try (Connection conn = DriverManager.getConnection(url)) {

  conn.setAutoCommit(false);

  int batchSize = 0;

  int commitSize = 1000; // number of rows you want to commit per batch.

  try (Statement stmt = conn.prepareStatement(upsert)) {

    stmt.set ... while (there are records to upsert) {

      stmt.executeUpdate();

      batchSize++;

      if (batchSize % commitSize == 0) {

        conn.commit();

      }

   }

 conn.commit(); // commit the last batch of records

 }