Issue #72: Updating API to include 2.1 improvements: a48bf3b

legacy/tripal_core/includes/tripal_core.toc.inc

@@ -28,7 +28,7 @@ function tripal_core_node_toc_form($form, &$form_state, $node) {
       the following order in the Table of Contents (TOC). You may rename
       the titles or drag and drop them to change the order.  <b>Any changes will
       only apply to this page</b>. If you would like to make changes apply to multiple
-      pages of the same tpye, please visit the $admin_link. ") . '</p>' .
+      pages of the same type, please visit the $admin_link. ") . '</p>' .
       '<p>' . t('The list below shows all possible content panes that can appear.
       However, those without content are automatically hidden and do not
       appear in the TOC.' . '</p>'),

tripal/api/tripal.notice.api.inc

@@ -134,8 +134,9 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
  * @param $message
  *   The message to be displayed to the tripal administrators
  * @param $importance
- *   The level of importance for this message. In the future this will be used to allow
- *   administrators to filter some of these messages. It can be one of the following:
+ *   The level of importance for this message. In the future this will be used
+ *   to allow administrators to filter some of these messages. It can be one of
+ *   the following:
  *     - TRIPAL_CRITICAL: Critical conditions.
  *     - TRIPAL_ERROR: Error conditions.
  *     - TRIPAL_WARNING: Warning conditions.
@@ -144,9 +145,9 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
  *     - TRIPAL_DEBUG: Debug-level messages.
  * @param $options
  *   Any options to apply to the current message. Supported options include:
- *     - return_html: return HTML instead of setting a drupal message. This can be
- *         used to place a tripal message in a particular place in the page.
- *         The default is FALSE.
+ *     - return_html: return HTML instead of setting a drupal message. This can
+ *       be used to place a tripal message in a particular place in the page.
+ *       The default is FALSE.
  */
 function tripal_set_message($message, $importance = TRIPAL_INFO, $options = array()) {
   global $user;

tripal_chado/api/tripal_chado.query.api.inc

@@ -1580,10 +1580,12 @@ function chado_select_record_check_value_type(&$op, &$value, $type) {
 }
 
 /**
- * Use this function instead of db_query() to avoid switching databases
- * when making query to the chado database
+ * A substitute for db_query() when querying from Chado.
  *
- * Will use a chado persistent connection if it already exists
+ * This function is needed to avoid switching databases when making query to
+ * the chado database.
+ *
+ * Will use a chado persistent connection if it already exists.
  *
  * @param $sql
  *   The sql statement to execute
@@ -1625,11 +1627,20 @@ function chado_query($sql, $args = array()) {
   // if Chado is local to the database then prefix the Chado table
   // names with 'chado'.
   if ($is_local) {
-    $sql = preg_replace('/\n/', '', $sql);  // remove carriage returns
+    // Remove carriage returns from the SQL.
+    $sql = preg_replace('/\n/', '', $sql);
+
+    // Prefix the tables with their correct schema.
+    // Chado tables should be enclosed in curly brackets (ie: {feature} )
+    // and Drupal tables should be enclosed in square brackets
+    // (ie: [tripal_jobs] ).
+    // @todo: remove assumption that the chado schema is called 'chado' and the
+    // drupal schema is called 'public'.
     $sql = preg_replace('/\{(.*?)\}/', 'chado.$1', $sql);
+    $sql = preg_replace('/\[(\w+)\]/', 'public.$1', $sql);
 
-    // the featureloc table has some indexes that use function that call other functions
-    // and those calls do not reference a schema, therefore, any tables with featureloc
+    // The featureloc table has some indexes that use function that call other
+    // functions and those calls do not reference a schema, therefore, any tables with featureloc
     // must automaticaly have the chado schema set as active to find
     if (preg_match('/chado.featureloc/i', $sql) or preg_match('/chado.feature/i', $sql)) {
       $previous_db = chado_set_active('chado') ;
@@ -1648,6 +1659,16 @@ function chado_query($sql, $args = array()) {
       $results = db_query($sql, $args);
     }
   }
+  // Check for any cross schema joins (ie: both drupal and chado tables
+  // represented and if present don't execute the query but instead warn the
+  // administrator.
+  else if (preg_match('/\[(\w*?)\]/', $sql)) {
+    tripal_report_error('chado_query', TRIPAL_ERROR,
+      'The following query does not support external chado databases. Please file an issue with the Drupal.org Tripal Project. Query: @query',
+       array('@query' => $sql)
+    );
+    return FALSE;
+  }
   // if Chado is not local to the Drupal database then we have to
   // switch to another database
   else {