Y26-125 dual index tags update in mlwh

app/models/aliquot/data_for_substitution.rb

@@ -7,6 +7,8 @@ module Aliquot::DataForSubstitution
   def substitution_hash
     return if id_previously_changed?
 
+    # Take care with saved_changes? - the Aliquot object in memory must be the same one that you called save on,
+    # otherwise you can't detect the changes.
     generate_substitution_hash if saved_changes?
   end
 

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

@@ -107,7 +107,8 @@ def disable_match_expectation
           true
         end
 
-        # if manifest is reuploaded, only aliquots, that are in 'fake' library tubes will be updated
+        # Comment is re: a multiplexed library tubes scenario, but this method is used for plates too.
+        # if manifest is re-uploaded, only aliquots, that are in 'fake' library tubes will be updated
         # actual aliquots in multiplexed library tube and other aliquots downstream are updated by this method
         # library updates all aliquots in one go, doing it row by row is inefficient and may trigger tag clash
         def update_downstream_aliquots

app/sample_manifest_excel/sample_manifest_excel/upload/row.rb

@@ -295,7 +295,11 @@ def create_specialised_fields
 
         specialised_fields =
           columns.with_specialised_fields.map do |column|
-            column.specialised_field.new(value: at(column.number), sample_manifest_asset: manifest_asset)
+            column.specialised_field.new(
+              value: at(column.number),
+              sample_manifest_asset: manifest_asset,
+              row: self
+            )
           end
 
         specialised_fields.tap { |fields| link_tag_groups_and_indexes(fields) }

app/sequencescape_excel/sequencescape_excel/specialised_field/base.rb

@@ -15,7 +15,7 @@ module Base
         end
       end
 
-      attr_accessor :value, :sample_manifest_asset
+      attr_accessor :value, :sample_manifest_asset, :row
 
       delegate :present?, to: :value, prefix: true
       delegate :asset, :sample, :sample_manifest, to: :sample_manifest_asset

app/sequencescape_excel/sequencescape_excel/specialised_field/dual_index_tag_well.rb

@@ -26,30 +26,36 @@ class DualIndexTagWell
       def update(_attributes = {})
         return unless valid?
 
-        # NB. asset here is a well, and a the well_has_single_aliquot? validation ensures there is only one aliquot
-        stock_aliquot = asset.aliquots.first
-
-        # Update all downstream aliquots as well as current aliquot
-        matching_aliquots = identify_all_matching_aliquots(stock_aliquot)
-        update_all_relevant_aliquots(matching_aliquots, tag, tag2)
+        # NB. the asset here is a well, and the well_has_single_aliquot? validation ensures there is only one aliquot
+        # NB. we are fetching via row so this is the same aliquot instance so saved_changes? works to detect
+        # substitutions
+        row.aliquots.first.assign_attributes(tag:, tag2:)
       end
 
       def link(other_fields)
         self.sf_dual_index_tag_set = other_fields[SequencescapeExcel::SpecialisedField::DualIndexTagSet]
       end
 
-      # From the validation in DualIndexTagSet, we know this tag set is a valid dual index tag set
+      # From the validation in DualIndexTagSet, we will know if this tag set is a valid dual index tag set
       # with a visible tag group and visible tag2 group
       def dual_index_tag_set
         @dual_index_tag_set = TagSet.find(sf_dual_index_tag_set.tag_set_id) if sf_dual_index_tag_set&.tag_set_id
       end
 
       def tag_group_id
-        @tag_group_id ||= ::TagGroup.find_by(id: dual_index_tag_set.tag_group_id, visible: true).id
+        # defensive guard to avoid NoMethodError being thrown when dual_index_tag_set is nil, caught by validation
+        # in DualIndexTagSet
+        return unless dual_index_tag_set
+
+        @tag_group_id ||= ::TagGroup.find_by(id: dual_index_tag_set.tag_group_id, visible: true)&.id
       end
 
       def tag2_group_id
-        @tag2_group_id ||= ::TagGroup.find_by(id: dual_index_tag_set.tag2_group_id, visible: true).id
+        # defensive guard to avoid NoMethodError being thrown when dual_index_tag_set is nil, caught by validation
+        # in DualIndexTagSet
+        return unless dual_index_tag_set
+
+        @tag2_group_id ||= ::TagGroup.find_by(id: dual_index_tag_set.tag2_group_id, visible: true)&.id
       end
 
       private
@@ -82,28 +88,6 @@ def well_has_single_aliquot?
         msg = "Expecting well #{asset.map.description} to have a single aliquot, but it has #{asset.aliquots.count}"
         errors.add(:base, msg)
       end
-
-      # Find all aliquots that need updating
-      # Aliquots must have a matching sample_id, library_id, tag_id and tag2_id to the given stock_aliquot.
-      def identify_all_matching_aliquots(stock_aliquot)
-        attributes = {
-          sample_id: stock_aliquot.sample_id,
-          library_id: stock_aliquot.library_id,
-          tag_id: stock_aliquot.tag_id,
-          tag2_id: stock_aliquot.tag2_id
-        }
-
-        Aliquot.where(attributes).ids
-      end
-
-      # Update the tags in all the matching aliquots
-      # NB. if active record sees that nothing has changed it will update the record
-      def update_all_relevant_aliquots(matching_aliquots, i7_tag, i5_tag)
-        Aliquot.where(id: matching_aliquots).find_each do |aq|
-          aq.update(tag: i7_tag, tag2: i5_tag)
-          aq.save!
-        end
-      end
     end
   end
 end

spec/sequencescape_excel/specialised_field_spec.rb

@@ -718,8 +718,9 @@ def self.name
 
     describe SequencescapeExcel::SpecialisedField::DualIndexTagWell do
       let(:sf_dual_index_tag_well) do
-        described_class.new(value: dual_index_tag_well, sample_manifest_asset: sample_manifest_asset)
+        described_class.new(value: dual_index_tag_well, sample_manifest_asset: sample_manifest_asset, row: row)
       end
+      let(:row) { instance_double(SampleManifestExcel::Upload::Row, aliquots: asset.aliquots) }
       let(:sf_dual_index_tag_set) do
         SequencescapeExcel::SpecialisedField::DualIndexTagSet.new(
           value: dual_index_tag_set.name,
@@ -742,6 +743,7 @@ def self.name
 
             it 'will apply the two tags associated with the map_id' do
               sf_dual_index_tag_well.update(aliquot: aliquot, tag_group: nil)
+              row.aliquots.first.save!
               # well location 'A1' => map_id '1'
               expect(asset.reload.aliquots.first.tag.map_id).to eq 1
               expect(asset.reload.aliquots.first.tag.tag_group).to eq tag_group1
@@ -763,6 +765,7 @@ def self.name
 
             it 'will apply the 2 tags associated with the updated map_id' do
               sf_dual_index_tag_well.update(aliquot: aliquot, tag_group: nil)
+              row.aliquots.first.save!
               # well location 'D1' => map_id '4'
               expect(asset.reload.aliquots.first.tag.map_id).to eq 4
               expect(asset.reload.aliquots.first.tag2.map_id).to eq 4
@@ -799,19 +802,13 @@ def self.name
               downstream_aliquot2
             end
 
-            it 'will apply the 2 tags associated with the updated map_id' do
+            it 'will apply the 2 tags associated with the updated map_id to the source aliquot' do
               sf_dual_index_tag_well.update(aliquot: aliquot, tag_group: nil)
+              row.aliquots.first.save!
 
               # well location 'D1' => map_id '4'
               expect(asset.reload.aliquots.first.tag.map_id).to eq 4
               expect(asset.reload.aliquots.first.tag2.map_id).to eq 4
-
-              # check downstream aliquots updated too
-              expect(downstream_aliquot1.reload.tag.map_id).to eq 4
-              expect(downstream_aliquot1.reload.tag2.map_id).to eq 4
-
-              expect(downstream_aliquot2.reload.tag.map_id).to eq 4
-              expect(downstream_aliquot2.reload.tag2.map_id).to eq 4
             end
           end