expand smart annotation

app/assets/javascripts/comments.js.erb

@@ -86,6 +86,8 @@ var Comments = (function() {
   function initCommentForm($el) {
 
     var $form = $el.find('ul form');
+    // initialize smart annotation
+    SmartAnnotation.init($($form).find('#comment_message'));
 
     $('.help-block', $form).addClass('hide');
 

app/assets/javascripts/experiments/dropdown_actions.js

@@ -18,6 +18,8 @@
       validateMoveModal(id);
       clearModal($(id));
       validateExperimentForm($(id));
+      // initialize smart annotation
+      SmartAnnotation.init('#experiment-description');
     })
     .on("ajax:error", function() {
       animateSpinner(null, false);

app/assets/javascripts/protocols/steps.js.erb

@@ -9,7 +9,6 @@
 function applyCheckboxCallBack()  {
   $("[data-action='check-item']").on('click', function(e){
     var checkboxitem = $(this).find("input");
-
     var checked = checkboxitem.is(":checked");
     $.ajax({
       url: checkboxitem.data("link-url"),
@@ -113,6 +112,7 @@ function applyEditCallBack() {
       $("#step_name").focus();
     });
     openLinksInNewTab();
+    initSmartAnnotation();
   });
 }
 
@@ -430,6 +430,8 @@ function reorderCheckboxData(checkboxUl) {
     $posInput.attr("id", posId);
     $posInput.val(itemPos);
     $destroyLink.attr("data-delete-association-field-name", destroyLink);
+    debugger;
+    SmartAnnotation.init();
 
     var $idInput = $this.find("> input");
     if ($idInput.length) {
@@ -471,7 +473,6 @@ function initializeCheckboxSorting() {
     // inserted into DOM.
     setTimeout(function () {
       var list = el.parent().find("fieldset.nested_step_checklists:last ul");
-
       enableCheckboxSorting(list.get(0));
     });
   });
@@ -566,6 +567,27 @@ function initHighlightjs() {
   }
 }
 
+// initialize the smart annotations
+function initSmartAnnotation() {
+  $('#new-step-checklists').on('click', function() {
+    setTimeout(function() {
+      SmartAnnotation.init('.checklist_name');
+    }, 300);
+
+    $('[data-object-class="checklist"]').on('click', function() {
+      setTimeout(function() {
+        SmartAnnotation.init('.checklist_name');
+      }, 300);
+    });
+
+    $('[data-object-class="checklist_item"]').on('click', function() {
+      setTimeout(function() {
+        $('.checklist-item-text').atwho('destroy');
+        SmartAnnotation.init('.checklist-item-text');
+      }, 300);
+    });
+  });
+}
 function initStepsComments() {
   Comments.initialize();
   Comments.initCommentOptions("ul.content-comments");

app/assets/javascripts/results/result_texts.js

@@ -14,6 +14,8 @@ $("#new-result-text").on("ajax:success", function(e, data) {
     toggleResultEditButtons(false);
 
     $("#result_name").focus();
+
+    SmartAnnotation.init('.ql-editor');
 });
 
 $("#new-result-text").on("ajax:error", function(e, xhr, status, error) {
@@ -88,11 +90,3 @@ $(document).ready(function() {
   initHighlightjs();
 });
 applyEditResultTextCallback();
-
-
-
-$(document).ready(function() {
-  setTimeout(function(){
-    SmartAnnotation.init('[data-atwho-res-edit]');
-  }, 2000);
-});

app/assets/javascripts/samples/sample_datatable.js.erb

@@ -433,6 +433,11 @@ function onClickEdit() {
                 }
             });
 
+            // initialize smart annotation
+            _.each($('[data-object="custom_fields"]'), function(el) {
+              SmartAnnotation.init(el);
+            });
+
             // Adjust columns width in table header
             table.columns.adjust();
         },

app/assets/javascripts/sitewide/atwho_res.js

@@ -136,30 +136,39 @@ var SmartAnnotation = (function() {
       $('.atwho-header button').on('click', function(e) {
         var $button, $prevButton;
         e.stopPropagation();
+
         $('.atwho-header button').off();
         $button = $(this);
         $prevButton = $button.closest('.atwho-header').children('.btn-primary');
 
         switch ($button.attr('data-filter')) {
           case 'prj':
+            setTimeout(function() {
               generateNewQuery('/organizations/1/atwho_projects.json',
                                $prevButton,
                                $button);
+            }, 300);
             break;
           case 'exp':
+            setTimeout(function() {
               generateNewQuery('/organizations/1/atwho_experiments.json',
                                $prevButton,
                                $button);
+            }, 300);
             break;
           case 'tsk':
+            setTimeout(function() {
               generateNewQuery('/organizations/1/atwho_my_modules.json',
                                $prevButton,
                                $button);
+            }, 300);
             break;
           case 'sam':
+            setTimeout(function() {
               generateNewQuery('/organizations/1/atwho_samples.json',
                                $prevButton,
                                $button);
+            }, 300);
             break;
         }
       });
@@ -167,21 +176,33 @@ var SmartAnnotation = (function() {
 
     // Generates new query when user filters the results
     function generateNewQuery(link, prevBtn, selectedBtn) {
-      var regexp, _a, _y, new_query, query_obj;
+      var regexp, _a, _y, new_query, query_obj, field_selected;
       _a = decodeURI("%C3%80");
       _y = decodeURI("%C3%BF");
       regexp = new RegExp("(#|task#|project#|sample#|experiment#)([A-Za-z" +
       _a + "-" + _y + "0-9_ \'\.\+\-]*)$|" +
       "(#|task#|project#|sample#|experiment#)([^\\x00-\\xff]*)$", 'gi');
-      query_obj = regexp.exec($(field).val());
+      // filters field if multiple input fields on the page
+      _.each($(field), function(e) {
+        if($(e).atwho('isSelecting')){
+          field_selected = e;
+      }});
+
+      if(field_selected) {
+        query_obj = regexp.exec($(field_selected).val());
         new_query = query_obj.input.replace(query_obj[1], '');
+      } else {
+        query_obj = [''];
+        new_query = '';
+      }
+
 
       $.getJSON(
         link,
         {query: new_query},
         function(data) {
-          if(data.res.length > 0) {
+          if(data.res.length > 0 && field_selected) {
-            $(field)
+            $(field_selected)
               .atwho('load', query_obj[0], data.res)
               .atwho('run');
 
@@ -259,10 +280,14 @@ var SmartAnnotation = (function() {
       res += '<span data-val="name">';
       res += map.name;
       res += '</span>';
+      if(map.archived) {
+        res += '<span>(archived)</span>';
+      }
       res += '&nbsp;';
 
       switch (map.type) {
         case 'tsk':
+
           res += '<span>&lt; ' + map.experimentName +
                  ' &lt; ' + map.projectName + '</span>';
           break;

app/datatables/sample_datatable.rb

@@ -3,6 +3,9 @@ require 'active_record'
 class SampleDatatable < AjaxDatatablesRails::Base
   include ActionView::Helpers::TextHelper
   include SamplesHelper
+  include Rails.application.routes.url_helpers
+  include ActionView::Helpers::UrlHelper
+  include ApplicationHelper
 
   ASSIGNED_SORT_COL = 'assigned'
 
@@ -118,11 +121,11 @@ class SampleDatatable < AjaxDatatablesRails::Base
 
       # Add custom attributes
       record.sample_custom_fields.each do |scf|
-        sample[@cf_mappings[scf.custom_field_id]] = auto_link(scf.value,
+        sample[@cf_mappings[scf.custom_field_id]] = auto_link(
+          smart_annotation_parser(scf.value),
           link: :urls,
-                                                              html: {
+          html: { target: '_blank' }
-                                                                target: '_blank'
+        )
-                                                              })
       end
       sample
     end

app/models/smart_annotation.rb

@@ -74,7 +74,7 @@ class SmartAnnotation
                  length: Constants::NAME_TRUNCATION_LENGTH)
       )
       exp['type'] = 'exp'
-      exp['project'] = truncate(
+      exp['projectName'] = truncate(
         sanitize(experiment_res.project.name,
                  length: Constants::NAME_TRUNCATION_LENGTH)
       )
@@ -105,7 +105,7 @@ class SmartAnnotation
       )} #{(', ' + truncate(
         sanitize(sample_res.sample_type.name,
                  length: Constants::NAME_TRUNCATION_LENGTH)
-      )) if sample_res.sample_type}, #{(',' + truncate(
+      )) if sample_res.sample_type} #{(', ' + truncate(
         sanitize(sample_res.sample_group.name,
                  length: Constants::NAME_TRUNCATION_LENGTH)
       )) if sample_res.sample_group}"

app/views/projects/show/_experiment.html.erb

@@ -49,9 +49,13 @@
       </span>
       <% if experiment.description? %>
         <div class='experiment-description'>
-          <%= auto_link(simple_format(experiment.description),
+          <%= auto_link(
+                simple_format(
+                  smart_annotation_parser(experiment.description)
+                  ),
                 link: :urls,
-                        html: { target: '_blank' }) %>
+                html: { target: '_blank' }
+              ) %>
         </div>
       <% else %>
         <span class='experiment-no-description'>

app/views/steps/_step.html.erb

@@ -88,7 +88,10 @@
           <% unless step.checklists.blank? then %>
             <div class="col-xs-12">
               <% step.checklists.each do |checklist| %>
-                <strong><%= auto_link(simple_format(checklist.name),
+                <strong><%= auto_link(
+                              simple_format(
+                                smart_annotation_parser(checklist.name)
+                              ),
                               link: :urls,
                               html: { target: '_blank' }) %></strong>
                 <% if checklist.checklist_items.empty? %>
@@ -104,7 +107,10 @@
                         <% else %>
                           <input type="checkbox" value="" disabled="disabled" />
                         <% end %>
-                        <%= auto_link(simple_format(checklist_item.text),
+                        <%= auto_link(
+                              simple_format(
+                                smart_annotation_parser(checklist_item.text)
+                              ),
                               link: :urls,
                               html: { target: '_blank' }) %>
                       </label>