Fixes #83 by exposing chado linking tables to the Drupal Schema API through hook_schema().

tripal_chado/tripal_chado.install

@@ -182,6 +182,55 @@ function tripal_chado_schema() {
   // Map cvterm usage to chado tables
   $schema['chado_cvterm_mapping'] = tripal_chado_chado_cvterm_mapping_schema();
 
+  // When a chado Tripal content type is created, a linking table is also created to
+  // link the entity to it's record in chado (@see tripal_chado_bundle_create() ).
+  // This table is created via db_create_table() but in order to expose it to
+  // the Drupal Schema API, we also need to define each one here.
+  if (db_table_exists('chado_bundle')) {
+    $resource = db_query('SELECT tb.name FROM chado_bundle cb LEFT JOIN tripal_bundle tb ON tb.id=cb.bundle_id');
+    foreach ($resource as $r) {
+      $bundle_name = $r->name;
+      // This makes an assumption about the name of the linking table.
+      // @todo: Switch to tripal_chado_get_bundle_entity_table($bundle).
+      $chado_entity_table = 'chado_' . $bundle_name;
+      $schema[$chado_entity_table] = array(
+        'description' => 'The linker table that associates TripalEntities with Chado records for entities of type ' . $bundle_name . '.',
+        'fields' => array(
+          'mapping_id' => array(
+            'type' => 'serial',
+            'not null' => TRUE
+          ),
+          'entity_id' => array(
+            'description' => 'The unique entity id.',
+            'type' => 'int',
+            'not null' => TRUE,
+          ),
+          'record_id' => array(
+            'description' => 'The unique numerical identifier for the record that this entity is associated with (e.g. feature_id, stock_id, library_id, etc.).',
+            'type' => 'int',
+            'not null' => TRUE,
+          ),
+          'nid' => array(
+            'description' => 'Optional. For linking nid to the entity when migrating Tripal v2 content',
+            'type' => 'int',
+          )
+        ),
+        'primary key' => array(
+          'mapping_id',
+        ),
+        'indexes' => array(
+          'record_id' => array('record_id'),
+          'entity_id' => array('entity_id'),
+          'nid' => array('nid'),
+        ),
+        'unique keys' => array(
+          'table_record' => array('record_id'),
+          'entity_id' => array('entity_id'),
+        ),
+      );
+    }
+  }
+
   return $schema;
 }