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Escriba una consulta nativa de sql con combinación izquierda y paginación en hibernación (springboot)

Lo resolví...

La consulta debe tener este aspecto:

@Query(
        value = "SELECT * FROM \n" +
                "(institution INNER JOIN user ON institution.user_id = user.id) \n" +
                "LEFT JOIN \n" +
                "(SELECT * FROM \n" +
                "building_institutions \n" +
                "WHERE building_id = :userId)\n" +
                " AS reserved_institutions \n" +
                "ON reserved_institutions.institutions_user_id = kits_nwt.institution.user_id \n" +
                " where reserved_institutions.institutions_user_id IS null \n"
                + "ORDER BY ?#{#pageable}"
        ,
        countQuery = "SELECT count(*) FROM \n" +
                "(institution INNER JOIN user ON institution.user_id = user.id) \n" +
                "LEFT JOIN \n" +
                "(SELECT * FROM \n" +
                "building_institutions \n" +
                "WHERE building_id =:userId)\n" +
                " AS reserved_institutions \n" +
                "ON reserved_institutions.institutions_user_id = kits_nwt.institution.user_id \n" +
                "where reserved_institutions.institutions_user_id IS null \n" +
                "ORDER BY ?#{#pageable}",
        nativeQuery = true)
Page<Institution> findPotentialInstitutionsByBuildingId(@Param("userId") Long userId, Pageable pageable);

Estaba recibiendo el error en la línea 4 cerca de DONDE, cuando mi consulta se veía así:

@Query(
        value = "SELECT username, password, description, location, title, user_id FROM (institution INNER JOIN user ON institution.user_id = user.id) LEFT JOIN\n" +
                "(SELECT * FROM building_institutions WHERE building_institutions.building_id = 1) AS reserved_institutions\n" +
                "ON reserved_institutions.institutions_user_id = kits_nwt.institution.user_id\n" +
                "WHERE reserved_institutions.institutions_user_id IS null ORDER BY ?#{#pageable}",
        nativeQuery = true)
Page<Institution> findPotentialInstitutionsByBuildingId(Long userId, Pageable pageable);

y eso fue porque no agregué countQuery parámetro a @Query anotación.

Muchas gracias a todos los que intentaron ayudar.

Espero que le ahorre a alguien más muchas horas de miseria.

¡Salud! :)