Cannot issue data manipulation statements with executeQuery()

To manipulate data you actually need executeUpdate() rather than executeQuery().

Here's an extract from the executeUpdate() javadoc which is already an answer at its own:

Executes the given SQL statement, which may be an INSERT, UPDATE, or DELETE statement or an SQL statement that returns nothing, such as an SQL DDL statement.

If you're using spring boot, just add an @Modifying annotation.

@Modifying
@Query
(value = "UPDATE user SET middleName = 'Mudd' WHERE id = 1", nativeQuery = true)
void updateMiddleName();

For Delete query - Use @Modifying and @Transactional before the @Query like:-

@Repository
public interface CopyRepository extends JpaRepository<Copy, Integer> {

    @Modifying
    @Transactional
    @Query(value = "DELETE FROM tbl_copy where trade_id = ?1 ; ", nativeQuery = true)
    void deleteCopyByTradeId(Integer id);

}

It won't give the java.sql.SQLException: Can not issue data manipulation statements with executeQuery() error.

Edit:

Since this answer is getting many upvotes, I shall refer you to the documentation as well for more understanding.

@Transactional

By default, CRUD methods on repository instances are transactional. For read operations, 
the transaction configuration readOnly flag is set to true. 
All others are configured with a plain @Transactional so that default transaction 
configuration applies.

@Modifying

Indicates a query method should be considered as modifying query as that changes the way 
it needs to be executed. This annotation is only considered if used on query methods defined 
through a Query annotation). It's not applied on custom implementation methods or queries 
derived from the method name as they already have control over the underlying data access 
APIs or specify if they are modifying by their name.

Queries that require a @Modifying annotation include INSERT, UPDATE, DELETE, and DDL 
statements.

Use executeUpdate() to issue data manipulation statements. executeQuery() is only meant for SELECT queries (i.e. queries that return a result set).

That's what executeUpdate is for.

Here's a very brief summary of the difference: http://www.coderanch.com/t/301594/JDBC/java/Difference-between-execute-executeQuery-executeUpdate

@Modifying
@Transactional
@Query(value = "delete from cart_item where cart_cart_id=:cart", nativeQuery = true)
public void deleteByCart(@Param("cart") int cart); 

Do not forget to add @Modifying and @Transnational before @query. it works for me.

To delete the record with some condition using native query with JPA the above mentioned annotations are important.

executeQuery() returns a ResultSet. I'm not as familiar with Java/MySQL, but to create indexes you probably want a executeUpdate().

Connection conn = DriverManager.getConnection("jdbc:mysql://localhost:3306/java_swing_db", "root", "root");

Statement smt = conn.createStatement();

String sql = "SELECT * FROM `users` WHERE `email` = " + email + " AND `password` = " + password + " LIMIT 1;";

String registerSql = "INSERT INTO `users`(`email`, `password`, `name`) VALUES ('" + email + "','" + password + "','" + name + "')";

System.out.println("SQL: " + registerSql);
            
int result = smt.executeUpdate(registerSql);
System.out.println("Result: " + result);

if (result == 0) {
   JOptionPane.showMessageDialog(this, "This is alredy exist");
} else {
  JOptionPane.showMessageDialog(this, "Welcome, Your account is sucessfully created");
  App.isLogin = true;
  this.dispose();
  new HomeFrame().show();
}
conn.close();