fix call to tripal_load_entity to account for missing reset parameter and cleaned up formatting.

tripal/includes/tripal.bulk_update.inc

@@ -1,35 +1,36 @@
 <?php
+
 /**
  * Updates all existing url aliases for an entity.
  *
  * @param $bundle_id
  * @param $update
  * @param $type
-*/
+ */
 function tripal_update_all($bundle_id, $update, $type) {
-  //Load all the entity_ids.
+  // Load all the entity_ids.
   $entity_table = 'chado_'.$bundle_id;
   $entities = db_select($entity_table, 'e')
-  ->fields('e', array('entity_id'))
-  ->execute()->fetchAll();
+    ->fields('e', array('entity_id'))
+    ->execute()->fetchAll();
   $num_entities = count($entities);
-  //Parse the $update variable for tokens and load those tokens.
+  // Parse the $update variable for tokens and load those tokens.
   preg_match_all("/\[[^\]]*\]/", $update, $bundle_tokens);
-  //Get the queue so we can add to it.  Use a
-  //descriptive name. It's ok if it doesn't exist yet.
+  // Get the queue so we can add to it.  Use a
+  // descriptive name. It's ok if it doesn't exist yet.
   $queue = DrupalQueue::get('entityQueue');
-  //Push all the items into the queue, one at a time.
-  //You can push any data in with (arrays, objects, etc).
-  foreach($entities as $entity) {
+  // Push all the items into the queue, one at a time.
+  // You can push any data in with (arrays, objects, etc).
+  foreach ($entities as $entity) {
     $queue->createItem($entity);
   }
   $i = 0;
-  //Pull items out one at a time.
-  while($entity = $queue->claimItem()) {
-    $arg = tripal_load_entity('TripalEntity', [$entity->data->entity_id], $bundle_tokens);
+  // Pull items out one at a time.
+  while ($entity = $queue->claimItem()) {
+    $arg = tripal_load_entity('TripalEntity', [$entity->data->entity_id], FALSE, $bundle_tokens);
     if ($type == 'alias') {
       if (!empty($arg)) {
-        if(is_array($arg)){
+        if (is_array($arg)) {
           $ent = reset($arg);
         }
         // Get the entity controller and clear the cache if requested (default).
@@ -39,7 +40,7 @@ function tripal_update_all($bundle_id, $update, $type) {
     }
     elseif ($type == 'title') {
       if (!empty($arg)) {
-        if(is_array($arg)){
+        if (is_array($arg)) {
           $ent = reset($arg);
         }
         $ec = entity_get_controller('TripalEntity');
@@ -48,11 +49,10 @@ function tripal_update_all($bundle_id, $update, $type) {
     }
     $i++;
     // Check if 50 items have been updated, if so print message.
-    if ($i < $num_entities){
-      print $i."/".$num_entities." entities have been updated.\r";
+    if ($i < $num_entities) {
+      print $i . "/" . $num_entities . " entities have been updated.\r";
     }
-    //Good, we succeeded.  Delete the item as it is no longer needed.
+    // Good, we succeeded.  Delete the item as it is no longer needed.
     $queue->deleteItem($entity);
   }
 }
-