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CREATE TABLE `timer` (
    `id` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
    `user_id` INT(10) UNSIGNED  NOT NULL,
    `action` VARCHAR(5) NOT NULL,
    `timestamp` INT(10) UNSIGNED NOT NULL,
    PRIMARY KEY(`id`)
);

<script src="http://code.jquery.com/jquery.js"></script>
<script>
var format = function(seconds) {
    var tempos = {
        segundos: 60
    ,   minutos: 60
    ,   horas: 24
    ,   dias: ''
    };
    var parts = [], string = '', resto, dias;
    for (var unid in tempos) {
        if (typeof tempos[unid] === 'number') {
            resto = seconds % tempos[unid];
            seconds = (seconds - resto) / tempos[unid];
        } else {
            resto = seconds;
        }
        parts.unshift(resto);
    }
    dias = parts.shift();
    if (dias) {
        string = dias + (dias > 1 ? ' dias ' : ' dia ');
    }
    for (var i = 0; i < 3; i++) {
        parts[i] = ('0' + parts[i]).substr(-2);
    }
    string += parts.join(':');
    return string;
};
$(function(){
    var tempo = 0;
    var interval = 0;
    var timer = function(){
        $('.timer').html(format(++tempo));
    };
    $.post('get_timer.php', function(resp){
        $('button').text(resp.running ? 'Pausar' : 'Iniciar');
        tempo = resp.seconds;
        timer();
        if (resp.running) {
            interval = setInterval(timer, 1000);
        }
    });
    $('button').on('click', function(){
        var btn = this;
        btn.disabled = true;
        $.post('grava_acao.php', function(resp){
            btn.disabled = false;
            $(btn).text(resp.running ? 'Pausar' : 'Iniciar');
            if (resp.running) {
                timer();
                interval = setInterval(timer, 1000);
            } else {
                clearInterval(interval);
            }
        });
    });
});
</script>
<div class="timer">0 segundos</div>
<button>Iniciar</button>

<?php
// definir no seu código
$pdo = new PDO($dsn, $username, $passwd);
$user_id = 1; // $_SESSION['user_id'];

$params = array(':user' => $user_id);
$stt = $pdo->prepare('SELECT `action`, `timestamp` FROM `timer` WHERE `user_id` = :user ORDER BY `id`');
$stt->execute($params);
$tempos = $stt->fetchAll(PDO::FETCH_ASSOC);
$seconds = 0;
$action = 'pause'; // sempre inicia pausado
foreach ($tempos as $tempo) {
    $action = $tempo['action'];
    switch ($action) {
        case 'start':
            $seconds -= $tempo['timestamp'];
            break;
        case 'pause':
            // para evitar erro se a primeira ação for pause
            if ($seconds !== 0) {
                $seconds += $tempo['timestamp'];
            }
            break;
    }
}
if ($action === 'start') {
    $seconds += time();
}
header('Content-Type: application/json');
echo json_encode(array(
    'seconds' => $seconds,
    'running' => $action === 'start',
));

<?php
// definir no seu código
$pdo = new PDO($dsn, $username, $passwd);
$user_id = 1; // $_SESSION['user_id'];

$params = array(':user' => $user_id);
$stt1 = $pdo->prepare('SELECT `action` FROM `timer` WHERE `user_id` = :user ORDER BY `id` DESC LIMIT 1');
$stt1->execute($params);
$newAction = 'start';
if ($stt1->rowCount() && $stt1->fetchColumn() === 'start') {
    $newAction = 'pause';
}
$stt2 = $pdo->prepare('INSERT INTO `timer` (`user_id`, `action`, `timestamp`) VALUES (:user, :action, :time)');
$params[':action'] = $newAction;
$params[':time'] = time();
$stt2->execute($params);
header('Content-Type: application/json');
echo json_encode(array(
   'running' => $newAction === 'start',
)); // para atualizar status, no caso de concorrência

<body onload="restore_timer();">
    <form name="form">
        <input type="text" name="cronometro" value="00:00:00" />
        <br />
        <button type="button" onclick="timer(this); return false;">Play</button>
    </form>
</body>

$(document).ready(function() {
    var t = form.cronometro.value;
    var hora = t.substring(0, 2);
    var minuto = t.substring(3, 5);
    var segundo = t.substring(6, 8);

    restore_timer = function() {
        send_ajax("get_time");
    }

    var interval;
    send_ajax = function(opt) {
        $.ajax({
            method: "POST",
            async: "false",
            url: "timer.php",
            data: {"opt": opt}
        }).done(function(msg) {
            if (opt == "get_time") {
                if (msg.status == "started") {
                    $('button').html('Pause');
                    interval = setInterval('tempo()', 983);
                }
                form.cronometro.value = msg.time;
                t = msg.time;
                hora = t.substring(0, 2);
                minuto = t.substring(3, 5);
                segundo = t.substring(6, 8);
            }
        });
    }

    timer = function(obj) {
        var html = $(obj).html();
        if (html == 'Play') {
            interval = setInterval('tempo()', 983);
            send_ajax("start_timer");
            $(obj).html('Pause');
        } else {
            clearInterval(interval);
            send_ajax("save_time");
            $(obj).html('Play');
        }
    }

    tempo = function(){
       if (segundo < 59) {
          segundo++;
          if (segundo < 10)
             segundo = "0" + segundo;
       } else if (segundo == 59 && minuto < 59) {
          segundo = 0 + "0";
          minuto++;
          if (minuto < 10)
             minuto = "0" + minuto;
       }
       if (minuto == 59 && segundo == 59) {
          segundo = 0 + "0";
          minuto = 0 + "0";
          hora++;
          if (hora < 10)
             hora = "0" + hora;
       }
       form.cronometro.value = hora + ":" + minuto + ":" + segundo;
    }
});

if ($_POST) {
    $opt = $_POST['opt'];

    $servername = "localhost";
    $username = "USUARIO";
    $password = "SENHA";
    $dbname = "BANCO_DE_DADOS";

    $conn = new mysqli($servername, $username, $password, $dbname);
    if ($conn->connect_error) {
        die("Connection failed: " . $conn->connect_error);
    }

    if ($opt == "get_time") {
        $sql = "SELECT * FROM time_stamps WHERE id = 1";
        $result = $conn->query($sql);

        $old_time_stamp;
        header('Content-Type: application/json');
        if ($result->num_rows > 0) {
            while($row = $result->fetch_assoc()) {
                $old_time_stamp = $row["time_stamp"];
            }

            $date = new DateTime();
            $time_stamp = $date->getTimestamp();

            echo json_encode(array("status" => "started", "time" => date('H:i:s', ($time_stamp - $old_time_stamp))));
        } else {
            $sql = "SELECT * FROM timer WHERE id = 1";
            $result = $conn->query($sql);

            if ($result->num_rows > 0) {
                while($row = $result->fetch_assoc()) {
                    echo json_encode(array("time" => $row["time"]));
                }
            }
        }
    } elseif ($opt == "start_timer") {
        $date = new DateTime();
        $time_stamp = $date->getTimestamp();
        $sql = "INSERT INTO time_stamps VALUES (1, '{$time_stamp}')";
        $result = $conn->query($sql);
    } elseif ($opt == "save_time") {
        $sql = "SELECT * FROM time_stamps WHERE id = 1";
        $result = $conn->query($sql);

        $old_time_stamp;
        if ($result->num_rows > 0) {
            while($row = $result->fetch_assoc()) {
                $old_time_stamp = $row["time_stamp"];
            }
        }

        $sql = "DELETE FROM time_stamps WHERE id = 1";
        $result = $conn->query($sql);

        $date = new DateTime();
        $time_stamp = $date->getTimestamp();

        $new_time = explode(":", date('H:i:s', ($time_stamp - $old_time_stamp)));

        $sql = "SELECT * FROM timer WHERE id = 1";
        $result = $conn->query($sql);

        $old_time;
        if ($result->num_rows > 0) {
            while($row = $result->fetch_assoc()) {
                $old_time = explode(":", $row["time"]);
            }
        }

        $hour = intval($old_time[0] + $new_time[0]);
        $minute = intval($old_time[1] + $new_time[1]);
        $second = intval($old_time[2] + $new_time[2]);
        while ($second >= 60) {
            $second = $second - 60;
            $minute++;
        }
        while ($minute >= 60) {
            $minute = $minute - 60;
            $hour++;
        }
        if ($second < 10)
            $second = "0" . strval($second);
        if ($minute < 10)
            $minute = "0" . strval($minute);
        if ($hour < 10)
            $hour = "0" . strval($hour);

        $time = "{$hour}:{$minute}:{$second}";

        $sql = "UPDATE timer SET time = '{$time}' WHERE id = 1";
        $result = $conn->query($sql);
    }
    $conn->close();
}

CREATE TABLE timer (
    id INT PRIMARY KEY,
    time VARCHAR(10) NOT NULL
);

CREATE TABLE time_stamps (
    id INT PRIMARY KEY,
    time_stamp VARCHAR(255) NOT NULL
);

INSERT INTO timer values (1, "00:00:00");

<?php

//
// Lib
//

const CHRON_PATH  = 'pathtodata\';

const CHRON_STOP  = 0x00;
const CHRON_PAUSE = 0x01;
const CHRON_PLAY  = 0x03;

class PersistentChronometer {
    // fields

    private $_id;
    private $_elapsed;
    private $_status;
    private $_statustime;

    // construtor privado

    private function __construct() {}

    // propriedades

    function __get($prop) {
        switch($prop) {
        case 'id':
            return $this->_id;
        case 'status':
            return $this->_status;
        case 'elapsed':
            $elapsed = $this->_elapsed;

            if ($this->_status == CHRON_PLAY)
                $elapsed += max(microtime(true) - $this->_statustime, 0);

            return $elapsed;
        }
    }

    // comandos

    public function play() {
        if($this->_status == CHRON_PLAY)
            return;

        $this->_statustime = microtime(true);
        $this->_status = CHRON_PLAY;
    }

    public function pause() {
        if($this->_status != CHRON_PLAY)
            return;

        $time = microtime(true);

        $this->_elapsed += max($time - $this->_statustime, 0);

        $this->_statustime = microtime(true);
        $this->_status = CHRON_PAUSE;
    }

    public function stop() {
        if($this->_status == CHRON_STOP)
            return;

        $this->_statustime = microtime(true);
        $this->_elapsed = 0;
        $this->_status = CHRON_STOP;
    }

    // persistência

    public static function create() {
        $chron = new PersistentChronometer();
        $chron->_statustime = microtime(true);
        $chron->_elapsed = 0;
        $chron->_status = CHRON_STOP;

        $i = 0;
        while (true) {
            $chron->_id = ((int)$chron->_statustime) . '$' . $i++;

            $fname = CHRON_PATH . $chron->_id . '.chron';
            if(file_exists($fname))
                continue;
            $f = fopen($fname, 'w');
            fwrite($f, $chron->serialize());
            fclose($f);
            break;
        }

        return $chron;
    }

    public static function load($id) {
        $fname = CHRON_PATH . $id . '.chron';

        if(!file_exists($fname))
            return false;
        $f = fopen($fname, 'r');
        $chron = PersistentChronometer::unserialize(fread($f, 255));
        fclose($f);

        return $chron;
    }

    public function save() {
        $fname = CHRON_PATH . $this->_id . '.chron';
        $f = fopen($fname, 'w');
        ftruncate($f, 0);
        fwrite($f, $this->serialize());
        fclose($f);
    }

    public function delete() {
        $fname = CHRON_PATH . $this->_id . '.chron';
        unlink($fname);
    }

    public function serialize() {
        return json_encode(array(
            'id' => $this->_id,
            'elapsed' => $this->_elapsed,
            'status' => $this->_status,
            'statustime' => $this->_statustime
        ));
    }

    public static function unserialize($string) {
        $data = json_decode($string);

        $chron = new PersistentChronometer();
        $chron->_id = $data->id;
        $chron->_elapsed = $data->elapsed;
        $chron->_status = $data->status;
        $chron->_statustime = $data->statustime;

        return $chron;
    }
}

//
// Comandos
//

if(isset($_GET['action'])) {
    switch($_GET['action']) {
    case 'play':
        if(isset($_GET['id'])
          && (($chron = PersistentChronometer::load($_GET['id'])) !== false)) {
            $chron->play();
            $chron->save();
        }
        break;
    case 'pause':
        if(isset($_GET['id'])
          && (($chron = PersistentChronometer::load($_GET['id'])) !== false)) {
            $chron->pause();
            $chron->save();
        }
        break;
    case 'stop':
        if(isset($_GET['id'])
          && (($chron = PersistentChronometer::load($_GET['id'])) !== false)) {
            $chron->stop();
            $chron->save();
        }
        break;
    case 'new':
        PersistentChronometer::create();
        break;
    case 'delete':
        if(isset($_GET['id'])
          && (($chron = PersistentChronometer::load($_GET['id'])) !== false)) {
            $chron->delete();
        }
        break;
    case 'get':
        if(isset($_GET['id'])
          && (($chron = PersistentChronometer::load($_GET['id'])) !== false)) {

            $data = new stdClass();
            $data->id = $chron->id;
            $data->elapsed = $chron->elapsed;
            $data->status = $chron->status;
            $data->result = true;

            echo json_encode($data);
        } else {
            echo '{"result": false}';
        }

        return;
    }
}

//
// Output
//

?>
<!DOCTYPE html>
<html>
<head>
    <script type="text/javascript" src="//code.jquery.com/jquery-2.1.3.min.js"></script>
    <script>
        $(function(){
            var cEl = $('#chron');
            if(!window.localStorage)
                cEl.text('Para esta solução é necessário o uso de localStorage. Mas também podem ser utilizados cookies ou variaveis de sessão!!!');
            else {
                var id = localStorage.getItem("chron-id");

                if(!id)
                    cEl.text('Nenhum cronômetro definido!');
                else {
                    loadChronometer(id);
                    cEl.text('Aguarde...');
                }
            }
        });

        function setChronometer(id) {
            localStorage.setItem("chron-id", id);
            loadChronometer(id);
        }

        function loadChronometer(id) {
            var status = {
                <?php echo CHRON_STOP ?>: 'Parado',
                <?php echo CHRON_PLAY ?>: 'Executando',
                <?php echo CHRON_PAUSE ?>: 'Interrompido'
            };
            var cEl = $('#chron');
            $.getJSON('?action=get&id=' + id, null, function(data) {
                if(data.result)
                    cEl.text(
                        'ID: ' + data.id + "n" +
                        'Estado: ' + status[data.status] + "n" +
                        'Tempo (seg): ' + data.elapsed + "n"
                    ).append(
                        '<a href="javascript:setChronometer('' + data.id + '')">Atualizar</a> | ' +
                        (data.status == <?php echo CHRON_STOP ?> ? '' : '<a href="?action=stop&id=' + data.id + '">Parar</a> | ') +
                        (data.status == <?php echo CHRON_PLAY ?> ? '' : '<a href="?action=play&id=' + data.id + '">Executar</a> | ') +
                        (data.status != <?php echo CHRON_PLAY ?> ? '' : '<a href="?action=pause&id=' + data.id + '">Interromper</a> | ') +
                        '<a href="javascript:setChronometer(null)">Remover</a>'
                    );
                else
                    cEl.text('Nenhum cronômetro definido!');
            });
        }
    </script>
</head>
<body>
<h1>Cronômetro padrão</h1>

<pre id="chron" style="white-space: pre"></pre>


<h1>Gerenciador</h1>
<table>
    <thead>
        <td>ID</td>
        <td>Estado</td>
        <td colspan="5">Comandos</td>
        <td>Tempo (seg)</td>
    </thead>
<?php

$files = scandir(CHRON_PATH);
$chrons = array();
foreach($files as $file) {
    if (substr($file, -6) == '.chron')
        $chrons[] = PersistentChronometer::load(substr($file, 0, -6));
}

$status = array(
    CHRON_STOP  => 'Parado',
    CHRON_PLAY  => 'Executando',
    CHRON_PAUSE => 'Interrompido'
);

foreach($chrons as $chron) {
    $td = array();
    $td[] = $chron->id;
    $td[] = $status[$chron->status];

    $td[] = $chron->status == CHRON_STOP ? '' : '<a href="?action=stop&id='. $chron->id .'">Parar</a>';
    $td[] = $chron->status == CHRON_PLAY ? '' : '<a href="?action=play&id='. $chron->id .'">Executar</a>';
    $td[] = $chron->status != CHRON_PLAY ? '' : '<a href="?action=pause&id='. $chron->id .'">Interromper</a>';
    $td[] = '<a href="?action=delete&id='. $chron->id .'">Destruir</a>';
    $td[] = '<a href="javascript:setChronometer(''. $chron->id .'')">Padrão</a>';
    $td[] = $chron->elapsed;
    echo '<tr id="cron-'. $chron->id .'"><td>'. implode('</td><td>', $td) .'</td></tr>';
}

?>
</table>
<a href="?action=new">Novo cronômetro</a>
</body>
</html>