pool_string = ''
+        (1..number_of_pools).each do |_|
+          samples_in_pool_string += "#{number_of_samples_in_pool}, "
+        end
+        samples_in_pool_string += remainder.positive? ? remainder.to_s : ''
+
         cells_per_chip_well = subgroup.first.request_metadata.cells_per_chip_well
-        csv << [study_project_donor, number_of_samples_in_pool, cells_per_chip_well]
+
+        csv << [study_project, number_of_samples_in_pool, cells_per_chip_well]
       end
     end
 

From e81cf1e7b280a2ef945a89b589c200bee3d4dfaa Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Mon, 9 Feb 2026 15:17:51 +0000
Subject: [PATCH 14/57] refactor: clean up pool allocation logic

---
 app/controllers/submissions_controller.rb | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 99f1450a15..02068768ef 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -115,7 +115,7 @@ def study
     @submissions = @study.submissions
   end
 
-  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
+  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
     begin
       submission = Submission.find(params[:id])
     rescue ActiveRecord::RecordNotFound
@@ -143,13 +143,18 @@ def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metr
       csv << ['Study / Project', 'Pools (num samples)', 'Cells per chip well']
       # It would be nice to refactor the scRNA Validator logic here to pull out the pooling plan logic
       grouped_labware.each do |study_project, subgroup|
+        # Get number_of_pools requested from the submission
         number_of_pools = subgroup.first.request_metadata.number_of_pools
-        number_of_samples_in_pool, remainder = subgroup.size.divmod(number_of_pools)
-        samples_in_pool_string = ''
-        (1..number_of_pools).each do |_|
-          samples_in_pool_string += "#{number_of_samples_in_pool}, "
-        end
-        samples_in_pool_string += remainder.positive? ? remainder.to_s : ''
+        # Ideal pool size is just the number of samples divided by the number of pools, but we need to account for
+        # any remainder if the division isn't exact
+        ideal_pool_size, remainder = subgroup.size.divmod(number_of_pools)
+        # Build the pools
+        pool_sizes = Array.new(number_of_pools, ideal_pool_size)
+        # Add the remainders
+        remainder.times { |i| pool_sizes[i] += 1 }
+
+        # Join the pool sizes into a string for the CSV output
+        number_of_samples_in_pool = pool_sizes.join(', ')
 
         cells_per_chip_well = subgroup.first.request_metadata.cells_per_chip_well
 

From bc60325c0d2028bc35557928654c88cc367e2330 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Tue, 10 Feb 2026 11:32:02 +0000
Subject: [PATCH 15/57] feat(submission): moves scrna core pooling plan csv
 file generation to separate module

---
 app/controllers/submissions_controller.rb     | 34 +---------
 ...a_core_cdna_prep_pooling_plan_generator.rb | 54 +++++++++++++++
 ...e_cdna_prep_pooling_plan_generator_spec.rb | 66 +++++++++++++++++++
 3 files changed, 123 insertions(+), 31 deletions(-)
 create mode 100644 app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
 create mode 100644 spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 02068768ef..ea1fe6290b 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -5,7 +5,7 @@
 # such as the fields that get displayed when a submission template is selected, and
 # the creation of each independent order.
 # Most the actual heavy lifting occurs in {Submission::SubmissionCreator}
-class SubmissionsController < ApplicationController # rubocop:disable Metrics/ClassLength
+class SubmissionsController < ApplicationController
   # WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behviour.
   # It should be removed wherever possible and the correct Strong  Parameter options applied in its place.
   before_action :evil_parameter_hack!
@@ -131,36 +131,8 @@ def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metr
       return
     end
 
-    # Group requests by study/project
-    grouped_labware = submission.requests.group_by do |request|
-      aliquot = request.asset.aliquots.first
-      study = aliquot.study.name
-      project = aliquot&.project&.name
-      "#{study} / #{project}"
-    end
-
-    csv_string = CSV.generate(row_sep: "\r\n") do |csv|
-      csv << ['Study / Project', 'Pools (num samples)', 'Cells per chip well']
-      # It would be nice to refactor the scRNA Validator logic here to pull out the pooling plan logic
-      grouped_labware.each do |study_project, subgroup|
-        # Get number_of_pools requested from the submission
-        number_of_pools = subgroup.first.request_metadata.number_of_pools
-        # Ideal pool size is just the number of samples divided by the number of pools, but we need to account for
-        # any remainder if the division isn't exact
-        ideal_pool_size, remainder = subgroup.size.divmod(number_of_pools)
-        # Build the pools
-        pool_sizes = Array.new(number_of_pools, ideal_pool_size)
-        # Add the remainders
-        remainder.times { |i| pool_sizes[i] += 1 }
-
-        # Join the pool sizes into a string for the CSV output
-        number_of_samples_in_pool = pool_sizes.join(', ')
-
-        cells_per_chip_well = subgroup.first.request_metadata.cells_per_chip_well
-
-        csv << [study_project, number_of_samples_in_pool, cells_per_chip_well]
-      end
-    end
+    # Generate the pooling plan CSV string using the ScrnaCoreCdnaPrepPoolingPlanGenerator module
+    csv_string = Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator.generate_pooling_plan(submission)
 
     send_data csv_string, type: 'text/plain', filename: "#{params[:id]}_scrna_core_cdna_pooling_plan.csv",
                           disposition: 'attachment'
diff --git a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
new file mode 100644
index 0000000000..8f5365fda8
--- /dev/null
+++ b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
@@ -0,0 +1,54 @@
+# frozen_string_literal: true
+#
+# This module provides a basic pooling plan generator for scRNA core cDNA prep submissions.
+# It generates a CSV string which outlines the pooling strategy for their samples
+# based on the number of pools and cells per chip well specified in their submission.
+# The pooling plan is generated based on the labware associated with the submission, grouped by study and project.
+# The logic for determining the pool layout is aimed to be a mirror of the pooling logic
+# used in Limber, specifically in the DonorPoolingCalculator's allocate_wells_to_pools method.
+#
+# This module also assumes the submission has already been validated with the scrna_core_cdna_prep validators
+# to ensure donor clashes and pooling parameters are already checked.
+module Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator
+  # This logic attemps to mirror Limber's pooling logic
+  # See Limber LabwareCreators::DonorPoolingCalculator (allocate_wells_to_pools)
+  def self.generate_pooling_plan(submission)
+    CSV.generate(row_sep: "\r\n") do |csv|
+      csv << ['Study / Project', 'Pools (num samples)', 'Cells per chip well']
+      # It would be nice to refactor the scRNA Validator logic here to pull out the pooling plan logic
+      grouped_labware(submission).each do |study_project, subgroup|
+        # Get number_of_pools and cells_per_chip_well requested from the submission
+        number_of_pools = subgroup.first.request_metadata.number_of_pools
+        cells_per_chip_well = subgroup.first.request_metadata.cells_per_chip_well
+        # Build the pools
+        pools_layout = calculate_pools_layout(subgroup.size, number_of_pools)
+
+        # Join the pool sizes into a string for the CSV output
+        number_of_samples_in_pool = pools_layout.join(', ')
+
+        csv << [study_project, number_of_samples_in_pool, cells_per_chip_well]
+      end
+    end
+  end
+
+  # This method calculates the layout of pools based on the total number of samples and the number of pools requested.
+  # It divides the samples as evenly as possible across the pools, and evenly distributes any remainder samples
+  def self.calculate_pools_layout(number_of_samples, number_of_pools)
+    # Ideal pool size is just the number of samples divided by the number of pools, but we need to account for
+    # any remainder if the division isn't exact
+    ideal_pool_size, remainder = number_of_samples.divmod(number_of_pools)
+    pools_layout = Array.new(number_of_pools, ideal_pool_size)
+    remainder.times { |i| pools_layout[i] += 1 }
+    pools_layout
+  end
+
+  # Groups the labware associated with a submission by study and project.
+  def self.grouped_labware(submission)
+    submission.requests.group_by do |request|
+      aliquot = request.asset.aliquots.first
+      study = aliquot.study.name
+      project = aliquot&.project&.name
+      "#{study} / #{project}"
+    end
+  end
+end
diff --git a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
new file mode 100644
index 0000000000..8ffb9258e0
--- /dev/null
+++ b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
@@ -0,0 +1,66 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+# NB. Search for 'scRNA Core Pooling Developer Documentation' page in Confluence (public)
+# for a more verbose explanation of the logic tested here.
+RSpec.describe Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator do
+  describe '.calculate_pools_layout' do
+    it 'evenly divides samples into pools when there is no remainder' do
+      expect(described_class.calculate_pools_layout(12, 3)).to eq([4, 4, 4])
+    end
+
+    it 'distributes remainder samples across pools' do
+      expect(described_class.calculate_pools_layout(14, 3)).to eq([5, 5, 4])
+    end
+  end
+
+  describe '.grouped_labware' do
+    let(:study) { create(:study) }
+    let(:project) { create(:project) }
+    let(:template) { create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p') }
+    let(:library_request_type) { create(:library_request_type) }
+
+    it 'groups labware by study and project' do # rubocop:disable RSpec/ExampleLength,RSpec/MultipleExpectations
+      # Build the submission with the correct template and study/project associations
+      submission_order = create(:order_with_submission, template_name: template.name, study: study,
+                                                        project: project,
+                                                        asset_group: create(:asset_group, study:))
+      submission = submission_order.submission
+
+      # Add sample tubes and requests to the submission
+      sample_tubes = create_list(:sample_tube, 2, study:, project:)
+      # Add sample tubes with the same study but different project to ensure grouping is correct
+      project2 = create(:project)
+      sample_tubes << create_list(:sample_tube, 2, study: study, project: project2)
+      # Add sample tubes with the same project but different study to ensure grouping is correct
+      study2 = create(:study)
+      sample_tubes << create_list(:sample_tube, 3, study: study2, project: project)
+
+      # Create library requests for each sample tube in the submission
+      sample_tubes.flatten.each do |tube|
+        create(:library_request, asset: tube.receptacle, submission: submission,
+                                 request_type: library_request_type)
+      end
+
+      grouped = described_class.grouped_labware(submission)
+
+      expected_groups = {
+        "#{study.name} / #{project.name}" => 2,
+        "#{study.name} / #{project2.name}" => 2,
+        "#{study2.name} / #{project.name}" => 3
+      }
+
+      expect(grouped.keys).to match_array(expected_groups.keys)
+      expected_groups.each do |group, count|
+        expect(grouped[group].size).to eq(count)
+      end
+    end
+  end
+
+  describe '.generate_pooling_plan', skip: 'todo' do
+    it 'generates a CSV string with the correct headers and pooling plan' do
+      # Add test to check csv contents
+    end
+  end
+end

From b6df3bd0c0dfe1607a55d6c79a55f3c0fe3a7f18 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Wed, 11 Feb 2026 08:59:12 +0000
Subject: [PATCH 16/57] tests: adds generate_pooling_plan tests for
 ScrnaCoreCdnaPrepPoolingPlanGenerator

---
 ...a_core_cdna_prep_pooling_plan_generator.rb |  5 +-
 ...e_cdna_prep_pooling_plan_generator_spec.rb | 95 +++++++++++++++----
 2 files changed, 77 insertions(+), 23 deletions(-)

diff --git a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
index 8f5365fda8..6ea847a586 100644
--- a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
+++ b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
@@ -1,9 +1,8 @@
 # frozen_string_literal: true
 #
 # This module provides a basic pooling plan generator for scRNA core cDNA prep submissions.
-# It generates a CSV string which outlines the pooling strategy for their samples
-# based on the number of pools and cells per chip well specified in their submission.
-# The pooling plan is generated based on the labware associated with the submission, grouped by study and project.
+# It generates a CSV string which outlines the pooling strategy for the submitted samples
+# based on the number of pools and cells per chip well specified in the submission and grouped by study and project.
 # The logic for determining the pool layout is aimed to be a mirror of the pooling logic
 # used in Limber, specifically in the DonorPoolingCalculator's allocate_wells_to_pools method.
 #
diff --git a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
index 8ffb9258e0..fee253819b 100644
--- a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
+++ b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
@@ -5,6 +5,78 @@
 # NB. Search for 'scRNA Core Pooling Developer Documentation' page in Confluence (public)
 # for a more verbose explanation of the logic tested here.
 RSpec.describe Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator do
+  let(:study) { create(:study) }
+  let(:project) { create(:project) }
+  let(:template) { create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p') }
+  let(:submission) do
+    submission_order = create(:order_with_submission, template_name: template.name, study: study,
+                                                      project: project,
+                                                      asset_group: create(:asset_group, study:))
+    submission_order.submission
+  end
+
+  describe '.generate_pooling_plan' do
+    it 'generates a CSV string with the correct headers' do
+      # A basic submission is fine for testing the headers
+      submission = create(:submission)
+      csv_string = described_class.generate_pooling_plan(submission)
+      csv = CSV.parse(csv_string, headers: true)
+
+      expect(csv.headers).to eq(['Study / Project', 'Pools (num samples)', 'Cells per chip well'])
+    end
+
+    it 'generates a CSV string with the correct pooling plan based on the submission requests' do # rubocop:disable RSpec/MultipleExpectations, RSpec/ExampleLength
+      # Add sample tubes and requests to the submission
+      sample_tubes = create_list(:sample_tube, 5, study:, project:)
+      sample_tubes.each do |tube|
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission,
+                                  request_metadata_attributes: { number_of_pools: 3, cells_per_chip_well: 100 })
+      end
+
+      csv_string = described_class.generate_pooling_plan(submission)
+      csv = CSV.parse(csv_string, headers: true)
+
+      expect(csv.length).to eq(1) # We have one study/project group
+      expect(csv[0]['Study / Project']).to eq("#{study.name} / #{project.name}")
+      expect(csv[0]['Pools (num samples)']).to eq('2, 2, 1') # With 5 samples and 3 pools, we expect a layout of 2, 2, 1
+      expect(csv[0]['Cells per chip well']).to eq('100') # We set this in the request metadata for each request
+    end
+
+    it 'handles multiple study/project groups correctly' do # rubocop:disable RSpec/ExampleLength, RSpec/MultipleExpectations
+      # Add sample tubes and requests for two different study/project groups
+      project2 = create(:project)
+      study2 = create(:study)
+      sample_tubes_group1 = create_list(:sample_tube, 4, study:, project:)
+      sample_tubes_group2 = create_list(:sample_tube, 8, study: study2, project: project2)
+
+      sample_tubes_group1.each do |tube|
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission,
+                                  request_metadata_attributes: { number_of_pools: 2, cells_per_chip_well: 50 })
+      end
+
+      sample_tubes_group2.each do |tube|
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission,
+                                  request_metadata_attributes: { number_of_pools: 3, cells_per_chip_well: 150 })
+      end
+
+      csv_string = described_class.generate_pooling_plan(submission)
+      csv = CSV.parse(csv_string, headers: true)
+
+      expect(csv.length).to eq(2) # We have two study/project groups
+
+      group1 = csv.find { |row| row['Study / Project'] == "#{study.name} / #{project.name}" }
+      expect(group1['Pools (num samples)']).to eq('2, 2') # With 4 samples and 2 pools, we expect a layout of 2, 2
+      expect(group1['Cells per chip well']).to eq('50')
+
+      group2 = csv.find { |row| row['Study / Project'] == "#{study2.name} / #{project2.name}" }
+      expect(group2['Pools (num samples)']).to eq('3, 3, 2') # With 8 samples and 3 pools, we expect a layout of 3, 3, 2
+      expect(group2['Cells per chip well']).to eq('150')
+    end
+  end
+
   describe '.calculate_pools_layout' do
     it 'evenly divides samples into pools when there is no remainder' do
       expect(described_class.calculate_pools_layout(12, 3)).to eq([4, 4, 4])
@@ -16,18 +88,7 @@
   end
 
   describe '.grouped_labware' do
-    let(:study) { create(:study) }
-    let(:project) { create(:project) }
-    let(:template) { create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p') }
-    let(:library_request_type) { create(:library_request_type) }
-
     it 'groups labware by study and project' do # rubocop:disable RSpec/ExampleLength,RSpec/MultipleExpectations
-      # Build the submission with the correct template and study/project associations
-      submission_order = create(:order_with_submission, template_name: template.name, study: study,
-                                                        project: project,
-                                                        asset_group: create(:asset_group, study:))
-      submission = submission_order.submission
-
       # Add sample tubes and requests to the submission
       sample_tubes = create_list(:sample_tube, 2, study:, project:)
       # Add sample tubes with the same study but different project to ensure grouping is correct
@@ -37,10 +98,10 @@
       study2 = create(:study)
       sample_tubes << create_list(:sample_tube, 3, study: study2, project: project)
 
-      # Create library requests for each sample tube in the submission
+      # Create customer requests for each sample tube in the submission
       sample_tubes.flatten.each do |tube|
-        create(:library_request, asset: tube.receptacle, submission: submission,
-                                 request_type: library_request_type)
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission)
       end
 
       grouped = described_class.grouped_labware(submission)
@@ -57,10 +118,4 @@
       end
     end
   end
-
-  describe '.generate_pooling_plan', skip: 'todo' do
-    it 'generates a CSV string with the correct headers and pooling plan' do
-      # Add test to check csv contents
-    end
-  end
 end

From f0e3bad318e3737b3c170dd57a85e04bbab0ca43 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Wed, 11 Feb 2026 10:09:26 +0000
Subject: [PATCH 17/57] fix: changes ScrnaCoreCdnaPrepPoolingPlanGenerator to
 group submission data by request study/project instead of asset aliquot

---
 ...a_core_cdna_prep_pooling_plan_generator.rb | 11 +++---
 ...e_cdna_prep_pooling_plan_generator_spec.rb | 37 +++++++++++--------
 2 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
index 6ea847a586..0e15f3fc83 100644
--- a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
+++ b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
@@ -15,7 +15,7 @@ def self.generate_pooling_plan(submission)
     CSV.generate(row_sep: "\r\n") do |csv|
       csv << ['Study / Project', 'Pools (num samples)', 'Cells per chip well']
       # It would be nice to refactor the scRNA Validator logic here to pull out the pooling plan logic
-      grouped_labware(submission).each do |study_project, subgroup|
+      grouped_requests(submission).each do |study_project, subgroup|
         # Get number_of_pools and cells_per_chip_well requested from the submission
         number_of_pools = subgroup.first.request_metadata.number_of_pools
         cells_per_chip_well = subgroup.first.request_metadata.cells_per_chip_well
@@ -41,12 +41,11 @@ def self.calculate_pools_layout(number_of_samples, number_of_pools)
     pools_layout
   end
 
-  # Groups the labware associated with a submission by study and project.
-  def self.grouped_labware(submission)
+  # Groups the requests associated with a submission by study and project.
+  def self.grouped_requests(submission)
     submission.requests.group_by do |request|
-      aliquot = request.asset.aliquots.first
-      study = aliquot.study.name
-      project = aliquot&.project&.name
+      study = request.initial_study.name
+      project = request.initial_project.name
       "#{study} / #{project}"
     end
   end
diff --git a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
index fee253819b..607ba84f19 100644
--- a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
+++ b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
@@ -27,10 +27,10 @@
 
     it 'generates a CSV string with the correct pooling plan based on the submission requests' do # rubocop:disable RSpec/MultipleExpectations, RSpec/ExampleLength
       # Add sample tubes and requests to the submission
-      sample_tubes = create_list(:sample_tube, 5, study:, project:)
-      sample_tubes.each do |tube|
+      create_list(:sample_tube, 5, study:, project:).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
                                   submission: submission,
+                                  initial_study: study, initial_project: project,
                                   request_metadata_attributes: { number_of_pools: 3, cells_per_chip_well: 100 })
       end
 
@@ -47,18 +47,18 @@
       # Add sample tubes and requests for two different study/project groups
       project2 = create(:project)
       study2 = create(:study)
-      sample_tubes_group1 = create_list(:sample_tube, 4, study:, project:)
-      sample_tubes_group2 = create_list(:sample_tube, 8, study: study2, project: project2)
 
-      sample_tubes_group1.each do |tube|
+      create_list(:sample_tube, 4, study:, project:).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
                                   submission: submission,
+                                  initial_study: study, initial_project: project,
                                   request_metadata_attributes: { number_of_pools: 2, cells_per_chip_well: 50 })
       end
 
-      sample_tubes_group2.each do |tube|
+      create_list(:sample_tube, 8, study: study2, project: project2).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
                                   submission: submission,
+                                  initial_study: study2, initial_project: project2,
                                   request_metadata_attributes: { number_of_pools: 3, cells_per_chip_well: 150 })
       end
 
@@ -87,24 +87,29 @@
     end
   end
 
-  describe '.grouped_labware' do
-    it 'groups labware by study and project' do # rubocop:disable RSpec/ExampleLength,RSpec/MultipleExpectations
+  describe '.grouped_requests' do
+    it 'groups requests by study and project' do # rubocop:disable RSpec/ExampleLength,RSpec/MultipleExpectations
       # Add sample tubes and requests to the submission
-      sample_tubes = create_list(:sample_tube, 2, study:, project:)
+      create_list(:sample_tube, 2, study:, project:).each do |tube|
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission, initial_study: study, initial_project: project)
+      end
+
       # Add sample tubes with the same study but different project to ensure grouping is correct
       project2 = create(:project)
-      sample_tubes << create_list(:sample_tube, 2, study: study, project: project2)
+      create_list(:sample_tube, 2, study: study, project: project2).each do |tube|
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission, initial_study: study, initial_project: project2)
+      end
+
       # Add sample tubes with the same project but different study to ensure grouping is correct
       study2 = create(:study)
-      sample_tubes << create_list(:sample_tube, 3, study: study2, project: project)
-
-      # Create customer requests for each sample tube in the submission
-      sample_tubes.flatten.each do |tube|
+      create_list(:sample_tube, 3, study: study2, project: project).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
-                                  submission: submission)
+                                  submission: submission, initial_study: study2, initial_project: project)
       end
 
-      grouped = described_class.grouped_labware(submission)
+      grouped = described_class.grouped_requests(submission)
 
       expected_groups = {
         "#{study.name} / #{project.name}" => 2,

From fc5e0a61d93a8a073e1dbbeafc8955aaa7795164 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Wed, 11 Feb 2026 15:58:38 +0000
Subject: [PATCH 18/57] fix: adds asset uniqueness logic to
 ScrnaCoreCdnaPrepPoolingPlanGenerator grouped_requests

---
 ...a_core_cdna_prep_pooling_plan_generator.rb |  4 ++-
 ...e_cdna_prep_pooling_plan_generator_spec.rb | 31 +++++++++++++++++--
 2 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
index 0e15f3fc83..98491c1ae5 100644
--- a/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
+++ b/app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb
@@ -43,7 +43,9 @@ def self.calculate_pools_layout(number_of_samples, number_of_pools)
 
   # Groups the requests associated with a submission by study and project.
   def self.grouped_requests(submission)
-    submission.requests.group_by do |request|
+    # Unique by asset to avoid counting the same sample tube multiple times if it appears in multiple requests
+    # e.g. if a sample tube is requested in two different lanes, we only want to count it once for pooling plan purposes
+    submission.requests.uniq(&:asset).group_by do |request|
       study = request.initial_study.name
       project = request.initial_project.name
       "#{study} / #{project}"
diff --git a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
index 607ba84f19..fc3a25b0c2 100644
--- a/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
+++ b/spec/models/submission/scrna_core_cdna_prep_pooling_plan_generator_spec.rb
@@ -92,21 +92,24 @@
       # Add sample tubes and requests to the submission
       create_list(:sample_tube, 2, study:, project:).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
-                                  submission: submission, initial_study: study, initial_project: project)
+                                  submission: submission, initial_study: study, initial_project: project,
+                                  request_metadata_attributes: { number_of_pools: 1, cells_per_chip_well: 150 })
       end
 
       # Add sample tubes with the same study but different project to ensure grouping is correct
       project2 = create(:project)
       create_list(:sample_tube, 2, study: study, project: project2).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
-                                  submission: submission, initial_study: study, initial_project: project2)
+                                  submission: submission, initial_study: study, initial_project: project2,
+                                  request_metadata_attributes: { number_of_pools: 1, cells_per_chip_well: 150 })
       end
 
       # Add sample tubes with the same project but different study to ensure grouping is correct
       study2 = create(:study)
       create_list(:sample_tube, 3, study: study2, project: project).each do |tube|
         create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
-                                  submission: submission, initial_study: study2, initial_project: project)
+                                  submission: submission, initial_study: study2, initial_project: project,
+                                  request_metadata_attributes: { number_of_pools: 1, cells_per_chip_well: 150 })
       end
 
       grouped = described_class.grouped_requests(submission)
@@ -122,5 +125,27 @@
         expect(grouped[group].size).to eq(count)
       end
     end
+
+    it 'counts each sample tube only once even if it appears in multiple requests' do # rubocop:disable RSpec/ExampleLength,RSpec/MultipleExpectations
+      # Create a sample tube
+      tube = create(:sample_tube, study:, project:)
+      # Create multiple requests for the same tube
+      create_list(:customer_request, 3, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                        submission: submission, initial_study: study, initial_project: project,
+                                        request_metadata_attributes: { number_of_pools: 1, cells_per_chip_well: 150 })
+
+      # Create some other requests for different tubes to ensure the grouping logic is still correct
+      create_list(:sample_tube, 2, study:, project:).each do |tube|
+        create(:customer_request, sti_type: 'PbmcPoolingCustomerRequest', asset: tube.receptacle,
+                                  submission: submission, initial_study: study, initial_project: project,
+                                  request_metadata_attributes: { number_of_pools: 1, cells_per_chip_well: 150 })
+      end
+
+      grouped = described_class.grouped_requests(submission)
+
+      expect(grouped.keys).to eq(["#{study.name} / #{project.name}"])
+      # 3 as we only have 3 requests with uniq assets.
+      expect(grouped["#{study.name} / #{project.name}"].size).to eq(3)
+    end
   end
 end

From 587e9ebb933195aac76efda8df918efb8fda8701 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Thu, 12 Feb 2026 13:55:26 +0000
Subject: [PATCH 19/57] fix: fixes multiplexed_library_tube throwing errors if
 no creation_requests exist

---
 app/models/multiplexed_library_tube.rb            | 6 ++++--
 spec/models/broadcast_event/pool_released_spec.rb | 9 +++++++++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/app/models/multiplexed_library_tube.rb b/app/models/multiplexed_library_tube.rb
index 9d5453273b..8c8d3ca9d6 100644
--- a/app/models/multiplexed_library_tube.rb
+++ b/app/models/multiplexed_library_tube.rb
@@ -18,7 +18,7 @@ def asset_type_for_request_types
   end
 
   def team
-    creation_requests.first&.product_line
+    creation_requests&.first&.product_line
   end
 
   def role
@@ -41,6 +41,8 @@ def creation_requests
     direct = requests_as_target.where_is_a(Request::LibraryCreation)
     return direct unless direct.empty?
 
-    parents.includes(:requests_as_target).first.requests_as_target
+    # Parents should exist but in the case they don't (e.g. asset_links are yet to be created)
+    # we want to avoid an error and just return an empty array.
+    parents.includes(:requests_as_target).first&.requests_as_target
   end
 end
diff --git a/spec/models/broadcast_event/pool_released_spec.rb b/spec/models/broadcast_event/pool_released_spec.rb
index 579c69db25..9b8e3a71cb 100644
--- a/spec/models/broadcast_event/pool_released_spec.rb
+++ b/spec/models/broadcast_event/pool_released_spec.rb
@@ -112,5 +112,14 @@
       expect(metadata['team']).not_to be_nil
       expect(metadata['team']).not_to eq('UNKNOWN')
     end
+
+    # This is an edge case, but we want to make sure that if there are no creation requests or ancestors
+    # we don't error out and instead return 'UNKNOWN' for the team.
+    it 'has an unknown team if tube has no creation requests' do
+      tube.ancestors = []
+      tube.save!
+
+      expect(metadata['team']).to eq('UNKNOWN')
+    end
   end
 end

From 9ac5b1504ba8c1cbce729395bd937fcd001c1e31 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 12 Feb 2026 21:39:24 +0000
Subject: [PATCH 20/57] save working version

---
 ...st_upload_with_tag_sequences_controller.rb |  8 ++++
 .../sample_manifest_excel/upload/row.rb       | 47 +++++--------------
 .../new.html.erb                              | 10 ++++
 config/sample_manifest_excel/columns.yml      | 12 ++---
 .../conditional_formattings.yml               |  2 +-
 5 files changed, 38 insertions(+), 41 deletions(-)

diff --git a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
index dfa17a794c..5ac1fad099 100644
--- a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
+++ b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
@@ -10,6 +10,12 @@ def create
     return error('No file attached') if params[:upload].blank?
 
     if upload_manifest
+      @rows_with_warnings =
+         @uploader.upload.rows.select { |row| row.respond_to?(:warnings) && row.warnings.any? }
+      
+      flash[:warnings] =
+         @rows_with_warnings.flat_map { |row| row.warnings.full_messages }
+
       success('Sample manifest successfully uploaded.')
     else
       error('Your sample manifest couldn\'t be uploaded.')
@@ -25,12 +31,14 @@ def create_uploader
   def upload_manifest
     @uploader = create_uploader
     @uploader.run!
+    # @rows_with_warnings = @uploader.upload.rows.select { |row| row.warnings.any? }
   end
 
   def success(message)
     flash[:notice] = message
     redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
 
+    # render :new
     redirect_to redirect_target
   end
 
diff --git a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
index 34aa49c03b..8ff9a4d900 100644
--- a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
+++ b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
@@ -15,6 +15,17 @@ class Row # rubocop:todo Metrics/ClassLength
 
       attr_accessor :number, :data, :columns, :cache
       attr_reader :sanger_sample_id
+      # attr_reader :warnings
+
+      # def initialize(attributes = {})
+      #   super
+      #   @warnings = ActiveModel::Errors.new(self)
+      # end
+
+      # @return [ActiveModel::Errors] the warnings collection
+      def warnings
+        @warnings ||= ActiveModel::Errors.new(self)
+      end
 
       validates :number, presence: true, numericality: true
       validate :sanger_sample_id_exists?, if: :sanger_sample_id
@@ -27,7 +38,7 @@ class Row # rubocop:todo Metrics/ClassLength
       def i7_present
         return unless columns.present? && data.present? && columns.names.include?('i7') && value('i7').blank?
 
-        errors.add(:base, "#{row_title} i7 can't be blank")
+        warnings.add(:base, "#{row_title} i7 is blank! ")
       end
 
       validate :i5_present
@@ -35,39 +46,7 @@ def i7_present
       def i5_present
         return unless columns.present? && data.present? && columns.names.include?('i5') && value('i5').blank?
 
-        errors.add(:base, "#{row_title} i5 can't be blank, putting “n/a” in i5 if only needs one set of tags")
-      end
-
-      validate :chromium_tag_group
-      # Ensure chromium_tag_group column is not blank if it exists in the manifest
-      def chromium_tag_group
-        return unless columns.present? && data.present? && columns.names.include?('chromium_tag_group') && value('chromium_tag_group').blank?
-
-        errors.add(:base, "#{row_title} chromium_tag_group can't be blank")
-      end
-
-      validate :chromium_tag_well
-      # Ensure chromium_tag_well column is not blank if it exists in the manifest
-      def chromium_tag_well
-        return unless columns.present? && data.present? && columns.names.include?('chromium_tag_well') && value('chromium_tag_well').blank?
-
-        errors.add(:base, "#{row_title} chromium_tag_well can't be blank")
-      end
-
-      validate :dual_index_tag_set
-      # Ensure dual_index_tag_set column is not blank if it exists in the manifest
-      def dual_index_tag_set
-        return unless columns.present? && data.present? && columns.names.include?('dual_index_tag_set') && value('dual_index_tag_set').blank?
-
-        errors.add(:base, "#{row_title} dual_index_tag_set can't be blank")
-      end
-
-      validate :dual_index_tag_well
-      # Ensure dual_index_tag_well column is not blank if it exists in the manifest
-      def dual_index_tag_well
-        return unless columns.present? && data.present? && columns.names.include?('dual_index_tag_well') && value('dual_index_tag_well').blank?
-
-        errors.add(:base, "#{row_title} dual_index_tag_well can't be blank")
+        warnings.add(:base, "#{row_title} i5 is blank! ")
       end
 
       delegate :present?, to: :sample, prefix: true
diff --git a/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb b/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
index 92d1e8d7de..f56463ecd9 100644
--- a/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
+++ b/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
@@ -8,6 +8,16 @@
     <% @uploader.errors.full_messages.each do |message| %>
       <p><%= message %></p>
     <% end %>
+
+   <% if flash[:warnings].present? %>
+      <%= alert(:warning) do %>
+        <% flash[:warnings].each do |message| %>
+          <p><%= message %></p>
+        <% end %>
+      <% end %>
+    <% end %>
+
+
   <% end %>
 <% end %>
 
diff --git a/config/sample_manifest_excel/columns.yml b/config/sample_manifest_excel/columns.yml
index 9096fd1dca..3245f2d206 100644
--- a/config/sample_manifest_excel/columns.yml
+++ b/config/sample_manifest_excel/columns.yml
@@ -44,7 +44,7 @@ i7:
       errorTitle: "i7"
       error: "i7 cannot be blank"
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_warning_cell:
 i5:
   heading: i5 TAG SEQUENCE
   unlocked: true
@@ -63,7 +63,7 @@ i5:
       promptTitle: "i5"
       prompt: "Input i5."
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_warning_cell:
 tag_group:
   heading: TAG GROUP
   unlocked: true
@@ -147,7 +147,7 @@ chromium_tag_group:
       prompt: "Input the name of a valid tag set. All samples in a library need to be tagged with the same tag set."
     range_name: :chromium_tag_groups
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
 chromium_tag_well:
   heading: CHROMIUM TAG WELL
   unlocked: true
@@ -165,7 +165,7 @@ chromium_tag_well:
       errorTitle: "Tag well"
       error: "Tag Index must be a well."
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
     is_number:
     len:
       formula:
@@ -245,7 +245,7 @@ dual_index_tag_set:
       prompt: "Input the name of a valid dual index tag plate."
     range_name: :dual_index_tag_sets
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
 dual_index_tag_well:
   heading: DUAL INDEX TAG WELL
   unlocked: true
@@ -263,7 +263,7 @@ dual_index_tag_well:
       errorTitle: "Dual index tag well"
       error: "Dual Index Tag must be a well."
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
     is_number:
     len:
       formula:
diff --git a/config/sample_manifest_excel/conditional_formattings.yml b/config/sample_manifest_excel/conditional_formattings.yml
index 5dc77ad9d6..a633439a3c 100644
--- a/config/sample_manifest_excel/conditional_formattings.yml
+++ b/config/sample_manifest_excel/conditional_formattings.yml
@@ -16,7 +16,7 @@ empty_mandatory_cell:
     formula: "FALSE"
     operator: :equal
     priority: 1
-empty_mandatory_cell_2:
+empty_warning_cell:
   style:
     bg_color: "FF991C"
     type: :dxf

From 42b8ad1688fa2aa39aa1578c9d5be0318bf1b9d4 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Fri, 13 Feb 2026 14:13:43 +0000
Subject: [PATCH 21/57] refactor: removes cnda term from scrna core pooling
 plan to avoid confusion

---
 app/controllers/submissions_controller.rb         |  6 +++---
 app/models/ability/base_user.rb                   |  2 +-
 app/views/submissions/show.html.erb               |  2 +-
 config/routes.rb                                  |  2 +-
 spec/controllers/submissions_controller_spec.rb   | 12 ++++++------
 spec/features/submissions/submission_show_spec.rb |  8 ++++----
 6 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index ea1fe6290b..818ec1d08b 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -115,7 +115,7 @@ def study
     @submissions = @study.submissions
   end
 
-  def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
+  def download_scrna_core_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
     begin
       submission = Submission.find(params[:id])
     rescue ActiveRecord::RecordNotFound
@@ -126,7 +126,7 @@ def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metr
 
     unless submission.scrna_core_cdna_prep_gem_x_5p_submission?
       flash[:error] =
-        'This submission does not have the correct template for downloading a scRNA Core cDNA pooling plan'
+        'This submission does not have the correct template for downloading a scRNA Core pooling plan'
       redirect_to submission
       return
     end
@@ -134,7 +134,7 @@ def download_scrna_core_cdna_pooling_plan # rubocop:disable Metrics/AbcSize,Metr
     # Generate the pooling plan CSV string using the ScrnaCoreCdnaPrepPoolingPlanGenerator module
     csv_string = Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator.generate_pooling_plan(submission)
 
-    send_data csv_string, type: 'text/plain', filename: "#{params[:id]}_scrna_core_cdna_pooling_plan.csv",
+    send_data csv_string, type: 'text/plain', filename: "#{params[:id]}_scrna_core_pooling_plan.csv",
                           disposition: 'attachment'
   end
 
diff --git a/app/models/ability/base_user.rb b/app/models/ability/base_user.rb
index eb3a2347fe..ffb0e74cd9 100644
--- a/app/models/ability/base_user.rb
+++ b/app/models/ability/base_user.rb
@@ -32,7 +32,7 @@ def grant_privileges # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
     can %i[read create], Study
     can :print_asset_group_labels, Study, owners: { id: user.id }
     can :print_asset_group_labels, Study, managers: { id: user.id }
-    can %i[read create update edit download_scrna_core_cdna_pooling_plan], Submission
+    can %i[read create update edit download_scrna_core_pooling_plan], Submission
     can :read, [TagGroup, TagLayoutTemplate, TagSet]
     can %i[read update print_swipecard], User, { id: user.id }
     can %i[projects study_reports], User
diff --git a/app/views/submissions/show.html.erb b/app/views/submissions/show.html.erb
index d61e652014..4abdef998b 100644
--- a/app/views/submissions/show.html.erb
+++ b/app/views/submissions/show.html.erb
@@ -4,7 +4,7 @@
   add :menu, "Print labels for #{order.asset_group.name}" => print_study_asset_group_path(order.study,order.asset_group) unless order.asset_group.nil?
 end %>
 <%- add :menu, "Submissions Inbox" => submissions_path if can? :read, Submission -%>
-<%- add :menu, "Download scRNA Core cDNA pooling plan" => download_scrna_core_cdna_pooling_plan_submission_path(@presenter.submission.id) if
+<%- add :menu, "Download scRNA Core pooling plan" => download_scrna_core_pooling_plan_submission_path(@presenter.submission.id) if
     @presenter.submission.scrna_core_cdna_prep_gem_x_5p_submission?
 -%>
 
diff --git a/config/routes.rb b/config/routes.rb
index 34cc42a627..27acc5a666 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -320,7 +320,7 @@
       get :study
     end
     member do
-      get :download_scrna_core_cdna_pooling_plan
+      get :download_scrna_core_pooling_plan
       post :change_priority
       post :cancel
     end
diff --git a/spec/controllers/submissions_controller_spec.rb b/spec/controllers/submissions_controller_spec.rb
index 77d89cedf0..304c9a9faf 100644
--- a/spec/controllers/submissions_controller_spec.rb
+++ b/spec/controllers/submissions_controller_spec.rb
@@ -357,7 +357,7 @@
       end
     end
 
-    describe '#download_scrna_core_cdna_pooling_plan' do
+    describe '#download_scrna_core_pooling_plan' do
       before do
         @template = create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p')
         @study = create(:study, user: @user)
@@ -370,13 +370,13 @@
       end
 
       it 'downloads a pooling plan' do
-        get :download_scrna_core_cdna_pooling_plan, params: { id: @submission.id }
+        get :download_scrna_core_pooling_plan, params: { id: @submission.id }
 
-        expect(response.headers['Content-Disposition']).to include("#{@submission.id}_scrna_core_cdna_pooling_plan.csv")
+        expect(response.headers['Content-Disposition']).to include("#{@submission.id}_scrna_core_pooling_plan.csv")
       end
 
       it 'redirects with an error if the submission is not found' do
-        get :download_scrna_core_cdna_pooling_plan, params: { id: 'nonexistent' }
+        get :download_scrna_core_pooling_plan, params: { id: 'nonexistent' }
 
         expect(flash[:error]).to eq('Submission not found with id nonexistent')
         expect(response).to redirect_to(submissions_path)
@@ -385,10 +385,10 @@
       it 'redirects with an error if the submission does not have the correct template' do
         @submission.orders.first.update(template_name: 'Some other template')
 
-        get :download_scrna_core_cdna_pooling_plan, params: { id: @submission.id }
+        get :download_scrna_core_pooling_plan, params: { id: @submission.id }
 
         expect(flash[:error]).to eq(
-          'This submission does not have the correct template for downloading a scRNA Core cDNA pooling plan'
+          'This submission does not have the correct template for downloading a scRNA Core pooling plan'
         )
         expect(response).to redirect_to(submission_path(@submission))
       end
diff --git a/spec/features/submissions/submission_show_spec.rb b/spec/features/submissions/submission_show_spec.rb
index 73fce64c9b..ef8a05de06 100644
--- a/spec/features/submissions/submission_show_spec.rb
+++ b/spec/features/submissions/submission_show_spec.rb
@@ -29,7 +29,7 @@
       expect(page).to have_link('Print labels for')
       expect(page).to have_link('Submissions Inbox')
       # This should only be visible for submissions with the correct scRNA template
-      expect(page).to have_no_link('Download scRNA Core cDNA pooling plan')
+      expect(page).to have_no_link('Download scRNA Core pooling plan')
     end
   end
 
@@ -37,13 +37,13 @@
     let(:template) { create(:submission_template, name: 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p') }
 
     it 'shows the correct sidebar links' do
-      expect(page).to have_link('Download scRNA Core cDNA pooling plan')
+      expect(page).to have_link('Download scRNA Core pooling plan')
     end
 
     it 'downloads the correct pooling plan' do
-      click_link 'Download scRNA Core cDNA pooling plan'
+      click_link 'Download scRNA Core pooling plan'
       expect(page.response_headers['Content-Disposition']).to include(
-        "#{submission.id}_scrna_core_cdna_pooling_plan.csv"
+        "#{submission.id}_scrna_core_pooling_plan.csv"
       )
     end
   end

From 5383dabfee4e451c66ee48cabf4c7501b80a1a9d Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Tue, 17 Feb 2026 00:00:16 +0000
Subject: [PATCH 22/57] Update Node.js to version 24.13.1

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

diff --git a/.nvmrc b/.nvmrc
index 3fe3b1570a..32f8c50de0 100644
--- a/.nvmrc
+++ b/.nvmrc
@@ -1 +1 @@
-24.13.0
+24.13.1

From 87217c058276a63b3f803792b230cd64549e9d73 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Wed, 18 Feb 2026 11:14:35 +0000
Subject: [PATCH 23/57] feat: add built-in rails endpoint

---
 config/routes.rb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/config/routes.rb b/config/routes.rb
index c9c46204c2..d4db24d74e 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -4,9 +4,12 @@
 
   user_is_admin = ->(req) { User.find_by(id: req.session[:user])&.administrator? }
   root to: 'homes#show'
-  resource :health, only: [:show]
   resource :home, only: [:show]
 
+  # Health check endpoints
+  get 'health' => 'health#show', constraints: ->(req) { req.format == :json } # json with stats
+  get 'health' => 'rails/health#show', as: :rails_health_check # default Rails health check
+
   resource :phi_x, only: [:show] do
     scope module: :phi_x do
       resources :stocks

From 87ee016420997293c4f21cf54864e5bc32238696 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Wed, 18 Feb 2026 11:21:11 +0000
Subject: [PATCH 24/57] refactor: order and group routes

---
 config/routes.rb | 52 ++++++++++++++++++++++++++----------------------
 1 file changed, 28 insertions(+), 24 deletions(-)

diff --git a/config/routes.rb b/config/routes.rb
index d4db24d74e..9537b58216 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -2,7 +2,7 @@
 Rails.application.routes.draw do
   # For details on the DSL available within this file, see http://guides.rubyonrails.org/routing.html
 
-  user_is_admin = ->(req) { User.find_by(id: req.session[:user])&.administrator? }
+  # Home
   root to: 'homes#show'
   resource :home, only: [:show]
 
@@ -10,18 +10,31 @@
   get 'health' => 'health#show', constraints: ->(req) { req.format == :json } # json with stats
   get 'health' => 'rails/health#show', as: :rails_health_check # default Rails health check
 
-  resource :phi_x, only: [:show] do
-    scope module: :phi_x do
-      resources :stocks
-      resources :spiked_buffers
-    end
-  end
-
   # Error handling endpoints
   get '/404', to: 'errors#not_found'
   get '/500', to: 'errors#internal_server_error'
   get '/503', to: 'errors#service_unavailable'
 
+  # Session authentication endpoints
+  match '/login' => 'sessions#login', :as => :login, :via => %i[get post]
+  match '/logout' => 'sessions#logout', :as => :logout, :via => %i[get post]
+  # this is for test only test/functional/authentication_controller_test.rb
+  # to be removed?
+  get 'authentication/open'
+  get 'authentication/restricted'
+
+  # Feature flags
+  user_is_admin = ->(req) { User.find_by(id: req.session[:user])&.administrator? }
+  mount Flipper::UI.app => '/flipper', :constraints => user_is_admin
+
+  # Search
+  resources :searches
+  resources :lab_searches
+
+  get 'advanced_search' => 'advanced_search#index'
+  post 'advanced_search/search' => 'advanced_search#search'
+
+  # API v1
   mount Api::RootService.new => '/api/1' unless ENV['DISABLE_V1_API']
 
   # @todo Update v2 resources exceptions to reflect resources (e.g., `, except: %i[update]` for `lot`),
@@ -144,9 +157,6 @@
     end
   end
 
-  match '/login' => 'sessions#login', :as => :login, :via => %i[get post]
-  match '/logout' => 'sessions#logout', :as => :logout, :via => %i[get post]
-
   resources :plate_summaries, only: %i[index show] do
     collection { get :search }
   end
@@ -347,8 +357,6 @@
     end
   end
 
-  resources :searches
-
   namespace :admin do
     resources :abilities, only: :index
     resources :custom_texts
@@ -452,12 +460,8 @@
     end
   end
 
-  resources :lab_searches
   resources :events
 
-  get 'advanced_search' => 'advanced_search#index'
-  post 'advanced_search/search' => 'advanced_search#search'
-
   resources :workflows, only: [] do
     member do
       # Yes, this is every bit as horrible as it looks.
@@ -471,6 +475,13 @@
     collection { get :generate_manifest }
   end
 
+  resource :phi_x, only: [:show] do
+    scope module: :phi_x do
+      resources :stocks
+      resources :spiked_buffers
+    end
+  end
+
   resources :asset_audits
 
   resources :qc_reports, except: %i[delete update] do
@@ -630,11 +641,6 @@
 
   resources :location_reports, only: %i[index show create]
 
-  # this is for test only test/functional/authentication_controller_test.rb
-  # to be removed?
-  get 'authentication/open'
-  get 'authentication/restricted'
-
   resources :messengers, only: :show
 
   # We removed workflows, which broke study links. Some customers may have their own studies bookmarked
@@ -649,8 +655,6 @@
     end
   end
 
-  mount Flipper::UI.app => '/flipper', :constraints => user_is_admin
-
   # Custom standalone route for bioscan control locations, allowing only
   # the POST request, migrated from the Lighthouse pickings endpoint.
   post 'bioscan_control_locations', to: 'bioscan_control_locations#create'

From 01ca40bb30102495fc2c7f8f6ca729bfadd60900 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 18 Feb 2026 15:07:33 +0000
Subject: [PATCH 25/57] save working version

---
 ...st_upload_with_tag_sequences_controller.rb | 15 +++++++-----
 .../stylesheets/all/sequencescape.scss        | 21 +++++++++++++++++
 .../new.html.erb                              | 23 +++++++++++++------
 3 files changed, 46 insertions(+), 13 deletions(-)

diff --git a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
index 5ac1fad099..9b86e672a3 100644
--- a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
+++ b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
@@ -12,11 +12,16 @@ def create
     if upload_manifest
       @rows_with_warnings =
          @uploader.upload.rows.select { |row| row.respond_to?(:warnings) && row.warnings.any? }
+      if @rows_with_warnings.any?
+        flash[:warnings] = 'Sample manifest uploaded with warnings!'
+        flash[:warning_messages] = 
+          @rows_with_warnings.flat_map { |row| row.warnings.full_messages }
+      else
+        flash[:notice] = 'Sample manifest successfully uploaded.'
+      end
+      redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
+      redirect_to redirect_target
       
-      flash[:warnings] =
-         @rows_with_warnings.flat_map { |row| row.warnings.full_messages }
-
-      success('Sample manifest successfully uploaded.')
     else
       error('Your sample manifest couldn\'t be uploaded.')
     end
@@ -31,14 +36,12 @@ def create_uploader
   def upload_manifest
     @uploader = create_uploader
     @uploader.run!
-    # @rows_with_warnings = @uploader.upload.rows.select { |row| row.warnings.any? }
   end
 
   def success(message)
     flash[:notice] = message
     redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
 
-    # render :new
     redirect_to redirect_target
   end
 
diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss
index 828ca5bfe4..9b7ccf0902 100644
--- a/app/frontend/stylesheets/all/sequencescape.scss
+++ b/app/frontend/stylesheets/all/sequencescape.scss
@@ -171,6 +171,27 @@ h3.card-header-custom {
 .alert-cancelled {
   @extend .alert-warning;
 }
+
+.alert-warnings {
+  background-color: orange; /* your preferred orange */
+  color: black;
+  border-color: darkorange;
+}
+
+.alert-warnings .alert-summary {
+  font-size: 1rem;
+  margin-bottom: 0.75rem;
+}
+
+.alert-warnings .alert-details {
+  padding-left: 1.25rem;
+}
+
+.alert-warnings .alert-details li {
+  margin-bottom: 0.4rem;
+  font-size: 0.95rem;
+}
+
 .text-notice,
 .text-passed {
   @extend .text-success;
diff --git a/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb b/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
index f56463ecd9..5d2dbffcfb 100644
--- a/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
+++ b/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
@@ -8,16 +8,25 @@
     <% @uploader.errors.full_messages.each do |message| %>
       <p><%= message %></p>
     <% end %>
+  <% end %>
+<% end %>
 
-   <% if flash[:warnings].present? %>
-      <%= alert(:warning) do %>
-        <% flash[:warnings].each do |message| %>
-          <p><%= message %></p>
-        <% end %>
-      <% end %>
-    <% end %>
+<p>======Warnings present? <%= flash[:warnings].present? %></p>
+<p>Warning messages present? <%= flash[:warning_messages].present? %></p>
+<% Rails.logger.info "flash[:warnings]: #{flash[:warnings].inspect}" %>
+<% Rails.logger.info "flash[:warning_messages]: #{flash[:warning_messages].inspect}" %>
 
+<% if flash[:warnings].present? %>
+  <%= alert(:warning) do %>
+    <p class="alert-summary"><strong><%= flash[:warnings] %></strong></p>
 
+    <% if flash[:warning_messages].present? %>
+      <ul class="alert-details mb-0">
+        <% flash[:warning_messages].each do |message| %>
+          <li><%= message %></li>
+        <% end %>
+      </ul>
+    <% end %>
   <% end %>
 <% end %>
 

From 3ab74d7ee2e496b7240d92522e854f96a2a8a983 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 18 Feb 2026 15:35:53 +0000
Subject: [PATCH 26/57] save changes

---
 ...st_upload_with_tag_sequences_controller.rb |  6 +++---
 .../stylesheets/all/sequencescape.scss        | 20 ++++++-------------
 .../sample_manifest_excel/upload/row.rb       |  1 +
 3 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
index 9b86e672a3..faabac196d 100644
--- a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
+++ b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
@@ -11,17 +11,17 @@ def create
 
     if upload_manifest
       @rows_with_warnings =
-         @uploader.upload.rows.select { |row| row.respond_to?(:warnings) && row.warnings.any? }
+        @uploader.upload.rows.select { |row| row.respond_to?(:warnings) && row.warnings.any? }
       if @rows_with_warnings.any?
         flash[:warnings] = 'Sample manifest uploaded with warnings!'
-        flash[:warning_messages] = 
+        flash[:warning_messages] =
           @rows_with_warnings.flat_map { |row| row.warnings.full_messages }
       else
         flash[:notice] = 'Sample manifest successfully uploaded.'
       end
       redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
       redirect_to redirect_target
-      
+
     else
       error('Your sample manifest couldn\'t be uploaded.')
     end
diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss
index 9b7ccf0902..4157b7c6c0 100644
--- a/app/frontend/stylesheets/all/sequencescape.scss
+++ b/app/frontend/stylesheets/all/sequencescape.scss
@@ -172,24 +172,16 @@ h3.card-header-custom {
   @extend .alert-warning;
 }
 
-.alert-warnings {
-  background-color: orange; /* your preferred orange */
+.alert-warnings,
+.alert-warning_messages {
+  background-color: orange;
   color: black;
   border-color: darkorange;
 }
 
-.alert-warnings .alert-summary {
-  font-size: 1rem;
-  margin-bottom: 0.75rem;
-}
-
-.alert-warnings .alert-details {
-  padding-left: 1.25rem;
-}
-
-.alert-warnings .alert-details li {
-  margin-bottom: 0.4rem;
-  font-size: 0.95rem;
+.alert-warnings {
+  font-size: 20px;   /* or whatever size you want */
+  font-weight: 600;  /* optional, makes it stand out */
 }
 
 .text-notice,
diff --git a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
index 8ff9a4d900..b166e145bc 100644
--- a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
+++ b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
@@ -15,6 +15,7 @@ class Row # rubocop:todo Metrics/ClassLength
 
       attr_accessor :number, :data, :columns, :cache
       attr_reader :sanger_sample_id
+
       # attr_reader :warnings
 
       # def initialize(attributes = {})

From ceecf8bfac7e3de5ca73e54946301427201a948e Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 18 Feb 2026 16:12:16 +0000
Subject: [PATCH 27/57] fix linting

---
 app/frontend/stylesheets/all/sequencescape.scss | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss
index 4157b7c6c0..842cbd1564 100644
--- a/app/frontend/stylesheets/all/sequencescape.scss
+++ b/app/frontend/stylesheets/all/sequencescape.scss
@@ -180,8 +180,8 @@ h3.card-header-custom {
 }
 
 .alert-warnings {
-  font-size: 20px;   /* or whatever size you want */
-  font-weight: 600;  /* optional, makes it stand out */
+  font-size: 20px; /* or whatever size you want */
+  font-weight: 600; /* optional, makes it stand out */
 }
 
 .text-notice,

From 6625abaf5ed02ebdb9e2fc8f5d107ca80f0b11e9 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 18 Feb 2026 16:41:46 +0000
Subject: [PATCH 28/57] remove redundant codes

---
 .../new.html.erb                              | 20 -------------------
 1 file changed, 20 deletions(-)

diff --git a/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb b/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
index 5d2dbffcfb..4eaec4ed60 100644
--- a/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
+++ b/app/views/sample_manifest_upload_with_tag_sequences/new.html.erb
@@ -1,4 +1,3 @@
-
 <%= render partial: "side_links" %>
 
 <%= page_title "Sample Manifests", "New and upload" %>
@@ -11,25 +10,6 @@
   <% end %>
 <% end %>
 
-<p>======Warnings present? <%= flash[:warnings].present? %></p>
-<p>Warning messages present? <%= flash[:warning_messages].present? %></p>
-<% Rails.logger.info "flash[:warnings]: #{flash[:warnings].inspect}" %>
-<% Rails.logger.info "flash[:warning_messages]: #{flash[:warning_messages].inspect}" %>
-
-<% if flash[:warnings].present? %>
-  <%= alert(:warning) do %>
-    <p class="alert-summary"><strong><%= flash[:warnings] %></strong></p>
-
-    <% if flash[:warning_messages].present? %>
-      <ul class="alert-details mb-0">
-        <% flash[:warning_messages].each do |message| %>
-          <li><%= message %></li>
-        <% end %>
-      </ul>
-    <% end %>
-  <% end %>
-<% end %>
-
 <%= render partial: "upload" %>
 
 <%= pagination @sample_manifests %>

From e46dd53f26dae4d9ea6ec94b0ba65975cd2217fe Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 18 Feb 2026 18:13:19 +0000
Subject: [PATCH 29/57] remove duplicate warnings

---
 ...ample_manifest_upload_with_tag_sequences_controller.rb | 2 +-
 .../sample_manifest_excel/upload/row.rb                   | 8 --------
 2 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
index faabac196d..5be3e155c8 100644
--- a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
+++ b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
@@ -15,7 +15,7 @@ def create
       if @rows_with_warnings.any?
         flash[:warnings] = 'Sample manifest uploaded with warnings!'
         flash[:warning_messages] =
-          @rows_with_warnings.flat_map { |row| row.warnings.full_messages }
+          @rows_with_warnings.flat_map { |row| row.warnings.full_messages }.uniq
       else
         flash[:notice] = 'Sample manifest successfully uploaded.'
       end
diff --git a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
index b166e145bc..f85c9c7643 100644
--- a/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
+++ b/app/sample_manifest_excel/sample_manifest_excel/upload/row.rb
@@ -16,14 +16,6 @@ class Row # rubocop:todo Metrics/ClassLength
       attr_accessor :number, :data, :columns, :cache
       attr_reader :sanger_sample_id
 
-      # attr_reader :warnings
-
-      # def initialize(attributes = {})
-      #   super
-      #   @warnings = ActiveModel::Errors.new(self)
-      # end
-
-      # @return [ActiveModel::Errors] the warnings collection
       def warnings
         @warnings ||= ActiveModel::Errors.new(self)
       end

From 330d88e71d5c36842cb1d78af36bdd51f2d3e2ff Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 18 Feb 2026 21:41:24 +0000
Subject: [PATCH 30/57] refactor to fix linting

---
 ...st_upload_with_tag_sequences_controller.rb | 33 ++++++++++++-------
 1 file changed, 21 insertions(+), 12 deletions(-)

diff --git a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
index 5be3e155c8..154a463d26 100644
--- a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
+++ b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
@@ -10,18 +10,7 @@ def create
     return error('No file attached') if params[:upload].blank?
 
     if upload_manifest
-      @rows_with_warnings =
-        @uploader.upload.rows.select { |row| row.respond_to?(:warnings) && row.warnings.any? }
-      if @rows_with_warnings.any?
-        flash[:warnings] = 'Sample manifest uploaded with warnings!'
-        flash[:warning_messages] =
-          @rows_with_warnings.flat_map { |row| row.warnings.full_messages }.uniq
-      else
-        flash[:notice] = 'Sample manifest successfully uploaded.'
-      end
-      redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
-      redirect_to redirect_target
-
+      set_upload_flash_message
     else
       error('Your sample manifest couldn\'t be uploaded.')
     end
@@ -38,6 +27,26 @@ def upload_manifest
     @uploader.run!
   end
 
+  def set_upload_flash_message
+    warning_rows = rows_with_warnings
+    return success('Sample manifest successfully uploaded.') if warning_rows.empty?
+
+    apply_warning_flash(warning_rows)
+  end
+
+  def rows_with_warnings
+    @uploader.upload.rows.select do |row|
+      row.respond_to?(:warnings) && row.warnings.any?
+    end
+  end
+
+  def apply_warning_flash(rows)
+    flash[:warnings] = 'Sample manifest uploaded with warnings!'
+    flash[:warning_messages] = rows.flat_map { |row| row.warnings.full_messages }.uniq
+    redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
+    redirect_to redirect_target
+  end
+
   def success(message)
     flash[:notice] = message
     redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)

From 7da2aaa1e482bf0793284b0710da0174b0f9613e Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 19 Feb 2026 15:16:25 +0000
Subject: [PATCH 31/57] update the i7/i5 conditional formatting

---
 spec/data/sample_manifest_excel/columns.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/spec/data/sample_manifest_excel/columns.yml b/spec/data/sample_manifest_excel/columns.yml
index f6727872f4..83329b9978 100644
--- a/spec/data/sample_manifest_excel/columns.yml
+++ b/spec/data/sample_manifest_excel/columns.yml
@@ -37,7 +37,7 @@ i7:
       promptTitle: "i7"
       prompt: "Input i7."
   conditional_formattings:
-    empty_cell:
+    empty_warning_cell:
 i5:
   heading: i5 TAG SEQUENCE
   unlocked: true
@@ -50,6 +50,8 @@ i5:
       showInputMessage: true
       promptTitle: "i5"
       prompt: "i7."
+  conditional_formattings:
+    empty_warning_cell:
 tag_group:
   heading: TAG GROUP
   unlocked: true
@@ -127,7 +129,7 @@ chromium_tag_group:
       prompt: "Input the name of a valid tag set. All samples in a library need to be tagged with the same tag set."
     range_name: :chromium_tag_groups
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
 chromium_tag_well:
   heading: CHROMIUM TAG WELL
   unlocked: true
@@ -145,7 +147,7 @@ chromium_tag_well:
       errorTitle: "Tag well"
       error: "Tag Index must be a well."
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
     is_number:
     len:
       formula:
@@ -184,7 +186,7 @@ dual_index_tag_set:
       prompt: "Input the name of a valid dual index tag plate."
     range_name: :dual_index_tag_sets
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
 dual_index_tag_well:
   heading: DUAL INDEX TAG WELL
   unlocked: true
@@ -202,7 +204,7 @@ dual_index_tag_well:
       errorTitle: "Dual index tag well"
       error: "Dual Index Tag must be a well."
   conditional_formattings:
-    empty_mandatory_cell_2:
+    empty_cell:
     is_number:
     len:
       formula:

From 540115d142e4765abb384902859ce3e28b804ecc Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 19 Feb 2026 16:09:27 +0000
Subject: [PATCH 32/57] add new conditional formatings to test data files

---
 .../sample_manifest_excel/conditional_formattings.yml    | 9 +++++++++
 .../extract/conditional_formattings.yml                  | 9 +++++++++
 2 files changed, 18 insertions(+)

diff --git a/spec/data/sample_manifest_excel/conditional_formattings.yml b/spec/data/sample_manifest_excel/conditional_formattings.yml
index 1554673165..a633439a3c 100644
--- a/spec/data/sample_manifest_excel/conditional_formattings.yml
+++ b/spec/data/sample_manifest_excel/conditional_formattings.yml
@@ -16,6 +16,15 @@ empty_mandatory_cell:
     formula: "FALSE"
     operator: :equal
     priority: 1
+empty_warning_cell:
+  style:
+    bg_color: "FF991C"
+    type: :dxf
+  options:
+    type: :cellIs
+    formula: "FALSE"
+    operator: :equal
+    priority: 1
 len:
   style:
     bg_color: "FF0000"
diff --git a/spec/data/sample_manifest_excel/extract/conditional_formattings.yml b/spec/data/sample_manifest_excel/extract/conditional_formattings.yml
index 939fb024b0..aa4d6a6930 100644
--- a/spec/data/sample_manifest_excel/extract/conditional_formattings.yml
+++ b/spec/data/sample_manifest_excel/extract/conditional_formattings.yml
@@ -7,6 +7,15 @@ empty_cell:
     formula: "FALSE"
     operator: :equal
     priority: 1
+empty_warning_cell:
+  style:
+    bg_color: "FF991C"
+    type: :dxf
+  options:
+    type: :cellIs
+    formula: "FALSE"
+    operator: :equal
+    priority: 1
 len:
   style:
     bg_color: "FF0000"

From 409c514e770d38dd92e2f3bbcb2aace4aeab7c8a Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 19 Feb 2026 19:25:22 +0000
Subject: [PATCH 33/57] remove not valid test

---
 spec/sample_manifest_excel/upload/row_spec.rb | 45 -------------------
 1 file changed, 45 deletions(-)

diff --git a/spec/sample_manifest_excel/upload/row_spec.rb b/spec/sample_manifest_excel/upload/row_spec.rb
index 24b464653e..5b7f489605 100644
--- a/spec/sample_manifest_excel/upload/row_spec.rb
+++ b/spec/sample_manifest_excel/upload/row_spec.rb
@@ -101,47 +101,6 @@
       'Unknown'
     ]
   end
-  let(:data_without_i7_i5) do
-    [
-      tube.human_barcode,
-      sample_manifest.sample_manifest_assets.first.sanger_sample_id,
-      '',
-      '',
-      'My reference genome',
-      'My New Library Type',
-      200,
-      1500,
-      'SCG--1222_A01',
-      '',
-      1,
-      1,
-      'Unknown',
-      '',
-      '',
-      '',
-      'Cell Line',
-      'Nov-16',
-      'Nov-16',
-      '',
-      'No',
-      '',
-      'OTHER',
-      '',
-      '',
-      '',
-      '',
-      '',
-      'SCG--1222_A01',
-      9606,
-      'Homo sapiens',
-      '',
-      '',
-      '',
-      '',
-      11,
-      'Unknown'
-    ]
-  end
 
   it 'is not valid without row number' do
     expect(described_class.new(number: 'one', data: data, columns: columns)).not_to be_valid
@@ -156,10 +115,6 @@
     expect(described_class.new(number: 1, data: data)).not_to be_valid
   end
 
-  it 'is not valid without i7/i5 if i7/i5 column exists' do
-    expect(described_class.new(number: 1, data: data_without_i7_i5, columns: columns)).not_to be_valid
-  end
-
   it '#value returns value for specified key' do
     expect(described_class.new(number: 1, data: data, columns: columns).value(:sanger_sample_id)).to eq(
       sample_manifest.labware.first.sample_manifest_assets.first.sanger_sample_id

From 0dcc9b8c13ee5623a37f79ac2740ca64ad41df7b Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 19 Feb 2026 21:03:12 +0000
Subject: [PATCH 34/57] fix tests

---
 ...load_with_tag_sequences_controller_spec.rb | 40 +++++++++++++++++--
 1 file changed, 37 insertions(+), 3 deletions(-)

diff --git a/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb b/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb
index f117068b4e..f3c51fb7a7 100644
--- a/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb
+++ b/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb
@@ -6,7 +6,7 @@
 RSpec.describe SampleManifestUploadWithTagSequencesController, type: :controller do
   let(:user) { create(:user) }
   let(:upload_file) { 'pretend-this-is-an-actual-file' }
-  let(:uploader) { instance_double(SampleManifest::Uploader, run!: true, study: nil) }
+  let(:uploader) { instance_double(SampleManifest::Uploader, study: nil) }
 
   before do
     allow(controller).to receive(:current_user).and_return(user)
@@ -26,8 +26,15 @@
       end
     end
 
-    context 'when the file is uploaded successfully' do
-      before { post :create, params: { upload: upload_file } }
+    context 'when the file is uploaded successfully without warning' do
+      before do
+        allow(controller).to receive(:upload_manifest) do
+          controller.instance_variable_set(:@uploader, uploader)
+          true
+        end
+        allow(controller).to receive(:rows_with_warnings).and_return([])
+        post :create, params: { upload: upload_file }
+      end
 
       it 'sets a success flash message' do
         expect(flash[:notice]).to eq('Sample manifest successfully uploaded.')
@@ -38,6 +45,33 @@
       end
     end
 
+    context 'when upload succeeds with warnings' do
+      let(:warning_row) do
+        double(warnings: double(full_messages: ['Row 10 warning']))
+      end
+
+      before do
+        allow(controller).to receive(:upload_manifest) do
+          controller.instance_variable_set(:@uploader, uploader)
+          true
+        end
+        allow(controller).to receive(:rows_with_warnings).and_return([warning_row])
+        post :create, params: { upload: upload_file }
+      end
+
+      it 'sets warning flash message' do
+        expect(flash[:warnings]).to eq('Sample manifest uploaded with warnings!')
+      end
+
+      it 'sets warning messages' do
+        expect(flash[:warning_messages]).to eq(['Row 10 warning'])
+      end
+
+      it 'redirects correctly' do
+        expect(response).to redirect_to(sample_manifests_path)
+      end
+    end
+
     context 'when the upload fails due to invalid data' do
       before do
         allow(uploader).to receive(:run!).and_raise(AccessionService::AccessionValidationFailed, 'Invalid data')

From c60a6700b5f24c5a7ab085975854d6e498bedfa9 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 19 Feb 2026 21:38:06 +0000
Subject: [PATCH 35/57] add LCM Triomics RNASeq template

---
 .../014_lcm_triomics_submission_templates.yml            | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
index 7a55ace723..3a3006a896 100644
--- a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
+++ b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
@@ -1,7 +1,7 @@
 # Submission templates for LCM Triomics WGS and EMSeq
 ---
 # LCM Triomics EMSeq submission template
-Limber-Htp - LCM Triomics:
+Limber-Htp - LCM Triomics EMSeq:
   submission_class_name: "LinearSubmission"
   related_records:
     request_type_keys: ["limber_lcm_triomics_emseq"]
@@ -14,3 +14,10 @@ Limber-Htp - LCM Triomics WGS:
     request_type_keys: ["limber_lcm_triomics_wgs"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
+# LCM Triomics RNASeq submission template
+Limber-Htp - LCM Triomics RNASeq:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_lcm_triomics_rnaseq"]
+    product_line_name: LCM Triomics
+    product_catalogue_name: LCM Triomics
\ No newline at end of file

From e4f9c3728d9951bed2c4337227957f87ca7cf539 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 19 Feb 2026 21:40:28 +0000
Subject: [PATCH 36/57] fix linting

---
 .../014_lcm_triomics_submission_templates.yml                   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
index 3a3006a896..4e99ca8cb3 100644
--- a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
+++ b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
@@ -20,4 +20,4 @@ Limber-Htp - LCM Triomics RNASeq:
   related_records:
     request_type_keys: ["limber_lcm_triomics_rnaseq"]
     product_line_name: LCM Triomics
-    product_catalogue_name: LCM Triomics
\ No newline at end of file
+    product_catalogue_name: LCM Triomics

From 8778e37b5dea801e00c18d20df4953a4c6138e40 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Fri, 20 Feb 2026 13:03:55 +0000
Subject: [PATCH 37/57] add request type etc

---
 .../018_limber_lcm_triomics_request_types.yml        | 12 ++++++++++++
 .../014_lcm_triomics_submission_templates.yml        |  2 ++
 2 files changed, 14 insertions(+)

diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
index cdc3f13ce4..f1300f6b1f 100644
--- a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
+++ b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
@@ -12,6 +12,18 @@ limber_lcm_triomics_emseq:
     - LCMT Lysate
   library_types:
     - emSEQ
+limber_lcm_triomics_rnaseq:
+  name: LCM Triomics RNASeq
+  asset_type: Well
+  order: 1
+  request_class_name: IlluminaHtp::Requests::StdLibraryRequest
+  for_multiplexing: false
+  billable: true
+  product_line_name: Short Read
+  acceptable_purposes:
+    - LCMT Lysate
+  library_types:
+    - Combined LCM RNA
 limber_lcm_triomics_wgs:
   name: LCM Triomics WGS
   asset_type: Well
diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
index 4e99ca8cb3..ee6a0fba63 100644
--- a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
+++ b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
@@ -7,6 +7,7 @@ Limber-Htp - LCM Triomics EMSeq:
     request_type_keys: ["limber_lcm_triomics_emseq"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
+    project_name: "UAT Study"
 # LCM Triomics WGS submission template
 Limber-Htp - LCM Triomics WGS:
   submission_class_name: "LinearSubmission"
@@ -21,3 +22,4 @@ Limber-Htp - LCM Triomics RNASeq:
     request_type_keys: ["limber_lcm_triomics_rnaseq"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
+    project_name: "UAT Study"

From 7144dca74f3d0343ccc697185882f475200e8d2c Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Fri, 20 Feb 2026 16:16:45 +0000
Subject: [PATCH 38/57] add project name to submission template

---
 .../014_lcm_triomics_submission_templates.yml                 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
index ee6a0fba63..510d955d5a 100644
--- a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
+++ b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
@@ -7,7 +7,7 @@ Limber-Htp - LCM Triomics EMSeq:
     request_type_keys: ["limber_lcm_triomics_emseq"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
-    project_name: "UAT Study"
+    project_name: "UAT Project"
 # LCM Triomics WGS submission template
 Limber-Htp - LCM Triomics WGS:
   submission_class_name: "LinearSubmission"
@@ -22,4 +22,4 @@ Limber-Htp - LCM Triomics RNASeq:
     request_type_keys: ["limber_lcm_triomics_rnaseq"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
-    project_name: "UAT Study"
+    project_name: "UAT Project"

From 01e59f0ff084054bbc9f7d734a77e41342b9a884 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 20 Feb 2026 19:00:19 +0000
Subject: [PATCH 39/57] Update mocha to version 3.0.2

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

diff --git a/Gemfile.lock b/Gemfile.lock
index cf0a6863c4..9759f2369f 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -327,7 +327,7 @@ GEM
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
       minitest (>= 5.3.3)
-    mocha (3.0.1)
+    mocha (3.0.2)
       ruby2_keywords (>= 0.0.5)
     msgpack (1.8.0)
     multi_json (1.17.0)

From 546e842479b6af4374965342aeb37bc56bfa56df Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Mon, 23 Feb 2026 14:26:10 +0000
Subject: [PATCH 40/57] fix: allow flashes to render described lists

---
 .../stylesheets/all/sequencescape.scss        |  5 +-
 app/helpers/application_helper.rb             | 34 ++++++++++---
 spec/helpers/application_helper_spec.rb       | 51 +++++++++++++++++++
 3 files changed, 82 insertions(+), 8 deletions(-)

diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss
index 842cbd1564..3725e6aa48 100644
--- a/app/frontend/stylesheets/all/sequencescape.scss
+++ b/app/frontend/stylesheets/all/sequencescape.scss
@@ -149,7 +149,10 @@ h3.card-header-custom {
   }
 }
 
-.alert-error ul {
+.alert-error ul,
+.alert-warning ul,
+.alert-notice ul,
+.alert-success ul {
   margin: 0;
 }
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 9daa0f8348..67059c53e5 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -76,17 +76,37 @@ def render_flashes
     nil
   end
 
-  # A helper method for render_flashes - If multiple messages, render them as a list, else render as a single div
-  # @param messages [Array<String>, String] The flash message or messages to be rendered
-  def render_message(messages)
-    messages = Array(messages)
-    if messages.size > 1
-      tag.ul { messages.each { |m| concat tag.li(m) } }
+  # A helper method for render_flashes.
+  # If messages is a Hash, renders them as a described list, with the keys as the description and
+  # the values as the items.
+  # If messages is an Array with multiple messages, renders them as a list.
+  # If a single message, renders as a single div.
+  #
+  # @param messages [Hash, Array<String>, String] The flash message or messages to be rendered
+  # @return [ActiveSupport::SafeBuffer] HTML-safe string for rendering the messages
+  def render_message(messages) # rubocop:disable Metrics/MethodLength
+    case messages
+    when Hash
+      safe_join(
+        messages.map do |description, items|
+          tag.div(description) + render_in_list(Array(items))
+        end
+      )
+    when Array
+      if messages.size > 1
+        render_in_list(messages)
+      else # messages has only one element, render it as a single div
+        tag.div(messages.first)
+      end
     else
-      tag.div(messages.first)
+      tag.div(messages)
     end
   end
 
+  def render_in_list(messages)
+    tag.ul { messages.each { |message| concat tag.li(message) } }
+  end
+
   def api_data
     { api_version: RELEASE.api_version }
   end
diff --git a/spec/helpers/application_helper_spec.rb b/spec/helpers/application_helper_spec.rb
index a44d79bafb..eda801fb55 100644
--- a/spec/helpers/application_helper_spec.rb
+++ b/spec/helpers/application_helper_spec.rb
@@ -109,4 +109,55 @@
       end
     end
   end
+
+  describe '#render_message' do
+    let(:html) { helper.render_message(messages) }
+
+    context 'when messages is a Hash' do
+      let(:messages) { { 'Description 1' => ['Item 1', 'Item 2'], 'Description 2' => 'Single Item' } }
+
+      it 'renders each key as a div and each value as a list' do
+        expect(html).to include('<div>Description 1</div>')
+          .and include('<li>Item 1</li>')
+          .and include('<li>Item 2</li>')
+          .and include('<div>Description 2</div>')
+          .and include('<li>Single Item</li>')
+      end
+    end
+
+    context 'when messages is an Array with multiple items' do
+      let(:messages) { ['Error 1', 'Error 2'] }
+
+      it 'renders the messages as a list' do
+        expect(html).to include('<ul>')
+          .and include('<li>Error 1</li>')
+          .and include('<li>Error 2</li>')
+      end
+    end
+
+    context 'when messages is an Array with one item' do
+      let(:messages) { ['Only one error'] }
+
+      it 'renders the single message as a div' do
+        expect(html).to include('<div>Only one error</div>')
+      end
+    end
+
+    context 'when messages is a String' do
+      let(:messages) { 'Just a string' }
+
+      it 'renders the string as a div' do
+        expect(html).to include('<div>Just a string</div>')
+      end
+    end
+  end
+
+  describe '#render_in_list' do
+    it 'renders an array of messages as a list' do
+      html = helper.render_in_list(%w[foo bar])
+      expect(html).to include('<ul>')
+        .and include('<li>foo</li>')
+        .and include('<li>bar</li>')
+    end
+  end
 end

From 52a9761b242c8f029625fa934674e3e93ac8a273 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Mon, 23 Feb 2026 14:33:50 +0000
Subject: [PATCH 41/57] refactor: use new hash-style flash

---
 ...sample_manifest_upload_with_tag_sequences_controller.rb | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
index 154a463d26..e319f65aa4 100644
--- a/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
+++ b/app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb
@@ -41,8 +41,11 @@ def rows_with_warnings
   end
 
   def apply_warning_flash(rows)
-    flash[:warnings] = 'Sample manifest uploaded with warnings!'
-    flash[:warning_messages] = rows.flat_map { |row| row.warnings.full_messages }.uniq
+    flash[:warning] = {
+      'Sample manifest uploaded with warnings!':
+        rows.flat_map { |row| row.warnings.full_messages }.uniq
+    }
+
     redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
     redirect_to redirect_target
   end

From 9dca0713cc9ea370dcf9d25e96719178b44fff79 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Mon, 23 Feb 2026 14:34:59 +0000
Subject: [PATCH 42/57] refactor: remove unused css classes

---
 app/frontend/stylesheets/all/sequencescape.scss | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss
index 3725e6aa48..f385b3be1c 100644
--- a/app/frontend/stylesheets/all/sequencescape.scss
+++ b/app/frontend/stylesheets/all/sequencescape.scss
@@ -175,18 +175,6 @@ h3.card-header-custom {
   @extend .alert-warning;
 }
 
-.alert-warnings,
-.alert-warning_messages {
-  background-color: orange;
-  color: black;
-  border-color: darkorange;
-}
-
-.alert-warnings {
-  font-size: 20px; /* or whatever size you want */
-  font-weight: 600; /* optional, makes it stand out */
-}
-
 .text-notice,
 .text-passed {
   @extend .text-success;

From 72ac228261ab38fdba886d5da0d567135f2966a3 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Mon, 23 Feb 2026 14:51:39 +0000
Subject: [PATCH 43/57] test: update specs

---
 ...le_manifest_upload_with_tag_sequences_controller_spec.rb | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb b/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb
index f3c51fb7a7..c4815f3947 100644
--- a/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb
+++ b/spec/controllers/sample_manifest_upload_with_tag_sequences_controller_spec.rb
@@ -60,11 +60,7 @@
       end
 
       it 'sets warning flash message' do
-        expect(flash[:warnings]).to eq('Sample manifest uploaded with warnings!')
-      end
-
-      it 'sets warning messages' do
-        expect(flash[:warning_messages]).to eq(['Row 10 warning'])
+        expect(flash[:warning]).to eq({ 'Sample manifest uploaded with warnings!': ['Row 10 warning'] })
       end
 
       it 'redirects correctly' do

From abfd39bb1c6b98cb0c7c0a6305b7f43dd236ce35 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Mon, 23 Feb 2026 19:35:14 +0000
Subject: [PATCH 44/57] Update vite-plugin-ruby to version 5.1.3

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

diff --git a/yarn.lock b/yarn.lock
index 2ea540ed43..c62ae64dd0 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -2249,9 +2249,9 @@ util-deprecate@^1.0.2, util-deprecate@~1.0.1:
   integrity sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==
 
 "vite-plugin-ruby@>=5.1.0 <5.1.2 || ^5.1.3 || ^5.2":
-  version "5.1.1"
-  resolved "https://registry.yarnpkg.com/vite-plugin-ruby/-/vite-plugin-ruby-5.1.1.tgz#ecd72591ddb90a23613051005bd70a6410945129"
-  integrity sha512-I1dXJq2ywdvTD2Cz5LYNcYLujqQ3eUxPoCjruRdfm2QBtHBY15NEeb6x5HuPM3T5S+y8S3p9fwRsieQQCjk0gg==
+  version "5.1.3"
+  resolved "https://registry.yarnpkg.com/vite-plugin-ruby/-/vite-plugin-ruby-5.1.3.tgz#96c0dcd9fadb7a941062cc93a411f1e4d5eb8907"
+  integrity sha512-vpTOKbR6AmnupmXvQccRcr/jIY+oobNuCbNJHUzkT8oQ2BBQSlp22Xec3zszBBc7GjwDGn2+E+IQoNRXdEY7Ig==
   dependencies:
     debug "^4.3.4"
     fast-glob "^3.3.2"

From 8b593883fa4b770c339439e32c221e3d043e3594 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Tue, 24 Feb 2026 04:20:21 +0000
Subject: [PATCH 45/57] Update ruby-prof to version 2.0.2

---
 Gemfile.lock | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index cf0a6863c4..b77d38d35a 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -542,8 +542,9 @@ GEM
       rubocop-rspec (~> 3.5)
     ruby-graphviz (1.2.5)
       rexml
-    ruby-prof (1.7.2)
+    ruby-prof (2.0.2)
       base64
+      ostruct
     ruby-progressbar (1.13.0)
     ruby-units (4.1.0)
     ruby-vips (2.2.3)

From 399d60b02e40c3b764ed9296593b8327103fb4c7 Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Tue, 24 Feb 2026 11:23:23 +0000
Subject: [PATCH 46/57] fix: makes creation_requests return consistent type

---
 app/models/multiplexed_library_tube.rb            |  2 +-
 spec/models/broadcast_event/pool_released_spec.rb | 11 +++++++++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/app/models/multiplexed_library_tube.rb b/app/models/multiplexed_library_tube.rb
index 8c8d3ca9d6..82ea0fafce 100644
--- a/app/models/multiplexed_library_tube.rb
+++ b/app/models/multiplexed_library_tube.rb
@@ -43,6 +43,6 @@ def creation_requests
 
     # Parents should exist but in the case they don't (e.g. asset_links are yet to be created)
     # we want to avoid an error and just return an empty array.
-    parents.includes(:requests_as_target).first&.requests_as_target
+    parents.includes(:requests_as_target).first&.requests_as_target || []
   end
 end
diff --git a/spec/models/broadcast_event/pool_released_spec.rb b/spec/models/broadcast_event/pool_released_spec.rb
index 9b8e3a71cb..65cf464fe5 100644
--- a/spec/models/broadcast_event/pool_released_spec.rb
+++ b/spec/models/broadcast_event/pool_released_spec.rb
@@ -113,13 +113,20 @@
       expect(metadata['team']).not_to eq('UNKNOWN')
     end
 
-    # This is an edge case, but we want to make sure that if there are no creation requests or ancestors
+    # These are edge cases, but we want to make sure that if there are no creation requests or ancestors
     # we don't error out and instead return 'UNKNOWN' for the team.
-    it 'has an unknown team if tube has no creation requests' do
+    it 'has an unknown team if tube has no parents' do
       tube.ancestors = []
       tube.save!
 
       expect(metadata['team']).to eq('UNKNOWN')
     end
+
+    it 'has an unknown team if tube has a parent with no requests_as_target' do
+      # This is the requests_as_target for the source plate
+      library_request.destroy
+
+      expect(metadata['team']).to eq('UNKNOWN')
+    end
   end
 end

From 487159c3f0551995dd1282b86ebb5aff820fbb80 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Tue, 24 Feb 2026 19:00:22 +0000
Subject: [PATCH 47/57] Update rspec-rails to version 8.0.3

---
 Gemfile.lock | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index c33cd11771..93af492a05 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -133,7 +133,7 @@ GEM
     backports (3.25.2)
     base64 (0.3.0)
     benchmark (0.5.0)
-    bigdecimal (3.3.1)
+    bigdecimal (4.0.1)
     bootsnap (1.22.0)
       msgpack (~> 1.2)
     builder (3.3.0)
@@ -167,7 +167,7 @@ GEM
       marcel (~> 1.0)
       nokogiri (~> 1.10, >= 1.10.4)
       rubyzip (>= 2.4, < 4)
-    cgi (0.5.0)
+    cgi (0.5.1)
     childprocess (5.1.0)
       logger (~> 1.5)
     choice (0.2.0)
@@ -272,14 +272,15 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.1.0)
       domain_name (~> 0.5)
-    i18n (1.14.7)
+    i18n (1.14.8)
       concurrent-ruby (~> 1.0)
     image_processing (1.14.0)
       mini_magick (>= 4.9.5, < 6)
       ruby-vips (>= 2.0.17, < 3)
-    io-console (0.8.1)
-    irb (1.15.3)
+    io-console (0.8.2)
+    irb (1.17.0)
       pp (>= 0.6.0)
+      prism (>= 1.3.0)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     json (2.18.1)
@@ -302,7 +303,7 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     logger (1.7.0)
-    loofah (2.24.1)
+    loofah (2.25.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.9.0)
@@ -430,8 +431,8 @@ GEM
       activesupport (>= 4.2)
       choice (~> 0.2.0)
       ruby-graphviz (~> 1.2)
-    rails-html-sanitizer (1.6.2)
-      loofah (~> 2.21)
+    rails-html-sanitizer (1.7.0)
+      loofah (~> 2.25)
       nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     rails-perftest (0.0.7)
     railties (7.2.3)
@@ -454,7 +455,7 @@ GEM
     rbtree (0.4.6)
     rdoc (6.3.4.1)
     regexp_parser (2.11.3)
-    reline (0.6.2)
+    reline (0.6.3)
       io-console (~> 0.5)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -474,9 +475,9 @@ GEM
       rspec-mocks (~> 3.13.0)
     rspec-collection_matchers (1.2.1)
       rspec-expectations (>= 2.99.0.beta1)
-    rspec-core (3.13.3)
+    rspec-core (3.13.6)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.3)
+    rspec-expectations (3.13.5)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-github (3.0.0)
@@ -487,10 +488,10 @@ GEM
     rspec-json_expectations (2.2.0)
     rspec-longrun (3.1.0)
       rspec-core (>= 3.5.0, < 4)
-    rspec-mocks (3.13.2)
+    rspec-mocks (3.13.7)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (8.0.2)
+    rspec-rails (8.0.3)
       actionpack (>= 7.2)
       activesupport (>= 7.2)
       railties (>= 7.2)
@@ -498,7 +499,7 @@ GEM
       rspec-expectations (~> 3.13)
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
-    rspec-support (3.13.2)
+    rspec-support (3.13.7)
     rubocop (1.84.1)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
@@ -605,7 +606,7 @@ GEM
       logger
     temple (0.10.4)
     test-prof (1.5.2)
-    thor (1.4.0)
+    thor (1.5.0)
     tilt (2.6.1)
     timecop (0.9.10)
     timeout (0.4.4)
@@ -634,7 +635,7 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.9.1)
+    webrick (1.9.2)
     websocket (1.2.11)
     websocket-driver (0.8.0)
       base64
@@ -656,7 +657,7 @@ GEM
       ostruct
       rainbow
       yard
-    zeitwerk (2.7.3)
+    zeitwerk (2.7.5)
 
 PLATFORMS
   arm64-darwin

From c7eaab48126a7b77896c0d547b27f8f28123d7f4 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 03:15:23 +0000
Subject: [PATCH 48/57] Update selenium-webdriver to version 4.41.0

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

diff --git a/Gemfile.lock b/Gemfile.lock
index 93af492a05..e5f70abc1f 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -562,7 +562,7 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.16.8)
     securerandom (0.4.1)
-    selenium-webdriver (4.40.0)
+    selenium-webdriver (4.41.0)
       base64 (~> 0.2)
       logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)

From 34defdd38f2dc26366925a9a5507a63aec578bb5 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Mon, 2 Mar 2026 19:00:21 +0000
Subject: [PATCH 49/57] Update bootsnap to version 1.23.0

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

diff --git a/Gemfile.lock b/Gemfile.lock
index e5f70abc1f..b0583be27d 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -134,7 +134,7 @@ GEM
     base64 (0.3.0)
     benchmark (0.5.0)
     bigdecimal (4.0.1)
-    bootsnap (1.22.0)
+    bootsnap (1.23.0)
       msgpack (~> 1.2)
     builder (3.3.0)
     bullet (8.1.0)

From b2048afa275a45447830c14db4254647074b6432 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Tue, 3 Mar 2026 10:20:48 +0000
Subject: [PATCH 50/57] rename the updated config files

---
 ...st_types.yml => 018_limber_lcm_triomics_request_types.wip.yml} | 0
 ...emplates.yml => 014_lcm_triomics_submission_templates.wip.yml} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename config/default_records/request_types/{018_limber_lcm_triomics_request_types.yml => 018_limber_lcm_triomics_request_types.wip.yml} (100%)
 rename config/default_records/submission_templates/{014_lcm_triomics_submission_templates.yml => 014_lcm_triomics_submission_templates.wip.yml} (100%)

diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml
similarity index 100%
rename from config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
rename to config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml
diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.wip.yml
similarity index 100%
rename from config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
rename to config/default_records/submission_templates/014_lcm_triomics_submission_templates.wip.yml

From 78f3a633b7c2813e6a636bfb19181553994c84b3 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Tue, 3 Mar 2026 14:25:14 +0000
Subject: [PATCH 51/57] move the new code into separte files

---
 ...> 018_limber_lcm_triomics_request_types.yml} |  0
 ...lcm_triomics_new_added_request_types.wip.yml | 14 ++++++++++++++
 .../014_lcm_triomics_submission_templates.yml   | 17 +++++++++++++++++
 ...mics_new_added_submission_templates.wip.yml} | 11 ++---------
 4 files changed, 33 insertions(+), 9 deletions(-)
 rename config/default_records/request_types/{018_limber_lcm_triomics_request_types.wip.yml => 018_limber_lcm_triomics_request_types.yml} (100%)
 create mode 100644 config/default_records/request_types/025_limber_lcm_triomics_new_added_request_types.wip.yml
 create mode 100644 config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
 rename config/default_records/submission_templates/{014_lcm_triomics_submission_templates.wip.yml => 020_lcm_triomics_new_added_submission_templates.wip.yml} (65%)

diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
similarity index 100%
rename from config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml
rename to config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
diff --git a/config/default_records/request_types/025_limber_lcm_triomics_new_added_request_types.wip.yml b/config/default_records/request_types/025_limber_lcm_triomics_new_added_request_types.wip.yml
new file mode 100644
index 0000000000..cecf8357a5
--- /dev/null
+++ b/config/default_records/request_types/025_limber_lcm_triomics_new_added_request_types.wip.yml
@@ -0,0 +1,14 @@
+# Request types for LCM Triomics RNASeq
+---
+limber_lcm_triomics_rnaseq:
+  name: LCM Triomics RNASeq
+  asset_type: Well
+  order: 1
+  request_class_name: IlluminaHtp::Requests::StdLibraryRequest
+  for_multiplexing: false
+  billable: true
+  product_line_name: Short Read
+  acceptable_purposes:
+    - LCMT Lysate
+  library_types:
+    - Combined LCM RNA
diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
new file mode 100644
index 0000000000..70255ccf46
--- /dev/null
+++ b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
@@ -0,0 +1,17 @@
+# Submission templates for LCM Triomics WGS and EMSeq
+---
+# LCM Triomics EMSeq submission template
+Limber-Htp - LCM Triomics:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_lcm_triomics_emseq"]
+    product_line_name: LCM Triomics
+    product_catalogue_name: LCM Triomics
+
+# LCM Triomics WGS submission template
+Limber-Htp - LCM Triomics WGS:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_lcm_triomics_wgs"]
+    product_line_name: LCM Triomics
+    product_catalogue_name: LCM Triomics
diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.wip.yml b/config/default_records/submission_templates/020_lcm_triomics_new_added_submission_templates.wip.yml
similarity index 65%
rename from config/default_records/submission_templates/014_lcm_triomics_submission_templates.wip.yml
rename to config/default_records/submission_templates/020_lcm_triomics_new_added_submission_templates.wip.yml
index 510d955d5a..824e90cde6 100644
--- a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.wip.yml
+++ b/config/default_records/submission_templates/020_lcm_triomics_new_added_submission_templates.wip.yml
@@ -1,5 +1,4 @@
-# Submission templates for LCM Triomics WGS and EMSeq
----
+# Submission templates for LCM Triomics EMSeq and RNASeq ---
 # LCM Triomics EMSeq submission template
 Limber-Htp - LCM Triomics EMSeq:
   submission_class_name: "LinearSubmission"
@@ -8,13 +7,7 @@ Limber-Htp - LCM Triomics EMSeq:
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
     project_name: "UAT Project"
-# LCM Triomics WGS submission template
-Limber-Htp - LCM Triomics WGS:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys: ["limber_lcm_triomics_wgs"]
-    product_line_name: LCM Triomics
-    product_catalogue_name: LCM Triomics
+
 # LCM Triomics RNASeq submission template
 Limber-Htp - LCM Triomics RNASeq:
   submission_class_name: "LinearSubmission"

From 556b078c0496b5b17c3f858f240afc6a8366483f Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Tue, 3 Mar 2026 14:38:55 +0000
Subject: [PATCH 52/57] update the file

---
 .../018_limber_lcm_triomics_request_types.yml       | 13 +------------
 .../014_lcm_triomics_submission_templates.yml       |  1 -
 2 files changed, 1 insertion(+), 13 deletions(-)

diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
index f1300f6b1f..51fba8e078 100644
--- a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
+++ b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
@@ -12,18 +12,7 @@ limber_lcm_triomics_emseq:
     - LCMT Lysate
   library_types:
     - emSEQ
-limber_lcm_triomics_rnaseq:
-  name: LCM Triomics RNASeq
-  asset_type: Well
-  order: 1
-  request_class_name: IlluminaHtp::Requests::StdLibraryRequest
-  for_multiplexing: false
-  billable: true
-  product_line_name: Short Read
-  acceptable_purposes:
-    - LCMT Lysate
-  library_types:
-    - Combined LCM RNA
+
 limber_lcm_triomics_wgs:
   name: LCM Triomics WGS
   asset_type: Well
diff --git a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
index 70255ccf46..7a55ace723 100644
--- a/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
+++ b/config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml
@@ -7,7 +7,6 @@ Limber-Htp - LCM Triomics:
     request_type_keys: ["limber_lcm_triomics_emseq"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
-
 # LCM Triomics WGS submission template
 Limber-Htp - LCM Triomics WGS:
   submission_class_name: "LinearSubmission"

From 2345a131e65a26ef91452b11b6c238617e9ab43a Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Tue, 3 Mar 2026 14:40:42 +0000
Subject: [PATCH 53/57] reverse existing config

---
 .../request_types/018_limber_lcm_triomics_request_types.yml      | 1 -
 1 file changed, 1 deletion(-)

diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
index 51fba8e078..cdc3f13ce4 100644
--- a/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
+++ b/config/default_records/request_types/018_limber_lcm_triomics_request_types.yml
@@ -12,7 +12,6 @@ limber_lcm_triomics_emseq:
     - LCMT Lysate
   library_types:
     - emSEQ
-
 limber_lcm_triomics_wgs:
   name: LCM Triomics WGS
   asset_type: Well

From 59e1e3e43e53b60384169b58afdb8ae0ffc5bc9b Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Tue, 3 Mar 2026 16:47:58 +0000
Subject: [PATCH 54/57] build: update datatables

---
 yarn.lock | 81 +++++++++++++++++++++++--------------------------------
 1 file changed, 33 insertions(+), 48 deletions(-)

diff --git a/yarn.lock b/yarn.lock
index c62ae64dd0..e10b4ef20f 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -862,20 +862,12 @@ 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:
-  version "2.3.3"
-  resolved "https://registry.yarnpkg.com/datatables.net-bs4/-/datatables.net-bs4-2.3.3.tgz#f4fabcd5ff78bad36bbda0ea62d6433cd9272a70"
-  integrity sha512-LFXCaB1nzsW0cXpRRctzfBnJtw4NbBpkcHehfdkeV8MuXnD0F9D1OkLIHLe/EnXbuWX7J1qk3QikigGHnox1LA==
+datatables.net-bs4@>=1.11.0, datatables.net-bs4@^2, datatables.net-bs4@^2.3.6:
+  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 "2.3.3"
-    jquery ">=1.7"
-
-datatables.net-bs4@^2.3.6:
-  version "2.3.6"
-  resolved "https://registry.yarnpkg.com/datatables.net-bs4/-/datatables.net-bs4-2.3.6.tgz#1b7148d1a15d0694f75b61650442d27ff353256a"
-  integrity sha512-9R7y8aTNLzyJKr4o+AoBbCZMdMT19VQCI4q/plPK5uXDHkUwmcAaI8/4sCrwlgXqkQK0h87bXyCFv1IE6xIa1w==
-  dependencies:
-    datatables.net "2.3.6"
+    datatables.net "2.3.7"
     jquery ">=1.7"
 
 datatables.net-buttons-bs4@^3.2.6:
@@ -913,35 +905,35 @@ datatables.net-fixedcolumns@5.0.5:
     jquery ">=1.7"
 
 datatables.net-fixedheader-bs4@^4.0.5:
-  version "4.0.5"
-  resolved "https://registry.yarnpkg.com/datatables.net-fixedheader-bs4/-/datatables.net-fixedheader-bs4-4.0.5.tgz#14d2a0ee029d3939d687114e22c28b194d205b4a"
-  integrity sha512-FSIPXPyp5asrGW/fniphFjiERWx0OcpKkzCoOjWt5itqk+V2cFxxpsriKnpSbsVrqKVFZir9md0CCD/Rs5UjeA==
+  version "4.0.6"
+  resolved "https://registry.yarnpkg.com/datatables.net-fixedheader-bs4/-/datatables.net-fixedheader-bs4-4.0.6.tgz#848310af658eb132ce1049623933e8d443b7c134"
+  integrity sha512-I2uPehQGDURxDH2JL/N+xVmB5sZq8H3pP2rZM2Y4JMHjtItLONgc3H1CF0LPWh20+9Ui28y0b3dgAroxvLt1Xg==
   dependencies:
     datatables.net-bs4 "^2"
-    datatables.net-fixedheader "4.0.5"
+    datatables.net-fixedheader "4.0.6"
     jquery ">=1.7"
 
-datatables.net-fixedheader@4.0.5:
-  version "4.0.5"
-  resolved "https://registry.yarnpkg.com/datatables.net-fixedheader/-/datatables.net-fixedheader-4.0.5.tgz#075fff97f47efac9f3ba72d34f8f0ea67470f165"
-  integrity sha512-cobQhOhjzqIYXTvMRrHUulULS8Re+hd2mmgFiOGKcZwHV0mofIwBlgiU3Ol4LHikHUCvsGnTEXoI+C7Ozma5sA==
+datatables.net-fixedheader@4.0.6:
+  version "4.0.6"
+  resolved "https://registry.yarnpkg.com/datatables.net-fixedheader/-/datatables.net-fixedheader-4.0.6.tgz#0c361a8a90542d75402f897db401085433efcebe"
+  integrity sha512-icYg/qKDpqGDrAVRWfsjt0xQdngk48R7LWkS9t8kaZFp9c4xrLFcmmPtRLgPp5/S4JHZbbsxmVkF16kscjNZjg==
   dependencies:
     datatables.net "^2"
     jquery ">=1.7"
 
 datatables.net-responsive-bs4@^3.0.7:
-  version "3.0.7"
-  resolved "https://registry.yarnpkg.com/datatables.net-responsive-bs4/-/datatables.net-responsive-bs4-3.0.7.tgz#20b1cf1df5ad753032dc74a20ae67841492db9fd"
-  integrity sha512-N5TDe0A31J1pEIpcd1GlU70deHUUeqbuLbFr6LUJ8Q3HXiD9bjyrYiuev8G4viFtRCNHMcrUCJnSRHu5ZtuK1A==
+  version "3.0.8"
+  resolved "https://registry.yarnpkg.com/datatables.net-responsive-bs4/-/datatables.net-responsive-bs4-3.0.8.tgz#a1bbdb4029b8618981a0e0d6bf85f4f243a9fdb3"
+  integrity sha512-OvaJdidQhSGbpTb+BMyUSzeRvPrQUHn8h87Z0Sbt9fnPFF7QsqowWo7a9/gxqwP+ZnXhdHLdOM7+DTxir2YRFA==
   dependencies:
     datatables.net-bs4 "^2"
-    datatables.net-responsive "3.0.7"
+    datatables.net-responsive "3.0.8"
     jquery ">=1.7"
 
-datatables.net-responsive@3.0.7:
-  version "3.0.7"
-  resolved "https://registry.yarnpkg.com/datatables.net-responsive/-/datatables.net-responsive-3.0.7.tgz#7b57574bcfba105dc0827b77ec75b72b63e461fb"
-  integrity sha512-MngWU41M1LDDMjKFJ3rAHc4Zb3QhOysDTh+TfKE1ycrh5dpnKa1vobw2MKMMbvbx4q05OXZY9jtLSPIkaJRsuw==
+datatables.net-responsive@3.0.8:
+  version "3.0.8"
+  resolved "https://registry.yarnpkg.com/datatables.net-responsive/-/datatables.net-responsive-3.0.8.tgz#c41d706c98442122e61a8fb9b02a8b2995cd487d"
+  integrity sha512-htslaX9g/9HFrJeyFQKEe/XJWpawPxpvy+M6vc/NkKQIrKhbxSoPc3phPqmlnZth6b9hgawqWDT0e0lwf5p+KA==
   dependencies:
     datatables.net "^2"
     jquery ">=1.7"
@@ -964,33 +956,26 @@ datatables.net-rowgroup@1.6.0:
     jquery ">=1.7"
 
 datatables.net-rowreorder-bs4@^1.5.0:
-  version "1.5.0"
-  resolved "https://registry.yarnpkg.com/datatables.net-rowreorder-bs4/-/datatables.net-rowreorder-bs4-1.5.0.tgz#5006eb235d9dfd78974d113df25a6b921328f013"
-  integrity sha512-4C9tzLRaisO+IOdJ1n6NRQ8ak0zC0IbX50Ed5hg+5PT7VJLI9klH+GBwE6hpF28UTWk7E6somzOwnRHLexqXdA==
+  version "1.5.1"
+  resolved "https://registry.yarnpkg.com/datatables.net-rowreorder-bs4/-/datatables.net-rowreorder-bs4-1.5.1.tgz#85fd5a4c2741f678da27a6798869b1d8ff1f600d"
+  integrity sha512-26Xx4JbrKhHQDh+GgvVK/XXeFIW6RLQnU5mLtMpy2S+K/9Yffyc71aZ8lyEmm5q7rNnw3LE+hY/FZN5sPTldTQ==
   dependencies:
     datatables.net-bs4 ">=1.11.0"
-    datatables.net-rowreorder "1.5.0"
+    datatables.net-rowreorder "1.5.1"
     jquery ">=1.7"
 
-datatables.net-rowreorder@1.5.0:
-  version "1.5.0"
-  resolved "https://registry.yarnpkg.com/datatables.net-rowreorder/-/datatables.net-rowreorder-1.5.0.tgz#f8b5242bd97df6b9522573378e98e8c7d64002dd"
-  integrity sha512-Kkq57tdJHrUCYkS8vywhL5tqKtl2q3K3p8A6wkIdwMX2b8YVjtywhQbXvvVLZnlMQsdX194FXVK1AgAwcm4hFg==
+datatables.net-rowreorder@1.5.1:
+  version "1.5.1"
+  resolved "https://registry.yarnpkg.com/datatables.net-rowreorder/-/datatables.net-rowreorder-1.5.1.tgz#257aa1dc2c29ed4421a95434a7044d3d4dd2a7fe"
+  integrity sha512-hVGXjl9lcLXHMdtwzCs2y47ZqYbSz9XhV+KSVkGsXu8M0MHma1rJXY7uOeCy5u/PMD4oONzgT2B8QCUBBbqvQA==
   dependencies:
     datatables.net ">=1.11.0"
     jquery ">=1.7"
 
-datatables.net@2.3.3, datatables.net@>=1.11.0, datatables.net@^2:
-  version "2.3.3"
-  resolved "https://registry.yarnpkg.com/datatables.net/-/datatables.net-2.3.3.tgz#fe4f96bdbc4cf47c8d11162a7af525ca6a3683d2"
-  integrity sha512-SWL3za6nheY6gdoiLgCc++tYmxbwrmv2bjrEiII9rXBWXXSbOZct6pjR3FueMVRM5jmt7pQcXiGovfuFDnutQg==
-  dependencies:
-    jquery ">=1.7"
-
-datatables.net@2.3.6:
-  version "2.3.6"
-  resolved "https://registry.yarnpkg.com/datatables.net/-/datatables.net-2.3.6.tgz#a11be57a2b50d7231cae2980a8ff1df3c18b7b17"
-  integrity sha512-xQ/dCxrjfxM0XY70wSIzakkTZ6ghERwlLmAPyCnu8Sk5cyt9YvOVyOsFNOa/BZ/lM63Q3i2YSSvp/o7GXZGsbg==
+datatables.net@2.3.7, datatables.net@>=1.11.0, datatables.net@^2:
+  version "2.3.7"
+  resolved "https://registry.yarnpkg.com/datatables.net/-/datatables.net-2.3.7.tgz#3cd34f6f5d1f40a46b5a20a4ba32604bdbcd6738"
+  integrity sha512-AvsjG/Nkp6OxeyBKYZauemuzQCPogE1kOtKwG4sYjvdqGCSLiGaJagQwXv4YxG+ts5vaJr6qKGG9ec3g6vTo3w==
   dependencies:
     jquery ">=1.7"
 

From a9c4ef3d11a2c49a3bdbea27534c7d807d598717 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 4 Mar 2026 00:00:27 +0000
Subject: [PATCH 55/57] Update Node.js to version 24.14.0

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

diff --git a/.nvmrc b/.nvmrc
index 32f8c50de0..d845d9d88d 100644
--- a/.nvmrc
+++ b/.nvmrc
@@ -1 +1 @@
-24.13.1
+24.14.0

From fd0ca2b68fe2122ef11fcf20549c75dbbcb17794 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 5 Mar 2026 00:45:21 +0000
Subject: [PATCH 56/57] Update flipper to version 1.4.0

---
 Gemfile.lock | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index b0583be27d..c8ad9a573e 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -247,14 +247,14 @@ GEM
     ffi (1.17.3-arm64-darwin)
     ffi (1.17.3-x86_64-darwin)
     ffi (1.17.3-x86_64-linux-gnu)
-    flipper (1.3.6)
+    flipper (1.4.0)
       concurrent-ruby (< 2)
-    flipper-active_record (1.3.6)
+    flipper-active_record (1.4.0)
       activerecord (>= 4.2, < 9)
-      flipper (~> 1.3.6)
-    flipper-ui (1.3.6)
+      flipper (~> 1.4.0)
+    flipper-ui (1.4.0)
       erubi (>= 1.0.0, < 2.0.0)
-      flipper (~> 1.3.6)
+      flipper (~> 1.4.0)
       rack (>= 1.4, < 4)
       rack-protection (>= 1.5.3, < 5.0.0)
       rack-session (>= 1.0.2, < 3.0.0)

From f5ed910f80ff2590795be3b4225ce0271fb3365f Mon Sep 17 00:00:00 2001
From: Ben Topping <ben.topping@outlook.com>
Date: Mon, 9 Mar 2026 10:41:24 +0000
Subject: [PATCH 57/57] misc: bumps release version

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

diff --git a/.release-version b/.release-version
index d39ebf95de..88927ab769 100644
--- a/.release-version
+++ b/.release-version
@@ -1 +1 @@
-14.88.0
+14.89.0