Dpl 917 scrna faculty input submission

.prettierignore

@@ -52,3 +52,4 @@ config/cucumber.yml
 config/database.yml
 *.min.js
 public/vite-*
+.ruby-lsp/vendor

app/uat_actions/uat_actions/generate_plates.rb

@@ -22,10 +22,18 @@ class UatActions::GeneratePlates < UatActions
   form_field :well_count,
              :number_field,
              label: 'Well Count',
-             help: 'The number of occupied wells on each plate',
+             help: 'The number of occupied wells on each plate (locations will be randomised if less than full)',
              options: {
                minimum: 1
              }
+  form_field :number_of_samples_in_each_well,
+             :number_field,
+             label: 'Number of samples in each well',
+             help: 'The number of samples to create in each well. Default is 1. Max 10.',
+             options: {
+               minimum: 1,
+               maximum: 10
+             }
   form_field :study_name,
              :select,
              label: 'Study',
@@ -38,11 +46,13 @@ class UatActions::GeneratePlates < UatActions
              select_options: %w[Column Row Random]
 
   validate :well_count_smaller_than_plate_size
+  validates :number_of_samples_in_each_well, numericality: { greater_than: 0, only_integer: true, allow_blank: false }
 
   def self.default
     new(
       plate_count: 1,
       well_count: 96,
+      number_of_samples_in_each_well: 1,
       study_name: UatActions::StaticRecords.study.name,
       plate_purpose_name: PlatePurpose.stock_plate_purpose.name,
       well_layout: 'Column'
@@ -69,21 +79,72 @@ def well_count_smaller_than_plate_size
     false
   end
 
+  # Ensures number of samples per occupied well is at least 1
+  def num_samples_per_well
+    @num_samples_per_well ||=
+      if number_of_samples_in_each_well.present? && number_of_samples_in_each_well.to_i.positive?
+        number_of_samples_in_each_well.to_i
+      else
+        1
+      end
+  end
+
+  # Constructs wells for the given plate.
+  # For each well in the plate, it creates the specified number of samples using the `create_sample` method.
+  # @param plate [Plate] the plate for which to construct wells
   def construct_wells(plate)
     wells(plate).each do |well|
-      sample_name = "sample_#{plate.human_barcode}_#{well.map.description}"
-      sample =
-        Sample.new(
-          name: sample_name,
-          sanger_sample_id: sample_name,
-          studies: [study],
-          sample_metadata_attributes: {
-            supplier_name: sample_name,
-            cohort: "Cohort#{plate.human_barcode}",
-            sample_description: "Description#{plate.human_barcode}"
-          }
-        )
-      sample.save!(validate: false)
+      num_samples_per_well.times { |sample_index| create_sample(plate, well, sample_index + 1) }
+    end
+  end
+
+  # Creates a new sample with a unique name based on the plate, well, and sample index.
+  # The sample is built using the `build_sample` method and saved using the `save_sample` method.
+  # If the sample fails to save due to an ActiveRecord::RecordInvalid error, the error message is
+  # added to the base errors.
+  # @param plate [Plate] the plate associated with the sample
+  # @param well [Well] the well associated with the sample
+  # @param sample_index [Integer] the index of the sample
+  # @raise [ActiveRecord::RecordInvalid] if the sample fails to save
+  def create_sample(plate, well, sample_index)
+    sample_name = "sample_#{sample_index}_#{plate.human_barcode}_#{well.map.description}"
+    sample = build_sample(sample_name, plate)
+    save_sample(sample, well, sample_index)
+  rescue ActiveRecord::RecordInvalid => e
+    errors.add(:base, "Failed to create sample: #{e.message}")
+  end
+
+  # Builds a new Sample object with the given name and associated plate.
+  # The sample's metadata attributes are also set, including the supplier name, cohort, and sample description.
+  # @param sample_name [String] the name of the sample, also used as the sanger_sample_id and supplier_name
+  # @param plate [Plate] the plate associated with the sample, its human_barcode is used in the cohort and
+  # sample_description
+  # @return [Sample] the newly built Sample object
+  def build_sample(sample_name, plate)
+    Sample.new(
+      name: sample_name,
+      sanger_sample_id: sample_name,
+      studies: [study],
+      sample_metadata_attributes: {
+        supplier_name: sample_name,
+        cohort: "Cohort#{plate.human_barcode}",
+        sample_description: "SD-#{plate.human_barcode}"
+      }
+    )
+  end
+
+  # Saves the given sample and creates an aliquot in the specified well.
+  # If there are multiple samples in each well, the aliquot is created with a tag depth.
+  # @param sample [Sample] the sample to be saved
+  # @param well [Well] the well where the aliquot will be created
+  # @param sample_index [Integer] the index of the sample in the well, used as tag depth
+  # if there are multiple samples per well
+  def save_sample(sample, well, sample_index)
+    sample.save!(validate: false)
+
+    if num_samples_per_well > 1
+      well.aliquots.create!(sample: sample, study: study, tag_depth: sample_index)
+    else
       well.aliquots.create!(sample: sample, study: study)
     end
   end

app/uat_actions/uat_actions/test_submission.rb

@@ -67,6 +67,18 @@ class UatActions::TestSubmission < UatActions # rubocop:todo Metrics/ClassLength
              options: {
                minimum: 1
              }
+  form_field :number_of_samples_in_each_well,
+             :number_field,
+             label: 'Number of samples per occupied well',
+             help:
+               'Use this option to create wells containing a pool of multiple samples. Enter ' \
+                 'the number of samples per well. All occupied wells will have this number of samples.' \
+                 'Useful for a pipeline where pools of starting samples is required.' \
+                 'Leave blank for 1 sample per well. Max 10 samples per well.',
+             options: {
+               minimum: 1,
+               maximum: 10
+             }
   form_field :number_of_wells_to_submit,
              :number_field,
              label: 'Number of wells to submit',
@@ -80,14 +92,15 @@ class UatActions::TestSubmission < UatActions # rubocop:todo Metrics/ClassLength
 
   validates :submission_template, presence: { message: 'could not be found' }
   validates :number_of_wells_with_samples, numericality: { greater_than: 0, only_integer: true, allow_blank: true }
+  validates :number_of_samples_in_each_well, numericality: { greater_than: 0, only_integer: true, allow_blank: true }
   validates :number_of_wells_to_submit, numericality: { greater_than: 0, only_integer: true, allow_blank: true }
 
   #
   # Returns a default copy of the UatAction which will be used to fill in the form
   #
   # @return [UatActions::TestSubmission] A default object for rendering a form
   def self.default
-    new
+    new(number_of_samples_in_each_well: 1)
   end
 
   def self.compatible_submission_templates
@@ -121,6 +134,7 @@ def perform # rubocop:todo Metrics/AbcSize
     report['primer_panel'] = order.request_options[:primer_panel_name] if order.request_options[:primer_panel_name]
       .present?
     report['number_of_wells_with_samples'] = labware.wells.with_aliquots.size
+    report['number_of_samples_in_each_well'] = labware.wells.with_aliquots.first.aliquots.size
     report['number_of_wells_to_submit'] = assets.size
     order.submission.built!
     true
@@ -166,24 +180,48 @@ def labware
     @labware ||= plate_barcode.blank? ? generate_plate : Plate.find_by_barcode(plate_barcode.strip)
   end
 
-  def generate_plate # rubocop:todo Metrics/MethodLength
-    generator = UatActions::GeneratePlates.default
-    generator.plate_purpose_name = plate_purpose_name.presence || default_purpose_name
-
-    num_sample_wells = number_of_wells_with_samples.to_i
-    generator.well_count =
-      if num_sample_wells.zero?
-        # default option, create a full plate
-        96
+  # Ensures number of samples per occupied well is at least 1
+  def num_samples_per_well
+    @num_samples_per_well ||=
+      if number_of_samples_in_each_well.present? && number_of_samples_in_each_well.to_i.positive?
+        number_of_samples_in_each_well.to_i
       else
-        # take the number entered in the form
-        num_sample_wells
+        1
       end
-    generator.well_layout = 'Random'
+  end
+
+  # Generates a new plate using a plate generator.
+  # The generator is set up with the appropriate parameters, then used to perform the plate generation.
+  # After the plate is generated, the barcode is retrieved.
+  # @return [Plate] the newly generated Plate object
+  def generate_plate
+    generator = setup_generator
     generator.perform
     Plate.find_by_barcode(generator.report['plate_0'])
   end
 
+  # Sets up a plate generator with the appropriate parameters.
+  # The generator is created with default settings, then its attributes are set based on the current object's state.
+  # The plate purpose name is set to the plate_purpose_name entered by the user, or to the default purpose name if
+  # plate_purpose_name is not present.
+  # The well count is determined by the `determine_well_count` method.
+  # The well layout is set to 'Random'.
+  # The number of samples in each well is set to num_samples_per_well.
+  # @return [UatActions::GeneratePlates] the configured plate generator
+  def setup_generator
+    generator = UatActions::GeneratePlates.default
+    generator.plate_purpose_name = plate_purpose_name.presence || default_purpose_name
+    generator.well_count = determine_well_count
+    generator.well_layout = 'Random'
+    generator.number_of_samples_in_each_well = num_samples_per_well
+    generator
+  end
+
+  def determine_well_count
+    num_sample_wells = number_of_wells_with_samples.to_i
+    num_sample_wells.zero? ? 96 : num_sample_wells
+  end
+
   def order_request_options
     default_request_options.merge(custom_request_options)
   end

config/default_records/plate_purposes/011_scrna_core_cdna_prep_plate_purposes.wip.yml

@@ -2,14 +2,10 @@
 # Most are defined in the Limber config, but the below also need to be defined in Sequencescape.
 # They are in a separate file so it can be 'feature flagged off' until needed.
 ---
-# The 'LRC PBMC Pools' purpose is controlled by Limber. However, it has been
-# added here to create submission and request type records for scRNA Core cDNA
-# Prep stage.
-LRC PBMC Pools:
-  stock_plate: false
-  cherrypickable_target: false
 # The 'LRC PBMC Pools Input' purpose is included here so that it's available for
-# sample manifests.
+# sample manifests, and also because it is an acceptable purpose for the scRNA Core cDNA Prep Input
+# submission template.
 LRC PBMC Pools Input:
+  input_plate: true
   stock_plate: true
   cherrypickable_target: false

config/default_records/request_types/014_limber_scrna_core_cdna_prep_request_types.wip.yml

@@ -20,3 +20,18 @@ limber_scrna_core_cdna_prep_v2:
     # - Chromium single cell 3 prime HT v3
     # - Chromium single cell BCR HT
     # - Chromium single cell TCR HT
+limber_scrna_core_cdna_prep_input:
+  name: scRNA Core cDNA Prep Input
+  asset_type: Well
+  order: 1
+  request_class_name: IlluminaHtp::Requests::StdLibraryRequest
+  for_multiplexing: false
+  billable: true
+  product_line_name: Short Read
+  acceptable_purposes:
+    - LRC PBMC Pools Input
+  library_types:
+    - Chromium single cell 5 prime HT v2
+    # - Chromium single cell 3 prime HT v3
+    # - Chromium single cell BCR HT
+    # - Chromium single cell TCR HT

config/default_records/submission_templates/004_novaseq.yml

@@ -1,3 +1,4 @@
+---
 Limber-Htp - WGS - NovaSeq 6000 Paired end sequencing:
   name: "Limber-Htp - WGS - NovaSeq 6000 Paired end sequencing"
   submission_class_name: "LinearSubmission"

config/default_records/submission_templates/011_scrna_core_cdna_prep_submission_templates.wip.yml

@@ -16,3 +16,9 @@ Limber-Htp - scRNA Core cDNA Prep:
     request_type_keys: ["limber_scrna_core_cdna_prep_v2"]
     product_line_name: Short Read
     product_catalogue_name: scRNA Core
+Limber-Htp - scRNA Core cDNA Prep Input:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_scrna_core_cdna_prep_input"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core

spec/uat_actions/generate_plates_spec.rb

@@ -11,13 +11,15 @@
     let(:plate_barcode_3) { build(:plate_barcode) }
 
     context 'when creating a single plate' do
+      let(:num_samples_per_well) { 1 }
       let(:parameters) do
         {
           plate_purpose_name: PlatePurpose.stock_plate_purpose.name,
           plate_count: 1,
           well_count: 1,
           study_name: study.name,
-          well_layout: 'Column'
+          well_layout: 'Column',
+          number_of_samples_in_each_well: num_samples_per_well
         }
       end
       let(:report) do
@@ -32,6 +34,16 @@
         expect(uat_action.perform).to be true
         expect(uat_action.report['plate_0']).to eq report['plate_0']
         expect(Plate.find_by_barcode(report['plate_0']).wells.first.aliquots.first.study).to eq study
+        expect(Plate.find_by_barcode(report['plate_0']).wells.first.aliquots.size).to eq 1
+      end
+
+      context 'with multiple samples per well' do
+        let(:num_samples_per_well) { 4 }
+
+        it 'can be performed' do
+          expect(uat_action.perform).to be true
+          expect(Plate.find_by_barcode(report['plate_0']).wells.first.aliquots.size).to eq 4
+        end
       end
     end
 

spec/uat_actions/test_submission_spec.rb

@@ -87,6 +87,16 @@
         expect(uat_action.report['number_of_wells_to_submit']).to be_a Integer
       end
     end
+
+    context 'with optional number of samples per well supplied' do
+      let(:parameters) { { submission_template_name: submission_template.name, number_of_samples_in_each_well: '2' } }
+
+      it 'can be performed' do
+        expect(uat_action.perform).to be true
+        expect(uat_action.report['plate_barcode_0']).to eq report['plate_barcode_0']
+        expect(uat_action.report['number_of_samples_in_each_well']).to be_a Integer
+      end
+    end
   end
 
   it 'returns a default' do