From b9f41defc97a319c2a0316804ff0b24f187e3608 Mon Sep 17 00:00:00 2001
From: Chloe Quignot <>
Date: Thu, 28 Mar 2024 09:38:31 +0100
Subject: [PATCH 1/3] fixes and changes applied to BIOI2 web server in
 production

---
 common.php          |  3 +-
 createdb.php        | 16 +++++++----
 createdb_status.php | 35 ++++++++++++-----------
 css/common.css      |  5 ++--
 direct_access.php   |  2 +-
 download.php        |  4 +--
 explore_db.php      | 55 +++++++++++++++++++++++++++++++------
 get_data.php        | 20 +++++++++-----
 help_pages.php      |  1 +
 index.php           |  2 +-
 js/aligner.js       |  2 --
 js/break_viewer.js  |  4 ---
 js/common.js        |  3 --
 js/createdb.js      | 39 +++++++++++---------------
 js/direct_access.js |  1 -
 js/index.js         | 67 +++++++++++++++++++++++++++------------------
 js/list.js          |  8 ------
 js/ranking_sort.js  |  3 --
 js/search.js        |  3 --
 js/search_status.js | 10 +++----
 js/seq_viewer.js    | 12 --------
 js/summary.js       |  4 ---
 lib_db.php          | 49 +++++++++++++++++++++++----------
 search.php          | 27 ++----------------
 send_qsub.php       |  2 +-
 25 files changed, 196 insertions(+), 181 deletions(-)

diff --git a/common.php b/common.php
index 0b6be26..34e1ac7 100755
--- a/common.php
+++ b/common.php
@@ -67,6 +67,7 @@ function print_header($type=null, $name=null) {
 
 function print_nav($type=null, $name=null) {
 	$dir = '.';
+	$sep = "&nbsp;> ";
 	echo "<div id='entete_links'>";
 	if ($type == 'viewer' || $type == 'aligner') {
 		# If the database is given
@@ -96,13 +97,13 @@ function print_sidebar() {
 	echo "<span class='mynav-logo-banner'>";
 	echo "<a href='$dir' style='padding: 1px; text-align: center;'><img src='" . "css/logo_bioi2_no_title_s.png" . "' alt='logo_bioi2' id='bioi2_menu_logo'/></a>";
 	// echo "<br>";
+	echo "<a href='index.php'>Home page</a>";
 	echo "<a href='explore_db.php'>Explore databases</a>";
 	echo "<a href='createdb.php'>Create database</a>";
 	echo "<a href='search.php'>Search databases</a>";
 	echo "<a href='direct_access.php'>Genomic islands</a>";
 	echo "<a href='help_pages.php'>Help page</a>";
 	echo "<a href='contact.php'>Contact us</a>";
-	echo "<a href='index.php'>Back to home page</a>";
 	echo "</span>";
 	echo "</div>";
 }
diff --git a/createdb.php b/createdb.php
index bea77dc..a3cce86 100755
--- a/createdb.php
+++ b/createdb.php
@@ -30,9 +30,10 @@
 <div id="content">
 <div class="centered_box">
 <h2><?php site_name(); ?> database creator</h2>
-<p>This page helps to create a <?php site_name(); ?> database (in sqlite3 format) based on genomes uploaded by the user.</p>
-<p> The final database can be downloaded for local analyzis, or it can be explored on the <?php site_name(); ?> site.</p>
-<p>Alternatively you can <a href="upload_db.php">upload a Synteruptor database</a> directly if you have generated a database yourself.</p>
+<p>Use this page to create a <?php site_name(); ?> database (in sqlite3 format) based on uploaded genomes.</p>
+<p> The final database can be downloaded for local analyzis, or it can be explored on the <?php site_name(); ?> web site.</p>
+<p>Alternatively you can <a href="upload_db.php">upload a <?php site_name(); ?> database</a> directly if you have already generated a database yourself.</p>
+
 <?php
 
 if (isset($_GET["id"])) {
@@ -57,7 +58,9 @@
 		echo "</div>";
 		echo "<div class='button_container'><a href='createdb_start.php'><div class='button_link'>Start a new project</div></a></div>";
 		exit;
-	}
+	}else{
+		if(!in_array($id,$_SESSION["db_ids"])){$_SESSION["db_ids"][]=$id;};
+	};
 
 	# List the genome files in the dir
 	$gbks = scan_gbks();
@@ -66,6 +69,7 @@
 	echo "<ol>";
 	print_gbks($gbks);
 	$config = get_config();
+
 	if ($ngbks < $max_gbks && (!isset($config) || $config['status'] == 'preparation')) {
 		$diff = $max_gbks - $ngbks;
 		echo '<form id="uploader" action="createdb_add.php?id=' . $id . '" method="post" enctype="multipart/form-data">';
@@ -86,7 +90,7 @@
 	echo '<div class="infobox">';
 	echo '<h3>Information about the data provided and generated</h3>';
 	echo "<ul>";
-	echo "<li>The job will send you an e-mail (mandatory) when the database creation starts and when it ends. You can also check the progress by bookmarking this page: <a href='$builder?id=$id'>$site_name job: $id</a>.</li>";
+	echo "<li>The job will send you an e-mail (if provided) when the database creation starts and when it ends. You can also check the progress on this page: <a href='$builder?id=$id'>$site_name job: $id</a> (if you didn't provide your email address, we strongly recommend that bookmark this page).</li>";
 	echo "<li>The mail provided will only be used to send the progress information.</li>";
 	echo "<li>The files uploaded will be conserved until the database has been built, and they will then be deleted from our servers.</li>";
 	echo "<li>The created database is not made public and can only be accessed with the random id created for it ($id).</li>";
@@ -97,6 +101,8 @@
 } else {
 	echo "<div class='button_container'><a href='createdb_start.php'><div class='button_link'>Start a new project</div></a></div>";
 }
+
+
 ?>
 </div>
 </div>
diff --git a/createdb_status.php b/createdb_status.php
index fd11daa..ec91d9b 100755
--- a/createdb_status.php
+++ b/createdb_status.php
@@ -37,41 +37,41 @@ function check_blocks_tol($btol) {
 
 function start_job() {
 	$config = get_config();
-
+	
 	# Change from "preparation" to "waiting"
 	if (isset($config) && isset($config['status']) && $config["status"] == 'preparation') {
 		$config["status"] = "waiting";
 		# Get a mail address too?
 		if (isset($_GET["mail"])) {
 			$mail = check_mail($_GET["mail"]);
-			if ($mail == '') {
-				return array(
-					'status' => "mail_error",
-				);
-			} else {
+			if ($mail != '') {
 				$config["mail"] = $mail;
+			// } else { // [CQ] 2024-03-22 -> remove this check to avoid error if mail not set
+			// 	return array(
+			// 		'status' => "mail_error",
+			// 	);
 			}
 		}
 		# Get an author?
 		if (isset($_GET["author"])) {
 			$author = check_text($_GET["author"]);
-			if ($author == '') {
-				return array(
-					'status' => "author_error",
-				);
-			} else {
+			if ($author != '') {
 				$config["author"] = $author;
+			// } else {
+			// 	return array(
+			// 		'status' => "author_error",
+			// 	);
 			}
 		}
 		# Get a description?
 		if (isset($_GET["description"])) {
 			$description = check_text($_GET["description"]);
-			if ($description == '') {
-				return array(
-					'status' => "description_error",
-				);
-			} else {
+			if ($description != '') {
 				$config["description"] = $description;
+			// } else {
+			// 	return array(
+			// 		'status' => "description_error",
+			// 	);
 			}
 		}
 		# Get a blocks tolerance value?
@@ -84,7 +84,7 @@ function start_job() {
 	} else {
 		return array(
 			'status' => "error",
-			'details' => "Status already exists (" . $status['status'] . ")",
+			'details' => "Status already exists (" . $config['status'] . ")",
 		);
 	}
 }
@@ -99,7 +99,6 @@ function start_job() {
 	);
 } else if (isset($_GET["command"])) {
 	$command = $_GET["command"];
-
 	# Check for the status of the current working dir
 	if ($command == "check") {
 		$output = get_config();
diff --git a/css/common.css b/css/common.css
index cb2d490..b19b62f 100755
--- a/css/common.css
+++ b/css/common.css
@@ -165,12 +165,13 @@ a.table-row {
 }
 
 @media screen and (max-width: 800px) {
-	#databases {
+	#databases,#userdatabases {
 		width: 100%;
 		overflow-x: auto;
 	}
 }
 
+
 /*
 #databases table {
 	border-spacing: 3px;
@@ -182,7 +183,7 @@ a.table-row {
 }
 */
 
-#databases td {
+#databases,#userdatabases td {
 	padding: 6px;
 }
 
diff --git a/direct_access.php b/direct_access.php
index 135ff4f..3bc8fa7 100755
--- a/direct_access.php
+++ b/direct_access.php
@@ -35,7 +35,7 @@
 		
 		<div class='index_box'>
 			<?php
-				$allowed = get_available_dbs_list(true, $_SESSION['db_ids']);
+				$allowed = get_available_dbs_list("all", $_SESSION['db_ids']);
 				if ($allowed) {
 					echo "<p>Select a public database:";
 					echo "<div id='databases'></div>";
diff --git a/download.php b/download.php
index 5871f05..133bb61 100755
--- a/download.php
+++ b/download.php
@@ -25,8 +25,8 @@
 			<div class='box'>
 				Downloads:<br />
 				<ul>
-				<li><a href='dl/synteruptor.tar.gz'><?php echo $site_name ?> scripts</a></li>
-				<li><a href='dl/synteruptor_web.tar.gz'><?php echo $site_name ?> website</a></li>
+				<li><a href='https://github.com/i2bc/synteruptor'><?php echo $site_name ?> scripts</a></li>
+				<li><a href='https://github.com/i2bc/synteruptor_web'><?php echo $site_name ?> website</a></li>
 				</ul>
 			</div>
 			<a href="index.php">&lt; Back to Main Page</a>
diff --git a/explore_db.php b/explore_db.php
index f2c82a3..db72be3 100755
--- a/explore_db.php
+++ b/explore_db.php
@@ -9,7 +9,7 @@
         ?>
 	<head>
 		<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-		<title><?php site_name(); ?> help pages</title>
+		<title><?php site_name(); ?> database exploration</title>
 		<link rel="icon" type="image/png" href="css/Synteruptor_logo_square.png">
 		<link rel="stylesheet" type="text/css" href="css/common.css">
 		<script type="text/javascript" src="js/jquery/jquery-1.12.min.js"></script>
@@ -17,6 +17,7 @@
 		<script type="text/javascript" src="js/index.js"></script>
 
 	</head>
+	
 	<nav>
 		<?php
 			print_sidebar();
@@ -26,15 +27,16 @@
 		<?php
 			print_header();
 		?>
+
 		<div id="content">
 			<div class="centered_box">
 				<h2>Available databases</h2>
                 <div class='index_box'>
                 <?php
                     // Display public databases (if any)
-                    $allowed = get_available_dbs_list();
+                    $allowed = get_available_dbs_list("dbs");
                     if ($allowed) {
-                        echo "<p>The following databases were generated with preselected genomes and can be freely explored:</p>";
+                        echo "<p>The following databases were generated with preselected genomes and can be freely explored (they might take a few seconds to load):</p>";
                         echo "<div id='databases'></div>";
                     } else {
                         echo "<p>No public database available</p>";
@@ -47,25 +49,60 @@
 				<h2>User databases</h2>
                 <div class='index_box'>
                 <?php
-					$available_dbs = get_available_dbs_list(true, $_SESSION['db_ids']);
+
+					// Check what user DBs are still available and list only those
+					$available_dbs = get_available_dbs_list("user", $_SESSION['db_ids']);
 					foreach ($_SESSION['db_ids'] as $key => $value){
 						if(!in_array($value.".sqlite",$available_dbs)){
+							console_log("removing".$value);
 							unset($_SESSION['db_ids'][$key]);
 						}
 					}
-					if (empty($_SESSION['db_ids'])){
-						echo "<p>No user databases found in web browser history</p>";
+					if (empty($available_dbs)){
+						echo "<p>No user databases found in web browser cache (/!\ note that jobs older than 30 days are automatically wiped)...</p>";
 					}else{
-						echo "<p>The following databases were generated:</p>";
-						foreach ($_SESSION['db_ids'] as &$value){
+						echo "<p>The following databases were found in your web cache:</p>";
+                        echo "<div id='userdatabases'></div>";
+						echo "<p>/!\ note that jobs older than 30 days are automatically wiped.</p>";
+
+						// foreach ($_SESSION['db_ids'] as &$value){
+						// 	$site_host = get_setting('site_host');
+						// 	$site_host_subdir = get_setting('site_host_subdir');
+						// 	echo "<p><a href='$site_host/$site_host_subdir/summary.php?version=$value'>$value</a></p>";
+						// }
+					}
+                ?>
+                </div>
+			</div>
+			<div class="centered_box">
+				<h2>User searches</h2>
+                <div class='index_box'>
+                <?php
+
+					// // Check what user DBs are still available and list only those
+					// $available_dbs = get_available_dbs_list("user", $_SESSION['db_ids']);
+					// foreach ($_SESSION['blast_ids'] as $key => $value){
+					// 	if(!in_array($value.".sqlite",$available_dbs)){
+					// 		console_log("removing".$value);
+					// 		unset($_SESSION['db_ids'][$key]);
+					// 	}
+					// }
+					if (empty($_SESSION['blast_ids'])){
+						echo "<p>No user searches found in web browser cache (/!\ note that jobs older than 30 days are automatically wiped)...</p>";
+					}else{
+						echo "<p>The following user searches were found in your web cache:</p>";
+						
+						foreach ($_SESSION['blast_ids'] as &$value){
 							$site_host = get_setting('site_host');
 							$site_host_subdir = get_setting('site_host_subdir');
-							echo "<p><a href='$site_host/$site_host_subdir/summary.php?version=$value'>$value</a></p>";
+							echo "<p><a href='$site_host/$site_host_subdir/search.php?id=$value'>$value</a></p>";
 						}
+						echo "<p>/!\ note that jobs older than 30 days are automatically wiped.</p>";
 					}
                 ?>
                 </div>
 			</div>
+
 		</div>
 	</body>
 </html>
diff --git a/get_data.php b/get_data.php
index 0695880..40bcde0 100755
--- a/get_data.php
+++ b/get_data.php
@@ -151,8 +151,8 @@ function get_genes_list($dbh) {
 	}
 }
 
-function get_databases($all = false, $authorised = array()) {
-	$data = get_databases_data($all, $authorised);
+function get_databases($show = 'dbs', $userauthorised = array()) {
+	$data = get_databases_data($show, $userauthorised);
 	return $data;
 }
 
@@ -174,14 +174,20 @@ function get_databases($all = false, $authorised = array()) {
 // MAIN
 // Special: list of all databases 
 if (isset($_GET['type']) && $_GET['type'] == 'databases') {
-	$all = false;
-	$authorised = array();
+	$show = 'dbs';
+	$userauthorised = array();
 	if (isset($_GET['userdb']) && $_GET['userdb']=='true'){
-		$all = true;
-		$authorised = $_SESSION['db_ids'];
+		$userauthorised = $_SESSION['db_ids'];
+		$show = 'all';
 	}
-	$data = get_databases($all, $authorised);
+	$data = get_databases($show, $userauthorised);
 	print json_encode($data);
+} elseif (isset($_GET['type']) && $_GET['type'] == 'userdatabases'){
+	$show = "user";
+	$userauthorised = $_SESSION['db_ids'];
+	$data = get_databases($show, $userauthorised);
+	print json_encode($data);
+	
 } else {
 	$dbh = get_db();
 
diff --git a/help_pages.php b/help_pages.php
index db210d7..b96aa35 100755
--- a/help_pages.php
+++ b/help_pages.php
@@ -31,6 +31,7 @@
 					<div class='index_box'>
 						<!--<img src='css/Synteruptor_logo_full.png' id='logo' alt='logo' />-->
 						<p><?php echo $site_name ?> is a tool designed to find synteny breaks between closely related bacterial genomes. The breaks found can be explored with this web interface to find clusters of genes of interest.</p>
+						<p>DOI on BioRxiv: <a href="https://www.biorxiv.org/content/10.1101/2024.01.03.573040v1">10.1101/2024.01.03.573040v1</a></p>
 						<br /><span id="last_update">Last update: <?php echo get_setting("last_update"); ?></span>
 						<br /><span id="contact">Contact: <?php echo get_mail(); ?></span>
 						<span style="float:right;"><a href="download.php">Download <?php echo $site_name ?></a></span>
diff --git a/index.php b/index.php
index 7511397..9e300cf 100755
--- a/index.php
+++ b/index.php
@@ -62,7 +62,7 @@
 			<?php
 				// Display public databases (if any)
 				echo "<h3 id='availdb'>Available databases</h3>";
-				$allowed = get_available_dbs_list();
+				$allowed = get_available_dbs_list("dbs");
 				if ($allowed) {
 					echo "<p>The following databases were generated with preselected genomes and can be freely explored:</p>";
 					echo "<div id='databases'></div>";
diff --git a/js/aligner.js b/js/aligner.js
index 85e349f..4fa5b16 100755
--- a/js/aligner.js
+++ b/js/aligner.js
@@ -73,7 +73,6 @@ function get_max(genes) {
 }
 
 function draw_alignment(data) {
-	console.log(data);
 	// Number of sequences in the alignment
 	var num = Object.keys(data.genomes).length;
 	
@@ -479,7 +478,6 @@ $(function() {
 			loading_off();
 		}).fail(function() {
 			$( "#message" ).html("<span>Error: data retrieval failed.</span>");
-			console.log(urls.get_data + '?' + $.param(pars));
 			loading_off();
 		});
 	}
diff --git a/js/break_viewer.js b/js/break_viewer.js
index caf86ce..6c8c9e8 100755
--- a/js/break_viewer.js
+++ b/js/break_viewer.js
@@ -1082,7 +1082,6 @@ function break_info(info, num) {
 	if (info.nCDS > 0) {
 		// Add GC content stats
 		var $gc_line = $("<li />");
-		console.log(info);
 		var gc = 'GC content diff: ' + (info.delta_GC > 0 ? "+" : '') + (info.delta_GC * 100).toFixed(1) + "%";
 		$gc_line.append(gc);
 		$ul.append( $gc_line );
@@ -1122,7 +1121,6 @@ $(function() {
 			// Create the page with the data
 			} else {
 				cached_data = data;
-				console.log(data);
 				$("#data_content").show();
 				text_stats(data);
 				display_all(data);
@@ -1134,7 +1132,6 @@ $(function() {
 			loading_off();
 		}).fail(function() {
 			$( "#message" ).text("Error: data retrieval failed");
-			console.log(urls.get_data + '?' + $.param(pars));
 			loading_off();
 		});
 	}
@@ -1179,7 +1176,6 @@ function change_break( breakid, new_window ) {
 	var url_pars = get_url_parameters();
 	url_pars.breakid = breakid;
 	var new_url = format_url(urls.current, url_pars);
-	console.log("Changing to break " + breakid + " : " + new_url);
 	if (new_window ) {
 		window.open( new_url );
 	} else {
diff --git a/js/common.js b/js/common.js
index a84bb36..6ece3e6 100755
--- a/js/common.js
+++ b/js/common.js
@@ -36,7 +36,6 @@ function set_par( key, val ) {
 		}
 	} else {
 		console.log( "Error: parameter key " + key + " with value " + val + " is not defined" );
-		console.log( get_pars() );
 		return null;
 	}
 }
@@ -46,7 +45,6 @@ function get_par( key ) {
 		return cur_pars[ key ];
 	} else {
 		console.log( "Error: parameter key " + key + " is not defined" );
-		console.log( get_pars() );
 		return null;
 	}
 }
@@ -138,7 +136,6 @@ function set_backtop() {
 		$(window).on('scroll', toggle_backtop);
 		$("#backtop").on('click', function(e) {
 			e.preventDefault();
-			console.log("Back to top?");
 			$('html,body').animate({ scrollTop: 0 }, 'fast');
 		});
 	}
diff --git a/js/createdb.js b/js/createdb.js
index 485d8f8..b96e49f 100755
--- a/js/createdb.js
+++ b/js/createdb.js
@@ -6,12 +6,8 @@ function status_checker(id) {
 		"id": id,
 		"command": "check",
 	};
-	console.log(pars);
 	// Check the status a first time to see if the building is already started/finished
-	console.log(format_url( urls.stat, pars ));
 	$.getJSON( urls.stat, pars, function( config ) {
-		console.log(config);
-		console.log(config.status);
 		if (config.status == 'preparation') {
 			start_button(id);
 		} else {
@@ -22,50 +18,48 @@ function status_checker(id) {
 
 function start_button(id) {
 
-	console.log("Start button created");
 	$form = $("<form id='mailform' style='text-align:left;' />");
 	$btol = $("<span><label for='btol'>Blocks tolerance: </label><input type='num' name='btol' class='btol' value=2 min=0 max=5 style='width:3em' /> genes gap allowed between pairs of orthologs in blocks (strict: 0)</span>");
 	$form
 		.append("<span>Finalization:</span><br>")
 		.append($btol)
 		.append("<br>")
-		.append( $("<label for='mail'>Mail: </label><input type='text' class='mail' name='mail' class='mail' placeholder='E-mail address required to get results' style='width:30em' />") )
+		.append( $("<label for='mail'>Mail: </label><input type='text' class='mail' name='mail' class='mail' placeholder='E-mail address to get results (optional)' style='width:30em' />") )
 		.append( $("<br /><label for='author'>Author: </label><input type='text' class='author' name='author' class='author' placeholder='Author name(s) (optional)' style='width:30em' />") )
 		.append( $("<br /><label for='description'>Description: </label><input type='text' class='description' name='description' class='description' placeholder='Description (optional)' style='width:30em' />") );
 	$form.append("<br>");
 	$button = $("<button type='submit' />")
 		.text("Start building the database with these genomes");
 	$form.append($button);
-	
-	/*
-	$form.on("submit", function(e) {
-		console.log("Submit");
-		e.preventDefault();
-		$(this).attr("disabled", "disabled");
-		validator.form();
-		start(id);
-	});
-	*/
+
 	$("#building").append($form);
+
 	validator = $( "#mailform" ).validate({
 		rules: {
 			mail: {
-				required: true,
+				required: false,
 				email: true
+			},
+			description: {
+				required: false
+			},
+			author: {
+				required: false
+			},
+			btol: {
+				required: true
 			}
 		},
 		submitHandler: function(form) {
 			$(this).attr("disabled", "disabled");
 			start(id);
 		}
-		       
 	});
 }
 
 function run_qsub(id) {
 	// run send_qsub.php to submit job to cluster
 	var qsub_url = format_url( urls.qsub, { 'id': id, 'run_script': "run_migenis.sh" } );
-	console.log(qsub_url);
 	$.ajax({
 		url : qsub_url
 	 }).done(function(data){
@@ -84,8 +78,8 @@ function start(id) {
 	pars.btol = $(".btol").val();
 	$("#addmore").closest("li").remove();
 	$("#uploader").remove();
-	run_qsub(id); // inspired by adeneo's comment, https://stackoverflow.com/questions/16941138/jquery-button-onclick-run-system-command
 	$.get( urls.stat, pars, function( stat ) {
+		run_qsub(id); // inspired by adeneo's comment, https://stackoverflow.com/questions/16941138/jquery-button-onclick-run-system-command
 		continuous_check(id);
 	});
 }
@@ -93,7 +87,6 @@ function start(id) {
 function continuous_check(id) {
 	$("#addmore").closest("li").remove();
 	$("#uploader").remove();
-	console.log("Continuous check for " + id);
 	var pars = {
 		"id": id,
 		"command": "check",
@@ -126,8 +119,8 @@ function finish(id) {
 	// $list.append( $( "<li />" ).append(summary) );
 	$("#building").empty()
 		.append( $("<p />").text("The database is ready:") )
-		.append( summary );
-	console.log("Check over");
+		.append( summary )
+		.append( $("<p />").text("/!\\ note that user databases older than 30 days are automatically wiped!"));
 }
 
 jQuery(function() {
diff --git a/js/direct_access.js b/js/direct_access.js
index 2ec3c8d..6657b26 100755
--- a/js/direct_access.js
+++ b/js/direct_access.js
@@ -3,7 +3,6 @@ init_pars( {
 });
 
 function create_menus(data) {
-                console.log(data);
                 var db = get_par( "db" );
                 // Init menu
                 var i = 0;
diff --git a/js/index.js b/js/index.js
index 81a1694..cf870ab 100755
--- a/js/index.js
+++ b/js/index.js
@@ -1,30 +1,46 @@
-//import { check_data_error } from "./utils.js";
-
-function print_db() {
+function print_db(type='databases',userdb=false,id="databases") {
 	pars = {};
-	pars.type = 'databases';
-	var str = "in print_db";
-	console.log(str);
-	console.log(format_url(urls.get_data, pars));
+	pars.type = type;
+	pars.userdb = userdb;
+	loading_on();
 	$.getJSON( urls.get_data, pars, function(data) {
-            error_msg = check_data_error(data);
-            if (error_msg) {
-                $( "#databases" ).append( error_msg );
-            } else {
-		print_db_table(data);
-            }
+		error_msg = check_data_error(data);
+		if (error_msg) {
+			$( "#" + id ).append( error_msg );
+		} else {
+			// Convert the object of objects to an array of objects and add 
+			// the key as an extra parameter of each object so as not to lose it
+			const arrayOfObjects = Object.keys(data).map(key => {
+				return { key, ...data[key] };
+			});
+			// Sort the array based on the date values in descending order
+			arrayOfObjects.sort(function(a, b) {
+				if (a.date < b.date) {return 1;}
+				if (b.date < a.date) {return -1;}
+				return 0;
+			});
+			// Convert the sorted array back to an object of objects	
+			data = arrayOfObjects.reduce((obj, item) => {
+				obj[item.key] = { description: item.description, author: item.author, date: item.date, num: item.num };
+				return obj;
+			}, {});
+			console.log(data);
+			print_db_table(data,id=id);
+		}
+		loading_off();
 	}).fail(function(){
 		console.log("Failed databases retrieval");
+		loading_off();
 	});
 }
 
 function check_data_error( data ) {
-    error_msg = ""
-    if ("outcome" in data && data["outcome"] == false) {
-        console.log("Error occurred: " + data["details"]);
-        error_msg = $("<p />").text("An error occurred: " + data["message"] + ". Check the console for more details.");
-    }
-    return error_msg;
+	error_msg = ""
+	if ("outcome" in data && data["outcome"] == false) {
+		console.log("Error occurred: " + data["details"]);
+		error_msg = $("<p />").text("An error occurred: " + data["message"] + ". Check the console for more details.");
+	}
+	return error_msg;
 }
 
 function get_dbs() {
@@ -32,21 +48,17 @@ function get_dbs() {
 	
 }
 
-function print_db_table( dbs ) {
-	var str = "in print_db_table";
-	console.log(str);
-	console.log(dbs);
+function print_db_table( dbs, id="databases" ) {
 	var table = $( "<table />" );
 	table.append( write_db_head() );
 	
 	for ( var db in dbs ) {
-		console.log( db );
 		var data = dbs[ db ];
 		data.db = db;
 		var row = write_db_line( db, data );
 		table.append( row );
 	}
-	$( "#databases" ).append( table );
+	$( "#" + id ).append( table );
 }
 
 var dbs_headers = {
@@ -88,7 +100,10 @@ function write_db_line( db, data ) {
 // First actions!
 $(function() {
 	if ($("#databases")) {
-		print_db();
+		print_db(type='databases',userdb=false,id="databases");
+	}
+	if ($("#userdatabases")) {
+		print_db(type='userdatabases',userdb=false,id="userdatabases");
 	}
 });
 
diff --git a/js/list.js b/js/list.js
index b806453..a4749af 100755
--- a/js/list.js
+++ b/js/list.js
@@ -12,7 +12,6 @@ function update_table(data) {
 	if (data['outcome'] && data['outcome'] == false) {
 		$('#message').text('List query error.');
 	} else {
-		console.log(data);
 		var $table = $('#list');
 		
 		if (!data || !data.genes || data.genes.length == 0) {
@@ -139,13 +138,11 @@ function update_table(data) {
 }
 
 function update() {
-	console.log("UPDATE");
 	$('#list').empty();
 	var pars = get_pars();
 	
 	// Cached?
 	if (cached_data[ pars.sp ]) {
-		console.log("Retrieve cached data.");
 		update_page( cached_data[ pars.sp ] );
 	} else {
 		var rankpars = {
@@ -155,9 +152,7 @@ function update() {
 			"version": get_par( "version" ),
 			"type": "genes_list",
 		};
-		console.log(rankpars);
 		// Retrieve all data between the genomes
-		console.log("Download data.");
 		loading_on();
 		$.getJSON( urls.get_data, rankpars, function(data) {
 			var predata = preprocess_data(data);
@@ -201,7 +196,6 @@ function preprocess_data(data) {
 
 function create_menus(data) {
 	genomes = data.genomes;
-	console.log(genomes);
 	var sp = get_par( "sp" );
 	
 	// Init menu
@@ -287,7 +281,6 @@ function jump_to() {
 	// Move the focus in the center of the page, not at the top or wheresnot
 	var pid = get_par( "pid" );
 	if (pid && !jumped) {
-		console.log("Scroll!" + pid);
 		var o = $("#" + pid).focus().offset().top;
 		var $w = $(window);
 		var diff = ($w.height() / 2);
@@ -302,7 +295,6 @@ $(function() {
 	// Init the parameters
 	pars = get_url_parameters();
 	set_pars( pars );
-	console.log( get_pars() );
 	
 	// Get all the genomes names for the menu
 	pars.type = 'genomes';
diff --git a/js/ranking_sort.js b/js/ranking_sort.js
index 2eaab14..be3ebd5 100755
--- a/js/ranking_sort.js
+++ b/js/ranking_sort.js
@@ -126,7 +126,6 @@ function get_custom_sort_vals() {
 	var sort;
 	if ( storage.isSet( store_name )) {
 		sort = storage.get( store_name );
-		console.log("Custom stored");
 	}
 	if (sort == null || Object.keys(sort).length == 0) {
 		console.log("Error, back to default");
@@ -146,7 +145,6 @@ function set_custom_sort_vals() {
 	});
 	
 	if (Object.keys(sort).length > 0) {
-		console.log("Custom saved in " + store_name);
 		sort_vals = sort;
 		storage.set( store_name, sort );
 	}
@@ -155,7 +153,6 @@ function set_custom_sort_vals() {
 function set_default_sort_vals() {
 	sort_vals = default_sort_vals;
 	storage.set( store_name, sort_vals );
-	console.log("Back to default sort");
 	build_sort_table();
 }
 
diff --git a/js/search.js b/js/search.js
index 4070c53..3f5aea1 100755
--- a/js/search.js
+++ b/js/search.js
@@ -63,9 +63,7 @@ $(function() {
 				'db': database,
 				'seq': $("#seq").val()
 			};
-			console.log(data);
 			var start_url = format_url( urls.start_search, { 'version': database } );
-			console.log(start_url);
 			$.post( start_url, data, function(ans) {
 				if (ans.status == 'success' && ans.id) {
 					var pars = {
@@ -73,7 +71,6 @@ $(function() {
 						'version': database
 					};
 					var new_url = format_url( urls.search, pars );
-					console.log( new_url );
 					window.location = new_url;
 				} else {
 					console.log( Sent );
diff --git a/js/search_status.js b/js/search_status.js
index 4f0ea34..4435a43 100755
--- a/js/search_status.js
+++ b/js/search_status.js
@@ -10,7 +10,6 @@ function status_checker(id) {
 		
 		// Check the status a first time to see if the building is already started/finished
 		$.getJSON( urls.stat, pars, function( stat ) {
-			console.log("Current status: " + stat.status);
 			if (stat.status == 'nostatus') {
 				// Do nothing: waiting for the form to be submitted
 			} else {
@@ -21,7 +20,6 @@ function status_checker(id) {
 }
 
 function start_button(id) {
-	console.log("Start button created");
 	$button = $("<button type='button' />")
 		.text("Search")
 		.on("click", function(e) {
@@ -43,7 +41,6 @@ function start(id) {
 }
 
 function continuous_check(id) {
-	console.log("Continuous check for " + id);
 	var pars = {
 		"id": id,
 		"command": "check",
@@ -88,7 +85,6 @@ function finish(id) {
 	};
 	// Ask the API to give the result in JSON
 	$.getJSON( urls.stat, pars, function( data ) {
-		console.log(data);
 		if (Object.keys(data.hits).length > 0) {
 			$("#results").empty();
 			
@@ -111,7 +107,6 @@ function finish(id) {
 				
 				for ( g in data.hits[q] ) {
 					var hit = data.hits[q][g];
-					console.log(hit);
 					
 					var breaks = [];
 					var brlist = hit.breaks;
@@ -132,6 +127,10 @@ function finish(id) {
 					$table.append($l);
 				}
 			}
+			$("#results_table")
+			.append( $("<p />")
+			.text("/!\\ note that user searches older than 30 days are automatically wiped!") );
+
 		} else {
 			$("#results").empty()
 				.append("No match found for the query '" + data.query + "' in the <a href='" + urls.summary + "?version=" + data.version + "'>" + data.version + " database</a>.");
@@ -140,7 +139,6 @@ function finish(id) {
 		var $redo = $( "<p><a href='" + redo_url + "'>Start another search</a></p>" );
 		$( "#results" ).append($redo);
 	});
-	console.log("Check over");
 }
 
 jQuery(function() {
diff --git a/js/seq_viewer.js b/js/seq_viewer.js
index 0dce419..3519ce2 100755
--- a/js/seq_viewer.js
+++ b/js/seq_viewer.js
@@ -30,25 +30,18 @@ function blast_ncbi_redirect( gene ) {
 		'QUERY': encodeURIComponent( get_fasta( gene ) )
 	};
 	var final_url = format_url( url_origin, commands );
-	console.log( final_url );
 	window.location.replace( final_url );
 }
 
 function blast_db_redirect( gene, db ) {
-	console.log(gene);
 	var data = {
 		'db': db,
 		'seq': encodeURIComponent( get_fasta( gene ) )
 	};
-	console.log(data);
-	console.log(urls.start_search);
 	$.post( urls.start_search, data, function(d) {
-		console.log("Successful");
-		console.log(d);
 		if (d.status == 'success' && d.id && urls.search) {
 			var pars = { 'id': d.id };
 			var final_url = format_url( urls.search, pars );
-			console.log( final_url );
 			setTimeout(function() {
 				window.location = final_url;
 			}, 1000);
@@ -65,7 +58,6 @@ function blast_db_redirect( gene, db ) {
 jQuery(function() {
 	// Retrieve the data
 	var pars = get_url_parameters();
-	console.log( pars );
 	
 	if (pars.pid) {
 		pars.type = 'gene';
@@ -75,7 +67,6 @@ jQuery(function() {
 		console.log("Error: no type");
 		return;
 	}
-	console.log( format_url(urls.get_data, pars) );
 	$.getJSON( urls.get_data, pars, function( gene ) {
 		$('#waiting').hide();
 		if ( gene.outcome === false ) {
@@ -89,11 +80,9 @@ jQuery(function() {
 				if ( pars.blast == 'ncbi') {
 					blast_ncbi_redirect( gene );
 				} else if ( pars.blast == 'db' ) {
-					console.log("Redirect to blast_db");
 					blast_db_redirect( gene, pars.version );
 				}
 			} else if (pars.breakid) {
-				console.log(gene);
 				var fasta_list = html_fasta_list( gene.break_genes );
 				$("#fasta").html(fasta_list);
        			} else if (pars.pid) {
@@ -103,7 +92,6 @@ jQuery(function() {
 		}
 	}).fail(function() {
 		console.log("Query failed");
-		console.log( urls.get_data + "?" + $.param(pars) );
 	});
 });
 
diff --git a/js/summary.js b/js/summary.js
index 1187b06..3453962 100755
--- a/js/summary.js
+++ b/js/summary.js
@@ -182,12 +182,9 @@ function create_table(pars) {
 		// Also get all the genomes orthologs numbers
 		pars.type = 'genomes_ortho';
 		loading_on();
-		console.log(pars);
-		console.log(urls.get_data);
 		$.getJSON( urls.get_data, pars, function(orthos) {
 			loading_off();
 			data.num_ortho = orthos.num_ortho;
-			console.log(data);
 			links_table(data);
 		});
 	});
@@ -198,7 +195,6 @@ $(function() {
 	// Init the parameters
 	pars = get_url_parameters();
 	set_pars( pars );
-	console.log( get_pars() );
 	if (get_par("version") && get_par("version") != "") {
 		create_table(pars);
 	} else {
diff --git a/lib_db.php b/lib_db.php
index 782dca6..8b5a683 100755
--- a/lib_db.php
+++ b/lib_db.php
@@ -30,7 +30,12 @@ function die_msg($message = '', $details = '') {
 }
 
 // Get available databases
-function get_available_dbs_list( $all = true , $authorised = array()) {
+function get_available_dbs_list( $show = "dbs" , $userauthorised = NULL) {
+	// show = "all" : list all dbs and userdbs, "dbs" : list all dbs only, "user" : list only user dbs
+	// authorised = array, all mgnXXXXXXX.sqlite that are allowed to be displayed
+	if (!in_array($show,array('all','dbs','user'))){
+		$show = 'all'; // defaults at "all" if unknown parameter value 
+	}
 	global $dbdir;
 	$files = scandir($dbdir);
 	$hfiles = array();
@@ -39,15 +44,28 @@ function get_available_dbs_list( $all = true , $authorised = array()) {
 	}
 	// remove dirs
 	for ($i = 0 ; $i < count($files); $i++) {
-		if ($files[$i] == '.'
-			or $files[$i] == '..'
-			or substr($files[$i], -7) != '.sqlite'
-			or (!$all and substr($files[$i], 0, 3) == 'mgn')
-		) {
+		if ($files[$i] == '.' 
+			or $files[$i] == '..' 
+			or substr($files[$i], -7) != '.sqlite') {
 			continue;
 		}
-if (!empty($authorised) and substr($files[$i], 0, 3) == 'mgn' and !in_array(substr($files[$i], 0, 9),$authorised)){
-			continue;
+		if ($show == "all"){
+			if (!is_null($userauthorised) 
+				and substr($files[$i], 0, 3) == 'mgn' 
+				and !in_array(substr($files[$i], 0, 9),$userauthorised)){
+				continue;
+			}
+		}elseif ($show == "dbs"){
+			if (substr($files[$i], 0, 3) == 'mgn'){
+				continue;
+			}
+		}else{ // $show == "user"
+			if (substr($files[$i], 0, 3) != 'mgn'){
+				continue;
+			}elseif (!is_null($userauthorised) 
+				and !in_array(substr($files[$i], 0, 9),$userauthorised)){
+				continue;
+			}
 		}
 		$hfiles[] = $files[$i];
 	}
@@ -56,15 +74,15 @@ function get_available_dbs_list( $all = true , $authorised = array()) {
 
 // Connects to the db and returns the database handler
 function get_db($version = null) {
-	$allowed = get_available_dbs_list();
+	
 	if (!isset($version)) {
 		if ( isset($_GET['version'])) {
 			$version = $_GET['version'] . ".sqlite";
 		} else {
-			$version = $allowed[0];
+			$version = get_available_dbs_list("dbs")[0];
 		}
 	}
-	if (in_array($version, $allowed)) {
+	if (in_array($version, get_available_dbs_list("all"))) {
 		return get_db_connection($version);
 	} else {
 		die_msg('Invalid database name: ' . $version, 'Undefined database name: there is no file with this name');
@@ -100,7 +118,7 @@ function check_db($dbh) {
 		$query = "SELECT * FROM $table LIMIT 1";
 		$data = get_db_data($dbh, $query);
 		if (count($data) != 1) {
-			error_log("Table $table has not data?");
+			error_log("Table $table has no data?");
 			return false;
 		}
 	}
@@ -163,8 +181,9 @@ function has_table($dbh, $table) {
 
 /*********************************************************/
 // Retrieve the list of available databases
-function get_databases_data($all = false, $authorised = array()) {
-	$dbs = get_available_dbs_list( $all, $authorised );
+function get_databases_data($show = 'dbs', $userauthorised = NULL) {
+	
+	$dbs = get_available_dbs_list( $show, $userauthorised );
 	$data = array();
 	foreach ($dbs as $db) {
 		$dbh = get_db($db);
@@ -500,7 +519,7 @@ function get_ranking_data($dbh) {
 	$joins .= 'LEFT JOIN genes gright2 ON (pnum_all_right2 = gright2.pnum_all and breaks_all.sp2 = gright2.sp) ';
 	$query = "$select $from $joins WHERE $condition $order $limit";
 	return get_db_data($dbh, $query, $vals);
-	return $query;
+	// return $query;
 }
 
 /************************************************************
diff --git a/search.php b/search.php
index 618f56a..e8ce3dc 100755
--- a/search.php
+++ b/search.php
@@ -42,15 +42,17 @@
 							if (!check_id($id)) {
 								echo "Invalid id ($id)<br>";
 								echo '<a href="search_search.php">Start a new search</a>';
+								if(in_array($id,$_SESSION["blast_ids"])){unset($_SESSION["blast_ids"][array_search($id,$_SESSION["blast_ids"])]);};
 								exit;
 							} else {
 								echo "<p id='results'>Waiting...</p>";
+								if(!in_array($id,$_SESSION["blast_ids"])){$_SESSION["blast_ids"][]=$id;};
 							}
 						} else {
 							# Form
 							echo '<form name="seqform" id ="blast_form" method="post">';
 							echo '<label>Choose the database to search:</label>' . print_select("db", list_dbs($_SESSION['db_ids'])) . ' <a id="summary"></a><br>';
-							echo "<p>Paste your sequence in the text area (fasta format):</p>";
+							echo "<p>Paste your (protein) sequence in the text area (fasta format):</p>";
 							echo '<textarea name="seq" cols=80 rows=10 value="" id="seq"></textarea>';
 							echo '<br><input id="submitter" type="submit"></input><button type="button" id="clear">Clear</button>';
 							echo '</form>';
@@ -63,29 +65,6 @@
 			</div>
 			<div id="results_table" />
 			<div id="tail" />
-			<!-- <div class="centered_box">
-				<h2>Previous searches</h2>
-                <div class='index_box'>
-                <?php
-					// $available_dbs = get_available_dbs_list(true, $_SESSION['db_ids']);
-					// foreach ($_SESSION['db_ids'] as $key => $value){
-					// 	if(!in_array($value.".sqlite",$available_dbs)){
-					// 		unset($_SESSION['db_ids'][$key]);
-					// 	}
-					// }
-					// if (empty($_SESSION['db_ids'])){
-					// 	echo "<p>No user databases found in web browser history</p>";
-					// }else{
-					// 	echo "<p>The following databases were generated:</p>";
-					// 	foreach ($_SESSION['db_ids'] as &$value){
-					// 		$site_host = get_setting('site_host');
-					// 		$site_host_subdir = get_setting('site_host_subdir');
-					// 		echo "<p><a href='$site_host/$site_host_subdir/summary.php?version=$value'>$value</a></p>";
-					// 	}
-					// }
-                ?>
-                </div>
-			</div> -->
 		</div>
 	</body>
 </html>
diff --git a/send_qsub.php b/send_qsub.php
index e2948de..e1acc50 100755
--- a/send_qsub.php
+++ b/send_qsub.php
@@ -28,6 +28,6 @@
         $queue = get_setting("search_queue");
         $ncpus = "1";
     }
-    echo shell_exec("echo sudo /home/scripts/run_job_as -u $userid -c 'qsub -N $id -q $queue -o $parent_dir/$id/$id.log -j oe -S /bin/sh -l ncpus=$ncpus -l walltime=$walltime -l mem=$mem -- $script_dir/$run_script -i $parent_dir/$id' > $parent_dir/$id/tmp.sh");
+    echo shell_exec("echo qsub -N $id -q $queue -o $parent_dir/$id/$id.log -j oe -S /bin/sh -l ncpus=$ncpus -l walltime=$walltime -l mem=$mem -- $script_dir/$run_script -i $parent_dir/$id > $parent_dir/$id/tmp.sh");
     $output = shell_exec("sudo /home/scripts/run_job_as -u $userid -c 'qsub -N $id -q $queue -o $parent_dir/$id/$id.log -j oe -S /bin/sh -l ncpus=$ncpus -l walltime=$walltime -l mem=$mem -- $script_dir/$run_script -i $parent_dir/$id'");
 ?>

From ab4391cf36eda0294501a931d125c20698e30ab4 Mon Sep 17 00:00:00 2001
From: Chloe Quignot <>
Date: Thu, 28 Mar 2024 09:48:21 +0100
Subject: [PATCH 2/3] a couple of aesthetic changes

---
 common.php    | 1 +
 settings.ini  | 2 +-
 upload_db.php | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/common.php b/common.php
index 34e1ac7..91f0cf7 100755
--- a/common.php
+++ b/common.php
@@ -100,6 +100,7 @@ function print_sidebar() {
 	echo "<a href='index.php'>Home page</a>";
 	echo "<a href='explore_db.php'>Explore databases</a>";
 	echo "<a href='createdb.php'>Create database</a>";
+	echo "<a href='upload_db.php'>Upload database</a>";
 	echo "<a href='search.php'>Search databases</a>";
 	echo "<a href='direct_access.php'>Genomic islands</a>";
 	echo "<a href='help_pages.php'>Help page</a>";
diff --git a/settings.ini b/settings.ini
index d2997f2..425734f 100755
--- a/settings.ini
+++ b/settings.ini
@@ -1,6 +1,6 @@
 [Site]
 site_name=Synteruptor
-last_update=2023-12-19
+last_update=2024-03-28
 contact= ; Email for admin contact
 db_dir=./db ; Where the databases are stored
 site_host= ; URL of the host
diff --git a/upload_db.php b/upload_db.php
index da96bca..55642c2 100755
--- a/upload_db.php
+++ b/upload_db.php
@@ -29,7 +29,7 @@
 <div id="content">
 <div class="centered_box">
 <h2><?php site_name(); ?> database upload</h2>
-<p>This page helps to upload <?php site_name(); ?> database (in sqlite3 format) to this website.</p>
+<p>Use this page to upload a <?php site_name(); ?> database (in sqlite3 format) to this website.</p>
 <?php
 
 if (isset($_GET["id"])) {

From b1e8b51bac0fca818726195f1223c63be21be964 Mon Sep 17 00:00:00 2001
From: Chloe Quignot <>
Date: Tue, 14 May 2024 12:02:32 +0200
Subject: [PATCH 3/3] fix: str_starts_with for php >v8 + upload_db_add modified
 because file extension has to be .sqlite

---
 common.php          |  6 ++++++
 lib_db.php          |  9 +++++----
 upload_db.php       |  2 +-
 upload_db_add.php   | 35 ++++++++++++++++++++++-------------
 upload_db_start.php |  1 +
 5 files changed, 35 insertions(+), 18 deletions(-)

diff --git a/common.php b/common.php
index 91f0cf7..a0803ab 100755
--- a/common.php
+++ b/common.php
@@ -11,6 +11,12 @@
 ini_set('display_errors', 'Off');
 // ini_set('error_log','../migenis.log');
 
+function console_log($output) {
+	echo '<script>';
+	echo 'console.log(' . json_encode($output) . ');';
+	echo '</script>';
+}
+
 function get_setting($key) {
 	global $settings;
 	if (isset($settings[ $key ])) {
diff --git a/lib_db.php b/lib_db.php
index 8b5a683..865c286 100755
--- a/lib_db.php
+++ b/lib_db.php
@@ -93,12 +93,13 @@ function get_db_connection($db) {
 	global $dbdir;
 	$dbh;
 	$dbpath = $db;
-	if (!str_starts_with($db, "/")) {
+	if (substr($db, 0, 1) != "/") {
 		$dbpath = "$dbdir/$dbpath";
-		if (! preg_match("/\.sqlite$/i", $dbpath)) {
-			$dbpath = "$dbpath.sqlite";
-		}
 	}
+	if (! preg_match("/\.sqlite$/i", $dbpath)) {
+		$dbpath = "$dbpath.sqlite";
+	}
+	
 	error_log("Get db connection to $dbpath");
 	try {
 		$dbh = new PDO("sqlite:$dbpath", '', '', array(PDO::ATTR_ERRMODE => PDO::ERRMODE_EXCEPTION));
diff --git a/upload_db.php b/upload_db.php
index 55642c2..6f49323 100755
--- a/upload_db.php
+++ b/upload_db.php
@@ -60,7 +60,7 @@
 		echo "Uploaded the database file to <a href=\"summary.php?version=$new_db\">$new_db</a>";
 	} else {
 		echo '<form id="uploader" action="upload_db_add.php?id=' . $id . '" method="post" enctype="multipart/form-data">';
-		echo " <input type='file' name='new_db' />";
+		echo "<input type='file' name='new_db' />";
 		echo '<input type="submit" value="Send" /></li>';
 	}
 	echo "</div>";
diff --git a/upload_db_add.php b/upload_db_add.php
index 0fde827..5ee5795 100755
--- a/upload_db_add.php
+++ b/upload_db_add.php
@@ -36,16 +36,6 @@
 			$errormsg .= "<li>File is empty</li>";
 			$nerrors++;
 		} else {
-			# Check there is data in the database
-			try {
-				$dbh = get_db_connection($tmp_name);
-				if (!check_db($dbh)) {
-					throw new DbException("Content of the db doesn't look right");
-				}
-			} catch(Exception $e) {
-				$errormsg .= "<li>Exception: ".$e->getMessage()."</li>";
-				$nerrors++;
-			}
 
 			if ($nerrors == 0) {
 				# Just in case, to avoid collisions
@@ -63,14 +53,33 @@
 					}
 				}
 				if ($nerrors == 0) {
-					if ( move_uploaded_file($tmp_name, $new_db_path) ) {
-						$uploaded_array[] .= "Uploaded file '".$name."'.<br/>\n";
-					} else {
+					if ( !move_uploaded_file($tmp_name, $new_db_path) ) {
 						$errormsg .= "<li>Could not move uploaded file '".$tmp_name."' to '".$name."'<li>";
 						$nerrors++;
 					}
 				}
+				if ($nerrors == 0) {
+					# Check there is data in the database
+					try {
+						$dbh = get_db_connection($new_db_path);
+						if (!check_db($dbh)) {
+							throw new DbException("Content of the db doesn't look right");
+							if (!unlink($new_db_path)) {
+								// Error occurred while deleting the file
+								$errormsg .= "<li>Could not remove the uploaded file from db<li>";
+								$nerrors++;
+							}
+							
+						}
+					} catch(Exception $e) {
+						$errormsg .= "<li>Exception: ".$e->getMessage()."</li>";
+						$nerrors++;
+					}
+					$uploaded_array[] .= "Uploaded file '".$name."'.<br/>\n";
+				}
 			}
+
+
 		}
 	}
 }
diff --git a/upload_db_start.php b/upload_db_start.php
index c4a20fc..04bfad8 100755
--- a/upload_db_start.php
+++ b/upload_db_start.php
@@ -12,6 +12,7 @@ function temp_file() {
 	
 	$tempfile = tempnam($basedir, 'mgn');
 	$id = basename($tempfile);
+	chmod($tempfile, 0777);
 	if(!in_array($id,$_SESSION["db_ids"])){$_SESSION["db_ids"][]=$id;}
 	return $id;
 }