File Upload - MySQL server has gone away

Question

I have the following file upload script. It is working great and my files are uploading perfectly. I am able to work with it. But this issue is not about file uploading, but the query being processed after the uploading. It throws error MySQL server has gone away . When I upload small files, the script works as expected and insert is working . Only when I upload big files, this issues happens. Even those big files are saved successfully, and the error only happens with MySQL Insert .

<?php
include('utils.php');
$result = array();
log_event("info", "Upload script initiated...");
log_event("info", "POST: ".json_encode($_POST, JSON_PRETTY_PRINT));
if(!isset($_FILES['file']['name'])){
    $result['error'] = "File not present";  echo json_encode($result); exit();
}
if(isset($_POST['auth'])){
    $is_valid = cookie_login($_POST['auth']);
    if($is_valid){
        log_event("info", "Authenticated for uploading.");
        if(isset($_POST['id'])){
            $exist = get_project($_POST['id']);
            if(!$exist){
                $result['error'] = "Project not specified";
            } else{
                log_event("info", "Project loaded. Analysing files for upload.");
                log_event("info", "FILES: ".json_encode($_FILES, JSON_PRETTY_PRINT));
                $file_name = $_FILES['file']['name'][0];
                $file_size = $_FILES['file']['size'][0];
                $file_tmp = $_FILES['file']['tmp_name'][0];
                $file_type = $_FILES['file']['type'][0];
                $file_name = mysql_real_escape_string($file_name);
                $file_ext=$ext = pathinfo($file_name, PATHINFO_EXTENSION);
                //print_r($_FILES['file']);

                $token = md5($file_name. $file_size.$file_tmp.$file_type. time() . rand(0, 99999) . rand(0, 99999));
                log_event("info", "Token Generated: $token");
                $filePath = "files/".$token;
                log_event("info", "Movable file path named after token: $filePath");
                if(!move_uploaded_file($file_tmp, $filePath)){
                    $result['error'] = "File Copying Error";
                    log_event("error", "File copying error");
                } else {
                    $sql = mysql_query("INSERT INTO files (name, path, package_name, token, username) VALUES ('$file_name', '$filePath', '$exist[package_name]', '$token', '$is_valid')");
                    if(!$sql){
                        $result['error'] = "Internal Server Error. Contact Administrator.";
                        log_event("error", mysql_error());
                    }
                }


            }
        } else {
            $result['error'] = "Project not specified";
        }
    } else {
        $result['error'] = "Authenticaton Failure";
    }
} else {
    $result['error'] = "Authenticaton Failure";
}

echo json_encode($result);

To analyse what is wrong, I created a log_event() method which just logs what the events to a file. These are the results.

[Wednesday 1st of June 2016 09:08:42 PM][info][http://www.example.com/bucket/upload.php] cookie_login(db64f68dee27eb08d29117c7da678f81): Success 
[Wednesday 1st of June 2016 09:08:42 PM][info][http://www.example.com/bucket/upload.php] Project loaded. Analysing files for upload. 
[Wednesday 1st of June 2016 09:08:42 PM][info][http://www.example.com/bucket/upload.php] FILES: {
    "file": {
        "name": [
            "Sibidharan_Software_Engineer_Android 3.zip"
        ],
        "type": [
            "application\/zip"
        ],
        "tmp_name": [
            "\/tmp\/phpTJJcQz"
        ],
        "error": [
            0
        ],
        "size": [
            97226470
        ]
    }
} 
[Wednesday 1st of June 2016 09:08:42 PM][info][http://www.example.com/bucket/upload.php] Token Generated: 599293ad3d30fd0d981f967df9d0f61f 
[Wednesday 1st of June 2016 09:08:42 PM][info][http://www.example.com/bucket/upload.php] Movable file path named after token: files/599293ad3d30fd0d981f967df9d0f61f 
[Wednesday 1st of June 2016 09:09:05 PM][error][http://www.example.com/bucket/upload.php] MySQL server has gone away 

If you see the time between the last 2 process, it took almost 23 seconds to process the query. I have no idea why it is happening. **

As I said above

When I upload small files, the script works as expected. Only when I upload big files, this issues happens.

** Moreover, the issue is not with my localhost, but only with the live server.

My PHP_MAX_UPLOAD is set to 128M and uploaded file size is around 98M which you can see in the log.

UPDATE - Here is how I connect to database

$db = NULL;
$logs_enabled = "yes";

function dbConnect(){

    $DB_SERVER = "localhost";
    $DB_USER = "root";
    $DB_PASSWORD = "";
    $DB = "bucket";

    $GLOBALS['db'] = mysql_pconnect($DB_SERVER,$DB_USER,$DB_PASSWORD);

    if (!$GLOBALS['db']){
        log_event("error", "mysql_pconnect(): ".mysql_error());
        return false;
    }
    if($GLOBALS['db']){
        log_event("success", "mysql_pconnect(): Connection obtained");
        $check = mysql_select_db($DB,$GLOBALS['db']);
        if($check){
            log_event("success", "mysql_pconnect(): Database selected");
             mysql_query ("set character_set_client='utf8'"); 
             mysql_query ("set character_set_results='utf8'"); 
             mysql_query ("set collation_connection='utf8_general_ci'");
        } else {
            log_event("error", "mysql_pconnect(): Couldn't select database. Error: ".mysql_error());
        }
        return true;
    }
}

This is done in the utils.php file which is included in the above script.

UPDATE 2 As said by Sasha Pachev I tried putting `dbConnect() before the query and I got the following log.

[Thursday 2nd of June 2016 12:41:57 AM][info][http://www.example.com/bucket/upload.php] Project loaded. Analysing files for upload. 
[Thursday 2nd of June 2016 12:41:57 AM][info][http://www.example.com/bucket/upload.php] FILES: {
    "file": {
        "name": [
            "Sibidharan_Software_Engineer_Android 3.zip"
        ],
        "type": [
            "application\/zip"
        ],
        "tmp_name": [
            "\/tmp\/php3Gtac3"
        ],
        "error": [
            0
        ],
        "size": [
            97226470
        ]
    }
} 
[Thursday 2nd of June 2016 12:41:57 AM][info][http://www.example.com/bucket/upload.php] Token Generated: f2131640ca97468b62e4ab2b2eed25f9 
[Thursday 2nd of June 2016 12:41:57 AM][info][http://www.example.com/bucket/upload.php] Movable file path named after token: files/f2131640ca97468b62e4ab2b2eed25f9 
[Thursday 2nd of June 2016 12:42:20 AM][success][http://www.example.com/bucket/upload.php] mysql_pconnect(): Connection obtained 
[Thursday 2nd of June 2016 12:42:20 AM][error][http://www.example.com/bucket/upload.php] mysql_pconnect(): Couldn't select database. Error: MySQL server has gone away 
[Thursday 2nd of June 2016 12:42:20 AM][error][http://www.example.com/bucket/upload.php] MySQL server has gone away

Result: The error still persists.

Answer 1

I think what is happening is that your file upload takes a long time, and the server times you out due to a low setting of wait_timeout . If you connect immediately after you have finished the upload and immediately before your insert, the "gone away" problem will likely be resolved. So put a call to dbConnect() right before mysql_query() with the insert.