class ProtocolsController < ApplicationController include RenamingUtil include ProtocolsImporter include ProtocolsExporter include ActionView::Helpers::TextHelper include ActionView::Helpers::UrlHelper include ApplicationHelper include InputSanitizeHelper include ProtocolsIoHelper include TeamsHelper include CommentHelper before_action :check_create_permissions, only: %i( create_new_modal create ) before_action :check_clone_permissions, only: [:clone] before_action :check_view_permissions, only: %i( protocol_status_bar updated_at_label preview linked_children linked_children_datatable ) before_action :switch_team_with_param, only: :index before_action :check_view_all_permissions, only: %i( index datatable ) # For update_from_parent and update_from_parent_modal we don't need to check # read permission for the parent protocol before_action :check_manage_permissions, only: %i( edit update_keywords update_description update_name update_authors edit_name_modal edit_keywords_modal edit_authors_modal edit_description_modal unlink unlink_modal revert revert_modal update_from_parent update_from_parent_modal ) before_action :check_manage_parent_in_repository_permissions, only: %i( update_parent update_parent_modal ) before_action :check_manage_all_in_repository_permissions, only: %i(make_private publish archive) before_action :check_restore_all_in_repository_permissions, only: :restore before_action :check_load_from_repository_views_permissions, only: %i( load_from_repository_modal load_from_repository_datatable ) before_action :check_load_from_repository_permissions, only: [ :load_from_repository ] before_action :check_load_from_file_permissions, only: [ :load_from_file ] before_action :check_copy_to_repository_permissions, only: %i( copy_to_repository copy_to_repository_modal ) before_action :check_import_permissions, only: :import before_action :check_export_permissions, only: :export before_action :check_protocolsio_import_permissions, only: %i(protocolsio_import_create protocolsio_import_save) def index; end def datatable respond_to do |format| format.json do render json: ::ProtocolsDatatable.new( view_context, @current_team, @type, current_user ) end end end def preview respond_to do |format| format.json do render json: { title: I18n.t('protocols.index.preview.title', protocol: escape_input(@protocol.name)), html: render_to_string( partial: 'protocols/index/protocol_preview_modal_body.html.erb', locals: { protocol: @protocol } ), footer: render_to_string( partial: 'protocols/index/protocol_preview_modal_footer.html.erb', locals: { protocol: @protocol } ) } end end end def linked_children respond_to do |format| format.json do render json: { title: I18n.t('protocols.index.linked_children.title', protocol: escape_input(@protocol.name)), html: render_to_string(partial: 'protocols/index/linked_children_modal_body.html.erb', locals: { protocol: @protocol }) } end end end def linked_children_datatable respond_to do |format| format.json do render json: ::ProtocolLinkedChildrenDatatable.new( view_context, @protocol, current_user, self ) end end end def make_private move_protocol('make_private') end def publish move_protocol('publish') end def archive move_protocol('archive') end def restore move_protocol('restore') end def edit # Switch to correct team current_team_switch(@protocol.team) end def update_keywords respond_to do |format| # sanitize user input if params[:keywords] params[:keywords].collect! do |keyword| escape_input(keyword) end end if @protocol.update_keywords(params[:keywords]) format.json do log_activity(:edit_keywords_in_protocol_repository, nil, protocol: @protocol.id) render json: { status: :ok } end else format.json { render json: {}, status: :unprocessable_entity } end end end def update_authors if @protocol.update(authors: params.require(:protocol)[:authors]) log_activity(:edit_authors_in_protocol_repository, nil, protocol: @protocol.id) render json: {}, status: :ok else render json: @protocol.errors, status: :unprocessable_entity end end def update_name if @protocol.update(name: params.require(:protocol)[:name]) render json: {}, status: :ok else render json: @protocol.errors, status: :unprocessable_entity end end def update_description respond_to do |format| format.json do if @protocol.update(description: params.require(:protocol)[:description]) log_activity(:edit_description_in_protocol_repository, nil, protocol: @protocol.id) TinyMceAsset.update_images(@protocol, params[:tiny_mce_images], current_user) render json: { html: custom_auto_link( @protocol.tinymce_render(:description), simple_format: false, tags: %w(img), team: current_team) } else render json: @protocol.errors, status: :unprocessable_entity end end end end def create @protocol = Protocol.new( team: @current_team, protocol_type: Protocol.protocol_types[@type == :public ? :in_repository_public : :in_repository_private], added_by: current_user ) @protocol.assign_attributes(create_params) ts = Time.now @protocol.record_timestamps = false @protocol.created_at = ts @protocol.updated_at = ts @protocol.published_on = ts if @type == :public respond_to do |format| if @protocol.save log_activity(:create_protocol_in_repository, nil, protocol: @protocol.id) TinyMceAsset.update_images(@protocol, params[:tiny_mce_images], current_user) format.json do render json: { url: edit_protocol_path( @protocol, team: @current_team, type: @type ) } end else format.json do render json: @protocol.errors, status: :unprocessable_entity end end end end def clone cloned = nil Protocol.transaction do begin cloned = @original.deep_clone_repository(current_user) rescue Exception raise ActiveRecord:: Rollback end end respond_to do |format| if !cloned.nil? flash[:success] = t( 'protocols.index.clone.success_flash', original: @original.name, new: cloned.name ) flash.keep(:success) format.json { render json: {}, status: :ok } else flash[:error] = t( 'protocols.index.clone.error_flash', original: @original.name ) flash.keep(:error) format.json { render json: {}, status: :bad_request } end end end def copy_to_repository link_protocols = params[:link] && can_manage_protocol_in_module?(@protocol) && can_create_protocols_in_repository?(@protocol.team) respond_to do |format| transaction_error = false Protocol.transaction do @new = @protocol.copy_to_repository( copy_to_repository_params[:name], copy_to_repository_params[:protocol_type], link_protocols, current_user ) rescue StandardError transaction_error = true raise ActiveRecord:: Rollback end if transaction_error # Bad request error format.json do render json: { message: t('my_modules.protocols.copy_to_repository_modal.error_400') }, status: :bad_request end elsif @new.invalid? # Render errors format.json do render json: @new.errors, status: :unprocessable_entity end else # Everything good, render 200 format.json { render json: { refresh: link_protocols }, status: :ok } end end end def unlink respond_to do |format| transaction_error = false Protocol.transaction do begin @protocol.unlink rescue Exception transaction_error = true raise ActiveRecord::Rollback end end if transaction_error # Bad request error format.json do render json: { message: t('my_modules.protocols.unlink_error') }, status: :bad_request end else # Everything good, display flash & render 200 flash[:success] = t( 'my_modules.protocols.unlink_flash' ) flash.keep(:success) format.json { render json: {}, status: :ok } end end end def revert respond_to do |format| if @protocol.can_destroy? transaction_error = false Protocol.transaction do # Revert is basically update from parent @protocol.update_from_parent(current_user) rescue StandardError transaction_error = true raise ActiveRecord::Rollback end if transaction_error # Bad request error format.json do render json: { message: t('my_modules.protocols.revert_error') }, status: :bad_request end else # Everything good, display flash & render 200 log_activity(:update_protocol_in_task_from_repository, @protocol.my_module.experiment.project, my_module: @protocol.my_module.id, protocol_repository: @protocol.parent.id) flash[:success] = t( 'my_modules.protocols.revert_flash' ) flash.keep(:success) format.json { render json: {}, status: :ok } end else format.json do render json: { message: t('my_modules.protocols.revert_error_locked') }, status: :bad_request end end end end def update_parent respond_to do |format| if @protocol.parent.can_destroy? transaction_error = false Protocol.transaction do @protocol.update_parent(current_user) rescue StandardError transaction_error = true raise ActiveRecord::Rollback end if transaction_error # Bad request error format.json do render json: { message: t('my_modules.protocols.update_parent_error') }, status: :bad_request end else # Everything good, record activity, display flash & render 200 log_activity(:update_protocol_in_repository_from_task, @protocol.my_module.experiment.project, my_module: @protocol.my_module.id, protocol_repository: @protocol.parent.id) flash[:success] = t( 'my_modules.protocols.update_parent_flash' ) flash.keep(:success) format.json { render json: {}, status: :ok } end else format.json do render json: { message: t('my_modules.protocols.update_parent_error_locked') }, status: :bad_request end end end end def update_from_parent respond_to do |format| if @protocol.can_destroy? transaction_error = false Protocol.transaction do @protocol.update_from_parent(current_user) rescue StandardError transaction_error = true raise ActiveRecord::Rollback end if transaction_error # Bad request error format.json do render json: { message: t('my_modules.protocols.update_from_parent_error') }, status: :bad_request end else # Everything good, display flash & render 200 log_activity(:update_protocol_in_task_from_repository, @protocol.my_module.experiment.project, my_module: @protocol.my_module.id, protocol_repository: @protocol.parent.id) flash[:success] = t( 'my_modules.protocols.update_from_parent_flash' ) flash.keep(:success) format.json { render json: {}, status: :ok } end else format.json do render json: { message: t('my_modules.protocols.update_from_parent_error_locked') }, status: :bad_request end end end end def load_from_repository respond_to do |format| if @protocol.can_destroy? transaction_error = false Protocol.transaction do @protocol.load_from_repository(@source, current_user) rescue StandardError transaction_error = true raise ActiveRecord::Rollback end if transaction_error # Bad request error format.json do render json: { message: t('my_modules.protocols.load_from_repository_error') }, status: :bad_request end else # Everything good, record activity, display flash & render 200 log_activity(:load_protocol_to_task_from_repository, @protocol.my_module.experiment.project, my_module: @protocol.my_module.id, protocol_repository: @protocol.parent.id) flash[:success] = t('my_modules.protocols.load_from_repository_flash') flash.keep(:success) format.json { render json: {}, status: :ok } end else format.json do render json: { message: t('my_modules.protocols.load_from_repository_error_locked') }, status: :bad_request end end end end def load_from_file # This is actually very similar to import respond_to do |format| if @protocol.can_destroy? transaction_error = false Protocol.transaction do begin import_into_existing( @protocol, @protocol_json, current_user, current_team ) rescue Exception transaction_error = true raise ActiveRecord:: Rollback end end if transaction_error format.json do render json: { status: :error }, status: :bad_request end else # Everything good, record activity, display flash & render 200 log_activity(:load_protocol_to_task_from_file, @protocol.my_module.experiment.project, my_module: @my_module.id) flash[:success] = t( 'my_modules.protocols.load_from_file_flash' ) flash.keep(:success) format.json do render json: { status: :ok }, status: :ok end end else format.json do render json: { status: :locked }, status: :bad_request end end end end def import protocol = nil respond_to do |format| transaction_error = false Protocol.transaction do begin protocol = import_new_protocol(@protocol_json, @team, @type, current_user) rescue StandardError => ex Rails.logger.error ex.message transaction_error = true raise ActiveRecord:: Rollback end end p_name = if @protocol_json['name'].present? && !@protocol_json['name'].empty? escape_input(@protocol_json['name']) else t('protocols.index.no_protocol_name') end if transaction_error format.json do render json: { name: p_name, status: :bad_request }, status: :bad_request end else Activities::CreateActivityService .call(activity_type: :import_protocol_in_repository, owner: current_user, subject: protocol, team: current_team, message_items: { protocol: protocol.id }) format.json do render json: { name: escape_input(p_name), new_name: escape_input(protocol.name), status: :ok }, status: :ok end end end end def protocolsio_import_create @protocolsio_too_big = false @protocolsio_invalid_file = false @protocolsio_no_file = false if params[:json_file].nil? @protocolsio_no_file = true respond_to do |format| format.js {} end return 0 # return 0 stops the rest of the controller code from executing end extension = File.extname(params[:json_file].path) file_size = File.size(params[:json_file].path) if extension != '.txt' && extension != '.json' @protocolsio_invalid_file = true respond_to do |format| format.js {} end return 0 # return 0 stops the rest of the controller code from executing end if file_size > Rails.configuration.x.file_max_size_mb.megabytes @protocolsio_too_big = true respond_to do |format| format.js {} # if file is too big, default to the js.erb file, # named the same as this controller # where a javascript alert is called end return 0 # return 0 stops the rest of the controller code from executing end json_file_contents = File.read(params[:json_file].path) json_file_contents.gsub! '\"', "'" # escaped double quotes too stressfull, html works with single quotes too # json double quotes dont get escaped since they dont match \" unless valid_protocol_json(json_file_contents) @protocolsio_invalid_file = true respond_to do |format| format.js {} end return 0 # return 0 stops the rest of the controller code from executing end @json_object = JSON.parse(json_file_contents) unless step_hash_null?(@json_object['steps']) @json_object['steps'] = protocols_io_guid_reorder_step_json( @json_object['steps'] ) end @protocol = Protocol.new respond_to do |format| format.js {} # go to the js.erb file named the same as this controller, # where a preview modal is rendered, # and some modals get closed and opened end rescue StandardError => e Rails.logger.error(e.message) @protocolsio_general_error = true respond_to do |format| format.js {} end end def protocolsio_import_save @json_object = JSON.parse(params['json_object']) @db_json = {} @toolong = false @db_json['name'] = pio_eval_title_len( sanitize_input(not_null(params['protocol']['name'])) ) # since scinote only has description field, and protocols.io has many others # ,here i am putting everything important from protocols.io into description @db_json['authors'] = pio_eval_title_len( sanitize_input(not_null(params['protocol']['authors'])) ) @db_json['created_at'] = pio_eval_title_len( sanitize_input(not_null(params['protocol']['created_at'])) ) @db_json['updated_at'] = pio_eval_title_len( sanitize_input(not_null(params['protocol']['last_modified'])) ) @db_json['steps'] = {} unless step_hash_null?(@json_object['steps']) @db_json['steps'] = protocols_io_fill_step( @json_object, @db_json['steps'] ) end protocol = nil respond_to do |format| transaction_error = false @protocolsio_general_error = false Protocol.transaction do begin protocol = import_new_protocol( @db_json, current_team, params[:type].to_sym, current_user ) rescue Exception transaction_error = true raise ActiveRecord:: Rollback end end p_name = if @db_json['name'].present? escape_input(@db_json['name']) else t('protocols.index.no_protocol_name') end if transaction_error @protocolsio_general_error = true # General something went wrong, upload to db failed error # format.json { # render json: { name: p_name, status: :bad_request }, # status: :bad_request # } else @protocolsio_general_error = false format.json do render json: { name: @db_json['name'], new_name: @db_json['name'], status: :ok }, status: :ok end end format.js {} end end def export # Make a zip output stream and send it to the client respond_to do |format| format.html do z_output_stream = Zip::OutputStream.write_buffer do |ostream| ostream.put_next_entry('scinote.xml') ostream.print(generate_envelope_xml(@protocols)) ostream.put_next_entry('scinote.xsd') ostream.print(generate_envelope_xsd) ostream.put_next_entry('eln.xsd') ostream.print(generate_eln_xsd) # Create folder and xml file for each protocol and populate it @protocols.each do |protocol| protocol_dir = get_guid(protocol.id).to_s ostream.put_next_entry("#{protocol_dir}/eln.xml") ostream.print(generate_protocol_xml(protocol)) ostream = protocol.tiny_mce_assets.save_to_eln(ostream, protocol_dir) # Add assets to protocol folder next if protocol.steps.count <= 0 protocol.steps.order(:id).each do |step| step_guid = get_guid(step.id) step_dir = "#{protocol_dir}/#{step_guid}" if step.assets.exists? step.assets.order(:id).each do |asset| next unless asset.file.attached? asset_guid = get_guid(asset.id) asset_file_name = asset_guid.to_s + File.extname(asset.file_name).to_s ostream.put_next_entry("#{step_dir}/#{asset_file_name}") ostream.print(asset.file.download) end end ostream = step.tiny_mce_assets.save_to_eln(ostream, step_dir) end end end z_output_stream.rewind protocol_name = get_protocol_name(@protocols[0]) # Now generate filename of the archive and send file to user if @protocols.count == 1 # Try to construct an OS-safe file name file_name = 'protocol.eln' unless protocol_name.nil? escaped_name = protocol_name.gsub(/[^0-9a-zA-Z\-.,_]/i, '_') .downcase[0..Constants::NAME_MAX_LENGTH] file_name = escaped_name + '.eln' unless escaped_name.empty? end elsif @protocols.length > 1 file_name = 'protocols.eln' end @protocols.each do |p| if params[:my_module_id] my_module = MyModule.find(params[:my_module_id]) Activities::CreateActivityService .call(activity_type: :export_protocol_from_task, owner: current_user, project: my_module.experiment.project, subject: my_module, team: current_team, message_items: { my_module: params[:my_module_id].to_i }) else Activities::CreateActivityService .call(activity_type: :export_protocol_in_repository, owner: current_user, subject: p, team: current_team, message_items: { protocol: p.id }) end end send_data(z_output_stream.read, filename: file_name) end end end def unlink_modal respond_to do |format| format.json do render json: { title: t('my_modules.protocols.confirm_link_update_modal.unlink_title'), message: t('my_modules.protocols.confirm_link_update_modal.unlink_message'), btn_text: t('my_modules.protocols.confirm_link_update_modal.unlink_btn_text'), url: unlink_protocol_path(@protocol) } end end end def revert_modal respond_to do |format| format.json do render json: { title: t('my_modules.protocols.confirm_link_update_modal.revert_title'), message: t('my_modules.protocols.confirm_link_update_modal.revert_message'), btn_text: t('my_modules.protocols.confirm_link_update_modal.revert_btn_text'), url: revert_protocol_path(@protocol) } end end end def update_parent_modal respond_to do |format| format.json do render json: { title: t('my_modules.protocols.confirm_link_update_modal.update_parent_title'), message: t('my_modules.protocols.confirm_link_update_modal.update_parent_message'), btn_text: t('general.update'), url: update_parent_protocol_path(@protocol) } end end end def update_from_parent_modal respond_to do |format| format.json do render json: { title: t('my_modules.protocols.confirm_link_update_modal.update_self_title'), message: t('my_modules.protocols.confirm_link_update_modal.update_self_message'), btn_text: t('general.update'), url: update_from_parent_protocol_path(@protocol) } end end end def load_from_repository_datatable @protocol = Protocol.find_by_id(params[:id]) @type = (params[:type] || 'public').to_sym respond_to do |format| format.json do render json: ::LoadFromRepositoryProtocolsDatatable.new( view_context, @protocol.team, @type, current_user ) end end end def load_from_repository_modal @protocol = Protocol.find_by_id(params[:id]) respond_to do |format| format.json do render json: { html: render_to_string({ partial: "my_modules/protocols/load_from_repository_modal_body.html.erb" }) } end end end def copy_to_repository_modal @new = Protocol.new @original = Protocol.find(params[:id]) respond_to do |format| format.json do render json: { html: render_to_string({ partial: "my_modules/protocols/copy_to_repository_modal_body.html.erb" }) } end end end def protocol_status_bar respond_to do |format| format.json do render json: { html: render_to_string({ partial: "my_modules/protocols/protocol_status_bar.html.erb" }) } end end end def updated_at_label respond_to do |format| format.json do render json: { html: render_to_string({ partial: "protocols/header/updated_at_label.html.erb" }) } end end end def create_new_modal @new_protocol = Protocol.new respond_to do |format| format.json do render json: { html: render_to_string({ partial: "protocols/index/create_new_modal_body.html.erb" }) } end end end def edit_name_modal respond_to do |format| format.json do render json: { title: I18n.t('protocols.header.edit_name_modal.title', protocol: escape_input(@protocol.name)), html: render_to_string({ partial: "protocols/header/edit_name_modal_body.html.erb" }) } end end end def edit_keywords_modal respond_to do |format| format.json do render json: { title: I18n.t('protocols.header.edit_keywords_modal.title', protocol: escape_input(@protocol.name)), html: render_to_string({ partial: "protocols/header/edit_keywords_modal_body.html.erb" }), keywords: @protocol.team.protocol_keywords_list } end end end def edit_authors_modal respond_to do |format| format.json do render json: { title: I18n.t('protocols.header.edit_authors_modal.title', protocol: escape_input(@protocol.name)), html: render_to_string({ partial: "protocols/header/edit_authors_modal_body.html.erb" }) } end end end def edit_description_modal respond_to do |format| format.json do render json: { title: I18n.t('protocols.header.edit_description_modal.title', protocol: escape_input(@protocol.name)), html: render_to_string({ partial: "protocols/header/edit_description_modal_body.html.erb" }) } end end end private def valid_protocol_json(json) JSON.parse(json) return true rescue JSON::ParserError => e return false end def move_protocol(action) rollbacked = false results = [] begin Protocol.transaction do @protocols.find_each do |protocol| result = { name: protocol.name } success = protocol.method(action).call(current_user) # Try renaming protocol unless success rename_record(protocol, :name) success = protocol.method(action).call(current_user) end result[:new_name] = protocol.name result[:type] = protocol.protocol_type result[:success] = success results << result end end rescue rollbacked = true end respond_to do |format| if rollbacked format.json do render json: {}, status: :bad_request end else format.json do render json: { html: render_to_string({ partial: "protocols/index/results_modal_body.html.erb", locals: { results: results, en_action: "#{action}_results" } }) } end end end end def load_team_and_type @current_team = current_team # :public, :private or :archive @type = (params[:type] || 'public').to_sym end def check_view_all_permissions load_team_and_type render_403 unless can_read_team?(@current_team) end def check_view_permissions @protocol = Protocol.find_by_id(params[:id]) unless @protocol.present? && (can_read_protocol_in_module?(@protocol) || can_read_protocol_in_repository?(@protocol)) respond_to { |f| f.json { render json: {}, status: :unauthorized } } end end def check_create_permissions load_team_and_type if !can_create_protocols_in_repository?(@current_team) || @type == :archive render_403 end end def check_clone_permissions load_team_and_type @original = Protocol.find_by_id(params[:id]) if @original.blank? || !can_clone_protocol_in_repository?(@original) || @type == :archive render_403 end end def check_manage_permissions @protocol = Protocol.find_by_id(params[:id]) render_403 unless @protocol.present? && (can_manage_protocol_in_module?(@protocol) || can_manage_protocol_in_repository?(@protocol)) end def check_manage_parent_in_repository_permissions @protocol = Protocol.find_by_id(params[:id]) render_403 unless @protocol.present? && can_read_protocol_in_module?(@protocol) && can_manage_protocol_in_repository?(@protocol.parent) end def check_manage_all_in_repository_permissions @protocols = Protocol.where(id: params[:protocol_ids]) @protocols.find_each do |protocol| unless can_manage_protocol_in_repository?(protocol) respond_to { |f| f.json { render json: {}, status: :unauthorized } } break end end end def check_restore_all_in_repository_permissions @protocols = Protocol.where(id: params[:protocol_ids]) @protocols.find_each do |protocol| unless can_restore_protocol_in_repository?(protocol) respond_to { |f| f.json { render json: {}, status: :unauthorized } } break end end end def check_load_from_repository_views_permissions @protocol = Protocol.find_by_id(params[:id]) render_403 if @protocol.blank? || !can_read_protocol_in_module?(@protocol) end def check_load_from_repository_permissions @protocol = Protocol.find_by_id(params[:id]) @source = Protocol.find_by_id(params[:source_id]) render_403 unless @protocol.present? && @source.present? && (can_manage_protocol_in_module?(@protocol) && can_read_protocol_in_repository?(@source)) end def check_load_from_file_permissions @protocol_json = params[:protocol] @protocol = Protocol.find_by_id(params[:id]) @my_module = @protocol.my_module if @protocol_json.blank? || @protocol.blank? || @my_module.blank? || !can_manage_protocol_in_module?(@protocol) render_403 end end def check_copy_to_repository_permissions @protocol = Protocol.find_by_id(params[:id]) @my_module = @protocol.my_module render_403 unless @my_module.present? && (can_read_protocol_in_module?(@protocol) || can_create_protocols_in_repository?(@protocol.team)) end def check_import_permissions @protocol_json = params[:protocol] @team = Team.find(params[:team_id]) @type = params[:type] ? params[:type].to_sym : nil unless @protocol_json.present? && @team.present? && (@type == :public || @type == :private) && can_create_protocols_in_repository?(@team) render_403 end end def check_export_permissions @protocols = Protocol.where(id: params[:protocol_ids]) render_403 if @protocols.blank? @protocols.each do |p| render_403 unless can_read_protocol_in_module?(p) || can_read_protocol_in_repository?(p) end end def copy_to_repository_params params.require(:protocol).permit(:name, :protocol_type) end def create_params params.require(:protocol).permit(:name) end def check_protocolsio_import_permissions render_403 unless can_create_protocols_in_repository?(current_team) end def log_activity(type_of, project = nil, message_items = {}) message_items = { protocol: @protocol&.id }.merge(message_items) Activities::CreateActivityService .call(activity_type: type_of, owner: current_user, subject: @protocol, team: current_team, project: project, message_items: message_items) end end