Merge pull request #1363 from sanger/1354-y24-180---bug-pacbio-libraries-not-updating-their-used_aliquots-when-they-are-edited

feat: Update used aliquots data when primary aliquot is updated for a library

Author: stevieing

app/models/pacbio/library.rb

@@ -49,6 +49,8 @@ class Library < ApplicationRecord
     # if the new volume is greater than the used volume.
     before_update :primary_aliquot_volume_sufficient
 
+    after_update :update_used_aliquots
+
     before_destroy :check_for_derived_aliquots, prepend: true
 
     def create_used_aliquot
@@ -65,6 +67,19 @@ def create_used_aliquot
       )
     end
 
+    # Updates the used aliquots data when the primary aliquot is updated
+    def update_used_aliquots
+      used_aliquots.each do |aliquot|
+        aliquot.update(
+          volume: primary_aliquot.volume,
+          concentration: primary_aliquot.concentration,
+          template_prep_kit_box_barcode: primary_aliquot.template_prep_kit_box_barcode,
+          insert_size: primary_aliquot.insert_size,
+          tag: primary_aliquot.tag
+        )
+      end
+    end
+
     # Always false for libraries, but always true for wells - a gross simplification
     def collection?
       false

lib/tasks/update_used_aliquots_with_primary_aliquot_tags.rake

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+namespace :used_aliquots do
+  task update_tags: :environment do
+    libraries = Pacbio::Library.all.reject { |library| library.used_aliquots.first.tag == library.tag }
+    libraries.each do |library|
+      library.used_aliquots.each do |used_aliquot|
+        used_aliquot.update!(tag: library.tag)
+      end
+    end
+    puts "-> #{libraries.count} instances of libraries updated."
+  end
+end

spec/lib/tasks/update_used_aliquots_with_primary_aliquot_tag.rake_spec.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+require 'rake'
+
+# only load Rake tasks if they haven't been loaded already
+Rails.application.load_tasks if Rake::Task.tasks.empty?
+
+RSpec.describe 'RakeTasks' do
+  describe 'used_aliquots:update_tags' do
+    it 'updates used aliquots with primary aliquot tag' do
+      libraries = create_list(:pacbio_library, 5)
+      tag = create(:tag)
+      libraries.each do |library|
+        library.used_aliquots.first.update!(tag:)
+      end
+
+      expect { Rake::Task['used_aliquots:update_tags'].invoke }.to output(
+        "-> #{libraries.count} instances of libraries updated.\n"
+      ).to_stdout
+
+      libraries.each do |library|
+        library.reload
+        expect(library.used_aliquots.first.tag).to eq(library.tag)
+      end
+    end
+  end
+end

spec/models/pacbio/library_spec.rb

@@ -310,4 +310,17 @@
       library.save
     end
   end
+
+  context 'after_update' do
+    it 'updates used_aliquots' do
+      library = create(:pacbio_library)
+      tag = create(:tag)
+      library.update(primary_aliquot_attributes: { tag_id: tag.id, volume: 1000, concentration: 1000, insert_size: 1000, template_prep_kit_box_barcode: 'LK456' })
+      expect(library.used_aliquots.first.tag).to eq(tag)
+      expect(library.used_aliquots.first.volume).to eq(1000)
+      expect(library.used_aliquots.first.concentration).to eq(1000)
+      expect(library.used_aliquots.first.insert_size).to eq(1000)
+      expect(library.used_aliquots.first.template_prep_kit_box_barcode).to eq('LK456')
+    end
+  end
 end

spec/requests/v1/pacbio/libraries_spec.rb

@@ -457,11 +457,6 @@
         library.reload
         expect(library.primary_aliquot.template_prep_kit_box_barcode).to eq('100')
       end
-
-      it 'does not update the used_aliquots' do
-        library.reload
-        expect(library.used_aliquots.first.template_prep_kit_box_barcode).not_to eq('100')
-      end
     end
 
     context 'on failure - when there is invalid library data' do