Bioi2 changes

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[ $key ])) {
@@ -67,6 +73,7 @@ function print_header($type=null, $name=null) {
 
 function print_nav($type=null, $name=null) {
 	$dir = '.';
+	$sep = "&nbsp;> ";
 	echo "<div id='entete_links'>";
 	if ($type == 'viewer' || $type == 'aligner') {
 		# If the database is given
@@ -96,13 +103,14 @@ function print_sidebar() {
 	echo "<span class='mynav-logo-banner'>";
 	echo "<a href='$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='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>";
 	echo "<a href='contact.php'>Contact us</a>";
-	echo "<a href='index.php'>Back to home page</a>";
 	echo "</span>";
 	echo "</div>";
 }

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>

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();

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;
 }
 

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>";

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>

explore_db.php

@@ -9,14 +9,15 @@
         ?>
 	<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>
 		<script type="text/javascript" src="js/common.js"></script>
 		<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>

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();
 

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>

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>";

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();
 		});
 	}