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$dql = "SELECT s, e, ie FROM Entities\Site s 
                        JOIN s.emails e JOIN e.incomingEmails ie ".
                        $this->buildFilterForDQL($filter).
                        " ORDER BY s.id {$order}";           
        
        $query = $this->getEntityManager()->createQuery($dql)
                      ->setFirstResult(0)
                      ->setMaxResults(PHP_INT_MAX);

        $paginator = new Paginator($query, true /* $fetchJoinCollection */);

// ... and

public function buildFilterForDQL($filter){
        switch($filter){
            case self::SHOW_ALL:
                return "";
            break;
            case self::NOT_AVAILABLE:
                return "WHERE s.lastCheckResult = ".\Entities\Site::SITE_DOWN." 
                              OR e.lastCheckResult = ".\Entities\Email::EMAIL_DOWN;
            break;
            case self::NOT_PAYED:
                return "WHERE DATE_DIFF(s.domainExpDate, CURRENT_DATE()) > 0 
                              OR DATE_DIFF(s.hostingExpDate, CURRENT_DATE()) > 0";
            break;
            case self::WITH_NEW_INFO_EMAILS:
                return "WHERE e.type = ".\Entities\Email::INFO_TYPE."
                              AND ie.state = ".\Entities\IncomingEmail::UNREAD;
            break;
            case self::WITH_NEW_TEH_EMAILS:
                return "WHERE e.type = ".\Entities\Email::TEH_TYPE."
                              AND ie.state = ".\Entities\IncomingEmail::UNREAD;
            break;
            default: throw new \InvalidArgumentException("Unknown filter {$filter} provided");
        }
    }