feat(pacbio-run-resource): adds adaptive_loading and sequencing_kit_b…

…ox_barcodes attributes

app/models/pacbio/run.rb

@@ -134,6 +134,16 @@ def used_aliquots_lib_source_in_pool(pools)
       end
     end
 
+    # @return [Boolean] true if all wells have adaptive loading enabled
+    def adaptive_loading
+      wells.all? { |w| w.use_adaptive_loading == 'True' }
+    end
+
+    # @return [Array<String>] the barcodes of the sequencing kits
+    def sequencing_kit_box_barcodes
+      plates.map { |p| "Plate #{p.plate_number}: #{p.sequencing_kit_box_barcode}" }
+    end
+
     private
 
     # We now have SMRT Link versioning

app/resources/v1/pacbio/run_resource.rb

@@ -32,9 +32,14 @@ class RunResource < JSONAPI::Resource
       #   @return [Integer] the ID of the PacBio SMRT Link version
       # @!attribute [rw] plates_attributes
       #   @return [Array<Hash>] the attributes of the plates
+      # @!attribute [r] adaptive_loading
+      #  @return [Boolean] whether adaptive loading is used
+      # @!attribute [r] sequencing_kit_box_barcodes
+      #  @return [Array<String>] the barcodes of the sequencing kits
       attributes :name, :dna_control_complex_box_barcode,
                  :system_name, :created_at, :state, :comments,
-                 :pacbio_smrt_link_version_id, :plates_attributes
+                 :pacbio_smrt_link_version_id, :plates_attributes,
+                 :adaptive_loading, :sequencing_kit_box_barcodes
 
       has_many :plates, foreign_key_on: :related, foreign_key: 'pacbio_run_id',
                         class_name: 'Runs::Plate'
@@ -86,6 +91,14 @@ def publish_messages
                                'volume_tracking')
       end
 
+      def self.creatable_fields(context)
+        super - %i[adaptive_loading sequencing_kit_box_barcodes]
+      end
+
+      def self.updatable_fields(context)
+        super - %i[adaptive_loading sequencing_kit_box_barcodes]
+      end
+
       private
 
       def plates_attributes=(plates_parameters) # rubocop:disable Metrics/MethodLength

config/pacbio_smrt_link_versions.yml

@@ -261,7 +261,6 @@ default: &default
         - v12_revio
         - v13_revio
         - v13_1_revio
-        - v25_1_revio
     library_type:
       key: library_type
       label: "Library Type"

spec/models/pacbio/run_spec.rb

@@ -233,6 +233,40 @@
     end
   end
 
+  context 'adaptive_loading' do
+    it 'is false if the wells do not have use_adaptive_loading' do
+      # Sequel run wells do not have use_adaptive_loading
+      run = create(:pacbio_sequel_run)
+      expect(run.adaptive_loading).to be false
+    end
+
+    it 'is false if the wells have use_adaptive_loading set to false' do
+      # Revio run wells have use_adaptive_loading set to false
+      run = create(:pacbio_revio_run)
+      expect(run.adaptive_loading).to be false
+    end
+
+    it 'is true if the wells have use_adaptive_loading set to true' do
+      # Revio run wells have use_adaptive_loading set to true
+      run = create(:pacbio_revio_run)
+      run.wells.each do |w|
+        w.use_adaptive_loading = 'True'
+        w.save
+      end
+      expect(run.adaptive_loading).to be true
+    end
+  end
+
+  context 'sequencing_kit_box_barcodes' do
+    it 'returns the barcodes of the sequencing kits' do
+      run = create(:pacbio_revio_run)
+      expect(run.sequencing_kit_box_barcodes).to eq([
+        "Plate 1: #{run.plates.first.sequencing_kit_box_barcode}",
+        "Plate 2: #{run.plates.second.sequencing_kit_box_barcode}"
+      ])
+    end
+  end
+
   describe '#create with nested attributes' do
     let!(:pools) { create_list(:pacbio_pool, 2) }
 

spec/requests/v1/pacbio/runs_spec.rb

@@ -125,7 +125,9 @@
             'state' => run.state,
             'comments' => run.comments,
             'pacbio_smrt_link_version_id' => run.pacbio_smrt_link_version_id,
-            'created_at' => run.created_at.to_fs(:us)
+            'created_at' => run.created_at.to_fs(:us),
+            'adaptive_loading' => run.adaptive_loading,
+            'sequencing_kit_box_barcodes' => run.sequencing_kit_box_barcodes
           )
         end
       end
@@ -157,7 +159,9 @@
             'state' => run1.state,
             'comments' => run1.comments,
             'pacbio_smrt_link_version_id' => run1.pacbio_smrt_link_version_id,
-            'created_at' => run1.created_at.to_fs(:us)
+            'created_at' => run1.created_at.to_fs(:us),
+            'adaptive_loading' => run1.adaptive_loading,
+            'sequencing_kit_box_barcodes' => run1.sequencing_kit_box_barcodes
           )
         end
       end
@@ -187,7 +191,9 @@
             'state' => run1.state,
             'comments' => run1.comments,
             'pacbio_smrt_link_version_id' => run1.pacbio_smrt_link_version_id,
-            'created_at' => run1.created_at.to_fs(:us)
+            'created_at' => run1.created_at.to_fs(:us),
+            'adaptive_loading' => run1.adaptive_loading,
+            'sequencing_kit_box_barcodes' => run1.sequencing_kit_box_barcodes
           )
         end
       end
@@ -497,6 +503,39 @@
         end
       end
 
+      context 'when there are read-only attributes' do
+        let(:body) do
+          {
+            data: {
+              type: 'runs',
+              attributes: {
+                adaptive_loading: 'True',
+                sequencing_kit_box_barcodes: ['Plate 1: DM0001100861800123121']
+              }
+            }
+          }.to_json
+        end
+
+        it 'has a bad_request status' do
+          post v1_pacbio_runs_path, params: body, headers: json_api_headers
+          expect(response).to have_http_status(:bad_request)
+        end
+
+        it 'does not create a run' do
+          expect do
+            post v1_pacbio_runs_path, params: body,
+                                      headers: json_api_headers
+          end.not_to change(Pacbio::Run, :count)
+        end
+
+        it 'has the correct error messages' do
+          post v1_pacbio_runs_path, params: body, headers: json_api_headers
+          json = ActiveSupport::JSON.decode(response.body)
+          errors = json['errors']
+          expect(errors[0]['detail']).to eq 'adaptive_loading is not allowed.'
+        end
+      end
+
       context 'when there no wells' do
         let(:body) do
           {