basics working

app/services/samples/file_import_service.rb

@@ -0,0 +1,163 @@
+# frozen_string_literal: true
+
+require 'roo'
+
+module Samples
+  # Service used to batch create samples via a file
+  class FileImportService < BaseService
+    SampleFileImportError = Class.new(StandardError)
+
+    # def initialize(namespace, user = nil, params = {})
+    def initialize(project, user = nil, params = {})
+      super(user, params)
+      @project = project
+      # @namespace = namespace
+      @file = params[:file]
+      @sample_name_column = params[:sample_name_column]
+      @sample_description_column = params[:sample_description_column] # TODO: do somthing with this
+      @spreadsheet = nil
+      @headers = nil
+    end
+
+    def execute
+      authorize! @project.namespace, to: :update_sample_metadata?
+
+      validate_sample_name_column
+
+      validate_file
+
+      perform_file_import
+    rescue Samples::FileImportService::SampleFileImportError => e
+      @namespace.errors.add(:base, e.message)
+      {}
+    end
+
+    private
+
+    def validate_sample_name_column
+      return unless @sample_name_column.nil?
+
+      raise SampleFileImportError,
+            I18n.t('services.samples.metadata.import_file.empty_sample_id_column')
+    end
+
+    def validate_file_extension
+      file_extension = File.extname(@file).downcase
+
+      return file_extension if %w[.csv .tsv .xls .xlsx].include?(file_extension)
+
+      raise SampleFileImportError,
+            I18n.t('services.samples.metadata.import_file.invalid_file_extension')
+    end
+
+    def validate_file_headers
+      duplicate_headers = @headers.find_all { |header| @headers.count(header) > 1 }.uniq
+      unless duplicate_headers.empty?
+        raise SampleFileImportError,
+              I18n.t('services.samples.metadata.import_file.duplicate_column_names')
+      end
+
+      unless @headers.include?(@sample_name_column)
+        raise SampleFileImportError,
+              I18n.t('services.samples.metadata.import_file.missing_sample_id_column')
+      end
+
+      # TODO: check if we have a project puid
+
+      # return if @headers.count { |header| header != @sample_name_column }.positive?
+
+      # raise SampleFileImportError,
+      #       I18n.t('services.samples.metadata.import_file.missing_metadata_column')
+    end
+
+    def validate_file_rows
+      # Should have at least 2 rows
+      first_row = @spreadsheet.row(2)
+      return unless first_row.compact.empty?
+
+      raise SampleFileImportError,
+            I18n.t('services.samples.metadata.import_file.missing_metadata_row')
+    end
+
+    def validate_file
+      if @file.nil?
+        raise SampleFileImportError,
+              I18n.t('services.samples.metadata.import_file.empty_file')
+      end
+
+      extension = validate_file_extension
+
+      @spreadsheet = if extension.eql? '.tsv'
+                       Roo::CSV.new(@file, csv_options: { col_sep: "\t" })
+                     else
+                       Roo::Spreadsheet.open(@file)
+                     end
+
+      @headers = @spreadsheet.row(1).compact
+
+      validate_file_headers
+
+      validate_file_rows
+    end
+
+    def perform_file_import
+      response = {}
+      parse_settings = @headers.zip(@headers).to_h
+
+      @spreadsheet.each_with_index(parse_settings) do |data, index|
+        next unless index.positive?
+
+        # TODO: next when all data is nil (empty line)
+
+        sample_name = data[@sample_name_column]
+
+        # TODO:  do work here
+
+        response[sample_name] = process_sample_row(sample_name, nil) # TODO
+      rescue ActiveRecord::RecordNotFound
+        @project.errors.add(:sample, error_message(sample_name))
+      end
+      response
+    end
+
+    def error_message(sample_id) # TODO: remove
+      if @namespace.type == 'Group'
+        I18n.t('services.samples.metadata.import_file.sample_not_found_within_group', sample_puid: sample_id)
+      else
+        I18n.t('services.samples.metadata.import_file.sample_not_found_within_project', sample_puid: sample_id)
+      end
+    end
+
+    def process_sample_row(name, description)
+      sample_params = { name:, description: }
+      sample = Samples::CreateService.new(current_user, @project, sample_params).execute
+
+      if sample.persisted?
+        sample
+      else
+        sample.errors.map do |error| # TODO: rework this error
+          {
+            path: ['sample', error.attribute.to_s.camelize(:lower)],
+            message: error.message
+          }
+        end
+      end
+    end
+
+    # def find_sample(sample_id)
+    #   if @namespace.type == 'Group'
+    #     authorized_scope(Sample, type: :relation, as: :namespace_samples,
+    #                              scope_options: { namespace: @namespace,
+    #                                               minimum_access_level: Member::AccessLevel::MAINTAINER })
+    #       .find_by!(puid: sample_id)
+    #   else
+    #     project = @namespace.project
+    #     if Irida::PersistentUniqueId.valid_puid?(sample_id, Sample)
+    #       Sample.find_by!(puid: sample_id, project_id: project.id)
+    #     else
+    #       Sample.find_by!(name: sample_id, project_id: project.id)
+    #     end
+    #   end
+    # end
+  end
+end