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<!DOCTYPE html>
<html>
<!-- NAVIGATION BAR-->
<?php include "header.html";?>
<?php include "title.html";?>
<div class="panel">
<?php
$debug=""; //put -d here when testing
$aResult = array();
if( !isset($_POST['code']) ) { $aResult['error'] = 'ERROR: No code passed to input_validation.php';}
$code=escapeshellcmd($_POST["code"]);
$uniqlength=escapeshellcmd($_POST["uniqlength"]);
$nickname = "my_assembly";
if( !isset($_POST['min_size']) ) { $aResult['error'] = 'ERROR: No min_size passed to input_validation.php';}
if( !isset($_POST['max_size']) ) { $aResult['error'] = 'ERROR: No max_size passed to input_validation.php';}
$min_size = escapeshellcmd($_POST["min_size"]);
$max_size = escapeshellcmd($_POST["max_size"]);
if( isset($_POST['nickname']) ) {
$nickname = escapeshellcmd($_POST['nickname']);
// Replace all non-alphanumeric characters with underscores
$nickname = preg_replace('/[^a-zA-Z0-9]/', '_', $nickname);
}
// if( !isset($_POST['read_length']) ) { echo shell_exec('echo ERROR: No read_length passed to run.php >> user_data/$code/run.log');}
// $kmer_length = $_POST["kmer_length"];
// $read_length = $_POST["read_length"];
$url="analysis.php?code=$code";
$run_url="run_algorithm.php";
$filename="user_uploads/$code";
$back_button= "<form action=\"./\" method=GET><button type=\"submit\" class=\"center btn btn-danger\">Back</button></form>";
//$continue_button= "<form action=\"$url\"><input type=\"hidden\" name = \"code\" value=\"$code\"><button type=\"submit\" class=\"center btn btn-success\">Continue</button></form>";
$continue_button= "<form
action=\"$run_url\"
method=\"post\">
<input type=\"hidden\" name = \"code\" value=\"$code\">
<input type=\"hidden\" name=\"nickname\" value=\"$nickname\">
<input type=\"hidden\" name=\"uniqlength\" value=\"$uniqlength\">
<input type=\"hidden\" name=\"max_size\" value=\"$max_size\">
<input type=\"hidden\" name=\"min_size\" value=\"$min_size\">
<button type=\"submit\" class=\"center btn btn-success\">Continue</button>
</form>";
// <input type=\"hidden\" name=\"read_length\" value=\"$read_length\">
if (!file_exists ($filename)) {
echo "<div class=\"alert center alert-danger\" role=\"alert\">No file uploaded</div>";
echo "$back_button";
exit;
}
$consistent=true;
// $myfile = fopen($filename, "r") or die("Unable to open file!");
// $line1 = fgets($myfile);
$myfile = gzopen($filename, "r") or die("Unable to open file!");
$line1 = gzgets($myfile);
$line1 = trim(preg_replace( '/\s+/', ' ', $line1 ));
$array=array_map("trim",explode(' ',$line1));
if (count($array)==2) {
// echo "GOOD first line";
} else {
echo "Bad first line. \n";
$consistent=false;
}
$line2 = fgets($myfile);
$line2 = trim(preg_replace( '/\s+/', ' ', $line2 ));
if ($line2 == "NUCMER") {
// echo "GOOD second line";
} else {
echo "Bad second line\n";
$consistent=false;
}
// fclose($myfile);
gzclose($myfile);
if ($consistent) {
// if ($previous_bins > 500) {
echo "<div class=\"alert center alert-success\" role=\"alert\">Great! File was uploaded and looks like a real delta file</div>";
// } else {
// echo "<div class=\"alert center alert-warning\" role=\"alert\">File was uploaded and has acceptable dimensions: $line_counter samples by $previous_bins bins, but the analysis is unlikely to work optimally without more bins. We recommend at least 500 bins for higher accuracy.</div>";
// }
if (!file_exists("user_data/$code")) {
}
else {
echo "<div class=\"alert center alert-info\" role=\"alert\">File already submitted once. Please continue.</div>";
}
echo "<div style=\"margin-left:1%;\"><div class=\"col-sm-1\">";
echo "$back_button";
echo "</div><div class=\"col-sm-1\">";
echo "$continue_button";
echo "</div></div>";
}
else {
echo "<div class=\"alert center alert-danger\" role=\"alert\">This doesn't look like a delta file. Are you sure it is the output from nucmer? The first line should list two file names separated by a space, and the second line should be the word 'NUCMER'. The remaining lines in the file specify alignments.";
echo "</div>";
echo "$back_button";
}
?>
</div>
</body>
</html>
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