Merge pull request #1455 from sanger/1451-y24-370---as-tree-of-life-w…

…e-would-like-the-sample-data-in-the-warehouse-when-a-library-is-created-so-that-we-can-track-back-to-the-original-plate-or-tube-barcode-to-make-the-top-up-process-more-efficient

Publishing filtered aliquots

app/exchanges/volume_tracking/message_builder.rb

@@ -46,6 +46,7 @@ def base_data
       }
     end
 
+    # rubocop:disable Metrics/MethodLength
     def populate_by_source_type(data)
       case object.source_type
       when 'Pacbio::Library'
@@ -56,8 +57,13 @@ def populate_by_source_type(data)
         data[:source_type] = 'pool'
         data[:source_barcode] = object.source.tube.barcode
         data[:sample_name] = pacbio_library_sample_names
+      when 'Pacbio::Request'
+        data[:source_type] = 'request'
+        data[:source_barcode] = object.source.container.barcode
+        data[:sample_name] = object.source.sample_name
       end
     end
+    # rubocop:enable Metrics/MethodLength
 
     def populate_by_used_type(data)
       case object.used_by_type
@@ -67,6 +73,9 @@ def populate_by_used_type(data)
       when 'Pacbio::Pool'
         data[:used_by_type] = 'pool'
         data[:used_by_barcode] = object.used_by.tube.barcode
+      when 'Pacbio::Library'
+        data[:used_by_type] = 'library'
+        data[:used_by_barcode] = object.used_by.tube.barcode
       end
     end
 

app/resources/v1/pacbio/library_resource.rb

@@ -75,7 +75,7 @@ def self.default_sort
       # to republish the messages for the run
       after_update :publish_messages
 
-      after_create :publish_volume_tracking_message
+      after_create :publish_volume_tracking_messages
 
       filter :sample_name, apply: lambda { |records, value, _options|
         # We have to join requests and samples here in order to find by sample name
@@ -130,11 +130,12 @@ def deactivated_at
 
       def publish_messages
         Messages.publish(@model.sequencing_runs, Pipelines.pacbio.message)
-        publish_volume_tracking_message
+        publish_volume_tracking_messages
       end
 
-      def publish_volume_tracking_message
-        Emq::Publisher.publish(@model.primary_aliquot, Pipelines.pacbio, 'volume_tracking')
+      def publish_volume_tracking_messages
+        Emq::Publisher.publish([@model.primary_aliquot, *@model.used_aliquots],
+                               Pipelines.pacbio, 'volume_tracking')
       end
     end
   end

config/pipelines/pacbio.yml

@@ -304,7 +304,7 @@ default: &default
     # The number suffix '1' is used to identify the schema version of message (created by the
     # message builder class defined in the message_class key) 
     # The schema version number should be present in bunny.yml for the same 'key'
-      avro_schema_version_1 : 
+      avro_schema_version_1: &avro_schema_version_1
         lims: Traction
         key: 'volume_tracking'
         message_class: VolumeTracking::MessageBuilder
@@ -351,6 +351,8 @@ default: &default
           usedByType:
             type: :self
             value: publish_data&.used_by_type
+      avro_schema_version_2:
+        <<: *avro_schema_version_1
 development: *default
 test: *default
 uat: *default

spec/exchanges/volume_tracking/message_builder_spec.rb

@@ -91,6 +91,24 @@
       end
     end
 
+    context 'with an aliquot with request as source and library as used_by' do
+      let(:configuration) { Pipelines.pacbio.volume_tracking.avro_schema_version_2 }
+      let(:aliquot) { create(:aliquot, source: pacbio_request, used_by: pacbio_library) }
+      let(:message_builder) { described_class.new(object: aliquot, configuration:) }
+      let(:pacbio_request) { create(:pacbio_request, tube: create(:tube, barcode: '123456789')) }
+
+      it 'produces the message in the correct format' do
+        expect(message_builder.publish_data).to include({
+                                                          source_type: 'request',
+                                                          source_barcode: pacbio_request.tube.barcode,
+                                                          sample_name: pacbio_request.sample_name,
+                                                          used_by_type: 'library',
+                                                          used_by_barcode: pacbio_library.tube.barcode,
+                                                          aliquot_uuid: aliquot.uuid
+                                                        })
+      end
+    end
+
     context 'with a aliquot with library as source and pool as used_by' do
       let(:aliquot) { create(:aliquot, source: pacbio_library, used_by: pacbio_pool) }
       let(:message_builder) { described_class.new(object: aliquot, configuration:) }

spec/messages/emq/publishing_job_spec.rb

@@ -38,7 +38,7 @@
           subjects: {
             volume_tracking: {
               subject: 'create-aliquot-in-mlwh',
-              version: 1
+              version: 2
             }
           }
         }
@@ -48,7 +48,7 @@
   let(:bunny_config_obj) { described_class.deep_open_struct(bunny_config) }
 
   let(:subject_obj) { 'create-aliquot-in-mlwh' }
-  let(:version_obj) { 1 }
+  let(:version_obj) { 2 }
 
   let(:volume_tracking_avro_response) do
     allow(Rails.configuration).to receive(:bunny).and_return(bunny_config)
@@ -86,9 +86,9 @@
   end
 
   it 'logs an error when the message building config misses the given avro schema version' do
-    bunny_config[:amqp][:schemas][:subjects][:volume_tracking][:version] = 2
+    bunny_config[:amqp][:schemas][:subjects][:volume_tracking][:version] = 3
     expect(emq_sender_mock).not_to receive(:send_message)
-    expect(Rails.logger).to receive(:error).with('Message builder configuration not found for schema key: volume_tracking and version: 2')
+    expect(Rails.logger).to receive(:error).with('Message builder configuration not found for schema key: volume_tracking and version: 3')
     publishing_job.publish(aliquot, Pipelines.pacbio, 'volume_tracking')
   end
 
@@ -102,7 +102,7 @@
     assert_equal 'traction', deep_struct.amqp.isg.exchange
     assert_equal 'http://test-redpanda/subjects/', deep_struct.amqp.schemas.registry_url
     assert_equal 'create-aliquot-in-mlwh', deep_struct.amqp.schemas.subjects.volume_tracking.subject
-    assert_equal 1, deep_struct.amqp.schemas.subjects.volume_tracking.version
+    assert_equal 2, deep_struct.amqp.schemas.subjects.volume_tracking.version
   end
 
   it 'logs error message when the EMQ is down' do