Merge branch 'master' of https://github.com/biosistemika/scinote-web into zd_SCI_939

2025-03-01 02:05:41 +08:00 · 2017-01-27 11:15:31 +01:00 · 2017-01-27 11:15:31 +01:00 · e59b2e039a
commit e59b2e039a
parent 61b260fb8a 77236f161b
36 changed files with 147 additions and 208 deletions
--- a/Gemfile.lock
+++ b/Gemfile.lock
@ -5,14 +5,6 @@ GIT
    sneaky-save (0.1.1)
      activerecord (>= 3.2.0)

-GIT
-  remote: https://github.com/biosistemika/quill-rails.git
-  revision: e765c042d9ff7ec22f8c51a0e08e39e783530f8b
-  ref: e765c04
-  specs:
-    quill-rails (0.1.4)
-      railties (>= 3.1.0, < 5.0)
-
 GEM
  remote: http://rubygems.org/
  specs:
@ -79,6 +71,7 @@ GEM
    babel-transpiler (0.7.0)
      babel-source (>= 4.0, < 6)
      execjs (~> 2.0)
+    base62 (1.0.0)
    bcrypt (3.1.11)
    better_errors (2.1.1)
      coderay (>= 1.0.0)
@ -314,6 +307,8 @@ GEM
    thor (0.19.1)
    thread_safe (0.3.5)
    tilt (2.0.1)
+    tinymce-rails (4.5.2)
+      railties (>= 3.1.1)
    turbolinks (2.5.3)
      coffee-rails
    tzinfo (1.2.2)
@ -347,6 +342,7 @@ DEPENDENCIES
  awesome_print
  aws-sdk (~> 2.2.8)
  aws-sdk-v1
+  base62
  bcrypt (~> 3.1.10)
  better_errors
  binding_of_caller
@ -382,7 +378,6 @@ DEPENDENCIES
  paperclip (~> 4.3)
  pg
  puma
-  quill-rails!
  rails (= 4.2.5)
  rails_12factor
  rails_autolink (~> 1.1, >= 1.1.6)
@ -392,6 +387,7 @@ DEPENDENCIES
  roo (~> 2.1.0)
  rubocop
  ruby-graphviz (~> 1.2)
+  rubyzip
  sass-rails (~> 5.0)
  scss_lint
  sdoc (~> 0.4.0)
@ -402,6 +398,7 @@ DEPENDENCIES
  sneaky-save!
  spinjs-rails
  starscope
+  tinymce-rails
  turbolinks
  tzinfo-data
  uglifier (>= 1.3.0)
--- a/app/assets/javascripts/protocols/steps.js.erb
+++ b/app/assets/javascripts/protocols/steps.js.erb
@ -107,7 +107,7 @@ function applyEditCallBack() {
    animateSpinner(null, false);
    initPreviewModal();

-    TinyMCE.init();
+    TinyMCE.refresh()
    $("#new-step-checklists fieldset.nested_step_checklists ul").each(function () {
      enableCheckboxSorting(this);
    });
@ -254,9 +254,6 @@ function formNewAjax($form) {
    initHandsOnTable($new_step);
    expandStep($new_step);
    toggleButtons(true);
-
-    TinyMCE.init();
-    TinyMCE.highlight();
    SmartAnnotation.preventPropagation('.atwho-user-popover');

    //Rerender tables
--- a/app/assets/javascripts/results/result_texts.js
+++ b/app/assets/javascripts/results/result_texts.js
@ -10,10 +10,8 @@ $("#new-result-text").on("ajax:success", function(e, data) {
        $form.remove();
        toggleResultEditButtons(true);
    });
-
-    TinyMCE.init();
    toggleResultEditButtons(false);
-
+    TinyMCE.refresh();
    $("#result_name").focus();
 });

@ -39,10 +37,8 @@ function applyEditResultTextCallback() {
            applyEditResultTextCallback();
            toggleResultEditButtons(true);
        });
-
-        TinyMCE.init();
        toggleResultEditButtons(false);
-
+        TinyMCE.refresh();
        $("#result_name").focus();
    });

--- a/app/assets/javascripts/samples/sample_datatable.js.erb
+++ b/app/assets/javascripts/samples/sample_datatable.js.erb
@ -162,6 +162,7 @@ function dataTableInit() {
      table.on('mousedown', function() {
        $('#samples-columns-dropdown').removeClass('open');
      });
+      initHeaderTooltip();
    }
  });

@ -350,6 +351,34 @@ function appendSamplesIdToForm(form) {
    });
 }

+function initHeaderTooltip() {
+  // Fix compatibility of fixed table header and column names modal-tooltip
+  $('.modal-tooltip').off();
+  $('.modal-tooltip').hover(function() {
+    var $tooltip = $(this).find('.modal-tooltiptext');
+    var offsetLeft = $tooltip.offset().left;
+    (offsetLeft + 200) > $(window).width() ? offsetLeft -= 150 : offsetLeft;
+    var offsetTop = $tooltip.offset().top;
+    $('body').append($tooltip);
+    $tooltip.css('background-color', '#d2d2d2');
+    $tooltip.css('border-radius', '6px');
+    $tooltip.css('color', '#333');
+    $tooltip.css('display', 'block');
+    $tooltip.css('left', offsetLeft + 'px');
+    $tooltip.css('padding', '5px');
+    $tooltip.css('position', 'absolute');
+    $tooltip.css('text-align', 'center');
+    $tooltip.css('top', offsetTop + 'px');
+    $tooltip.css('visibility', 'visible');
+    $tooltip.css('width', '200px');
+    $tooltip.css('word-wrap', 'break-word');
+    $(this).data('dropdown-tooltip', $tooltip);
+  }, function() {
+    $(this).append($(this).data('dropdown-tooltip'));
+    $(this).data('dropdown-tooltip').removeAttr('style');
+  });
+}
+
 //Show sample info
 function sampleInfoListener() {
    $(".sample_info").on("click", function(e){
@ -1076,6 +1105,7 @@ function changeToEditMode() {
        li.removeClass('col-invisible');
        column.visible(true);
        table.setColumnSearchable(column.index(), true);
+        initHeaderTooltip();
      }

      // Re-filter/search if neccesary
@ -1135,6 +1165,7 @@ function changeToEditMode() {
            .html(generateColumnNameTooltip(newName));

          cancelEditMode();
+          initHeaderTooltip();
        },
        error: function(xhr) {
          dropdownList.sortable('disable');
--- a/app/assets/javascripts/sitewide/atwho_res.js.erb
+++ b/app/assets/javascripts/sitewide/atwho_res.js.erb
@ -336,11 +336,11 @@ var SmartAnnotation = (function() {
              {query: query},
              function(data) {
                if (data.users.length < 1) {
-                   callback([{no_results: 1}]);
-                 } else {
-                   callback(data.users);
-                 }
-                initDismissButton();
+                  callback([{no_results: 1}]);
+                } else {
+                  callback(data.users);
+                }
+                initDismissButton($('.atwho-view[style]'));
              }
            );
          },
--- a/app/assets/javascripts/sitewide/tiny_mce.js.erb
+++ b/app/assets/javascripts/sitewide/tiny_mce.js.erb
@ -20,11 +20,15 @@ var TinyMCE = (function() {
        tinyMCE.init({
          selector: "textarea.tinymce",
          toolbar: ["undo redo | insert | styleselect | bold italic | alignleft aligncenter alignright alignjustify | bullist numlist outdent indent | link | forecolor backcolor | codesample"],
-          plugins: "link,advlist,codesample,autolink,lists,charmap,hr,anchor,searchreplace,wordcount,visualblocks,visualchars,insertdatetime,nonbreaking,save,contextmenu,directionality,paste,textcolor,colorpicker,textpattern,imagetools,toc",
+          plugins: "link,advlist,codesample,autolink,lists,charmap,hr,anchor,searchreplace,wordcount,visualblocks,visualchars,insertdatetime,nonbreaking,save,contextmenu,directionality,paste,textcolor,colorpicker,textpattern,imagetools",
          codesample_languages: [{"text":"R","value":"r"},{"text":"MATLAB","value":"matlab"},{"text":"Python","value":"python"},{"text":"JSON","value":"javascript"},{"text":"HTML/XML","value":"markup"},{"text":"JavaScript","value":"javascript"},{"text":"CSS","value":"css"},{"text":"PHP","value":"php"},{"text":"Ruby","value":"ruby"},{"text":"Java","value":"java"},{"text":"C","value":"c"},{"text":"C#","value":"csharp"},{"text":"C++","value":"cpp"}],
          removed_menuitems: 'newdocument',
          elementpath: false,
          default_link_target: "_blank",
+          target_list: [
+            {title: 'New page', value: '_blank'},
+            {title: 'Same page', value: '_self'}
+          ],
          style_formats: [
            {title: 'Headers', items: [
              {title: 'Header 1', format: 'h1'},
@ -59,7 +63,7 @@ var TinyMCE = (function() {
            initHighlightjsIframe($(this.iframeElement).contents());
          },
          setup: function(editor) {
-            editor.on('Change', function(e) {
+            editor.on('keydown', function(e) {
              if(e.keyCode == 13 && $(editor.contentDocument.activeElement).atwho('isSelecting')) {
                return false;
              }
--- a/app/controllers/at_who_controller.rb
+++ b/app/controllers/at_who_controller.rb
@ -15,8 +15,9 @@ class AtWhoController < ApplicationController
      user_obj['full_name'] =
        user_obj['full_name']
        .truncate(Constants::NAME_TRUNCATION_LENGTH_DROPDOWN)
-      user_obj['id'] = user_obj['id'].base62_encode
-      user_obj['img_url'] = avatar_path(user_obj['id'], :icon_small)
+      id = user_obj['id']
+      user_obj['id'] = id.base62_encode
+      user_obj['img_url'] = avatar_path(id, :icon_small)
    end

    respond_to do |format|
--- a/app/controllers/my_module_comments_controller.rb
+++ b/app/controllers/my_module_comments_controller.rb
@ -116,14 +116,7 @@ class MyModuleCommentsController < ApplicationController
              module: @my_module.name
            )
          )
-          message = auto_link(
-            smart_annotation_parser(
-              simple_format(sanitize_input(@comment.message))
-            ),
-            link: :urls,
-            sanitize: false,
-            html: { target: '_blank' }
-          ).html_safe
+          message = custom_auto_link(@comment.message)
          render json: { comment: message }, status: :ok
        else
          render json: { errors: @comment.errors.to_hash(true) },
--- a/app/controllers/project_comments_controller.rb
+++ b/app/controllers/project_comments_controller.rb
@ -113,14 +113,7 @@ class ProjectCommentsController < ApplicationController
              project: @project.name
            )
          )
-          message = auto_link(
-            smart_annotation_parser(
-              simple_format(sanitize_input(@comment.message))
-            ),
-            link: :urls,
-            sanitize: false,
-            html: { target: '_blank' }
-          ).html_safe
+          message = custom_auto_link(@comment.message)
          render json: { comment: message }, status: :ok
        else
          render json: { errors: @comment.errors.to_hash(true) },
--- a/app/controllers/result_comments_controller.rb
+++ b/app/controllers/result_comments_controller.rb
@ -114,14 +114,7 @@ class ResultCommentsController < ApplicationController
              result: @result.name
            )
          )
-          message = auto_link(
-            smart_annotation_parser(
-              simple_format(sanitize_input(@comment.message))
-            ),
-            link: :urls,
-            sanitize: false,
-            html: { target: '_blank' }
-          )
+          message = custom_auto_link(@comment.message)
          render json: { comment: message }, status: :ok
        else
          render json: { errors: @comment.errors.to_hash(true) },
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@ -11,12 +11,18 @@ class SamplesController < ApplicationController
    respond_to do |format|
      format.html
      if can_create_samples(@team)
-      format.json {
-        render json: {
-          sample_groups: @team.sample_groups.as_json(only: [:id, :name, :color]),
-          sample_types: @team.sample_types.as_json(only: [:id, :name])
-        }
-      }
+        groups = @team.sample_groups.map do |g|
+          { id: g.id, name: sanitize_input(g.name), color: g.color }
+        end
+        types = @team.sample_types.map do |t|
+          { id: t.id, name: sanitize_input(t.name) }
+        end
+        format.json do
+          render json: {
+            sample_groups: groups.as_json,
+            sample_types: types.as_json
+          }
+        end
      else
        format.json { render json: {}, status: :unauthorized }
      end
@ -122,8 +128,12 @@ class SamplesController < ApplicationController
        sample_group: @sample.sample_group.nil? ? "" : @sample.sample_group.id,
        custom_fields: {}
      },
-      sample_groups: @team.sample_groups.as_json(only: [:id, :name, :color]),
-      sample_types: @team.sample_types.as_json(only: [:id, :name])
+      sample_groups: @team.sample_groups.map do |g|
+        { id: g.id, name: sanitize_input(g.name), color: g.color }
+      end,
+      sample_types: @team.sample_types.map do |t|
+        { id: t.id, name: sanitize_input(t.name) }
+      end
    }

    # Add custom fields ids as key (easier lookup on js side)
--- a/app/controllers/step_comments_controller.rb
+++ b/app/controllers/step_comments_controller.rb
@ -119,14 +119,7 @@ class StepCommentsController < ApplicationController
              )
            )
          end
-          message = auto_link(
-            smart_annotation_parser(
-              simple_format(sanitize_input(@comment.message))
-            ),
-            link: :urls,
-            sanitize: false,
-            html: { target: '_blank' }
-          ).html_safe
+          message = custom_auto_link(@comment.message)
          render json: { comment: message }, status: :ok
        else
          render json: { errors: @comment.errors.to_hash(true) },
--- a/app/datatables/sample_datatable.rb
+++ b/app/datatables/sample_datatable.rb
@ -129,15 +129,9 @@ class SampleDatatable < AjaxDatatablesRails::Base

      # Add custom attributes
      record.sample_custom_fields.each do |scf|
-        sample[@cf_mappings[scf.custom_field_id]] = auto_link(
-          smart_annotation_parser(
-            simple_format(sanitize_input(scf.value)),
-            @team
-          ),
-          link: :urls,
-          sanitize: false,
-          html: { target: '_blank' }
-        ).html_safe
+        sample[@cf_mappings[scf.custom_field_id]] = custom_auto_link(scf.value,
+                                                                     true,
+                                                                     @team)
      end
      sample
    end
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@ -77,7 +77,7 @@ module ApplicationHelper
        if project.archived?
          "<span class='sa-type'>#{sanitize(match[2])}</span> " \
          "#{link_to project.name,
-                     projects_archive_path} #{t'atwho.res.archived'}"
+                     projects_archive_path} #{I18n.t('atwho.res.archived')}"
        else
          "<span class='sa-type'>#{sanitize(match[2])}</span> " \
          "#{link_to project.name,
@ -90,7 +90,7 @@ module ApplicationHelper
          "<span class='sa-type'>#{sanitize(match[2])}</span> " \
          "#{link_to experiment.name,
                     experiment_archive_project_path(experiment.project)} " \
-          "#{t'atwho.res.archived'}"
+          "#{I18n.t('atwho.res.archived')}"
        else
          "<span class='sa-type'>#{sanitize(match[2])}</span> " \
          "#{link_to experiment.name,
@ -103,7 +103,7 @@ module ApplicationHelper
          "<span class='sa-type'>#{sanitize(match[2])}</span> " \
          "#{link_to my_module.name,
                     module_archive_experiment_path(my_module.experiment)} " \
-          "#{t'atwho.res.archived'}"
+          "#{I18n.t('atwho.res.archived')}"
        else
          "<span class='sa-type'>#{sanitize(match[2])}</span> " \
          "#{link_to my_module.name,
@ -118,7 +118,7 @@ module ApplicationHelper
                     class: 'sample-info-link')}"
        else
          "<span class='glyphicon glyphicon-tint'></span> " \
-          "#{match[1]} #{t'atwho.res.deleted'}"
+          "#{match[1]} #{I18n.t('atwho.res.deleted')}"
        end
      end
    end
--- a/app/helpers/form_tag_helper.rb
+++ b/app/helpers/form_tag_helper.rb
@ -11,7 +11,7 @@ module FormTagHelper
        res << '</span>'
      end
      res << '</div>'
-      sanitize_input(res)
+      res.html_safe
    end
  end
 end
--- a/app/helpers/input_sanitize_helper.rb
+++ b/app/helpers/input_sanitize_helper.rb
@ -1,9 +1,13 @@
 module InputSanitizeHelper
-  def sanitize_input(text)
+  def sanitize_input(
+    text,
+    tags = [],
+    attributes = []
+  )
    ActionController::Base.helpers.sanitize(
      text,
-      tags: Constants::WHITELISTED_TAGS,
-      attributes: Constants::WHITELISTED_ATTRIBUTES
+      tags: Constants::WHITELISTED_TAGS + tags,
+      attributes: Constants::WHITELISTED_ATTRIBUTES + attributes
    )
  end

@ -11,8 +15,17 @@ module InputSanitizeHelper
    ERB::Util.html_escape(text)
  end

-  def custom_auto_link(text, args)
-    args[:sanitize] = false
-    auto_link(sanitize_input(text), args)
+  def custom_auto_link(text, simple_format = true, org = nil)
+    text = if simple_format
+             simple_format(sanitize_input(text))
+           else
+             sanitize_input(text)
+           end
+    auto_link(
+      smart_annotation_parser(text, org),
+      link: :urls,
+      sanitize: false,
+      html: { target: '_blank' }
+    ).html_safe
  end
 end
--- a/app/utilities/protocols_exporter.rb
+++ b/app/utilities/protocols_exporter.rb
@ -94,9 +94,9 @@ module ProtocolsExporter
            checklist_xml = "<checklist id=\"#{checklist.id}\" " \
                            "guid=\"#{get_guid(checklist.id)}\">\n"
            checklist_xml << "<name>#{checklist.name}</name>\n"
-            if checklist.items
+            if checklist.checklist_items
              checklist_xml << "<items>\n"
-              checklist.items.each do |item|
+              checklist.checklist_items.each do |item|
                item_xml = "<item id=\"#{item.id}\" " \
                           "guid=\"#{get_guid(item.id)}\" " \
                           "position=\"#{item.position}\">\n"
--- a/app/views/my_module_comments/_comment.html.erb
+++ b/app/views/my_module_comments/_comment.html.erb
@ -39,12 +39,5 @@
 </div>
 <strong><%= comment.user.full_name %>:</strong>
 <div data-role="comment-message-container">
-  <div data-role="comment-message"><%= auto_link(
-    smart_annotation_parser(simple_format(
-      sanitize_input(comment.message)),
-    ),
-    link: :urls,
-    sanitize: false,
-    html: { target: '_blank' }
-  ).html_safe %></div>
+  <div data-role="comment-message"><%= custom_auto_link(comment.message) %></div>
 </div>
--- a/app/views/my_modules/_description_label.html.erb
+++ b/app/views/my_modules/_description_label.html.erb
@ -1,6 +1,5 @@
 <% if @my_module.description.blank? %>
  <em><%=t "experiments.canvas.popups.no_description" %></em>
 <% else %>
-  <%= custom_auto_link(simple_format(@my_module.description),
-                       link: :urls, html: { target: '_blank' }) %>
+  <%= custom_auto_link(@my_module.description) %>
 <% end %>
--- a/app/views/project_comments/_comment.html.erb
+++ b/app/views/project_comments/_comment.html.erb
@ -39,12 +39,5 @@
 </div>
 <strong><%= comment.user.full_name %>:</strong>
 <div data-role="comment-message-container">
-  <div data-role="comment-message"><%= auto_link(
-    smart_annotation_parser(simple_format(
-      sanitize_input(comment.message)),
-    ),
-    link: :urls,
-    sanitize: false,
-    html: { target: '_blank' }
-  ).html_safe %></div>
+  <div data-role="comment-message"><%= custom_auto_link(comment.message) %></div>
 </div>
--- a/app/views/projects/experiment_archive/_experiment.html.erb
+++ b/app/views/projects/experiment_archive/_experiment.html.erb
@ -67,14 +67,7 @@
    </div>
    <div class="row">
      <div class="col-xs-12">
-        <%= auto_link(
-              smart_annotation_parser(
-                simple_format(experiment.description)
-              ),
-              link: :urls,
-              sanitize: false,
-              html: { target: '_blank' }
-            ).html_safe %>
+        <%= custom_auto_link(experiment.description) %>
      </div>
    </div>
  </div>
--- a/app/views/projects/show/_experiment.html.erb
+++ b/app/views/projects/show/_experiment.html.erb
@ -49,16 +49,7 @@
      </span>
      <% if experiment.description? %>
        <div class='experiment-description'>
-          <%= auto_link(
-                smart_annotation_parser(
-                  simple_format(
-                    sanitize_input(experiment.description)
-                  )
-                ),
-                link: :urls,
-                sanitize: false,
-                html: { target: '_blank' }
-              ).html_safe %>
+          <%= custom_auto_link(experiment.description) %>
        </div>
      <% else %>
        <span class='experiment-no-description'>
--- a/app/views/protocols/index/_protocol_preview_modal_body.html.erb
+++ b/app/views/protocols/index/_protocol_preview_modal_body.html.erb
@ -113,13 +113,24 @@
                      <% assets.each do |asset| %>
                        <li>
                          <% if can_view_or_download_step_assets(@protocol) %>
-                            <%= link_to download_asset_path(asset), data: {no_turbolink: true, id: true, status: "asset-present"} do %>
-                              <%= image_tag preview_asset_path(asset) if asset.is_image? %>
-                              <p><%= truncate(asset.file_file_name,
-                                              length: Constants::FILENAME_TRUNCATION_LENGTH) %></p>
+                            <% if asset.is_image? %>
+                              <%= link_to download_asset_path(asset),
+                                class: 'image-preview-link',
+                                id: "modal_link#{asset.id}",
+                                data: {no_turbolink: true, id: true, status: "asset-present",
+                                  description: "#{step.position + 1}. #{truncate(step.name, length: Constants::FILENAME_TRUNCATION_LENGTH)}"} do %>
+                                <%= image_tag asset.url(:medium), data: {'preview-url': large_image_url_asset_path(asset)} %>
+                                <p><%= truncate(asset.file_file_name,
+                                                length: Constants::FILENAME_TRUNCATION_LENGTH) %></p>
+                              <% end %>
+                            <% else %>
+                              <%= link_to download_asset_path(asset), data: {no_turbolink: true} do %>
+                                <p><%= truncate(asset.file_file_name,
+                                                length: Constants::FILENAME_TRUNCATION_LENGTH) %></p>
+                              <% end %>
                            <% end %>
                          <% else %>
-                            <%= image_tag preview_asset_path(asset) if asset.is_image? %>
+                            <%= image_tag asset.url(:medium) if asset.is_image? %>
                            <p><%= truncate(asset.file_file_name,
                                            length: Constants::FILENAME_TRUNCATION_LENGTH) %></p>
                          <% end %>
--- a/app/views/reports/elements/_experiment_element.html.erb
+++ b/app/views/reports/elements/_experiment_element.html.erb
@ -27,10 +27,7 @@
    <div class="row">
      <div class="col-xs-12">
        <% if experiment.description.present? %>
-          <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(experiment.description))),
-                        link: :urls,
-                        sanitize: false,
-                        html: { target: '_blank' }).html_safe %>
+          <%= custom_auto_link(experiment.description) %>
        <% else %>
           <em><%=t "projects.reports.elements.experiment.no_description" %></em>
        <% end %>
--- a/app/views/reports/elements/_my_module_element.html.erb
+++ b/app/views/reports/elements/_my_module_element.html.erb
@ -30,8 +30,7 @@
    <div class="row">
      <div class="col-xs-12">
        <% if my_module.description.present? %>
-          <%= custom_auto_link(simple_format(my_module.description),
-                               link: :urls, html: { target: '_blank' }) %>
+          <%= custom_auto_link(my_module.description) %>
        <% else %>
           <em><%=t "projects.reports.elements.module.no_description" %></em>
        <% end %>
--- a/app/views/reports/elements/_result_comments_element.html.erb
+++ b/app/views/reports/elements/_result_comments_element.html.erb
@ -31,10 +31,7 @@
                </span>
                <span class="comment-message">
                  &nbsp;
-                  <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(comment.message))),
-                                link: :urls,
-                                sanitize: false,
-                                html: { target: '_blank' }).html_safe %>
+                  <%= custom_auto_link(comment.message) %>
                </span>
              </li>
            <% end %>
--- a/app/views/reports/elements/_result_text_element.html.erb
+++ b/app/views/reports/elements/_result_text_element.html.erb
@ -23,10 +23,7 @@
  <div class="report-element-body">
    <div class="row">
      <div class="col-xs-12 text-container ql-editor">
-        <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(result_text.text))),
-                      link: :urls,
-                      sanitize: false,
-                      html: { target: '_blank' }).html_safe %>
+        <%= custom_auto_link(result_text.text, false) %>
      </div>
    </div>
  </div>
--- a/app/views/reports/elements/_step_checklist_element.html.erb
+++ b/app/views/reports/elements/_step_checklist_element.html.erb
@ -8,10 +8,7 @@
          <span class="glyphicon glyphicon-list"></span>
      </div>
      <div class="pull-left checklist-name">
-        <%= auto_link(smart_annotation_parser(simple_format(t 'projects.reports.elements.step_checklist.checklist_name', name: checklist.name)),
-                      link: :urls,
-                      sanitize: false,
-                      html: { target: '_blank' }).html_safe %>
+        <%= custom_auto_link(t('projects.reports.elements.step_checklist.checklist_name', name: checklist.name)) %>
      </div>
      <div class="pull-left user-time">
        <%=t 'projects.reports.elements.step_checklist.user_time', timestamp: l(timestamp, format: :full) %>
@ -27,10 +24,8 @@
        <li>
          <input type="checkbox" disabled="disabled" <%= "checked='checked'" if item.checked %>/>
          <span class="<%= 'checked' if item.checked %>">
-            <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(item.text))),
-                          link: :urls,
-                          sanitize: false,
-                          html: { target: '_blank' }).html_safe %></span>
+            <%= custom_auto_link(item.text) %>
+          </span>
        </li>
      <% end %>
    </ul>
--- a/app/views/reports/elements/_step_comments_element.html.erb
+++ b/app/views/reports/elements/_step_comments_element.html.erb
@ -31,10 +31,7 @@
                </span>
                <span class="comment-message">
                  &nbsp;
-                  <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(comment.message))),
-                                link: :urls,
-                                sanitize: false,
-                                html: { target: '_blank' }).html_safe %>
+                  <%= custom_auto_link(comment.message) %>
                </span>
              </li>
            <% end %>
--- a/app/views/reports/elements/_step_element.html.erb
+++ b/app/views/reports/elements/_step_element.html.erb
@ -27,10 +27,7 @@
    <div class="row">
      <div class="col-xs-12 ql-editor">
        <% if strip_tags(step.description).present? %>
-          <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(step.description))),
-                              link: :urls,
-                              sanitize: false,
-                              html: { target: '_blank' }).html_safe %>
+          <%= custom_auto_link(step.description, false) %>
        <% else %>
           <em><%=t "projects.reports.elements.step.no_description" %></em>
        <% end %>
--- a/app/views/reports/report.pdf.erb
+++ b/app/views/reports/report.pdf.erb
@ -9,7 +9,8 @@
  </head>
  <body class="print-report-body">
    <div class="print-report">
-      <%= sanitize_input(@html) %>
+      <% # Also whitelist <img> and <input type="checkbox"> tags %>
+      <%= sanitize_input(@html, ['img', 'input'], ['type', 'disabled', 'checked']) %>
    </div>
  </body>
 </html>
--- a/app/views/result_comments/_comment.html.erb
+++ b/app/views/result_comments/_comment.html.erb
@ -39,12 +39,5 @@
  <% end %>
 </div>
 <div data-role="comment-message-container">
-  <div data-role="comment-message"><%= auto_link(
-    smart_annotation_parser(simple_format(
-      sanitize_input(comment.message)),
-    ),
-    link: :urls,
-    sanitize: false,
-    html: { target: '_blank' }
-  ).html_safe %></div>
+  <div data-role="comment-message"><%= custom_auto_link(comment.message) %></div>
 </div>
--- a/app/views/results/_result_text.html.erb
+++ b/app/views/results/_result_text.html.erb
@ -1,6 +1,3 @@
 <div class="ql-editor">
-  <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(result.result_text.text))),
-                link: :urls,
-                sanitize: false,
-                html: { target: '_blank' }).html_safe %>
+  <%= custom_auto_link(result.result_text.text, false) %>
 </div>
--- a/app/views/step_comments/_comment.html.erb
+++ b/app/views/step_comments/_comment.html.erb
@ -1,4 +1,4 @@
-f<div>
+<div>
  <strong>
    <%=t "protocols.steps.comment_title", user: comment.user.full_name, time: l(comment.created_at, format: :time) %>
  </strong>
@ -40,12 +40,5 @@ f<div>
  <% end %>
 </div>
 <div data-role="comment-message-container">
-  <div data-role="comment-message"><%= auto_link(
-    smart_annotation_parser(simple_format(
-      sanitize_input(comment.message)),
-    ),
-    link: :urls,
-    sanitize: false,
-    html: { target: '_blank' }
-  ).html_safe %></div>
+  <div data-role="comment-message"><%= custom_auto_link(comment.message)%></div>
 </div>
--- a/app/views/steps/_step.html.erb
+++ b/app/views/steps/_step.html.erb
@ -37,10 +37,7 @@
              <em><%= t("protocols.steps.no_description") %></em>
            <% else %>
              <div class="ql-editor">
-                <%= auto_link(smart_annotation_parser(simple_format(sanitize_input(step.description))),
-                              link: :urls,
-                              sanitize: false,
-                              html: { target: '_blank' }).html_safe %>
+                <%= custom_auto_link(step.description, false) %>
              </div>
            <% end %>
          </div>
@ -51,7 +48,7 @@
            <div class="col-xs-12">
              <% step.tables.each do |table| %>
                <strong>
-                  <%= custom_auto_link(simple_format(table.name),
+                  <%= auto_link(simple_format(table.name),
                                      link: :urls,
                                      html: { target: '_blank' }) %>
                </strong>
@ -122,15 +119,7 @@
          <% unless step.checklists.blank? then %>
            <div class="col-xs-12">
              <% step.checklists.each do |checklist| %>
-                <strong><%= auto_link(
-                              smart_annotation_parser(
-                                simple_format(
-                                  sanitize_input(checklist.name)
-                                )
-                              ),
-                              link: :urls,
-                              sanitize: false,
-                              html: { target: '_blank' }).html_safe %></strong>
+                <strong><%= custom_auto_link(checklist.name) %></strong>
                <% if checklist.checklist_items.empty? %>
                  </br>
                  <%= t("protocols.steps.empty_checklist") %>
@ -144,15 +133,7 @@
                        <% else %>
                          <input type="checkbox" value="" disabled="disabled" />
                        <% end %>
-                        <%= auto_link(
-                                smart_annotation_parser(
-                                  simple_format(
-                                    sanitize_input(checklist_item.text)
-                                  )
-                                ),
-                              link: :urls,
-                              sanitize: false,
-                              html: { target: '_blank' }).html_safe %>
+                        <%= custom_auto_link(checklist_item.text) %>
                      </label>
                    </div>
                  <% end %>
--- a/config/initializers/constants.rb
+++ b/config/initializers/constants.rb
@ -190,7 +190,7 @@ class Constants
  #=============================================================================

  # Application version
-  APP_VERSION = '1.6.1'.freeze
+  APP_VERSION = '1.7.1'.freeze

  TEXT_EXTRACT_FILE_TYPES = [
    'application/pdf',
@ -213,7 +213,7 @@ class Constants

  WHITELISTED_TAGS = %w(
    a b strong i em li ul ol h1 del ins h2 h3 h4 h5 h6 br sub sup p code hr div
-    span u s blockquote pre
+    span u s blockquote pre col colgroup table thead tbody th tr td
  ).freeze

  WHITELISTED_ATTRIBUTES = %w(