Minor adjustments

tripal_chado/api/tripal_chado.api.inc

@@ -317,28 +317,28 @@ function tripal_replace_chado_tokens($string, $record) {
 }
 
 /**
- * Retrieve entity_id for a chado record
- * 
+ * Retrieve an entity_id for a chado record.
+ *
  * @param string $chado_table
- *   the chado_table where the record is stored
+ *   The chado_table where the record is stored.
  * @param integer $record_id
- *   the record_id which is the primary key of the chado_table
- *   
+ *   The record_id which is the primary key of the chado table.
+ *
  * @return
- *   Return an integer representing the entity_id or NULL if not found. The record is then 
- *   accessible on the website through URL /bio_data/<entity_id>
+ *   Return an integer representing the entity_id or NULL if not found. The
+ *   record is then accessible on the website through URL /bio_data/<entity_id>
  */
 function tripal_get_chado_entity_id ($chado_table, $record_id) {
-  // To find the bundle_table, check if type_column is used for the chado_table
-  $type_column = 
+  // To find the bundle_table, check if type_column is used for the chado table.
+  $type_column =
     db_select('chado_bundle', 'CB')
     ->fields('CB', array('type_column'))
     ->condition('data_table', $chado_table)
     ->execute()
     ->fetchField();
-  
-  // if there is a type_column, get bundle_id by specifying the data_table,  type_column, 
-  // and type_id
+
+  // If there is a type_column, get bundle_id by specifying the data_table,
+  // type_column, and type_id.
   $bundle_id = NULL;
   if ($type_column) {
     $schema = chado_get_schema($chado_table);
@@ -346,48 +346,48 @@ function tripal_get_chado_entity_id ($chado_table, $record_id) {
     $type_id = NULL;
     if (key_exists($type_column, $schema['fields'])) {
       $type_id =
-        db_select('chado.' . $chado_table, 'C')
-        ->fields('C', array($type_column))
-        ->condition($pkey, $record_id)
-        ->execute()
-        ->fetchField();
+        chado_select($chado_table, 'C')
+          ->fields('C', array($type_column))
+          ->condition($pkey, $record_id)
+          ->execute()
+          ->fetchField();
     }
     if ($type_id) {
       $bundle_id =
         db_select('chado_bundle', 'CB')
-        ->fields('CB', array('bundle_id'))
-        ->condition('data_table', $chado_table)
-        ->condition('type_column', $type_column)
-        ->condition('type_id', $type_id)
-        ->execute()
-        ->fetchField();
+          ->fields('CB', array('bundle_id'))
+          ->condition('data_table', $chado_table)
+          ->condition('type_column', $type_column)
+          ->condition('type_id', $type_id)
+          ->execute()
+          ->fetchField();
     }
   }
-  // if type_column is not used, get bundle_id by specifying the data_table
+  // If type_column is not used, get bundle_id by specifying the data_table.
   else {
-    $bundle_id = 
+    $bundle_id =
       db_select('chado_bundle', 'CB')
-      ->fields('CB', array('bundle_id'))
-      ->condition('data_table', $chado_table)
-      ->execute()
-      ->fetchField();
+        ->fields('CB', array('bundle_id'))
+        ->condition('data_table', $chado_table)
+        ->execute()
+        ->fetchField();
   }
-  
-  // if bundle_id is found, find the bundle table name and return the entity_id
+
+  // If bundle_id is found, find the bundle table name and return the entity_id.
   $entity_id = NULL;
   if ($bundle_id) {
-    $table_name = 
+    $table_name =
       db_select('tripal_bundle', 'TB')
-      ->fields('TB', array('name'))
-      ->condition('id', $bundle_id)
-      ->execute()
-      ->fetchField();
-    $entity_id = 
+        ->fields('TB', array('name'))
+        ->condition('id', $bundle_id)
+        ->execute()
+        ->fetchField();
+    $entity_id =
       db_select('chado_' . $table_name, 'CBD')
-      ->fields('CBD', array('entity_id'))
-      ->condition('record_id', $record_id)
-      ->execute()
-      ->fetchField();
-  }  
+        ->fields('CBD', array('entity_id'))
+        ->condition('record_id', $record_id)
+        ->execute()
+        ->fetchField();
+  }
   return $entity_id;
 }