Y24-402 - Specify 'no. pools' rather than 'no. samples per pool' in submission

.rubocop_todo.yml

@@ -297,6 +297,7 @@ Metrics/AbcSize:
     - 'app/controllers/api/v2/transfers/transfers_controller.rb'
     - 'app/jobs/export_pool_xp_to_traction_job.rb'
     - 'app/sample_manifest_excel/sample_manifest_excel/manifest_type_list.rb'
+    - 'spec/models/bulk_submission_scrna_spec.rb'
 
 # Offense count: 1
 # Configuration parameters: CountComments, Max, CountAsOne.
@@ -857,6 +858,7 @@ RSpec/LetSetup:
     - 'spec/models/transfer_request_collection_spec.rb'
     - 'spec/requests/api/v2/comments_spec.rb'
     - 'spec/requests/api/v2/plates_spec.rb'
+    - 'spec/models/bulk_submission_scrna_spec.rb'
 
 # Offense count: 40
 # Configuration parameters: EnforcedStyle.

app/models/bulk_submission.rb

@@ -231,7 +231,7 @@ def process # rubocop:todo Metrics/CyclomaticComplexity
     'gigabases expected',
     'priority',
     'flowcell type',
-    'scrna core number of samples per pool',
+    'scrna core number of pools',
     'scrna core cells per chip well'
   ].freeze
 
@@ -312,6 +312,12 @@ def add_study_to_assets(assets, study)
     assets.map(&:samples).flatten.uniq.each { |sample| sample.studies << study unless sample.studies.include?(study) }
   end
 
+  # Assigns a value from the source object to the target object if the source value is present.
+  #
+  # @param [Hash] source_obj The source object containing the value to be assigned.
+  # @param [String, Symbol] source_key The key to look up the value in the source object.
+  # @param [Hash] target_obj The target object where the value will be assigned.
+  # @param [String, Symbol] target_key The key to assign the value in the target object.
   def assign_value_if_source_present(source_obj, source_key, target_obj, target_key)
     target_obj[target_key] = source_obj[source_key] if source_obj[source_key].present?
   end
@@ -329,7 +335,7 @@ def extract_request_options(details)
         ['gigabases expected', 'gigabases_expected'],
         ['primer panel', 'primer_panel_name'],
         ['flowcell type', 'requested_flowcell_type'],
-        ['scrna core number of samples per pool', 'number_of_samples_per_pool'],
+        ['scrna core number of pools', 'number_of_pools'],
         ['scrna core cells per chip well', 'cells_per_chip_well']
       ].each do |source_key, target_key|
         assign_value_if_source_present(details, source_key, request_options, target_key)

app/models/pbmc_pooling_customer_request.rb

@@ -3,7 +3,7 @@
 # A class for customer requests that need the extra metadata fields used for PBMC pooling calculations
 class PbmcPoolingCustomerRequest < CustomerRequest
   has_metadata as: Request do
-    custom_attribute(:number_of_samples_per_pool, integer: true, required: false, default: nil)
     custom_attribute(:cells_per_chip_well, integer: true, required: false, default: nil)
+    custom_attribute(:number_of_pools, integer: true, required: false, default: nil)
   end
 end

app/models/submission/validations_by_template_name.rb

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+# rubocop:todo Metrics/ModuleLength
 module Submission::ValidationsByTemplateName
   # Template names
   SCRNA_CORE_CDNA_PREP_GEM_X_5P = 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p'
@@ -7,9 +8,13 @@
   HEADER_TEMPLATE_NAME = 'template name'
   HEADER_STUDY_NAME = 'study name'
   HEADER_PROJECT_NAME = 'project name'
-  HEADER_NUM_SAMPLES = 'scrna core number of samples per pool'
+  HEADER_BARCODE = 'barcode'
+  HEADER_PLATE_WELLS = 'plate well'
+  HEADER_NUMBER_OF_POOLS = 'scrna core number of pools'
   HEADER_CELLS_PER_CHIP_WELL = 'scrna core cells per chip well'
 
+  SAMPLES_PER_POOL = { max: 25, min: 5 }.freeze
+
   # Applies additional validations based on the submission template type.
   #
   # This method determines the submission template type from the CSV data and calls the appropriate
@@ -32,11 +37,23 @@
     case submission_template_name
     # this validation is for the scRNA pipeline cDNA submission
     when SCRNA_CORE_CDNA_PREP_GEM_X_5P
-      validate_consistent_column_value(HEADER_NUM_SAMPLES)
+      validate_consistent_column_value(HEADER_NUMBER_OF_POOLS)
       validate_consistent_column_value(HEADER_CELLS_PER_CHIP_WELL)
+      validate_samples_per_pool_for_labware
     end
   end
 
+  def apply_number_of_samples_per_pool_validation
+    # Creates groups of rows based on the study and project name (pool_number, study-project) combinations
+    group_rows_by_study_and_project
+  end
+
+  def group_rows_by_study_and_project
+    index_of_study_name = headers.index(HEADER_STUDY_NAME)
+    index_of_project_name = headers.index(HEADER_PROJECT_NAME)
+    csv_data_rows.group_by { |row| [row[index_of_study_name], row[index_of_project_name]] }
+  end
+
   # Validates that the specified column is consistent for all rows with the same study and project name.
   #
   # This method groups the rows in the CSV data by the study name and project name, and checks if the specified column
@@ -45,25 +62,219 @@
   #
   # @param column_header [String] The header of the column to validate.
   # @return [void]
-  # rubocop:disable Metrics/MethodLength,Metrics/AbcSize
   def validate_consistent_column_value(column_header)
-    index_of_study_name = headers.index(HEADER_STUDY_NAME)
-    index_of_project_name = headers.index(HEADER_PROJECT_NAME)
     index_of_column = headers.index(column_header)
-
-    grouped_rows = csv_data_rows.group_by { |row| [row[index_of_study_name], row[index_of_project_name]] }
+    grouped_rows = group_rows_by_study_and_project
 
     grouped_rows.each do |study_project, rows|
-      unique_values = rows.pluck(index_of_column).uniq
+      validate_unique_values(study_project, rows, index_of_column, column_header)
+    end
+  end
+
+  # Validates the number of samples per pool for labware.
+  #
+  # This method checks if the headers for barcode and plate wells are present.
+  # If they are, it groups the rows by study and project, and processes each group.
+  # The processing involves determining if the labware is a plate or tube and
+  # validating the number of samples per pool accordingly.
+  #
+  # @return [void]
+  def validate_samples_per_pool_for_labware
+    return if headers.index(HEADER_BARCODE).nil? && headers.index(HEADER_PLATE_WELLS).nil?
+
+    grouped_rows = group_rows_by_study_and_project
+    grouped_rows.each_value { |rows| process_rows(rows) }
+  end
+
+  private
+
+  # Validates that the specified column has unique values for each study and project.
+  #
+  # This method checks if the specified column has unique values for each study and project.
+  # If inconsistencies are found, an error is added to the errors collection.
+  #
+  # @param study_project [Array<String>] The study and project names.
+  # @param rows [Array<Array<String>>] The rows of CSV data to process.
+  # @param index_of_column [Integer] The index of the column to validate.
+  # @param column_header [String] The header of the column to validate.
+  # @return [void]
+  def validate_unique_values(study_project, rows, index_of_column, column_header)
+    unique_values = rows.pluck(index_of_column).uniq
+    return unless unique_values.size > 1
+
+    errors.add(
+      :spreadsheet,
+      "Inconsistent values for column '#{column_header}' for Study name '#{study_project[0]}' and Project name " \
+        "'#{study_project[1]}', all rows for a specific study and project must have the same value"
+    )
+  end
+
+  # Processes the rows to determine the type of labware and validate accordingly.
+  #
+  # This method extracts the barcodes and well locations from the rows and determines if the labware is a plate or tube.
+  # It then calls the appropriate validation method based on the labware type.
+  #
+  # @param rows [Array<Array<String>>] The rows of CSV data to process.
+  # @return [void]
+  # rubocop:disable Metrics/MethodLength
+  def process_rows(rows)
+    barcodes = rows.pluck(headers.index(HEADER_BARCODE))
+    well_locations = rows.pluck(headers.index(HEADER_PLATE_WELLS))
+
+    if plate?(barcodes, well_locations)
+      validate_for_plates(barcodes, well_locations, rows)
+    elsif tube?(barcodes, well_locations)
+      validate_for_tubes(barcodes, rows)
+    else
+      errors.add(
+        :spreadsheet,
+        'Invalid labware type. Please provide either a plate barcode with well locations or tube barcodes only'
+      )
+    end
+  end
+  # rubocop:enable Metrics/MethodLength
+
+  # Validates the number of samples per pool for plates.
+  #
+  # This method finds the plate using the provided barcodes and retrieves the wells located at the specified well
+  # locations.
+  # It then calculates the total number of samples per study and project and the number of pools.
+  # Finally, it validates the number of samples per pool.
+  #
+  # @param barcodes [Array<String>] The barcodes of the plates.
+  # @param well_locations [Array<String>] The well locations on the plate.
+  # @param rows [Array<Array<String>>] The rows of CSV data to process.
+  # @return [void]
+  # rubocop:disable Metrics/AbcSize
+  def validate_for_plates(barcodes, well_locations, rows)
+    plate = Plate.find_from_any_barcode(barcodes.uniq.first)
+    return if plate.nil?
+
+    wells = plate.wells.for_bulk_submission.located_at(well_locations)
+    total_number_of_samples_per_study_project = wells.map(&:samples).flatten.count.to_i
+    number_of_pools = rows.pluck(headers.index(HEADER_NUMBER_OF_POOLS)).uniq.first.to_i
+
+    validate_samples_per_pool(rows, total_number_of_samples_per_study_project, number_of_pools)
+  end
+  # rubocop:enable Metrics/AbcSize
+
+  # Validates the number of samples per pool for tubes.
+  #
+  # This method finds the tubes using the provided barcodes and calculates the total number of samples per study and
+  # project.
+  # It then retrieves the number of pools from the rows and validates the number of samples per pool.
+  #
+  # @param barcodes [Array<String>] The barcodes of the tubes.
+  # @param rows [Array<Array<String>>] The rows of CSV data to process.
+  # @return [void]
+  def validate_for_tubes(barcodes, rows)
+    tubes = find_tubes(barcodes)
+    total_number_of_samples_per_study_project = calculate_total_samples(tubes)
+    number_of_pools = extract_number_of_pools(rows)
+
+    validate_samples_per_pool(rows, total_number_of_samples_per_study_project, number_of_pools)
+  end
+
+  # Finds the tubes using the provided barcodes.
+  #
+  # This method retrieves the tubes that match the provided barcodes and raises an error if any barcodes are missing.
+  #
+  # @param barcodes [Array<String>] The barcodes of the tubes.
+  # @return [Array<Receptacle>] The found tubes.
+  def find_tubes(barcodes)
+    Receptacle
+      .on_a(Tube)
+      .for_bulk_submission
+      .with_barcode(barcodes)
+      .tap do |found|
+        missing = find_missing_barcodes(barcodes, found)
+        raise ActiveRecord::RecordNotFound, "Could not find Tubes with barcodes #{missing.inspect}" if missing.present?
+      end
+  end
+
+  # Finds the missing barcodes from the found tubes.
+  #
+  # This method checks which barcodes are not present in the found tubes.
+  #
+  # @param barcodes [Array<String>] The barcodes of the tubes.
+  # @param found [Array<Receptacle>] The found tubes.
+  # @return [Array<String>] The missing barcodes.
+  def find_missing_barcodes(barcodes, found)
+    barcodes.reject { |barcode| found.any? { |tube| tube.any_barcode_matching?(barcode) } }
+  end
+
+  # Calculates the total number of samples from the tubes.
+  #
+  # This method calculates the total number of samples by flattening the samples from the tubes and counting them.
+  #
+  # @param tubes [Array<Receptacle>] The tubes to calculate samples from.
+  # @return [Integer] The total number of samples.
+  def calculate_total_samples(tubes)
+    tubes.map(&:samples).flatten.count.to_i
+  end
+
+  # Extracts the number of pools from the rows.
+  #
+  # This method retrieves the number of pools from the specified column in the rows.
+  #
+  # @param rows [Array<Array<String>>] The rows of CSV data to process.
+  # @return [Integer] The number of pools.
+  def extract_number_of_pools(rows)
+    rows.pluck(headers.index(HEADER_NUMBER_OF_POOLS)).uniq.first.to_i
+  end
+
+  # Determines if the labware is a plate based on the presence of barcodes and well locations.
+  #
+  # This method checks if both barcodes and well locations are present to determine if the labware is a plate.
+  #
+  # @param barcodes [Array<String>] The barcodes of the labware.
+  # @param well_locations [Array<String>] The well locations on the labware.
+  # @return [Boolean] Returns true if both barcodes and well locations are present, indicating the labware is a plate.
+  def plate?(barcodes, well_locations)
+    barcodes.present? && well_locations.none?(&:nil?)
+  end
+
+  # Determines if the labware is a tube based on the presence of barcodes and absence of well locations.
+  #
+  # This method checks if barcodes are present and well locations are absent to determine if the labware is a tube.
+  #
+  # @param barcodes [Array<String>] The barcodes of the labware.
+  # @param well_locations [Array<String>] The well locations on the labware.
+  # @return [Boolean] Returns true if barcodes are present and well locations are absent, indicating the labware is a
+  # tube.
+  def tube?(barcodes, well_locations)
+    barcodes.present? && well_locations.all?(&:nil?)
+  end
+
+  # Validates the number of samples per pool.
+  #
+  # This method calculates the number of samples per pool by dividing the total number of samples by the number of
+  # pools.
+  # It then iterates through each pool and checks if the number of samples per pool is within the allowed range.
+  # If the number of samples per pool is less than the minimum or greater than the maximum allowed, an error is added.
+  #
+  # @param rows [Array<Array<String>>] The rows of CSV data to process.
+  # @param total_samples [Integer] The total number of samples.
+  # @param number_of_pools [Integer] The number of pools.
+  # @return [void]
+  # rubocop:disable Metrics/MethodLength
+  def validate_samples_per_pool(rows, total_samples, number_of_pools)
+    int_division = total_samples / number_of_pools
+    remainder = total_samples % number_of_pools
+
+    number_of_pools.times do |pool_number|
+      samples_per_pool = int_division
+      samples_per_pool += 1 if pool_number < remainder
+      next unless samples_per_pool > SAMPLES_PER_POOL[:max] || samples_per_pool < SAMPLES_PER_POOL[:min]
 
-      next unless unique_values.size > 1
       errors.add(
         :spreadsheet,
-        "Inconsistent values for column '#{column_header}' for Study name '#{study_project[0]}' and Project name " \
-          "'#{study_project[1]}', " \
-          'all rows for a specific study and project must have the same value'
+        "Number of samples per pool for Study name '#{rows.first[headers.index(HEADER_STUDY_NAME)]}' " \
+          "and Project name '#{rows.first[headers.index(HEADER_PROJECT_NAME)]}' " \
+          "is less than 5 or greater than 25 for pool number #{pool_number}"
       )
     end
   end
-  # rubocop:enable Metrics/MethodLength,Metrics/AbcSize
+  # rubocop:enable Metrics/MethodLength
 end
+# rubocop:enable Metrics/ModuleLength

config/bulk_submission_excel/columns.yml

@@ -269,26 +269,26 @@ requested_flowcell_type:
   conditional_formattings:
     empty_cell:
     is_error:
-number_of_samples_per_pool:
-  heading: scRNA Core Number of Samples per Pool
-  attribute: :number_of_samples_per_pool
+number_of_pools:
+  heading: scRNA Core Number of Pools
+  attribute: :number_of_pools
   unlocked: true
   type: :integer
   validation:
     options:
       type: :whole
       operator: :between
-      formula1: "5"
-      formula2: "25"
+      formula1: "1"
+      formula2: "8"
       allowBlank: true
       showInputMessage: true
-      promptTitle: "Samples per Pool"
-      prompt: "The requested number of samples per pool (between 5 and 25 inclusive)"
+      promptTitle: "Number of pools"
+      prompt: "The requested number pools (between 1 and 8 inclusive)"
   conditional_formattings:
     empty_cell:
     is_text:
-    is_num_samples_per_pool_in_valid_range:
-    is_num_samples_per_pool_outside_valid_range:
+    is_num_of_pools_in_valid_range:
+    is_num_of_pools_outside_valid_range:
 cells_per_chip_well:
   heading: scRNA Core Cells per Chip Well
   attribute: :cells_per_chip_well