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 1/8] 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 2/8] 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 3/8] 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 4/8] 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 5/8] 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 6/8] 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 7/8] 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 8/8] 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: