debug.txt

function get_next_id(){
    $file_handle = fopen("INCREMENTFILE.num", "r+");
    while (!flock($file_handle, LOCK_EX)){
        //print "Please reset INCREMENTFILE.num, php flock() error";
        //exit(1);
    }
    $id = stream_get_contents($file_handle);
    $next = ($id+1)%10000;
    fseek($file_handle,0);
    ftruncate($file_handle,0);
    fwrite($file_handle, $next);
    flock($file_handle, LOCK_UN);
    fclose($file_handle);
    return $id;
}
    

    
    
echo '<table style="margin:0 auto;"><tr><td>';
    #echo '<div>';

    #get information
    $email = $_POST['email'];
    $ct = $_POST['ct'];
    $cl = $_POST['cl'];
    $min = $_POST['min'];
    $max = $_POST['max'];
    $dComp = $_POST['dcomp'];
    $dRed = $_POST['dred'];
    $dLen = $_POST['dlen'];
    $dFis = $_POST['dfis'];
    $zj = $_POST['zj'];
    $xs = $_POST['xs'];
    $ms = $_POST['ms'];
    #$fft = $_POST['fft'];
    #$ffl = $_POST['ffl'];
    #$rg = $_POST['refgm'];

    if ($dLen == "on"){
        $dLen = " -nolen ";
    }else{
        $dLen = "";
    }
    if ($dRed == "on"){
        $dRed = " -nored ";
    }else{
        $dRed = "";
    }
    if ($dComp == "on"){
        $dComp = " -nocomp ";
    }else{
        $dComp = "";
    }
//         if ($dFis == "on"){
//             $dFis = " -nofis ";
//         }else{
//             $dFis = "";
//         }
    if ($ms == "on"){
        $ms = " -ms ";
    }else{
        $ms = "";
    }
    $target_dir = "uploaded_fasta/";
    $next_id = get_next_id();
    $fname = $_FILES['fastaseq']['name'];
    $target_fname = substr($fname,0,strpos($fname,'.')) . '_' . $next_id;
    $target_file = $target_dir . $target_fname;



    #move file into uploaded folder
    if(!move_uploaded_file($_FILES['fastaseq']['tmp_name'], $target_file)){
        echo '<div class="notout">';
        echo 'Error Uploading Input File <br>';

    }else{

//             if($rg == "custom"){
//                 $rfname = $_FILES['fastaseq']['name'];
//                 $target_reference_file = $target_dir . substr($rfname,0,strpos($rfname,'.')) . '_' . $next_id;
//                 if(!move_uploaded_file($_FILES['refgm_file']['tmp_name'], $target_reference_file)){
//                     echo '<div class="notout">';
//                     echo 'Error Uploading Reference Genome File';
//                     echo '<form action="index.php"><input type="button" value="Back" onClick="history.go(-1);return true;"></form>';
//                     echo "</div></td></tr></table>";
//                     die();
//                 }
//                 $rg = $target_reference_file;
//             }


        echo '<div class="outputs">';

        $headers = 'From: "CoreCop Pipeline" <noreply@kirschner.med.harvard.edu>\r\n';
        $headers .= "MIME-Version: 1.0\r\n";
        $headers .= "Content-Type: text/html; charset=ISO-8859-1\r\n";

        $fullpath = substr(getcwd(),strpos(getcwd(), "/www/") + 5) . "/logs/" . $target_fname . ".log";
        $fullpath = str_replace("/docroot/", "/", $fullpath);
        $sent = @mail($email, "CoreCop REQUEST SENT", "We are processing your file as: " . $target_file . " size: " . filesize($target_file) . ' bytes.<br> ' . $fullpath . '<br>', $headers);
        if($sent){
            echo "<p> Email Validated... </p>";
        }else{
            echo "<p> INVALID EMAIL! TERMINATING JOB! </p>";
            echo '<form action="index.php"><input type="button" value="Back" onClick="history.go(-1);return true;"></form>';
            echo "</div></td></tr></table>";
            die();
        }

        echo "<p> We are processing your file as: " . $target_file . " size: " . filesize($target_file) . " bytes </p>";
        echo 'python run_cra_interface.py ' . $target_file . ' ' . $target_file . '.clean.fa ' . $target_file . '.messy.fa ' . $email . ' -ct ' . $ct . ' -cl ' . $cl . ' -0j ' . $zj . ' -min ' . $min . ' -max ' . $max . $ms . ' -xs ' . $xs . $dComp . $dLen . $dRed .' > superlog 2>&1 &';
        exec('python run_cra_interface.py ' . $target_file . ' ' . $target_file . '.clean.fa ' . $target_file . '.messy.fa ' . $email . ' -ct ' . $ct . ' -cl ' . $cl . ' -0j ' . $zj . ' -min ' . $min . ' -max ' . $max . $ms . ' -xs ' . $xs . $dComp . $dLen . $dRed .' > superlog 2>&1 &');

        if(!$_POST['email']){
            echo '<p> You will receive an email when the results are ready. </p>';
        }
        echo '<p><a href="logs/' . $target_fname . '.log"> Log file for job </a></p>';

    }

    echo '<form action="index.php"><input type="button" value="Back" onClick="history.go(-1);return true;"></form>';

    echo "</div></td></tr></table>";