Merge pull request #1365 from sanger/y24-096-add-uuid-to-aliquot

refactor: add uuid field to aliquot

Author: seenanair

app/exchanges/volume_tracking/message_builder.rb

@@ -11,7 +11,7 @@ class MessageBuilder < Message::Message
     #    "messageUuid"=>"0a62ee15-bbf6-46f0-ba95-01d42622d076",
     #    "recordedAt"=>Mon, 15 Jul 2024 15:16:54.867713000 UTC +00:00,
     #    "volume"=>1.5, "concentration"=>10.0, "insertSize"=>100, "aliquotType"=>"primary",
-    #    "aliquotId"=>"", "sourceType"=>"library", "sourceBarcode"=>"TRAC-2-35805",
+    #    "aliquotUuid"=>"", "sourceType"=>"library", "sourceBarcode"=>"TRAC-2-35805",
     #    "sampleName"=>"Sample1", "usedByBarcode"=>"TRAC-2-35806", "usedByType"=>"pool"}}
 
     def publish_data # rubocop:disable Metrics/MethodLength
@@ -20,7 +20,7 @@ def publish_data # rubocop:disable Metrics/MethodLength
 
       aliquot = object
       data = { source_type: '', source_barcode: '', sample_name: '',
-               used_by_type: 'nil', used_by_barcode: '', aliquot_id: aliquot.id.to_s || '' }
+               used_by_type: 'nil', used_by_barcode: '', aliquot_uuid: aliquot.uuid || '' }
 
       case aliquot.source_type
       when 'Pacbio::Library'

app/models/aliquot.rb

@@ -6,6 +6,7 @@
 # An aliquot can be used to track volumes and concentrations of samples
 class Aliquot < ApplicationRecord
   include SampleSheet::Aliquot
+  include Uuidable
 
   enum state: { created: 0, used: 1 }
   enum aliquot_type: { primary: 0, derived: 1 }

config/pipelines/pacbio.yml

@@ -333,9 +333,9 @@ default: &default
           aliquotType:
             type: :model
             value: aliquot_type
-          aliquotId:
+          aliquotUuid:
             type: :self
-            value: publish_data&.aliquot_id
+            value: publish_data&.aliquot_uuid
           sourceType:
             type: :self
             value: publish_data&.source_type

lib/tasks/update_aliquots_with_uuids.rake

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+namespace :aliquots do
+  #  A rake task to be run to add UUIDs to all aliquots that do not have one
+  desc 'Update aliquots with UUID'
+
+  task add_missing_uuids: :environment do
+    puts '-> Updating aliquots with UUID'
+
+    ActiveRecord::Base.transaction do
+      # If an aliquot does not have a UUID set it
+      Aliquot.where(uuid: nil).find_each do |aliquot|
+        aliquot.update!(uuid: SecureRandom.uuid)
+      end
+    end
+  end
+end

spec/exchanges/volume_tracking/message_builder_spec.rb

@@ -21,7 +21,7 @@
                                                      sample_name: pacbio_library.sample_name,
                                                      used_by_type: 'nil',
                                                      used_by_barcode: '',
-                                                     aliquot_id: aliquot.id.to_s || ''
+                                                     aliquot_uuid: aliquot.uuid
                                                    })
       end
     end
@@ -37,7 +37,7 @@
                                                      sample_name: pacbio_library.sample_name,
                                                      used_by_type: 'pool',
                                                      used_by_barcode: pacbio_pool.tube.barcode,
-                                                     aliquot_id: aliquot.id.to_s || ''
+                                                     aliquot_uuid: aliquot.uuid
                                                    })
       end
     end
@@ -53,7 +53,7 @@
                                                      sample_name: pacbio_library.sample_name,
                                                      used_by_type: 'well',
                                                      used_by_barcode: "#{pacbio_well.plate.sequencing_kit_box_barcode}:#{pacbio_well.plate.plate_number}:#{pacbio_well.position}",
-                                                     aliquot_id: aliquot.id.to_s || ''
+                                                     aliquot_uuid: aliquot.uuid
                                                    })
       end
     end

spec/fixtures/volume_tracking_avro_response.json

@@ -2,5 +2,5 @@
   "subject": "create-aliquot-in-mlwh",
   "version": 1,
   "id": 14,
-  "schema": "{\"type\":\"record\",\"name\":\"CreateAliquotInMLWH\",\"namespace\":\"uk.ac.sanger.psd\",\"doc\":\"Create an Aliquot in MLWH coming from Traction.\",\"fields\":[{\"name\":\"messageUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"Unique message ID.\"},{\"name\":\"messageCreateDateUtc\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"Date (UTC) that the message was created.\"},{\"name\":\"limsId\",\"type\":\"string\",\"doc\":\"The LIMS system that the aliquot was created in\"},{\"name\":\"aliquotId\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"The UUID of the aliquot in the LIMS system\"},{\"name\":\"aliquotType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedAliquotType\",\"symbols\":[\"primary\",\"derived\"]},\"doc\":\"The type of the aliquot\"},{\"name\":\"sourceType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedSourceType\",\"symbols\":[\"well\",\"sample\",\"library\",\"pool\"]},\"doc\":\"The type of the source of the aliquot\"},{\"name\":\"sourceBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the source of the aliquot\"},{\"name\":\"sampleName\",\"type\":\"string\",\"doc\":\"The name of the sample that the aliquot was created from\"},{\"name\":\"usedByType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedUsedByType\",\"symbols\":[\"library\",\"pool\",\"run\",\"none\"],\"default\":\"none\"},\"doc\":\"The type of the entity that the aliquot is used by\"},{\"name\":\"usedByBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the entity that the aliquot is used by\"},{\"name\":\"volume\",\"type\":\"float\",\"doc\":\"The volume of the aliquot (uL)\"},{\"name\":\"concentration\",\"type\":[\"null\",\"float\"],\"doc\":\"The concentration of the aliquot (ng/ul)\",\"default\":null},{\"name\":\"insertSize\",\"type\":[\"null\",\"int\"],\"doc\":\"The insert size for the aliquot\",\"default\":null},{\"name\":\"recordedAt\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"The date and time that the aliquot was recorded\"}]}"
+  "schema": "{\"type\":\"record\",\"name\":\"CreateAliquotInMLWH\",\"namespace\":\"uk.ac.sanger.psd\",\"doc\":\"Create an Aliquot in MLWH coming from Traction.\",\"fields\":[{\"name\":\"messageUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"Unique message ID.\"},{\"name\":\"messageCreateDateUtc\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"Date (UTC) that the message was created.\"},{\"name\":\"limsId\",\"type\":\"string\",\"doc\":\"The LIMS system that the aliquot was created in\"},{\"name\":\"aliquotUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"The UUID of the aliquot in the LIMS system\"},{\"name\":\"aliquotType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedAliquotType\",\"symbols\":[\"primary\",\"derived\"]},\"doc\":\"The type of the aliquot\"},{\"name\":\"sourceType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedSourceType\",\"symbols\":[\"well\",\"sample\",\"library\",\"pool\"]},\"doc\":\"The type of the source of the aliquot\"},{\"name\":\"sourceBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the source of the aliquot\"},{\"name\":\"sampleName\",\"type\":\"string\",\"doc\":\"The name of the sample that the aliquot was created from\"},{\"name\":\"usedByType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedUsedByType\",\"symbols\":[\"library\",\"pool\",\"run\",\"none\"],\"default\":\"none\"},\"doc\":\"The type of the entity that the aliquot is used by\"},{\"name\":\"usedByBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the entity that the aliquot is used by\"},{\"name\":\"volume\",\"type\":\"float\",\"doc\":\"The volume of the aliquot (uL)\"},{\"name\":\"concentration\",\"type\":[\"null\",\"float\"],\"doc\":\"The concentration of the aliquot (ng/ul)\",\"default\":null},{\"name\":\"insertSize\",\"type\":[\"null\",\"int\"],\"doc\":\"The insert size for the aliquot\",\"default\":null},{\"name\":\"recordedAt\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"The date and time that the aliquot was recorded\"}]}"
 }

spec/lib/tasks/update_aliquots_with_uuids.rake_spec.rb

@@ -0,0 +1,45 @@
+# 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
+  # Create a default SMRTLink version to be used by factories
+  before do
+    Pacbio::SmrtLinkVersion.find_by(name: 'v13_sequel_iie') || create(:pacbio_smrt_link_version, name: 'v13_sequel_iie', default: true)
+  end
+
+  describe 'aliquots:add_missing_uuids' do
+    define_negated_matcher :not_change, :change
+
+    it 'assigns a random UUID to all aliquots that currently lack one.' do
+      aliquots_with_empty_uuid = create_list(:aliquot, 5, used_by: create(:pacbio_pool), uuid: nil)
+      aliquots_with_uuid = create_list(:aliquot, 5, used_by: create(:pacbio_pool))
+
+      # Get uuids to check they are not affected
+      uuids = aliquots_with_uuid.map(&:uuid)
+
+      # We shouldnt change the amount of aliquots
+      expect { Rake::Task['aliquots:add_missing_uuids'].invoke }.to not_change(Aliquot, :count).and output(
+        <<~HEREDOC
+          -> Updating aliquots with UUID
+        HEREDOC
+      ).to_stdout
+
+      # Aliquots without uuids should have a uuid set
+      aliquots_with_empty_uuid.each do |aliquot|
+        aliquot.reload
+        expect(aliquot.uuid).not_to be_nil
+      end
+
+      # Other aliquots should not be affected
+      aliquots_with_uuid.each do |aliquot|
+        aliquot.reload
+        expect(uuids).to include aliquot.uuid
+      end
+    end
+  end
+end

spec/models/aliquot_spec.rb

@@ -3,6 +3,12 @@
 require 'rails_helper'
 
 RSpec.describe Aliquot do
+  context 'uuidable aliquot' do
+    let(:uuidable_model) { :aliquot }
+
+    it_behaves_like 'uuidable'
+  end
+
   it 'is invalid without volume' do
     expect(build(:aliquot, volume: nil)).not_to be_valid
   end