require_relative '../../app/services/tasks/samples_to_repository_migration_service' namespace :samples_to_repository_migration do desc 'Migrates all data from samples to custom repository' task :run, [:last_id] => :environment do |_, args| include ActiveRecord::Sanitization::ClassMethods params = { batch_size: 10 } migration_service = Tasks::SamplesToRepositoryMigrationService conn = ActiveRecord::Base.connection if args.present? && args[:last_id].present? params[:start] = args[:last_id].to_i end Team.find_each(params) do |team| puts "******************************* \n\n" puts "Processing Team id => [#{team.id}] \n\n" puts '*******************************' ActiveRecord::Base.transaction do team_samples = migration_service.fetch_all_team_samples(team) repository = migration_service.prepare_repository(team) custom_columns = migration_service.get_custom_columns(team, repository) sample_mappings = {} team_samples.each do |item| created_by = item['sample_created_by_id'] || team.created_by_id last_modified_by = item['sample_last_modified_by_id'] last_modified_by ||= team.created_by_id timestamp = conn.quote(Time.now.to_s(:db)) values = [repository.id, created_by, last_modified_by, conn.quote(item['sample_name']), timestamp, timestamp] list_item_sql = <<-SQL INSERT INTO repository_rows (repository_id, created_by_id, last_modified_by_id, name, created_at, updated_at) VALUES (#{values.join(', ')}) RETURNING id SQL result = conn.execute(list_item_sql) row_id = result[0]['id'] sample_mappings[item['sample_id']] = row_id # check if sample has sample type assigned if item['sample_type_name'] column = custom_columns.detect { |el| el['name'] == 'Sample type' } list_item = column.repository_list_items.where( data: item['sample_type_name'] ).take migration_service.create_list_cell( row_id, column.id, list_item.id, list_item.created_by_id, list_item.last_modified_by_id ) end # check if sample has sample group assigned if item['sample_group_name'] column = custom_columns.detect { |el| el['name'] == 'Sample group' } list_item = column.repository_list_items.where( data: item['sample_group_name'] ).take migration_service.create_list_cell( row_id, column.id, list_item.id, list_item.created_by_id, list_item.last_modified_by_id ) # assign sample group color to the sample if item['sample_group_color'] column = custom_columns.detect do |el| el['name'] == 'Sample group color hex' end migration_service.create_text_cell( row_id, column.id, item['sample_group_color'], created_by, last_modified_by ) end end # append custom fields custom_fields = migration_service.get_sample_custom_fields( item['sample_id'] ) custom_fields.each do |field| column = custom_columns.detect do |el| el['name'] == field['column_name_reference'] end migration_service .create_text_cell(row_id, column.id, field['value'], created_by, last_modified_by) end # assign repository item to a tasks assigned_modules = migration_service.get_assigned_sample_module( item['sample_id'] ) assigned_modules.each do |element| assigned_by = element['assigned_by_id'] || created_by values = [row_id, element['my_module_id'], assigned_by, timestamp, timestamp] cell_sql = <<-SQL INSERT INTO my_module_repository_rows (repository_row_id, my_module_id, assigned_by_id, created_at, updated_at) VALUES (#{values.join(', ')}) SQL conn.execute(cell_sql) end end # Update report elements team.reports.each do |r| r.report_elements.where(type_of: 7).each do |e| e.update_attributes(type_of: 17, repository_id: repository.id) end end # Now update smart annotations migration_service.update_smart_annotations(team, sample_mappings) end end end end