Y25-598 - scRNA - add tube size options

app/uat_actions/uat_actions/generate_tubes.rb

@@ -48,7 +48,10 @@ def perform
             sanger_sample_id: sample_name,
             studies: [study],
             sample_metadata_attributes: {
-              supplier_name: sample_name
+              supplier_name: sample_name,
+              collected_by: UatActions::StaticRecords.collection_site,
+              donor_id: "#{sample_name}_donor",
+              sample_common_name: 'human'
             }
           ),
         study: study

config/default_records/request_types/014_limber_scrna_core_cdna_prep_request_types.yml

@@ -15,7 +15,8 @@ limber_scrna_core_cdna_prep_gem_x_5p:
   acceptable_purposes:
     - LRC Bank Seq
     - LRC Bank Spare
-    - LRC Bank Input
+    - LRC Bank Input 1ml
+    - LRC Bank Input 08ml
 limber_scrna_core_cdna_prep_gem_x_5p_gems_input:
   name: scRNA Core cDNA Prep GEM-X 5p GEMs Input
   asset_type: Well

config/default_records/tube_purposes/008_scrna_core_cdna_prep_tube_purposes.yml

@@ -12,7 +12,12 @@ LRC Bank Spare:
   target_type: SampleTube
   stock_plate: false
 
-LRC Bank Input:
+LRC Bank Input 1ml:
+  type: Tube::Purpose
+  target_type: SampleTube
+  stock_plate: true
+
+LRC Bank Input 08ml:
   type: Tube::Purpose
   target_type: SampleTube
   stock_plate: true

config/initializers/scrna_config.rb

@@ -33,7 +33,7 @@
   # Key for the required number of cells metadata stored on Study (in poly_metadata)
   study_required_number_of_cells_per_sample_in_pool_key: 'scrna_core_pbmc_donor_pooling_required_number_of_cells',
   # Default viability threshold when passing/failing samples (in percent)
-  viability_default_threshold: 65,
+  viability_default_threshold: 50,
   # Default total cell count threshold when passing/failing samples
   total_cell_count_default_threshold: 50_000,
   # Key for the number of cells per chip well metadata stored on pool wells (in poly_metadata)

spec/uat_actions/generate_tubes_spec.rb

@@ -19,10 +19,31 @@
 
       before { allow(AssetBarcode).to receive(:new_barcode).and_return('2') }
 
-      it 'can be performed' do
+      it 'performs the action successfully' do
         expect(uat_action.perform).to be true
+      end
+
+      it 'returns the expected barcode in the report' do
+        uat_action.perform
         expect(uat_action.report['tube_0']).to eq report['tube_0']
-        expect(Tube.find_by_barcode(report['tube_0']).aliquots.first.study).to eq study
+      end
+
+      it 'assigns the correct study to the tube' do
+        uat_action.perform
+        tube = Tube.find_by_barcode(report['tube_0'])
+        expect(tube.aliquots.first.study).to eq study
+      end
+
+      it 'sets the correct sample metadata values' do
+        uat_action.perform
+        tube = Tube.find_by_barcode(report['tube_0'])
+        sample_metadata = tube.aliquots.first.sample.sample_metadata
+        expect(sample_metadata).to have_attributes(
+          supplier_name: 'sample_NT2P_0',
+          collected_by: UatActions::StaticRecords.collection_site,
+          donor_id: 'sample_NT2P_0_donor',
+          sample_common_name: 'human'
+        )
       end
     end
 
@@ -38,12 +59,29 @@
 
       before { allow(AssetBarcode).to receive(:new_barcode).and_return('3', '4', '5') }
 
-      it 'can be performed' do
+      it 'performs the action successfully' do
         expect(uat_action.perform).to be true
+      end
+
+      it 'returns the expected barcodes in the report' do
+        uat_action.perform
         expect(uat_action.report['tube_0']).to eq report['tube_0']
         expect(uat_action.report['tube_1']).to eq report['tube_1']
         expect(uat_action.report['tube_2']).to eq report['tube_2']
       end
+
+      it 'sets the correct sample metadata values for each tube' do
+        uat_action.perform
+        uat_action.report.each_with_index do |(_key, barcode), i|
+          sample_metadata = Tube.find_by_barcode(barcode).aliquots.first.sample.sample_metadata
+          expect(sample_metadata).to have_attributes(
+            supplier_name: "sample_#{barcode}_#{i}",
+            collected_by: UatActions::StaticRecords.collection_site,
+            donor_id: "sample_#{barcode}_#{i}_donor",
+            sample_common_name: 'human'
+          )
+        end
+      end
     end
 
     context 'when creating the tube with a fluidx foreign barcode' do
@@ -55,17 +93,38 @@
           foreign_barcode_type: 'FluidX'
         }
       end
-      let(:report) do
+      let(:expected_report) do
         # Tube NT6T created with foreign barcode based on machine barcode
         { 'tube_0' => 'SA00006844' }
       end
 
       before { allow(AssetBarcode).to receive(:new_barcode).and_return('6') }
 
-      it 'can be performed' do
+      it 'performs the action successfully' do
         expect(uat_action.perform).to be true
-        expect(uat_action.report['tube_0']).to eq report['tube_0']
-        expect(Tube.find_by_barcode(report['tube_0']).aliquots.first.study).to eq study
+      end
+
+      it 'returns the expected barcode in the report' do
+        uat_action.perform
+        expect(uat_action.report['tube_0']).to eq expected_report['tube_0']
+      end
+
+      it 'assigns the correct study to the tube' do
+        uat_action.perform
+        tube = Tube.find_by_barcode(expected_report['tube_0'])
+        expect(tube.aliquots.first.study).to eq study
+      end
+
+      it 'sets the correct sample metadata values' do
+        uat_action.perform
+        tube = Tube.find_by_barcode(expected_report['tube_0'])
+        sample_metadata = tube.aliquots.first.sample.sample_metadata
+        expect(sample_metadata).to have_attributes(
+          supplier_name: 'sample_NT6T_0',
+          collected_by: UatActions::StaticRecords.collection_site,
+          donor_id: 'sample_NT6T_0_donor',
+          sample_common_name: 'human'
+        )
       end
     end
   end