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4579-y25-002---bug-duplicate-samples-per-pool-validations_v2 #4660

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Feb 6, 2025
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4579-y25-002---bug-duplicate-samples-per-pool-validations_v2 #4660

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116 changes: 1 addition & 115 deletions app/models/submission/validations_by_template_name.rb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# frozen_string_literal: true
# rubocop:todo Metrics/ModuleLength

module Submission::ValidationsByTemplateName
include Submission::ScrnaCoreCdnaPrepFeasibilityValidator

Expand Down Expand Up @@ -41,7 +41,6 @@ def apply_additional_validations_by_template_name
when SCRNA_CORE_CDNA_PREP_GEM_X_5P
validate_consistent_column_value(HEADER_NUMBER_OF_POOLS)
validate_consistent_column_value(HEADER_CELLS_PER_CHIP_WELL)
validate_samples_per_pool_for_labware
validate_scrna_core_cdna_prep_feasibility
end
end
Expand Down Expand Up @@ -73,21 +72,6 @@ def validate_consistent_column_value(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.
Expand All @@ -111,72 +95,6 @@ def validate_unique_values(study_project, rows, index_of_column, column_header)
)
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.
Expand Down Expand Up @@ -247,36 +165,4 @@ def plate?(barcodes, well_locations)
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]

errors.add(
:spreadsheet,
"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
end
# rubocop:enable Metrics/ModuleLength
2 changes: 1 addition & 1 deletion app/views/bulk_submissions/_upload.html.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<strong>none</strong> of them will be processed. You will get feedback about any problems.</p>
<% end %>
<%= semantic_form_for @bulk_submission, html: { multipart: true } do |form| %>
<%= form.semantic_errors :base %>

<%= form.inputs do %>
<%= form.input :spreadsheet, as: :file, required: true %>
<%= form.input :encoding, as: :select, collection: Encoding.list.map(&:to_s) %>
Expand Down