# frozen_string_literal: true class SpreadsheetParser # Based on file's extension opens file (used for importing) def self.open_spreadsheet(file) file_path = file.path filename = if file.class.name.split('::')[-1] == 'UploadedFile' file.original_filename else File.basename(file.path) end case File.extname(filename) when '.csv' Roo::CSV.new(file_path, extension: :csv) when '.tsv' Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) when '.txt' # This assumption is based purely on biologist's habits Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) when '.xlsx' Roo::Excelx.new(file_path) else raise TypeError end end def self.spreadsheet_enumerator(sheet) if sheet.is_a?(Roo::CSV) sheet elsif sheet.is_a?(Roo::Excelx) sheet.each_row_streaming(pad_cells: true) else sheet.rows end end def self.first_two_rows(sheet, date_format: nil) rows = spreadsheet_enumerator(sheet) header = [] columns = [] rows.take(2).each_with_index do |row_values, i| row = parse_row(row_values, sheet, header: i.zero?, date_format: date_format) if row && i.zero? header = row else escaped_row = row.map do |cell| cell.to_s.gsub("\\n", "\n") end columns = escaped_row end end return header, columns end def self.parse_row(row, sheet, header: false, date_format: nil) if sheet.is_a?(Roo::Excelx) && !header row.map do |cell| if cell.is_a?(Roo::Excelx::Cell::Number) && cell.format == 'General' cell&.value&.to_d elsif date_format && cell&.value.is_a?(Date) cell&.value&.strftime(date_format) else cell&.formatted_value end end else row.map(&:to_s) end end def self.duplicate_ids(sheet) # Extracting IDs from sheet and removing header row ids = sheet.drop(1).map(&:first) # Selecting duplicate IDs ids.group_by { |id| id }.select { |_, group| group.size > 1 }.keys end end