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mysql-collation-fixer.php

<?php
  /**
   * @package MySQL_Collation_Fixer
   * @version 1.6
   */
  /*
  Plugin Name: MySQL Collation fixer
  Description: Change database tables collation to utf8_general__ci after DB upgrade
  Version:     1.0
  Author:      Federico Parodi - weLaika
  Author URI:  http://dev.welaika.com
  License:     MIT
  License URI: http://opensource.org/licenses/MIT
  */

  // If this file is called directly, abort.
  if ( !defined( 'WPINC' ) ) {
    die;
  }

  function tables_list() {
    global $wpdb;
    $sqlTablesResults = $wpdb->get_results( 'SHOW TABLES' );
    $outputColumnName = "Tables_in_" . DB_NAME;
    $tables = array();
    foreach ($sqlTablesResults as $value) {
      array_push($tables, $value->$outputColumnName);
    }
    return $tables;
  }

  function fix_tables() {
    global $wpdb;
    $tables = tables_list();

    foreach ($tables as $table) {
      $wpdb->get_results( "alter table $table CONVERT TO CHARACTER SET utf8 COLLATE utf8_general_ci" );
    }
  }

  add_action( 'after_db_upgrade', 'fix_tables' );
  //or calling directly fix_tables(); if you already have an upgraded database