Y25-687 - Aviti additional information

app/models/api/messages/eseq_flowcell_io.rb

@@ -0,0 +1,77 @@
+# frozen_string_literal: true
+# Generates warehouse messages describing an Element Aviti flowcell.
+# This is a subset of FlowcellIo containing only fields required by Eseq.
+class Api::Messages::EseqFlowcellIo < Api::Base
+  self.includes = {
+    requests: [
+      {
+        target_asset: {
+          aliquots: [
+            :library,
+            :bait_library,
+            :primer_panel,
+            { tag: :tag_group, tag2: :tag_group, sample: :uuid_object, study: :uuid_object }
+          ]
+        }
+      },
+      :batch_request
+    ]
+  }
+
+  # The following modules add methods onto the relevant models, which are used below in generation of the
+  # eseq flowcel  MLWH message.
+  # Included in SequencingRequest model
+  module LaneExtensions
+    def self.included(base)
+      base.class_eval do
+        def quant_method_used
+          detect_descriptor('Quant method used')
+        end
+
+        def custom_primer_kit_used
+          detect_descriptor('Custom primer kit used')
+        end
+      end
+    end
+  end
+
+  renders_model(::Batch)
+
+  map_attribute_to_json_attribute(:id, 'flowcell_id')
+  map_attribute_to_json_attribute(:updated_at)
+
+  with_nested_has_many_association(:requests, as: :lanes) do
+    map_attribute_to_json_attribute(:position, 'lane')
+    map_attribute_to_json_attribute(:mx_library, 'id_pool_lims')
+    map_attribute_to_json_attribute(:lane_identifier, 'entity_id_lims')
+    map_attribute_to_json_attribute(:request_purpose, 'purpose')
+    map_attribute_to_json_attribute(:quant_method_used)
+    map_attribute_to_json_attribute(:custom_primer_kit_used)
+
+    with_nested_has_many_association(:lane_samples, as: :samples) do
+      with_association(:tag) { map_attribute_to_json_attribute(:oligo, 'tag_sequence') }
+      with_association(:tag2) { map_attribute_to_json_attribute(:oligo, 'tag2_sequence') }
+      map_attribute_to_json_attribute(:library_type, 'pipeline_id_lims')
+      with_association(:bait_library) { map_attribute_to_json_attribute(:name, 'bait_name') }
+      map_attribute_to_json_attribute(:insert_size_from, 'requested_insert_size_from')
+      map_attribute_to_json_attribute(:insert_size_to, 'requested_insert_size_to')
+      with_association(:sample) { map_attribute_to_json_attribute(:uuid, 'sample_uuid') }
+      with_association(:study) { map_attribute_to_json_attribute(:uuid, 'study_uuid') }
+      with_association(:primer_panel) { map_attribute_to_json_attribute(:name, 'primer_panel') }
+      with_association(:library) { map_attribute_to_json_attribute(:external_identifier, 'id_library_lims') }
+      map_attribute_to_json_attribute(:aliquot_type, 'entity_type')
+    end
+
+    # The following methods come from the Aliquot model or the relevant module above.
+    # They are included in the MLWH message under 'controls'.
+    with_nested_has_many_association(:controls) do
+      with_association(:tag) { map_attribute_to_json_attribute(:oligo, 'tag_sequence') }
+      with_association(:tag2) { map_attribute_to_json_attribute(:oligo, 'tag2_sequence') }
+      map_attribute_to_json_attribute(:library_type, 'pipeline_id_lims')
+      with_association(:sample) { map_attribute_to_json_attribute(:uuid, 'sample_uuid') }
+      with_association(:study) { map_attribute_to_json_attribute(:uuid, 'study_uuid') }
+      with_association(:library) { map_attribute_to_json_attribute(:external_identifier, 'id_library_lims') }
+      map_attribute_to_json_attribute(:control_aliquot_type, 'entity_type')
+    end
+  end
+end

app/models/element_aviti_sequencing_pipeline.rb

@@ -5,6 +5,6 @@ class ElementAvitiSequencingPipeline < SequencingPipeline
   def post_release_batch(batch, _user)
     # Same logic as the superclass, but with a different Messenger root
     batch.assets.compact.uniq.each(&:index_aliquots)
-    Messenger.create!(target: batch, template: 'FlowcellIo', root: 'eseq_flowcell')
+    Messenger.create!(target: batch, template: 'EseqFlowcellIo', root: 'eseq_flowcell')
   end
 end

app/models/sequencing_request.rb

@@ -3,6 +3,7 @@
 
 class SequencingRequest < CustomerRequest
   include Api::Messages::FlowcellIo::LaneExtensions
+  include Api::Messages::EseqFlowcellIo::LaneExtensions
 
   class_attribute :flowcell_identifier
 

config/default_records/descriptors/002_element_aviti_descriptors.yml

@@ -1,3 +1,14 @@
+Quant method used:
+  name: Quant method used
+  task: Loading
+  workflow: Element Aviti
+  kind: Selection
+  value: Tapestation
+  selection:
+    Tapestation: Tapestation
+    Tapestation & qPCR: Tapestation & qPCR
+  required: true
+  sorter: -1
 Pipette Carousel:
   name: Pipette Carousel
   task: Loading
@@ -12,6 +23,17 @@ Final Loading Concentration (pM):
   kind: Text
   required: false
   sorter: 1
+Custom primer kit used:
+  name: Custom primer kit used
+  task: Loading
+  workflow: Element Aviti
+  kind: Selection
+  value: Yes
+  selection:
+    Yes: Yes
+    No: No
+  required: true
+  sorter: 1
 "200mM Tris PH7 lot#":
   name: "200mM Tris PH7 lot#"
   task: Loading

spec/models/api/messages/eseq_flowcell_io_spec.rb

@@ -0,0 +1,158 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe Api::Messages::EseqFlowcellIo do
+  let(:message) { described_class.to_hash(sequencing_batch.reload) }
+
+  context 'with a batch' do
+    let(:sequencing_pipeline) { create(:element_aviti_sequencing_pipeline) }
+    let(:sequencing_batch) { create(:sequencing_batch, pipeline: sequencing_pipeline) }
+
+    let!(:request) do
+      create(
+        :complete_sequencing_request,
+        asset: mx_tube1,
+        batch: sequencing_batch,
+        target_asset: lane1,
+        request_type: request_type,
+        event_descriptors: request_data
+      )
+    end
+
+    let(:mx_tube1) { create(:multiplexed_library_tube, sample_count: 1) }
+    let(:request_type) { sequencing_pipeline.request_types.first }
+
+    let(:lane1) do
+      create(:lane, aliquots: mx_tube1.aliquots.map(&:dup)).tap do |lane|
+        lane.labware.parents << phix
+        lane.index_aliquots
+      end
+    end
+
+    let(:phix) { create(:spiked_buffer, :tube_barcode, tag_option: 'Dual') }
+
+    let(:tags) { lane1.aliquots.map(&:tag) }
+    let(:tag2s) { lane1.aliquots.map(&:tag2) }
+    let(:aliquots) { lane1.aliquots }
+
+    let(:expected_json) do
+      {
+        'flowcell_id' => sequencing_batch.id,
+        'lanes' => [
+          {
+            'lane' => 1,
+            'id_pool_lims' => mx_tube1.human_barcode,
+            'entity_id_lims' => lane1.id,
+            'purpose' => 'standard',
+            'quant_method_used' => 'Tapestation',
+            'custom_primer_kit_used' => 'No',
+            'samples' => [
+              {
+                'tag_sequence' => tags[0].oligo,
+                'tag2_sequence' => tag2s[0].oligo,
+                'pipeline_id_lims' => 'Standard',
+                'bait_name' => aliquots[0].bait_library.name,
+                'requested_insert_size_from' => 100,
+                'requested_insert_size_to' => 200,
+                'sample_uuid' => aliquots[0].sample.uuid,
+                'study_uuid' => aliquots[0].study.uuid,
+                'primer_panel' => aliquots[0].primer_panel.name,
+                'id_library_lims' => aliquots[0].library.human_barcode,
+                'entity_type' => 'library_indexed'
+              }
+            ],
+            'controls' => [
+              {
+                'tag_sequence' => 'TGTGCAGC',
+                'tag2_sequence' => 'ACTGATGT',
+                'pipeline_id_lims' => nil,
+                'sample_uuid' => phix.aliquots[0].sample.uuid,
+                'id_library_lims' => phix.human_barcode,
+                'entity_type' => 'library_indexed_spike'
+              }
+            ]
+          }
+        ]
+      }
+    end
+
+    let(:request_data) do
+      {
+        'Quant method used' => 'Tapestation',
+        'Custom primer kit used' => 'No'
+      }
+    end
+
+    context 'with all request data' do
+      it 'generates valid json' do
+        expect(message.as_json).to include_json(expected_json)
+      end
+    end
+
+    context 'with some missing request data' do
+      let(:request_data) do
+        {
+          'Quant method used' => 'Tapestation',
+          'Custom primer kit used' => nil
+        }
+      end
+
+      it 'generates valid json' do
+        # Should have an empty primer kit used
+        expected_json['lanes'][0]['custom_primer_kit_used'] = nil
+
+        expect(message.as_json).to include_json(expected_json)
+      end
+    end
+
+    context 'with updated events' do
+      before do
+        create(
+          :lab_event,
+          eventful: request,
+          batch: request.batch,
+          descriptors: {
+            'Quant method used' => 'Tapestation & qPCR',
+            'Custom primer kit used' => 'Yes'
+          }
+        )
+      end
+
+      let(:expected_json) do
+        {
+          'flowcell_id' => sequencing_batch.id,
+          'lanes' => [
+            {
+              'lane' => 1,
+              'id_pool_lims' => mx_tube1.human_barcode,
+              'entity_id_lims' => lane1.id,
+              'purpose' => 'standard',
+              'quant_method_used' => 'Tapestation & qPCR',
+              'custom_primer_kit_used' => 'Yes',
+              'samples' => [
+                {
+                  'tag_sequence' => tags[0].oligo,
+                  'tag2_sequence' => tag2s[0].oligo,
+                  'pipeline_id_lims' => 'Standard',
+                  'bait_name' => aliquots[0].bait_library.name,
+                  'requested_insert_size_from' => 100,
+                  'requested_insert_size_to' => 200,
+                  'sample_uuid' => aliquots[0].sample.uuid,
+                  'study_uuid' => aliquots[0].study.uuid,
+                  'primer_panel' => aliquots[0].primer_panel.name,
+                  'id_library_lims' => aliquots[0].library.human_barcode,
+                  'entity_type' => 'library_indexed'
+                }
+              ]
+            }
+          ]
+        }
+      end
+
+      it 'generates valid json' do
+        expect(message.as_json).to include_json(expected_json)
+      end
+    end
+  end
+end

spec/models/element_aviti_sequencing_pipeline_spec.rb

@@ -11,7 +11,7 @@
       pipeline.post_release_batch(batch, create(:user))
 
       expect(Messenger).to have_received(:create!).with(
-        hash_including(target: batch, template: 'FlowcellIo', root: 'eseq_flowcell')
+        hash_including(target: batch, template: 'EseqFlowcellIo', root: 'eseq_flowcell')
       )
     end
   end