Fixed incompatibility with PHP 5.4

tripal_contact/includes/tripal_contact.form.inc

@@ -4,7 +4,7 @@
  *
  *
  *
- *  @parm &$node
+ *  @parm $node
  *    The node that is created when the database is initialized
  *
  *  @parm $form_state

tripal_contact/tripal_contact.install

@@ -154,7 +154,7 @@ function tripal_contact_add_custom_tables(){
       ),
     ),
   );
-  tripal_core_create_custom_table(&$ret, 'contactprop', $schema, TRUE);
+  tripal_core_create_custom_table($ret, 'contactprop', $schema, TRUE);
 }
 /**
  *  Update for Drupal 6.x, Tripal 1.0

tripal_project/tripal_project.module

@@ -185,7 +185,7 @@ function tripal_project_theme() {
  *
  *  This form takes the Project Title information and description from the user.
  *
- *  @parm &$node
+ *  @parm $node
  *    The initialized node
  *
  *  @parm $form_state

tripal_pub/includes/importers/AGL.inc

@@ -329,7 +329,7 @@ function tripal_pub_remote_search_AGL($search_array, $num_to_retrieve, $pager_id
     );
     yaz_ccl_conf($yazc, $fields);
 
-    if (!yaz_ccl_parse($yazc, $ccl, &$cclresult)) {
+    if (!yaz_ccl_parse($yazc, $ccl, $cclresult)) {
       drupal_set_message('Error parsing search string: ' . $cclresult["errorstring"], "error");
       watchdog('tripal_pub', 'Error: %errstr', array('%errstr' => $cclresult["errorstring"]), WATCHDOG_ERROR);
       return array();

tripal_pub/tripal_pub.install

@@ -117,39 +117,39 @@ function tripal_pub_add_custom_tables() {
       'pubauthor_contact_id' => array (
         'type' => 'serial',
         'not null' => true,
-  ),
+      ),
       'contact_id' => array (
         'type' => 'int',
         'not null' => true,
-  ),
+      ),
       'pubauthor_id' => array (
         'type' => 'int',
         'not null' => true,
-  ),
-  ),
+      ),
+    ),
     'primary key' => array (
-  0 => 'pubauthor_contact_id',
-  ),
+      0 => 'pubauthor_contact_id',
+    ),
     'unique keys' => array (
       'pubauthor_contact_c1' => array (
-  0 => 'contact_id',
-  1 => 'pubauthor_id',
-  ),
-  ),
+        0 => 'contact_id',
+        1 => 'pubauthor_id',
+      ),
+    ),
     'foreign keys' => array (
       'contact' => array (
         'table' => 'contact',
         'columns' => array (
           'contact_id' => 'contact_id',
-  ),
-  ),
+        ),
+      ),
       'pubauthor' => array (
         'table' => 'pubauthor',
         'columns' => array (
           'pubauthor_id' => 'pubauthor_id',
-  ),
-  ),
-  ),
+        ),
+      ),
+    ),
   );
-  tripal_core_create_custom_table(&$ret, 'pubauthor_contact', $schema, TRUE);
+  tripal_core_create_custom_table($ret, 'pubauthor_contact', $schema, TRUE);
 }

tripal_views/api/tripal_views.api.inc

@@ -617,7 +617,7 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
 /**
  * Adds the joins necessary to link a chado table to it's node counterpart
  *
- * @param &$defn_array
+ * @param $defn_array
  *   The current definition array for a given table
  *
  * @ingroup tripal_views_api

tripal_views/includes/tripal_views_integration.inc

@@ -196,7 +196,7 @@ function tripal_views_integration_delete($setup_id) {
  *   handlers when integrating a table with views.  This form is used for both
  *   creating a new record and editing an existing record.
  *
- * @param &$form_state
+ * @param $form_state
  *    The form state which is passed automatically by drupal
  *
  * @param $setup_id
@@ -847,7 +847,7 @@ function tripal_views_integration_form(&$form_state, $setup_id = NULL) {
  * @param $form
  *    The form object which is passed automatically by drupal
  *
- * @param &$form_state
+ * @param $form_state
  *    The form state pbject which is passed automatically by drupal
  *
  * @ingroup tripal_views_integration
@@ -883,7 +883,7 @@ function tripal_views_integration_form_validate($form, &$form_state) {
  * @param $form
  *    The form object which is passed automatically by drupal
  *
- * @param &$form_state
+ * @param $form_state
  *    The form state pbject which is passed automatically by drupal
  *
  * @ingroup tripal_views_integration