Fixed bug with node template and other content being added (e.g. form comment form)

tripal_core/theme/css/tripal.css

@@ -29,7 +29,10 @@
   width: 100%;
 }
 
-#tripal-contents_table {
+.tripal-contents-links {
+}
+
+.tripal-contents_table {
   padding: 0px !important;
   margin:  0px !important;
 }
@@ -42,7 +45,7 @@
  * the table settings. 
  */
  
-#tripal-contents-table tbody {
+.tripal-contents-table tbody {
   padding: 0px !important;
   margin:  0px !important;
   border:  none !important;
@@ -116,7 +119,6 @@
    margin:  0;
    width: 100%;
 }
-
 .tripal-data-block-title {
   font-size: 1.5em;
   padding-bottom: 5px;

tripal_core/theme/node--chado-generic.tpl.php

@@ -30,23 +30,30 @@ else {
           if(block != null){
             $(".tripal-data-block").hide().filter("#" + block[1] + "-tripal-data-block").show();
           }
+          // remove the 'active' class from the links section, as it doesn't
+          // make sense for this layout
+          $("a.active").removeClass('active');
         }
       };
     })(jQuery);
   </script>
   
-  <div id="tripal_<?php print $node_type?>_content" class="tripal-contents"> 
-    <table id="tripal-contents-table">
+  <div id="tripal_<?php print $node_type?>_contents" class="tripal-contents">
+    <table id ="tripal-<?php print $node_type?>-contents-table" class="tripal-contents-table">
       <tr class="tripal-contents-table-tr">
         <td nowrap class="tripal-contents-table-td tripal-contents-table-td-toc"  align="left"><?php
         
           // print the table of contents. It's found in the content array 
           print $content['tripal_toc']['#markup'];
           
-          // remove the table of contents so it doesn't show up in the 
-          // data section with the $content array is rendered
-          unset($content['tripal_toc']); ?>
+          // we may want to add the links portion of the contents to the sidebar
+          //print render($content['links']);
           
+          // remove the table of contents and links so thye doent show up in the 
+          // data section when the rest of the $content array is rendered
+          unset($content['tripal_toc']);
+          unset($content['links']); ?>
+
         </td>
         <td class="tripal-contents-table-td-data" align="left" width="100%"> <?php
          

tripal_core/tripal_core.module

@@ -553,6 +553,8 @@ function tripal_core_views_api() {
 function tripal_core_node_view_alter(&$build) {
   global $theme;
   
+  //dpm($build);
+  
   // if the $build['tripal_toc'] element is not present, then this is not
   // a full node view so we do not want to alter 
   if (!array_key_exists('tripal_toc', $build)) {
@@ -571,50 +573,46 @@ function tripal_core_node_view_alter(&$build) {
 
     // iterate through all the elements of the $build array and for those
     // that are wanting to provide content for this node
-    $markup_list = array();
+    $markup = array();
     foreach ($build as $key => $value) {
 
       // examine elements without a '#' prefix as these should be adding 
-      // contents to the page. Skip the table of contents and any teasers
-      if (!preg_match('/^#/', $key) and $key != 'tripal_toc') {
+      // contents to the page. Skip the table of contents and links as those
+      // will be placed elsewhere
+      if (!preg_match('/^#/', $key) and $key != 'tripal_toc' and $key != 'links') {
+        $markup = '';
         
         // find the markup. Some fields will have a '#markup' and others, such
         // as CCK elements may have a set of '#markup' elements organized by 
         // numerical keys. 
         if (array_key_exists('#markup', $build[$key]) and trim($build[$key]['#markup'])) {
-          $markup_list[$key][] = $build[$key]['#markup'];
+          $markup = $build[$key]['#markup'];
         }
         // For backwards copmatibility we should support the '#value' element as well.
         elseif (array_key_exists('#value', $build[$key]) and trim($build[$key]['#value'])) {
-          $markup_list[$key][] = $build[$key]['#markup'];
+          $markup = $build[$key]['#markup'];
         }
-        else {
-          // we don't have a '#markup' field so look to see if this is a CCK
-          // element with numerical fields and a '#markup' inside
-          foreach ($value as $subkey => $subvalue) {
-            if (is_array($subvalue) and array_key_exists('#markup', $value[$subkey]) and trim($value[$subkey]['#markup'])) {
-              $markup_list[$key][] = $value[$subkey]['#markup'];
-            }
-          }
+        
+        // if we have no '#markup' field then this element has not yet
+        // been rendered.  Let's render it and substitute that for markup
+        if (!$markup) {
+          $markup = trim(render($build[$key]));
+          $build[$key] = array(
+            '#markup' => $markup,
+          );
+        }
+        
+        // if we still don't have markup then skip this one
+        if (!$markup) {
+          continue;
         }
-      }
-    }
-
-    // if we have markup for this node then format it for display with Tripal
-    // basically, we just wrap it with a container, give it a title, and
-    // build the table of contents for the page.  The user theme can handle
-    // how to display it.  The default tripal node template will handle it 
-    // by default.
-    foreach ($markup_list as $key => $markup) {
-      foreach ($markup as $i => $html_text) {
-        $is_teaser = FALSE;
 
         // intialize the item title, key and id
         $toc_item_title = $key;
         $toc_item_id    = $key;
         $toc_item_link  = '';
         
-        // BUILD THE TEMPLATE PATH
+        // FIND THE TEMPLATE PATH
         // get the template path so we can put it in an admin message box
         $path = '';
         if (array_key_exists($key, $cache->data) and array_key_exists('path', $cache->data[$key])) {
@@ -629,7 +627,7 @@ function tripal_core_node_view_alter(&$build) {
             Currently, the content above is provided by this template: <br><br>$path")
           );
         }
-  
+
         // BUILD THE TOC LINKS
         // get the title for the table of contents.  Tripal templates should
         // have a '#tripal_toc_title' element in the build array
@@ -639,14 +637,6 @@ function tripal_core_node_view_alter(&$build) {
         if (array_key_exists('#tripal_toc_id', $build[$key])) {
           $toc_item_id = $build[$key]['#tripal_toc_id'];
         }
-        
-        // for any content items that have more than one entry (such
-        // as CCK fields with unlimited values, we want to add the index to the
-        // id 
-        if($i > 0) {
-          $toc_item_id .= '-' . $i;
-          $toc_item_title .= '-' . $i;
-        }
         $toc_item_link = "<div class=\"tripal_toc_list_item\"><a id=\"$toc_item_id\" class=\"tripal_toc_list_item_link\" href=\"?block=$toc_item_id\">$toc_item_title</a></div>";
         
         // next check the database. If the title has been overridden then 
@@ -662,19 +652,13 @@ function tripal_core_node_view_alter(&$build) {
         $updated_markup = "
           <div id=\"$toc_item_id-tripal-data-block\" class=\"tripal-data-block\">
             <div class=\"$toc_item_id-tripal-data-block-title tripal-data-block-title\">$toc_item_title</div>  
-              $html_text  
+              $markup
               $path 
             </div>
           </div>
         ";
         
-        // subtitute back in the #markup into the correct field.
-        if (array_key_exists($i, $build[$key])) {
-          $build[$key][$i]['#markup'] = $updated_markup;
-        }
-        else {
-          $build[$key]['#markup'] = $updated_markup;
-        }
+        $build[$key]['#markup'] = $updated_markup;
       }
     }
   }