class OrganizationsController < ApplicationController before_action :load_vars, only: [:parse_sheet, :import_samples, :export_samples] before_action :check_create_sample_permissions, only: [:parse_sheet, :import_samples] before_action :check_view_samples_permission, only: [:export_samples] def parse_sheet session[:return_to] ||= request.referer respond_to do |format| if params[:file] begin if params[:file].size > FILE_MAX_SIZE.megabytes error = t("organizations.parse_sheet.errors.file_size_exceeded") format.html { flash[:alert] = error redirect_to session.delete(:return_to) } format.json { render json: {message: error}, status: :unprocessable_entity } else sheet = Organization.open_spreadsheet(params[:file]) # Check if we actually have any rows (last_row > 1) if sheet.last_row.between?(0, 1) flash[:notice] = t( "organizations.parse_sheet.errors.empty_file") redirect_to session.delete(:return_to) and return end # Get data (it will trigger any errors as well) @header = sheet.row(1) @rows = []; @rows << Hash[[@header, sheet.row(2)].transpose] # Fill in fields for dropdown @available_fields = @organization.get_available_sample_fields # Save file for next step (importing) @temp_file = TempFile.new( session_id: session.id, file: params[:file] ) if @temp_file.save # format.html format.json { render :json => { :html => render_to_string({ :partial => "samples/parse_samples_modal.html.erb" }) } } else error = t("organizations.parse_sheet.errors.temp_file_failure") format.html { flash[:alert] = error redirect_to session.delete(:return_to) } format.json { render json: {message: error}, status: :unprocessable_entity } end end rescue ArgumentError, CSV::MalformedCSVError error = t("organizations.parse_sheet.errors.invalid_file") format.html { flash[:alert] = error redirect_to session.delete(:return_to) } format.json { render json: {message: error}, status: :unprocessable_entity } rescue TypeError error = t("organizations.parse_sheet.errors.invalid_extension") format.html { flash[:alert] = error redirect_to session.delete(:return_to) } format.json { render json: {message: error}, status: :unprocessable_entity } end else error = t("organizations.parse_sheet.errors.no_file_selected") format.html { flash[:alert] = error session[:return_to] ||= request.referer redirect_to session.delete(:return_to) } format.json { render json: {message: error}, status: :unprocessable_entity } end end end def import_samples session[:return_to] ||= request.referer respond_to do |format| if params[:file_id] @temp_file = TempFile.find_by_id(params[:file_id]) if @temp_file # Check if session_id is equal to prevent file stealing if @temp_file.session_id == session.id # Check if mappings exists or else we don't have anything to parse if params[:mappings] @sheet = Organization.open_spreadsheet(@temp_file.file) # Check for duplicated values h1 = params[:mappings].clone.delete_if { |k, v| v.empty? } if h1.length == h1.invert.length # Check if there exist mapping for sample name (it's mandatory) if params[:mappings].has_value?("-1") result = @organization.import_samples(@sheet, params[:mappings], current_user) nr_of_added = result[:nr_of_added] total_nr = result[:total_nr] if result[:status] == :ok # If no errors are present, redirect back # to samples table flash[:success] = t( "organizations.import_samples.success_flash", nr: nr_of_added, samples: t( "organizations.import_samples.sample", count: total_nr ) ) @temp_file.destroy format.html { redirect_to session.delete(:return_to) } format.json { flash.keep(:success) render json: { status: :ok } } else # Otherwise, also redirect back, # but display different message flash[:alert] = t( "organizations.import_samples.partial_success_flash", nr: nr_of_added, samples: t( "organizations.import_samples.sample", count: total_nr ) ) @temp_file.destroy format.html { redirect_to session.delete(:return_to) } format.json { flash.keep(:alert) render json: { status: :unprocessable_entity } } end else # This is currently the only AJAX error response flash_alert = t( "organizations.import_samples.errors.no_sample_name") format.html { flash[:alert] = flash_alert redirect_to session.delete(:return_to) } format.json { render json: { html: render_to_string({ partial: "parse_error.html.erb", locals: { error: flash_alert } }) }, status: :unprocessable_entity } end else # This code should never execute unless user tampers with # JS (selects same column in more than one dropdown) flash_alert = t( "organizations.import_samples.errors.duplicated_values") format.html { flash[:alert] = flash_alert redirect_to session.delete(:return_to) } format.json { render json: { html: render_to_string({ partial: "parse_error.html.erb", locals: { error: flash_alert } }) }, status: :unprocessable_entity } end else @temp_file.destroy flash[:alert] = t( "organizations.import_samples.errors.no_data_to_parse") format.html { redirect_to session.delete(:return_to) } format.json { flash.keep(:alert) render json: { status: :unprocessable_entity } } end else @temp_file.destroy flash[:alert] = t( "organizations.import_samples.errors.session_expired") format.html { redirect_to session.delete(:return_to) } format.json { flash.keep(:alert) render json: { status: :unprocessable_entity } } end else # No temp file to begin with, so no need to destroy it flash[:alert] = t( "organizations.import_samples.errors.temp_file_not_found") format.html { redirect_to session.delete(:return_to) } format.json { flash.keep(:alert) render json: { status: :unprocessable_entity } } end else flash[:alert] = t( "organizations.import_samples.errors.temp_file_not_found") format.html { redirect_to session.delete(:return_to) } format.json { flash.keep(:alert) render json: { status: :unprocessable_entity } } end end end def export_samples require "csv" respond_to do |format| if params[:sample_ids].present? and params[:header_ids].present? samples = [] params[:sample_ids].each do |id| sample = Sample.find_by_id(id) if sample samples << sample end end format.csv { send_data @organization.to_csv(samples, params[:header_ids]) } else format.csv { render nothing: true } end end end def load_vars @organization = Organization.find_by_id(params[:id]) unless @organization render_404 end end def check_create_sample_permissions unless can_create_samples(@organization) render_403 end end def check_view_samples_permission unless can_view_samples(@organization) render_403 end end def routing_error(error = 'Routing error', status = :not_found, exception=nil) redirect_to root_path end end