vacuum sqlite after pruning data (#2697)

* vaccum sqlite database

* use pruned height table for opening sqlite write txn

* move vacuum after each batch delete

hotshot-query-service/src/data_source/storage/sql.rs

@@ -731,6 +731,13 @@ impl PruneStorage for SqlStorage {
             }
         }
 
+        #[cfg(feature = "embedded-db")]
+        {
+            let mut conn = self.pool().acquire().await?;
+            query("VACUUM").execute(conn.as_mut()).await?;
+            conn.close().await?;
+        }
+
         // If threshold is set, prune data exceeding minimum retention in batches
         // This parameter is needed for SQL storage as there is no direct way to get free space.
         if let Some(threshold) = cfg.pruning_threshold() {
@@ -765,6 +772,13 @@ impl PruneStorage for SqlStorage {
                             message: format!("failed to commit {e}"),
                         })?;
 
+                        #[cfg(feature = "embedded-db")]
+                        {
+                            let mut conn = self.pool().acquire().await?;
+                            query("VACUUM").execute(conn.as_mut()).await?;
+                            conn.close().await?;
+                        }
+
                         pruner.pruned_height = Some(height);
 
                         return Ok(Some(height));

hotshot-query-service/src/data_source/storage/sql/transaction.rs

@@ -124,7 +124,7 @@ impl TransactionMode for Write {
         // statement that has no actual effect on the database is suitable for this purpose, hence
         // the `WHERE false`.
         #[cfg(feature = "embedded-db")]
-        conn.execute("UPDATE header SET height = height WHERE false")
+        conn.execute("UPDATE pruned_height SET id = id WHERE false")
             .await?;
 
         // With Postgres things are much more straightforward: just tell Postgres we want a write