Y26-129 - Add sample manifest uploads controls for volume and concentration

app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb

@@ -19,7 +19,10 @@ def create
   end
 
   def create_uploader
-    SampleManifest::Uploader.new(params[:upload], SampleManifestExcel.configuration, current_user, params[:override])
+    samples = params[:override_samples].present?
+
+    overrides = { samples:, exclude_fields: }
+    SampleManifest::Uploader.new(params[:upload], SampleManifestExcel.configuration, current_user, overrides)
   end
 
   def upload_manifest
@@ -82,4 +85,11 @@ def prepare_manifest_pagination # rubocop:todo Metrics/MethodLength
     @display_manifests = pending_sample_manifests | completed_sample_manifests
     @sample_manifests = SampleManifest.paginate(page: params[:page])
   end
+
+  def exclude_fields
+    excluded_fields = []
+    excluded_fields << :volume if params[:overwrite_volume].blank?
+    excluded_fields << :concentration if params[:overwrite_concentration].blank?
+    excluded_fields.compact
+  end
 end

app/models/sample_manifest.rb

@@ -51,7 +51,7 @@ def self.included(base)
   has_uploaded_document :uploaded, differentiator: 'uploaded'
   has_uploaded_document :generated, differentiator: 'generated'
 
-  attr_accessor :override, :only_first_label, :barcode_type
+  attr_accessor :overrides, :only_first_label, :barcode_type
   attr_writer :rows_per_well, :invalid_wells
 
   class_attribute :spreadsheet_offset

app/models/sample_manifest/uploader.rb

@@ -9,7 +9,7 @@
 class SampleManifest::Uploader
   include ActiveModel::Validations
 
-  attr_reader :file, :configuration, :tag_group, :upload, :user, :override
+  attr_reader :file, :configuration, :tag_group, :upload, :user
 
   validates :tag_group, presence: { message: 'is not correctly configured for manifest generation' }
   validates :file, :configuration, :user, presence: true
@@ -18,14 +18,12 @@ class SampleManifest::Uploader
 
   delegate :processed?, :study, to: :upload
 
-  def initialize(file, configuration, user, override)
+  def initialize(file, configuration, user, overrides)
     @file = file
     @configuration = configuration || SequencescapeExcel::NullObjects::NullConfiguration.new
     @user = user
-    @override = override
     @tag_group = create_tag_group
-    @upload =
-      SampleManifestExcel::Upload::Base.new(file: file, column_list: self.configuration.columns.all, override: override)
+    @upload =  SampleManifestExcel::Upload::Base.new(file:, column_list:, overrides:)
   end
 
   def run! # rubocop:disable Metrics/MethodLength
@@ -54,6 +52,10 @@ def run! # rubocop:disable Metrics/MethodLength
 
   private
 
+  def column_list
+    configuration.columns.all
+  end
+
   def process_upload_and_callbacks
     return false unless upload.process(tag_group)
 

app/sample_manifest_excel/sample_manifest_excel/upload/base.rb

@@ -19,7 +19,7 @@ class Base # rubocop:todo Metrics/ClassLength
       include AccessionHelper
       include ActiveModel::Model
 
-      attr_accessor :file, :column_list, :start_row, :override
+      attr_accessor :file, :column_list, :start_row, :overrides
 
       # rubocop:todo Layout/LineLength
       attr_reader :spreadsheet, :columns, :sanger_sample_id_column, :rows, :sample_manifest, :data, :processor, :cache # TODO: probably shouldn't add the cache here, do it another way
@@ -47,7 +47,7 @@ def initialize(attributes = {}) # rubocop:todo Metrics/AbcSize
         @cache = Cache.new(self)
         @rows = Upload::Rows.new(data, columns, @cache)
         @sample_manifest = derive_sample_manifest
-        @override = override || false
+        @overrides = overrides || { samples: false, exclude_fields: [] }
         @processor = create_processor
       end
 

app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb

@@ -49,7 +49,7 @@ def samples_valid?
           all_valid = true
 
           upload.rows.each do |row|
-            unless row.validate_sample
+            unless row.validate_sample(upload.overrides)
               upload.errors.add(:base, row.errors.full_messages.join(', ').to_s)
               all_valid = false
             end
@@ -60,7 +60,7 @@ def samples_valid?
 
         def update_samples_and_aliquots(tag_group)
           upload.rows.each do |row|
-            row.update_sample(tag_group, upload.override)
+            row.update_sample(tag_group, upload.overrides)
             substitutions.concat(row.aliquots.filter_map(&:substitution_hash)) if row.reuploaded?
           end
           update_downstream_aliquots unless no_substitutions?

app/sample_manifest_excel/sample_manifest_excel/upload/processor/multiplexed_library_tube.rb

@@ -24,7 +24,7 @@ def run(tag_group)
 
         def update_samples_and_aliquots(tag_group)
           upload.rows.each do |row|
-            row.update_sample(tag_group, upload.override)
+            row.update_sample(tag_group, upload.overrides)
             row.transfer_aliquot # Requests are smart enough to only transfer once
             substitutions.concat(row.aliquots.filter_map(&:substitution_hash)) if row.reuploaded?
           end

app/sample_manifest_excel/sample_manifest_excel/upload/row.rb

@@ -88,30 +88,41 @@
       # - Updating all of the specialised fields in the aliquot
       # - Updating the sample metadata
       # - Saving the asset, metadata and sample
-      def update_sample(tag_group, override)
+      def update_sample(tag_group, overrides)
         return unless valid?
 
         @reuploaded = sample.updated_by_manifest
 
-        if skip_sample_update?(override)
+        if skip_sample_update?(overrides)
           @sample_skipped = true
           return
         end
 
-        @sample_updated = save_sample(tag_group)
+        exclude_fields = overrides[:exclude_fields]
+        @sample_updated = save_sample(tag_group, exclude_fields)
       end
 
       def changed?
         (@sample_updated && sample.previous_changes.present?) || metadata.previous_changes.present? ||
           aliquots.any? { |a| a.previous_changes.present? }
       end
 
-      def update_specialised_fields(tag_group)
-        specialised_fields.each { |specialised_field| specialised_field.update(tag_group:) }
+      def update_specialised_fields(tag_group, exclude_fields)
+        specialised_fields.each do |specialised_field|
+          puts "Exclude specialised fields: #{exclude_fields.inspect}, Processing column: #{specialised_field.name.to_sym}"
+          next if exclude_fields.include?(specialised_field.name.to_sym)
+
+          puts "Updating specialised field: #{specialised_field.name}"
+
+          specialised_field.update(tag_group:)
+        end
       end
 
-      def update_metadata_fields
+      def update_metadata_fields(exclude_fields)
         columns.with_metadata_fields.each do |column|
+          puts "Exclude metadata fields: #{exclude_fields.inspect}, Processing column: #{column.name}"
+          next if exclude_fields.include?(column.name.to_sym)
+
           value = at(column.number)
           column.update_metadata(metadata, value) if value.present?
         end
@@ -172,9 +183,9 @@
         sample.primary_receptacle.labware
       end
 
-      def validate_sample
+      def validate_sample(overrides)
         check_sample_present
-        sample_can_be_updated
+        sample_can_be_updated(overrides)
         errors.empty?
       end
 
@@ -247,12 +258,14 @@
       #
       # This confirms that the sample can be updated by attempting to apply the updates
       # and raising errors if any of the updates are invalid. It does not (seem to!) save any changes to the database.
-      def sample_can_be_updated
+      def sample_can_be_updated(overrides)
         return unless errors.empty?
 
+        exclude_fields = overrides[:exclude_fields]
+
         check_primary_receptacle
-        check_specialised_fields
-        check_sample_metadata
+        check_specialised_fields(exclude_fields)
+        check_sample_metadata(exclude_fields)
       end
 
       def check_primary_receptacle
@@ -261,19 +274,21 @@
         errors.add(:base, "#{row_title} Does not have a primary receptacle.")
       end
 
-      def check_specialised_fields
+      def check_specialised_fields(exclude_fields)
         return unless errors.empty?
 
         specialised_fields.each do |specialised_field|
+          next if exclude_fields.include?(specialised_field.name.to_sym)
+
           unless specialised_field.valid?
             errors.add(:base, "#{row_title} #{specialised_field.errors.full_messages.join(', ')}")
           end
         end
       end
 
-      def check_sample_metadata
+      def check_sample_metadata(exclude_fields)
         # it has to be called here, otherwise metadata errors will not appear
-        update_metadata_fields
+        update_metadata_fields(exclude_fields)
         return if metadata.valid?
 
         errors.add(:base, "#{row_title} #{metadata.errors.full_messages.join(', ')}")
@@ -302,10 +317,10 @@
         fields.each { |field| field.link(indexed_fields) }
       end
 
-      def save_sample(tag_group)
-        update_specialised_fields(tag_group)
+      def save_sample(tag_group, exclude_fields)
+        update_specialised_fields(tag_group, exclude_fields)
         asset.save!
-        update_metadata_fields
+        update_metadata_fields(exclude_fields)
         metadata.save!
         sample.updated_by_manifest = true
         sample.empty_supplier_sample_name = false

app/views/sdb/sample_manifests/_upload.html.erb

@@ -6,11 +6,43 @@
         <%= file_field_tag :upload, required: true %>
       </div>
       <div class="form-group">
-        <%= check_box_tag :override %>&nbsp;<%= label_tag :override, 'Override previously uploaded samples' %>
+        <div class="form-check">
+          <%= check_box_tag :override_samples, class: 'form-check-input'%>
+          <%= label_tag :override_samples, 'Override previously uploaded samples', class: 'form-check-label' %>
+        </div>
+
+        <div class="ml-3"><%# Indent the volume and concentration checkboxes, since they depend on override_samples %>
+          <div class="form-check">
+            <%= check_box_tag :overwrite_volume, class: 'form-check-input', disabled: true %>
+            <%= label_tag :overwrite_volume, 'Overwrite volume', class: 'form-check-label' %>
+          </div>
+          <div class="form-check">
+            <%= check_box_tag :overwrite_concentration, class: 'form-check-input', disabled: true %>
+            <%= label_tag :overwrite_concentration, 'Overwrite concentration', class: 'form-check-label' %>
+          </div>
+        </div>
       </div>
       <div class="form-group mb-0">
         <%= submit_tag 'Upload manifest', class: 'btn btn-success' %>
       </div>
     </fieldset>
   <% end -%>
 <% end %>
+
+<script>
+  // Add JavaScript to enable/disable the volume and concentration checkboxes based on the state of the override-samples checkbox
+  document.addEventListener('DOMContentLoaded', function() {
+    const overrideSamples = document.getElementById('override_samples');
+    const overwriteVolume = document.getElementById('overwrite_volume');
+    const overwriteConcentration = document.getElementById('overwrite_concentration');
+
+    // Enable the vol and conc checkboxes when override-samples is checked, otherwise disable them
+    function updateCheckboxStates() {
+      overwriteVolume.disabled = !overrideSamples.checked;
+      overwriteConcentration.disabled = !overrideSamples.checked;
+    }
+
+    // Listen for changes
+    overrideSamples.addEventListener('change', updateCheckboxStates);
+  });
+</script>

app/views/shared/metadata/show/_sample.html.erb

@@ -9,12 +9,15 @@
     <%= metadata_fields.plain_value(:geographical_region) %>
     <%= metadata_fields.plain_value(:ethnicity) %>
     <%= metadata_fields.plain_value(:dna_source) %>
-    <%= metadata_fields.plain_value(:volume) %>
     <%= metadata_fields.plain_value(:mother) %>
     <%= metadata_fields.plain_value(:father) %>
     <%= metadata_fields.plain_value(:replicate) %>
     <%= metadata_fields.plain_value(:collected_by) %>
 
+    <!-- Physical properties -->
+    <%= metadata_fields.plain_value(:volume) %>
+    <%= metadata_fields.plain_value(:concentration) %>
+
     <%# Fields for 'Next-gen sequencing' %>
     <%= metadata_fields.plain_value(:organism) %>
     <%= metadata_fields.plain_value(:gc_content) %>