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

tripal_chado/api/tripal_chado.api.inc

@@ -316,4 +316,78 @@ function tripal_replace_chado_tokens($string, $record) {
   return $string;
 }
 
-
+/**
+ * Retrieve entity_id for a chado record
+ * 
+ * @param string $chado_table
+ *   the chado_table where the record is stored
+ * @param integer $record_id
+ *   the record_id which is the primary key of the chado_table
+ *   
+ * @return
+ *   Return an integer representing the entity_id or NULL if not found. The record is then 
+ *   accessible on the website through URL /bio_data/<entity_id>
+ */
+function tripal_get_chado_entity_id ($chado_table, $record_id) {
+  // To find the bundle_table, check if type_column is used for the chado_table
+  $type_column = 
+    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
+  $bundle_id = NULL;
+  if ($type_column) {
+    $schema = chado_get_schema($chado_table);
+    $pkey = is_array($schema['primary key']) ? $schema['primary key'][0] : $schema['primary key'];
+    $type_id = NULL;
+    if (key_exists($type_column, $schema['fields'])) {
+      $type_id =
+        db_select('chado.' . $chado_table, 'C')
+        ->fields('C', array($type_column))
+        ->condition($pkey, $record_id)
+        ->execute()
+        ->fetchField();
+    }
+    if ($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();
+    }
+  }
+  // if type_column is not used, get bundle_id by specifying the data_table
+  else {
+    $bundle_id = 
+      db_select('chado_bundle', 'CB')
+      ->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
+  $entity_id = NULL;
+  if ($bundle_id) {
+    $table_name = 
+      db_select('tripal_bundle', 'TB')
+      ->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();
+  }  
+  return $entity_id;
+}