scinote-web/app/controllers/protocols_controller.rb

class ProtocolsController < ApplicationController
  include RenamingUtil
  include ProtocolsImporter
  include ProtocolsExporter
  include InputSanitizeHelper

  before_action :check_create_permissions, only: [
    :create_new_modal,
    :create
  ]
  before_action :check_clone_permissions, only: [ :clone ]
  before_action :check_view_permissions, only: [
    :protocol_status_bar,
    :updated_at_label,
    :preview,
    :linked_children,
    :linked_children_datatable
  ]
  before_action :check_edit_permissions, only: [
    :edit,
    :update_metadata,
    :update_keywords,
    :edit_name_modal,
    :edit_keywords_modal,
    :edit_authors_modal,
    :edit_description_modal
  ]
  before_action :check_view_all_permissions, only: [
    :index,
    :datatable
  ]
  before_action :check_unlink_permissions, only: [
    :unlink,
    :unlink_modal
  ]
  before_action :check_revert_permissions, only: [
    :revert,
    :revert_modal
  ]
  before_action :check_update_parent_permissions, only: [
    :update_parent,
    :update_parent_modal
  ]
  before_action :check_update_from_parent_permissions, only: [
    :update_from_parent,
    :update_from_parent_modal
  ]
  before_action :check_load_from_repository_views_permissions, only: [
    :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: [
    :copy_to_repository,
    :copy_to_repository_modal
  ]
  before_action :check_make_private_permissions, only: [ :make_private ]
  before_action :check_publish_permissions, only: [ :publish ]
  before_action :check_archive_permissions, only: [ :archive ]
  before_action :check_restore_permissions, only: [ :restore ]
  before_action :check_import_permissions, only: [ :import ]
  before_action :check_export_permissions, only: [ :export ]


  def index
  end

  def datatable
    respond_to do |format|
      format.json {
        render json: ::ProtocolsDatatable.new(
          view_context,
          @current_team,
          @type,
          current_user
        )
      }
    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 {
        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

  def linked_children_datatable
    respond_to do |format|
      format.json {
        render json: ::ProtocolLinkedChildrenDatatable.new(
          view_context,
          @protocol,
          current_user,
          self
        )
      }
    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
  end

  def update_metadata
    @protocol.record_timestamps = false
    @protocol.assign_attributes(metadata_params)

    respond_to do |format|
      if @protocol.save
        format.json {
          render json: {
            updated_at_label: render_to_string(
              partial: "protocols/header/updated_at_label.html.erb"
            ),
            name_label: render_to_string(
              partial: "protocols/header/name_label.html.erb"
            ),
            authors_label: render_to_string(
              partial: "protocols/header/authors_label.html.erb"
            ),
            description_label: render_to_string(
              partial: "protocols/header/description_label.html.erb"
            )
          }
        }
      else
        format.json {
          render json: @protocol.errors,
            status: :unprocessable_entity
        }
      end
    end
  end

  def update_keywords
    respond_to do |format|
      # sanitize user input
      params[:keywords].collect! do |keyword|
        escape_input(keyword)
      end
      if @protocol.update_keywords(params[:keywords])
        format.json {
          render json: {
            updated_at_label: render_to_string(
              partial: "protocols/header/updated_at_label.html.erb"
            ),
            keywords_label: render_to_string(
              partial: "protocols/header/keywords_label.html.erb"
            )
          }
        }
      else
        format.json { render json: {}, status: :unprocessable_entity }
      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
    if @type == :public
      @protocol.published_on = ts
    end

    respond_to do |format|
      if @protocol.save
        format.json {
          render json: {
            url: edit_protocol_path(
              @protocol,
              team: @current_team,
              type: @type
            )
          }
        }
      else
        format.json {
          render json: @protocol.errors,
            status: :unprocessable_entity
        }
      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 = can_link_copied_protocol_in_repository(@protocol) && params[:link]
    respond_to do |format|
      transaction_error = false
      Protocol.transaction do
        begin
          @new = @protocol.copy_to_repository(
            copy_to_repository_params[:name],
            copy_to_repository_params[:protocol_type],
            link_protocols,
            current_user
          )
        rescue Exception
          transaction_error = true
          raise ActiveRecord:: Rollback
        end
      end

      if transaction_error
        # Bad request error
        format.json {
          render json: {
            message: t("my_modules.protocols.copy_to_repository_modal.error_400")
          },
          status: :bad_request
        }
      elsif @new.invalid?
        # Render errors
        format.json {
          render json: @new.errors,
          status: :unprocessable_entity
        }
      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 {
          render json: {
            message: t("my_modules.protocols.unlink_error")
          },
          status: :bad_request
        }
      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
          begin
            # Revert is basically update from parent
            @protocol.update_from_parent(current_user)
          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.revert_error')
            },
            status: :bad_request
          end
        else
          # Everything good, display flash & render 200
          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
          begin
            @protocol.update_parent(current_user)
          rescue Exception
            transaction_error = true
            raise ActiveRecord:: Rollback
          end
        end

        if transaction_error
          # Bad request error
          format.json {
            render json: {
              message: t("my_modules.protocols.update_parent_error")
            },
            status: :bad_request
          }
        else
          # Everything good, record activity, display flash & render 200
          Activity.create(
            type_of: :revert_protocol,
            project: @protocol.my_module.experiment.project,
            experiment: @protocol.my_module.experiment,
            my_module: @protocol.my_module,
            user: current_user,
            message: I18n.t(
              'activities.revert_protocol',
              user: current_user.full_name,
              protocol: @protocol.name
            )
          )
          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
          begin
            @protocol.update_from_parent(current_user)
          rescue Exception
            transaction_error = true
            raise ActiveRecord:: Rollback
          end
        end

        if transaction_error
          # Bad request error
          format.json {
            render json: {
              message: t("my_modules.protocols.update_from_parent_error")
            },
            status: :bad_request
          }
        else
          # Everything good, display flash & render 200
          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
          begin
            @protocol.load_from_repository(@source, current_user)
          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.load_from_repository_error')
            },
            status: :bad_request
          end
        else
          # Everything good, record activity, display flash & render 200
          Activity.create(
            type_of: :load_protocol_from_repository,
            project: @protocol.my_module.experiment.project,
            experiment: @protocol.my_module.experiment,
            my_module: @protocol.my_module,
            user: current_user,
            message: I18n.t(
              'activities.load_protocol_from_repository',
              user: current_user.full_name,
              protocol: @source.name
            )
          )
          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 {
            render json: { status: :error }, status: :bad_request
          }
        else
          # Everything good, record activity, display flash & render 200
          Activity.create(
            type_of: :load_protocol_from_file,
            project: @protocol.my_module.experiment.project,
            experiment: @protocol.my_module.experiment,
            my_module: @protocol.my_module,
            user: current_user,
            message: I18n.t(
              'activities.load_protocol_from_file',
              user: current_user.full_name,
              protocol: @protocol_json[:name]
            )
          )
          flash[:success] = t(
            'my_modules.protocols.load_from_file_flash',
          )
          flash.keep(:success)
          format.json {
            render json: { status: :ok }, status: :ok
          }
        end
      else
        format.json do
          render json: { status: :locked }, status: :bad_request
        end
      end
    end
  end

  def import #tega uporabi .eln 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 Exception
          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 {
          render json: { name: p_name, status: :bad_request }, status: :bad_request
        }
      else
        format.json {
          render json: {
            name: p_name, new_name: protocol.name, status: :ok
          },
          status: :ok
        }
      end
    end
  end
#
#tule
def protocolsio_import_create


  json_file_contents=File.read(params[:json_file].path)
  json_file_contents.gsub! '\"', "'"


  @json_object=JSON.parse(json_file_contents)
  @protocol=Protocol.new

  respond_to do |format|
    #format.html {}
    format.js {}
  end

end


def protocolsio_import_save
  #@temp_json=JsonTemp.new
  @json_object=JSON.parse(params["json_object"])
  @import_object=Hash.new
  @import_object["name"]=params["protocol"]["name"]

  @import_object["description"]=params["protocol"]["description"]
  # will have to fit various things in here (guidelines, manuscript citations etc etc)

  @import_object["authors"]=params["protocol"]["authors"]
  @import_object["created_at"]=params["protocol"]["created_at"]
  @import_object["updated_at"]=params["protocol"]["last_modified"]
  #@import_object["steps"]


  @import_object["steps"]=Hash.new
  counter=0
  step_pos=-1
  #these whitelists are there to not let some useless step components true, that always have data set to null (data doesnt get imported over to json)
  whitelist_simple=["1","6","17"] #(simple to map) id 1= step description, id 6= section (title), id 17= expected result
  whitelist_complex=["8","9","15","18","19","20"] #(complex mapping with nested hashes) id 8 = software package, id 9 = dataset, id 15 = command, id 18 = attached sub protocol
  # id 19= safety information ,id 20= regents (materials, like scinote samples kind of)
  @json_object["steps"].each do |step|
    #@import_object["steps"][step_pos.to_s]=step
        step_pos+=1
        counter+=1

        @import_object["steps"][step_pos.to_s]=Hash.new
        @import_object["steps"][step_pos.to_s]["position"]=step_pos
        
        step["components"].each do |key,value|

          if counter>1 #here i made an if to distinguish the first step from the others, because the first step
         #sometimes has weird nesting that requires different handling
       if whitelist_simple.include?(key["component_type_id"])

         case key["component_type_id"]
         when "1"
           if !key["data"].nil? && key["data"]!=""
             @import_object["steps"][step_pos.to_s]["description"]=key["data"]
            else
              @import_object["steps"][step_pos.to_s]["description"]="Description missing!"
            end
         when "6"
           if !key["data"].nil? && key["data"]!=""
          @import_object["steps"][step_pos.to_s]["name"]=key["data"]
          else
          @import_object["steps"][step_pos.to_s]["name"]="Protocols.io"
        end
         when "17"

        else

        end

      elsif key && whitelist_complex.include?(key["component_type_id"])
        case key["component_type_id"]
        when "8"

        when "9"

         when "15"

         when "18"

         if key["source_data"]["link"]&&key["source_data"]["link"]!=""

         end
         when "19"

         when "20"

         else

         end
       end #finished step component loop

     else #it is first step

       unless value
       value=key #some json files have random empty arrays in beggining of step components
       end

         if whitelist_simple.include?(value["component_type_id"])

           case value["component_type_id"]
           when "1"
             if !value["data"].nil? && value["data"]!=""
               @import_object["steps"][step_pos.to_s]["description"]=value["data"]
              else
                @import_object["steps"][step_pos.to_s]["description"]="Description missing!"
              end
           when "6"
             if !value["data"].nil? && value["data"]!=""
            @import_object["steps"][step_pos.to_s]["name"]=value["data"]
            else
            @import_object["steps"][step_pos.to_s]["name"]="Protocols.io"
          end
           when "17"

          else

          end

         elsif value && whitelist_complex.include?(value["component_type_id"])

         case value["component_type_id"]
         when "8"

         when "9"

         when "15"

         when "18"

         if value["source_data"]["link"]&&value["source_data"]["link"]!=""

         end
         when "19"

         when "20"

         else

          end
        end #if statement to check if its first step or not
      end #finished step component looping, onto next step component
    end #finished looping over step components
  end #steps

  protocol = nil
  respond_to do |format|
    transaction_error = false
    #@steps_object=JSON.parse(params["steps"]["steps_object"])

    Protocol.transaction do
      begin
        #byebug
        protocol = import_new_protocol(@import_object, current_team, params[:type].to_sym, current_user)

      rescue Exception

        transaction_error = true
        raise ActiveRecord:: Rollback
      end
    end

    p_name =
      if @import_object['name'].present? && !@import_object['name'].empty?
        escape_input(@import_object['name'])
      else
        t('protocols.index.no_protocol_name')
      end

    if transaction_error

      format.json {
        render json: { name: p_name, status: :bad_request }, status: :bad_request
      }
      format.js{}

      #:location => root_url
        #  protocolsDatatable.ajax.reload();
        #  $('#modal-import-json-protocol-preview').modal('hide');
    else
      format.json {
        render json: {
          name: p_name, new_name: protocol.name, status: :ok
        },
        status: :ok
      }
      format.js{}
    end
  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))
            # 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}"
              next if step.assets.count <= 0
              step.assets.order(:id).each do |asset|
                asset_guid = get_guid(asset.id)
                asset_file_name = asset_guid.to_s +
                                  File.extname(asset.file_file_name).to_s
                ostream.put_next_entry("#{step_dir}/#{asset_file_name}")
                input_file = asset.open
                ostream.print(input_file.read)
                input_file.close
              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.empty?
          end
        elsif @protocols.length > 1
          file_name = 'protocols.eln'
        end
        send_data(z_output_stream.read, filename: file_name)
      end
    end
  end

  def unlink_modal
    respond_to do |format|
      format.json {
        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

  def revert_modal
    respond_to do |format|
      format.json {
        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

  def update_parent_modal
    respond_to do |format|
      format.json {
        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

  def update_from_parent_modal
    respond_to do |format|
      format.json {
        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

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

  def load_from_repository_modal
    @protocol = Protocol.find_by_id(params[:id])
    respond_to do |format|
      format.json {
        render json: {
          html: render_to_string({
            partial: "my_modules/protocols/load_from_repository_modal_body.html.erb"
          })
        }
      }
    end
  end

  def copy_to_repository_modal
    @new = Protocol.new
    @original = Protocol.find(params[:id])
    respond_to do |format|
      format.json {
        render json: {
          html: render_to_string({
            partial: "my_modules/protocols/copy_to_repository_modal_body.html.erb"
          })
        }
      }
    end
  end

  def protocol_status_bar
    respond_to do |format|
      format.json {
        render json: {
          html: render_to_string({
            partial: "my_modules/protocols/protocol_status_bar.html.erb"
          })
        }
      }
    end
  end

  def updated_at_label
    respond_to do |format|
      format.json {
        render json: {
          html: render_to_string({
            partial: "protocols/header/updated_at_label.html.erb"
          })
        }
      }
    end
  end

  def create_new_modal
    @new_protocol = Protocol.new
    respond_to do |format|
      format.json {
        render json: {
          html: render_to_string({
            partial: "protocols/index/create_new_modal_body.html.erb"
          })
        }
      }
    end
  end

  def edit_name_modal
    respond_to do |format|
      format.json {
        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

  def edit_keywords_modal
    respond_to do |format|
      format.json {
        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

  def edit_authors_modal
    respond_to do |format|
      format.json {
        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

  def edit_description_modal
    respond_to do |format|
      format.json {
        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

  private

  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|
      unless rollbacked
        format.json {
          render json: {
            html: render_to_string({
              partial: "protocols/index/results_modal_body.html.erb",
              locals: { results: results, en_action: "#{action}_results" }
            })
          }
        }
      else
        format.json {
          render json: {}, status: :bad_request
        }
      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_view_team_protocols(@current_team)
  end

  def check_view_permissions
    @protocol = Protocol.find_by_id(params[:id])
    if @protocol.blank? || !can_view_protocol(@protocol)
      respond_to { |f| f.json { render json: {}, status: :unauthorized } }
    end
  end

  def check_create_permissions
    load_team_and_type

    if !can_create_new_protocol(@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(@original) || @type == :archive
      render_403
    end
  end

  def check_edit_permissions
    load_team_and_type
    @protocol = Protocol.find_by_id(params[:id])

    unless can_edit_protocol(@protocol)
      render_403
    end
  end

  def check_unlink_permissions
    @protocol = Protocol.find_by_id(params[:id])

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

  def check_revert_permissions
    @protocol = Protocol.find_by_id(params[:id])

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

  def check_update_parent_permissions
    @protocol = Protocol.find_by_id(params[:id])

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

  def check_update_from_parent_permissions
    @protocol = Protocol.find_by_id(params[:id])

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

  def check_load_from_repository_views_permissions
    @protocol = Protocol.find_by_id(params[:id])

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

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

    if @protocol.blank? || @source.blank? || !can_load_protocol_from_repository(@protocol, @source)
      render_403
    end
  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_load_protocol_into_module(@my_module)
      render_403
    end
  end

  def check_copy_to_repository_permissions
    @protocol = Protocol.find_by_id(params[:id])
    @my_module = @protocol.my_module

    if @my_module.blank? or !can_copy_protocol_to_repository(@my_module)
      render_403
    end
  end

  def check_make_private_permissions
    @protocols = Protocol.where(id: params[:protocol_ids])
    @protocols.find_each do |protocol|
      unless can_make_protocol_private(protocol) then
        respond_to { |f| f.json { render json: {}, status: :unauthorized } }
        return
      end
    end
  end

  def check_publish_permissions
    @protocols = Protocol.where(id: params[:protocol_ids])
    @protocols.find_each do |protocol|
      unless can_publish_protocol(protocol) then
        respond_to { |f| f.json { render json: {}, status: :unauthorized } }
        return
      end
    end
  end

  def check_archive_permissions
    @protocols = Protocol.where(id: params[:protocol_ids])
    @protocols.find_each do |protocol|
      unless can_archive_protocol(protocol) then
        respond_to { |f| f.json { render json: {}, status: :unauthorized } }
        return
      end
    end
  end

  def check_restore_permissions
    @protocols = Protocol.where(id: params[:protocol_ids])
    @protocols.find_each do |protocol|
      unless can_restore_protocol(protocol) then
        respond_to { |f| f.json { render json: {}, status: :unauthorized } }
        return
      end
    end
  end

  def check_import_permissions
    @protocol_json = params[:protocol]
    @team = Team.find(params[:team_id])
    @type = params[:type] ? params[:type].to_sym : nil
    if !(
      @protocol_json.present? &&
      @team.present? &&
      (@type == :public || @type == :private) &&
      can_import_protocols(@team)
    )
      render_403
    end
  end

  def check_export_permissions
    @protocols = Protocol.where(id: params[:protocol_ids])
    if @protocols.blank? || @protocols.any? { |p| !can_export_protocol(p) }
      render_403
    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 metadata_params
    params.require(:protocol).permit(:name, :authors, :description)
  end

end