Fully support extender

tripal_chado/includes/ChadoPrefixExtender.inc

@@ -1,36 +1,147 @@
 <?php
 
 /**
- * SelectQueryExtender to use chado_replace_table_prefix().
+ * ChadoPrefixExtender
  *
- *   Note that extenders can only be called on an existing db_select().
- * Therefore the table name in the initial select must be prefixed prior to
- * initialization. Read more about extenders:
- * https://www.drupal.org/docs/7/api/database-api/dynamic-queries/extenders.
+ * A query extender that for select queries. By extending the
+ * SelectQueryExtender class, we can make sure that chado tables
+ *
+ * @see https://www.drupal.org/docs/7/api/database-api/dynamic-queries/extenders
  */
 class ChadoPrefixExtender extends SelectQueryExtender {
 
+  /**
+   * A static cache for Chado tables.
+   *
+   * @var array
+   */
+  protected static $chado_tables = [];
+
+  /**
+   * A replacement for db_select when querying Chado.
+   *
+   * Use this function instead of db_select when querying Chado tables.
+   *
+   * @param string|\SelectQuery $table
+   *   The base table for this query. May be a
+   *   string or another SelectQuery object. If a query object is passed, it
+   *   will be used as a subselect.
+   * @param string $alias
+   *   The alias for the base table of this query.
+   * @param array $options
+   *   An array of options to control how the query
+   *   operates.
+   *
+   * @return \SelectQuery
+   *   A new SelectQuery object for this connection.
+   *
+   * @ingroup tripal_chado_query_api
+   */
+  public static function select($table, $alias = NULL, array $options = []) {
+    // Since the table could also be a SelectQuery object, we should verify that
+    // it is a string first.
+    if (is_string($table)) {
+      $table = static::getTable($table);
+    }
+
+    // If the alias is null, determine a safe alias. db_select fails to generate
+    // a safe alias when the table name is prefixed with "public.".
+    if (is_null($alias)) {
+      $alias = static::makeAlias($table);
+    }
+
+    // Create a select query
+    $query = db_select($table, $alias, $options);
+    return $query->extend('ChadoPrefixExtender');
+  }
+
   /**
    * Overwrites the join to prefix table names.
    *
    * @param string $table
    *   Table to join.
-   * @param null $alias
+   * @param string $alias
    *   Alias for joined table.
-   * @param null $condition
+   * @param string $condition
    *   Operation for joining.
    * @param array $arguments
    *   Additional arguments.
    *
    * @return $this
+   *   The current object.
+   *
+   * @ingroup tripal_chado_query_api
    */
   public function join($table, $alias = NULL, $condition = NULL, $arguments = []) {
-    if(strpos($table, '[') !== 0 && strpos($table, ']') !== strlen($table)) {
-      $table = "{{$table}}";
+    $table = static::getTable($table);
+
+    if (is_null($alias)) {
+      $alias = static::makeAlias($table);
     }
-    $table = chado_replace_table_prefix($table);
+
     $this->query->join($table, $alias, $condition, $arguments);
+
     return $this;
   }
 
+
+  /**
+   * Checks if a table is a chado table.
+   *
+   * @param string $table
+   *
+   * @return bool
+   */
+  public static function isChadoTable($table) {
+    if (empty(static::$chado_tables)) {
+      static::$chado_tables = chado_get_table_names(TRUE);
+    }
+
+    return in_array($table, static::$chado_tables);
+  }
+
+  /**
+   * If the table name has a schema name as a prefix, replace it with the
+   * correct schema name.
+   *
+   * @param string $table
+   *   The table name.
+   *
+   * @return string
+   *   The table with the correct prefix.
+   *
+   * @see chado_replace_schema_prefix()
+   */
+  public static function getTable($table) {
+    // No schema was provided.
+    if (strpos($table, '.') === FALSE) {
+      // If this is a chado table, add the chado prefix. Otherwise, add the
+      // public prefix.
+      if (static::isChadoTable($table)) {
+        $table = "chado.{$table}";
+      }
+      else {
+        $table = "public.{$table}";
+      }
+    }
+
+    // Now that the schema has been set, we can replace it with the correct
+    // name. Note that schema names can be altered by developers so we need to
+    // to run the following function to obtain the final name.
+    $table = chado_replace_schema_prefix($table);
+
+    return $table;
+  }
+
+  /**
+   * Create a safe alias.
+   *
+   * @param string $table Table name.
+   *
+   * @return string
+   *    The safe alias.
+   */
+  public static function makeAlias($table) {
+    return str_replace('.', '_', $table);
+  }
 }