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(); 
        batchSize = 0;
      } 
   } 
 conn.commit(); // commit the last batch of records 
 }