Merge branch '7.x-3.x' of github.com:tripal/tripal into 7.x-3.x

tripal/includes/tripal.bulk_update.inc

@@ -12,18 +12,12 @@ function tripal_update_all_urls_and_titles($bundle_id, $update, $type) {
   $entity_table = 'chado_'.$bundle_id;
   $entities = db_select($entity_table, 'e')
     ->fields('e', array('entity_id'))
-    ->execute()->fetchAll();
-  $num_entities = count($entities);
+    ->orderBy('entity_id', 'ASC')
+    ->execute();
+  $num_entities = $entities->rowCount();
   // 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.
-  $queue = DrupalQueue::get('entityQueue');
-  // Push all the items into the queue, one at a time.
-  // You can push any data in with (arrays, objects, etc).
-  foreach ($entities as $entity) {
-    $queue->createItem($entity);
-  }
+
   $fields = array();
   foreach ($bundle_tokens as $bundle_token) {
     foreach ($bundle_token as $token) {
@@ -32,10 +26,11 @@ function tripal_update_all_urls_and_titles($bundle_id, $update, $type) {
       $fields[] = $field_array['id'];
     }
   }
-  $i = 0;
+
+  $i = 1;
   // Pull items out one at a time.
-  while ($entity = $queue->claimItem()) {
-    $arg = tripal_load_entity('TripalEntity', [$entity->data->entity_id], FALSE, $fields);
+  while ($entity = $entities->fetchObject()) {
+    $arg = tripal_load_entity('TripalEntity', [$entity->entity_id], FALSE, $fields);
     if ($type == 'alias') {
       if (!empty($arg)) {
         if (is_array($arg)) {
@@ -44,6 +39,7 @@ function tripal_update_all_urls_and_titles($bundle_id, $update, $type) {
         // Get the entity controller and clear the cache if requested (default).
         $ec = entity_get_controller('TripalEntity');
         $ec->setAlias($ent, $update);
+        $ec->resetCache();
       }
     }
     elseif ($type == 'title') {
@@ -54,14 +50,16 @@ function tripal_update_all_urls_and_titles($bundle_id, $update, $type) {
 
         $ec = entity_get_controller('TripalEntity');
         $ec->setTitle($ent, $update);
+        $ec->resetCache();
       }
     }
-    $i++;
     // Check if 50 items have been updated, if so print message.
-    if ($i < $num_entities) {
-      print $i . "/" . $num_entities . " entities have been updated.\r";
+    if ($i <= $num_entities) {
+      $mem = number_format(memory_get_usage());
+      print $i . "/" . $num_entities . " entities have been updated. Memory usage: $mem bytes.\r";
     }
-    // Good, we succeeded.  Delete the item as it is no longer needed.
-    $queue->deleteItem($entity);
+    $i++;
   }
+
+  print "\nDone.";
 }