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geneInfo.php
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<!DOCTYPE html>
<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
<head><title>MetGENE: Gene Information</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<?php
$curDirPath = dirname(htmlentities($_SERVER['PHP_SELF']));
$METGENE_BASE_DIR_NAME = $curDirPath;
?>
<?php
echo "<link rel=\"apple-touch-icon\" sizes=\"180x180\" href=\"".$METGENE_BASE_DIR_NAME."/images/apple-touch-icon.png\">";
echo "<link rel=\"apple-touch-icon\" sizes=\"180x180\" href=\"".$METGENE_BASE_DIR_NAME."/images/apple-touch-icon.png\">";
echo "<link rel=\"icon\" type=\"image/png\" sizes=\"32x32\" href=\"".$METGENE_BASE_DIR_NAME."/images/favicon-32x32.png\">";
echo "<link rel=\"icon\" type=\"image/png\" sizes=\"16x16\" href=\"".$METGENE_BASE_DIR_NAME."/images/favicon-16x16.png\">";
echo "<link rel=\"manifest\" href=\"".$METGENE_BASE_DIR_NAME."/site.webmanifest\">";
?>
<?php include($_SERVER['DOCUMENT_ROOT'].$METGENE_BASE_DIR_NAME."/nav.php");?>
<?php
$_SESSION['prev_geneInfo_species'] = isset($_SESSION['prev_geneInfo_species'])?$_SESSION['prev_geneInfo_species']:'';
$_SESSION['prev_geneInfo_geneList'] = isset($_SESSION['prev_geneInfo_geneList'])?$_SESSION['prev_geneInfo_geneList']:'';
$_SESSION['prev_geneInfo_anatomy'] = isset($_SESSION['prev_geneInfo_anatomy'])?$_SESSION['prev_geneInfo_anatomy']:'';
$_SESSION['prev_geneInfo_disease'] = isset($_SESSION['prev_geneInfo_disease'])?$_SESSION['prev_geneInfo_disease']:'';
$_SESSION['prev_geneInfo_pheno'] = isset($_SESSION['prev_geneInfo_pheno'])?$_SESSION['prev_geneInfo_pheno']:'';
if (strcmp($_SESSION['prev_geneInfo_species'],$_SESSION['species']) != 0) {
$_SESSION['prev_geneInfo_species'] = $_SESSION['species'];
// echo "prev geneInfo species updated=".$_SESSION['prev_geneInfo_species'];
$_SESSION['geneInfo_changed'] = 1;
// echo "species geneInfo_changed= ".$_SESSION['geneInfo_changed'];
} else if (strcmp($_SESSION['prev_geneInfo_geneList'], $_SESSION['geneList']) != 0) {
$_SESSION['prev_geneInfo_geneList'] = $_SESSION['geneList'];
// echo "prev geneList updated=".$_SESSION['prev_geneInfo_geneList'];
$_SESSION['geneInfo_changed'] = 1;
// echo "geneList geneInfo_changed= ".$_SESSION['geneInfo_changed'];
} else if (strcmp($_SESSION['prev_geneInfo_disease'], $_SESSION['disease']) != 0) {
$_SESSION['prev_geneInfo_disease'] = $_SESSION['disease'];
// echo "prev geneInfo disease updated=".$_SESSION['prev_geneInfo_disease'];
$_SESSION['geneInfo_changed'] = 1;
// echo "disease geneInfo_changed= ".$_SESSION['geneInfo_changed'];
} else if (strcmp($_SESSION['prev_geneInfo_anatomy'], $_SESSION['anatomy']) != 0) {
$_SESSION['prev_geneInfo_anatomy'] = $_SESSION['anatomy'];
// echo "prev geneInfo anatomy updated=".$_SESSION['prev_geneInfo_anatomy'];
$_SESSION['geneInfo_changed'] = 1;
// echo "anatomy geneInfo_changed= ".$_SESSION['geneInfo_changed'];
} else if (strcmp($_SESSION['prev_geneInfo_pheno'], $_SESSION['phenotype']) != 0) {
$_SESSION['prev_geneInfo_pheno'] = $_SESSION['phenotype'];
// echo "prev geneInfo phenotype updated=".$_SESSION['prev_geneInfo_phenotype'];
$_SESSION['geneInfo_changed'] = 1;
// echo "phenotype geneInfo_changed= ".$_SESSION['geneInfo_changed'];
} else {
$_SESSION['geneInfo_changed'] = 0;
}
?>
</head>
<body>
<div id="constrain">
<div class="constrain">
<br>
<br>
<p>
<?php
// top-cache.php
$url = $_SERVER["SCRIPT_NAME"];
$break = explode('/', $url);
$file = $break[count($break) - 1];
$cachefile = 'cache/cached-'.session_id().'-'.substr_replace($file ,"",-4).'.html';
$_SESSION['geneInfo_cache_file'] = $cachefile;
$cachetime = 18000;
//echo "<h3>Session changed ".$_SESSION['geneInfo_changed']."</h3>";
// Serve from the cache if it is younger than $cachetime
if ( $_SESSION['geneInfo_changed'] == False && isset($_SESSION['geneInfo_cache_file']) && file_exists($_SESSION['geneInfo_cache_file']) && time() - $cachetime < filemtime($_SESSION['geneInfo_cache_file'])) {
echo "<!-- Cached copy, generated ".date('H:i', filemtime($cachefile))." -->\n";
// echo "<h3>loaded cache file</h3>";
readfile($cachefile);
exit;
}
ob_start(); // Start the output buffer
///////
$gene_array = (isset($_SESSION['geneArray']))?$_SESSION['geneArray']:'';
$gene_syms = (isset($_SESSION['geneSymbols']))?$_SESSION['geneSymbols']:'';
//echo "Gene array = ".$gene_array;
if(isset($_SESSION['species']) && isset($_SESSION['geneArray']) && isset($_SESSION['geneInfo_changed']) && $_SESSION['geneInfo_changed'] == 1) {
$gene_vec_arr = array();
$gene_sym_arr = array();
$gene_sym_str_arr = explode(",", $gene_syms);
for ($i=0; $i<count($gene_array); $i++) {
if ($gene_array[$i] != "NA") {
$gene_vec_arr[$i] = $gene_array[$i];
$gene_sym_arr[$i] = $gene_sym_str_arr[$i];
}
}
$gene_vec_str = implode("__", $gene_vec_arr);
// echo "<h3>Gene vec str =".$gene_vec_str."</h3>";
$gene_sym_str = implode(",", $gene_sym_arr);
if (!empty($gene_vec_str)) {
$h3_str = "<h3>Gene Information for <i><b>".$_SESSION['org_name']."</b></i> gene(s) <i><b>".$gene_sym_str."</b></i></h3>";
echo $h3_str;
// $gene_array = $_SESSION['geneArray'];
$output = array();
$htmlbuff = array();
$domainName = $_SERVER['SERVER_NAME'];
exec("/usr/bin/Rscript extractGeneInfoTable.R $species $gene_vec_str $domainName", $output, $retvar);
$htmlbuff = implode($output);
echo "<pre>";
echo $htmlbuff;
$btnStr = "<p><button id=\"json\">TO JSON</button> <button id=\"csv\">TO CSV</button> </p>";
echo $btnStr;
echo "</pre>";
} else {
echo "<h3><i>No gene information found for <b>".$organism_name."</b> gene(s) <b>".$gene_syms."</b></i></h3>";
}
}?>
</p>
</div>
</div>
<script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
<?php echo "<script src=\"".$METGENE_BASE_DIR_NAME."/src/tableHTMLExport.js\"></script>"; ?>
<script>
$('#json').on('click',function(){
$("#Table1").tableHTMLExport({type:'json',filename:'GeneInfo.json', ignoreColumns:"SELECT"});
})
$('#csv').on('click',function(){
$("#Table1").tableHTMLExport({type:'csv',filename:'GeneInfo.csv'});
})
</script>
<?php include($_SERVER['DOCUMENT_ROOT'].$METGENE_BASE_DIR_NAME."/footer.php");?>
<?php
// bottom-cache.php
// Cache the contents to a cache file
//echo "creating cached file ".$cachefile;
$cachefile = $_SESSION['geneInfo_cache_file'];
$cached = fopen($cachefile, 'w');
fwrite($cached, ob_get_contents());
fclose($cached);
ob_end_flush(); // Send the output to the browser
?>
</body>
</html>