scinote-web/app/controllers/protocols_controller.rb

class ProtocolsController < ApplicationController
  include RenamingUtil
  include ActionView::Helpers::TextHelper
  include ActionView::Helpers::UrlHelper
  include ApplicationHelper
  include InputSanitizeHelper
  include ProtocolsIoHelper
  include TeamsHelper
  include CommentHelper
  include ProtocolsExporterV2

  before_action :check_create_permissions, only: %i(
    create
  )
  before_action :check_clone_permissions, only: [:clone]
  before_action :check_view_permissions, only: %i(
    show
    versions_modal
    protocol_status_bar
    linked_children
    linked_children_datatable
    permissions
  )
  before_action :switch_team_with_param, only: %i(index protocolsio_index)
  before_action :check_view_all_permissions, only: %i(
    index
    protocolsio_index
    datatable
  )
  before_action :check_manage_permissions, only: %i(
    update_keywords
    update_description
    update_version_comment
    update_name
    update_authors
    unlink
    unlink_modal
    delete_steps
  )

  before_action :check_manage_with_read_protocol_permissions, only: %i(
    revert
    revert_modal
    update_from_parent
    update_from_parent_modal
  )
  before_action :check_restore_all_in_repository_permissions, only: :restore
  before_action :check_archive_all_in_repository_permissions, only: :archive
  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
  )

  before_action :check_publish_permission, only: %i(publish version_comment update_version_comment)
  before_action :check_import_permissions, only: :import
  before_action :check_export_permissions, only: :export
  before_action :check_delete_draft_permissions, only: :destroy_draft
  before_action :check_save_as_draft_permissions, only: :save_as_draft

  before_action :check_protocolsio_import_permissions,
                only: %i(protocolsio_import_create protocolsio_import_save)

  before_action :set_importer, only: %i(load_from_file import)
  before_action :set_inline_name_editing, only: :show
  before_action :set_breadcrumbs_items, only: %i(index show)

  layout 'fluid'

  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 versions_modal
    return render_403 unless @protocol.in_repository_published_original? || @protocol.initial_draft?

    @published_versions = @protocol.published_versions_with_original.order(version_number: :desc)
    render json: {
      html: render_to_string(partial: 'protocols/index/protocol_versions_modal.html.erb')
    }
  end

  def print
    @protocol = Protocol.find(params[:id])
    render_403 && return unless @protocol.my_module.blank? || can_read_protocol_in_module?(@protocol)

    render layout: 'protocols/print'
  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 publish
    Protocol.transaction do
      @protocol.update!(
        published_by: current_user,
        published_on: DateTime.now,
        version_comment: params[:version_comment] || @protocol.version_comment,
        protocol_type: (@protocol.parent_id.nil? ? :in_repository_published_original : :in_repository_published_version)
      )
      log_activity(:protocol_template_published,
                   nil,
                   protocol: @protocol.id,
                   version_number: @protocol.version_number)
    rescue ActiveRecord::RecordInvalid => e
      flash[:error] = @protocol.errors&.map(&:message)&.join(',')
      Rails.logger.error e.message
      raise ActiveRecord::Rollback
    rescue StandardError => e
      flash[:error] = I18n.t('errors.general')
      Rails.logger.error e.message
      raise ActiveRecord::Rollback
    end

    if params[:view] == 'show'
      redirect_to protocol_path(@protocol)
    else
      redirect_to protocols_path
    end
  end

  def destroy_draft
    Protocol.transaction do
      parent = @protocol.parent
      @protocol.destroy!
      @protocol = parent
      log_activity(:protocol_template_draft_deleted,
                   nil,
                   protocol: @protocol.id)

      flash[:success] = I18n.t('protocols.delete_draft_modal.success')
      redirect_to protocols_path
    rescue ActiveRecord::RecordNotDestroyed => e
      Rails.logger.error e.message
      render json: { message: e.message }, status: :unprocessable_entity
      raise ActiveRecord::Rollback
    rescue StandardError => e
      render json: { message: I18n.t('errors.general') }, status: :unprocessable_entity
      Rails.logger.error e.message
      raise ActiveRecord::Rollback
    end
  end

  def archive
    move_protocols('archive')
  end

  def restore
    move_protocols('restore')
  end

  def edit
    render :show
  end

  def show
    respond_to do |format|
      format.json { render json: @protocol, serializer: ProtocolSerializer, user: current_user }
      format.html
    end
  end

  def update_keywords
    respond_to do |format|
      if @protocol.update_keywords(params[:keywords], current_user)
        format.json do
          log_activity(:edit_keywords_in_protocol_repository, nil, protocol: @protocol.id)
          render json: @protocol, serializer: ProtocolSerializer, user: current_user
        end
      else
        format.json { render json: I18n.t('errors.general'), status: :unprocessable_entity }
      end
    end
  end

  def update_authors
    if @protocol.update(authors: params.require(:protocol)[:authors], last_modified_by: current_user)
      log_activity(:edit_authors_in_protocol_repository, nil, protocol: @protocol.id)
      render json: @protocol, serializer: ProtocolSerializer, user: current_user
    else
      render json: @protocol.errors, status: :unprocessable_entity
    end
  end

  def update_name
    if @protocol.update(name: params.require(:protocol)[:name], last_modified_by: current_user)
      log_activity(:edit_protocol_name_in_repository, nil, protocol: @protocol.id)
      render json: {}, status: :ok
    else
      render json: @protocol.errors, status: :unprocessable_entity
    end
  end

  def update_description
    old_description = @protocol.description
    respond_to do |format|
      format.json do
        if @protocol.update(description: params.require(:protocol)[:description], last_modified_by: current_user)
          log_activity(:edit_description_in_protocol_repository, nil, protocol: @protocol.id)
          TinyMceAsset.update_images(@protocol, params[:tiny_mce_images], current_user)
          protocol_annotation_notification(old_description)
          render json: @protocol, serializer: ProtocolSerializer, user: current_user
        else
          render json: @protocol.errors, status: :unprocessable_entity
        end
      end
    end
  end

  def create
    @protocol = Protocol.new(create_params)
    ts = Time.now
    @protocol.team = current_team
    @protocol.protocol_type = :in_repository_draft
    @protocol.added_by = current_user
    @protocol.record_timestamps = false
    @protocol.created_at = ts
    @protocol.updated_at = ts
    @protocol.last_modified_by = current_user

    if @protocol.save
      log_activity(:create_protocol_in_repository, nil, protocol: @protocol.id)
      redirect_to protocol_path(@protocol)
    else
      render json: { error: @protocol.errors.messages.map { |_k, v| v }.join(', ') }, status: :unprocessable_entity
    end
  end

  def delete_steps
    @protocol.with_lock do
      team = @protocol.team
      previous_size = 0
      @protocol.steps.each do |step|
        previous_size += step.space_taken

        if @protocol.in_module?
          log_activity(:destroy_step, @protocol.my_module.experiment.project,
                       my_module: @protocol.my_module.id,
                       step: step.id,
                       step_position: { id: step.id, value_for: 'position_plus_one' })
        else
          log_activity(:delete_step_in_protocol_repository, nil, step: step.id,
            step_position: { id: step.id, value_for: 'position_plus_one' })
        end

        # skip adjusting positions after destroy as this is a bulk delete
        step.skip_position_adjust = true
        step.destroy!
      end

      team.release_space(previous_size)
      team.save!
      render json: { status: 'ok' }
    rescue ActiveRecord::RecordNotDestroyed
      render json: { status: 'error' }, status: :unprocessable_entity
      raise ActiveRecord::Rollback
    end
  end

  def clone
    cloned = nil
    Protocol.transaction do
      cloned = @original.deep_clone_repository(current_user)
    rescue StandardError
      raise ActiveRecord::Rollback
    end

    respond_to do |format|
      format.json do
        if cloned.present?
          render json: { message: t('protocols.index.clone.success_flash', original: @original.name, new: cloned.name) }
        else
          render json: { message: t('protocols.index.clone.error_flash', original: @original.name) },
                 status: :bad_request
        end
      end
    end
  end

  def copy_to_repository
    respond_to do |format|
      transaction_error = false
      Protocol.transaction do
        @new_protocol = @protocol.copy_to_repository(Protocol.new(create_params), current_user)
        log_activity(:task_protocol_save_to_template, @my_module.experiment.project, protocol: @new_protocol.id)
      rescue StandardError => e
        transaction_error = true
        Rails.logger.error(e.message)
        Rails.logger.error(e.backtrace.join("\n"))
        raise ActiveRecord::Rollback
      end

      format.json do
        if transaction_error
          # Bad request error
          render json: {
            message: t('my_modules.protocols.copy_to_repository_modal.error_400')
          },
          status: :bad_request
        elsif @new_protocol.invalid?
          render json: { error: @new_protocol.errors.messages.map { |_, value| value }.join(' ') }, status: :unprocessable_entity
        else
          # Everything good, render 200
          render json: { message: t('my_modules.protocols.copy_to_repository_modal.success_message') }
        end
      end
    end
  end

  def save_as_draft
    Protocol.transaction do
      draft = @protocol.save_as_draft(current_user)

      if draft.invalid?
        flash[:error] = draft.errors.full_messages.join(', ')
        redirect_to protocols_path
      else
        log_activity(:protocol_template_draft_created, nil, protocol: @protocol.id)
        redirect_to protocol_path(draft)
      end
    rescue StandardError => e
      Rails.logger.error(e.message)
      Rails.logger.error(e.backtrace.join("\n"))
      flash[:error] = I18n.t('errors.general')
      redirect_to protocols_path
      raise ActiveRecord::Rollback
    end
  end

  def unlink
    respond_to do |format|
      transaction_error = false
      Protocol.transaction do
        begin
          @protocol.unlink
        rescue StandardError
          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, @protocol.parent)
        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_from_parent
    protocol_can_destroy = @protocol.can_destroy?
    respond_to do |format|
      if protocol_can_destroy
        transaction_error = false
        Protocol.transaction do
          # Find original published protocol template
          source_parent = if @protocol.parent.in_repository_published_original?
                            @protocol.parent
                          else
                            @protocol.parent.parent
                          end
          @protocol.update_from_parent(current_user, source_parent.latest_published_version_or_self)
        rescue StandardError
          transaction_error = true
          raise ActiveRecord::Rollback
        end
      end

      format.json do
        if !protocol_can_destroy
          render json: { message: t('my_modules.protocols.update_from_parent_error_locked') }, status: :bad_request
        elsif transaction_error
          render json: { message: t('my_modules.protocols.update_from_parent_error') }, status: :bad_request
        else
          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)
          render json: {}, status: :ok
        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
          @importer.import_into_existing(
            @protocol, @protocol_json
          )
        rescue StandardError => e
          transaction_error = true
          Rails.logger.error(e.message)
          Rails.logger.error(e.backtrace.join("\n"))
          raise ActiveRecord::Rollback
        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 protocolsio_index
    render json: {
      html: render_to_string({ partial: 'protocols/index/protocolsio_modal_body.html.erb' })
    }
  end

  def import
    protocol = nil
    respond_to do |format|
      transaction_error = false
      Protocol.transaction do
        protocol = @importer.import_new_protocol(@protocol_json)
      rescue StandardError => e
        Rails.logger.error e.backtrace.join("\n")
        transaction_error = true
        raise ActiveRecord::Rollback
      end

      if transaction_error
        format.json do
          render json: { status: :bad_request }, status: :bad_request
        end
      else
        Activities::CreateActivityService
          .call(activity_type: :import_protocol_in_repository,
                owner: current_user,
                subject: protocol,
                team: protocol.team,
                message_items: {
                  protocol: protocol.id
                })

        format.json do
          render json: { 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.backtrace.join("\n"))
    @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(
      escape_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(
      escape_input(not_null(params['protocol']['authors']))
    )
    @db_json['created_at'] = pio_eval_title_len(
      escape_input(not_null(params['protocol']['created_at']))
    )
    @db_json['updated_at'] = pio_eval_title_len(
      escape_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 = @importer.import_new_protocol(@db_json)
        rescue StandardError
          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 = protocol.latest_published_version_or_self
            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)

              step.step_texts.each do |step_text|
                ostream = step_text.tiny_mce_assets.save_to_eln(ostream, step_dir)
              end
            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.blank?
          end
        elsif @protocols.length > 1
          file_name = 'protocols.eln'
        end

        @protocols.each do |protocol|
          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.project,
                    subject: my_module,
                    team: my_module.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: protocol,
                    team: protocol.team,
                    message_items: {
                      protocol: protocol.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_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('my_modules.protocols.confirm_link_update_modal.update_self_btn_text'),
          url: update_from_parent_protocol_path(@protocol)
        }
      end
    end
  end

  def load_from_repository_datatable
    @protocol = Protocol.find_by_id(params[:id])
    respond_to do |format|
      format.json do
        render json: ::LoadFromRepositoryProtocolsDatatable.new(
          view_context,
          @protocol.team,
          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 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 version_comment
    respond_to do |format|
      format.json do
        render json: { version_comment: @protocol.version_comment }
      end
    end
  end

  def update_version_comment
    respond_to do |format|
      format.json do
        if @protocol.update(version_comment: params.require(:protocol)[:version_comment])
          log_activity(:protocol_template_revision_notes_updated,
                       nil,
                       protocol: @protocol.id)
          render json: { version_comment: @protocol.version_comment }
        else
          render json: { errors: @protocol.errors }, status: :unprocessable_entity
        end
      end
    end
  end

  def permissions
    if stale?([@protocol, @protocol.team.user_assignments])
      render json: {
        copyable: can_clone_protocol_in_repository?(@protocol),
        archivable: can_archive_protocol_in_repository?(@protocol),
        restorable: can_restore_protocol_in_repository?(@protocol),
        readable: can_read_protocol_in_repository?(@protocol)
      }
    end
  end

  private

  def set_importer
    case params.dig('protocol', 'elnVersion')
    when '1.0'
      @importer = ProtocolsImporter.new(current_user, current_team)
    when '1.1'
      @importer = ProtocolsImporterV2.new(current_user, current_team)
    end
  end

  def valid_protocol_json(json)
    JSON.parse(json)
    return true
  rescue JSON::ParserError => e
    return false
  end

  def move_protocols(action)
    Protocol.transaction do
      @protocols.find_each do |protocol|
        protocol = protocol.parent if protocol.parent_id
        unless protocol.method(action).call(current_user)
          raise StandardError, protocol.errors&.messages&.values&.join(' ') || I18n.t('errors.general')
        end
      end
    end
    render json: { message: t("protocols.index.#{action}_flash_html", count: @protocols.size) }
  rescue StandardError => e
    Rails.logger.error(e.message)
    Rails.logger.error(e.backtrace.join("\n"))
    render json: { message: e.message }, status: :unprocessable_entity
  end

  def set_inline_name_editing
    return unless @protocol.initial_draft?
    return unless can_manage_protocol_draft_in_repository?(@protocol)

    @inline_editable_title_config = {
      name: 'title',
      params_group: 'protocol',
      item_id: @protocol.id,
      field_to_udpate: 'name',
      path_to_update: name_protocol_path(@protocol)
    }
  end

  def load_team_and_type
    @current_team = current_team
    # :public, :private or :archive
    @type = (params[:type] || 'active').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])
    current_team_switch(@protocol.team) if current_team != @protocol.team
    unless @protocol.present? &&
           (can_read_protocol_in_module?(@protocol) ||
           can_read_protocol_in_repository?(@protocol) ||
           (@protocol.in_repository? && can_manage_team?(@protocol.team)))
      render_403
    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
    protocol = Protocol.find_by(id: params[:ids][0])
    @original = protocol.latest_published_version_or_self

    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_draft_in_repository?(@protocol))
  end

  def check_manage_with_read_protocol_permissions
    @protocol = Protocol.find_by(id: params[:id])
    render_403 unless @protocol.present? && @protocol.parent.present? &&
                      (can_manage_protocol_in_module?(@protocol) &&
                       can_read_protocol_in_repository?(@protocol.parent))
  end

  def check_save_as_draft_permissions
    @protocol = Protocol.find_by(id: params[:id])
    render_403 unless @protocol.present? && can_save_protocol_version_as_draft?(@protocol)
  end

  def check_delete_draft_permissions
    @protocol = Protocol.find_by(id: params[:id])
    render_403 unless @protocol.present? &&
                      can_delete_protocol_draft_in_repository?(@protocol)
  end

  def check_archive_all_in_repository_permissions
    @protocols = Protocol.where(id: params[:protocol_ids])
    @protocols.find_each do |protocol|
      unless can_archive_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_publish_permission
    @protocol = Protocol.find_by(id: params[:id])

    render_403 if @protocol.blank? || !can_publish_protocol_in_repository?(@protocol)
  end

  def check_load_from_repository_permissions
    @protocol = Protocol.find_by(id: params[:id])
    @source = Protocol.find_by(id: params[:source_id])&.latest_published_version_or_self

    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])
    render_403 unless @protocol_json.present? && @team.present? && can_create_protocols_in_repository?(@team)
  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, :default_public_user_role_id, :visibility)
  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: @protocol.team,
            project: project,
            message_items: message_items)
  end

  def protocol_annotation_notification(old_text)
    smart_annotation_notification(
      old_text: old_text,
      new_text: @protocol.description,
      title: t('notifications.protocol_description_annotation_title',
               user: current_user.full_name,
               protocol: @protocol.name),
      message: t('notifications.protocol_description_annotation_message_html',
                 protocol: link_to(@protocol.name, protocol_url(@protocol)))
    )
  end

  def set_breadcrumbs_items
    @breadcrumbs_items = []

    @breadcrumbs_items.push({
                              label: t('breadcrumbs.protocols'),
                              url: protocols_path
                            })

    if @protocol
      @breadcrumbs_items.push({
                                label: @protocol.name,
                                url: protocol_path(@protocol),
                                archived: @protocol.archived?
                              })
    end
  end
end