/**
* Opens a connection to a Tokyo Tyrant server
* <code>
* try {
* $tt = Tyrant::connect('localhost', 1978);
* } catch (Tyrant_Exception $e) {
* echo $e->getMessage();
* }
* </code>
*
* @param string Server hostname or IP address
* @param string Server port
* @param string Optional existing connection id
* @return object Database connection
*/
public static function connect($host = 'localhost', $port = '1978', $id = 0)
{
$id = implode(':', array($host, $port, $id));
// Check if connection already exists
if (isset(self::$connections[$id])) {
$connection =& self::$connections[$id];
return $connection;
}
// Start a new connection
if ($port == 0) {
$addr = $host;
$socket = socket_create(AF_UNIX, SOCK_STREAM, 0);
} else {
$ip = gethostbyname($host);
$addr = ip2long($ip);
if (empty($addr)) {
throw new Tyrant_Exception("Host not found");
}
$socket = socket_create(AF_INET, SOCK_STREAM, SOL_TCP);
}
if (!is_resource($socket)) {
throw new Tyrant_Exception("Connection refused");
}
if (!socket_connect($socket, $addr, $port)) {
throw new Tyrant_Exception("Connection refused");
}
if ($port > 0) {
if (defined('TCP_NODELAY')) {
socket_set_option($socket, SOL_TCP, TCP_NODELAY, 1);
} else {
// See http://bugs.php.net/bug.php?id=46360
socket_set_option($socket, SOL_TCP, 1, 1);
}
}
// Determine the database type
if (socket_write($socket, pack('CC', 0xc8, 0x88)) === false) {
throw new Tyrant_Exception("Unable to get database type");
}
$str = '';
if (socket_recv($socket, $str, 1, 0) === false) {
throw new Tyrant_Exception("Unable to get database type");
}
$c = unpack("C", $str);
if (!isset($c[1]) || $c[1] !== 0) {
throw new Tyrant_Exception("Unable to get database type");
}
$str = '';
if (socket_recv($socket, $str, 4, 0) === false) {
throw new Tyrant_Exception("Unable to get database type");
}
$num = unpack("N", $str);
if (!isset($num[1])) {
throw new Tyrant_Exception("Unable to get database type");
}
$size = unpack("l", pack("l", $num[1]));
$len = $size[1];
$str = '';
if (socket_recv($socket, $str, $len, 0) === false) {
throw new Tyrant_Exception("Unable to get database type");
}
$value = explode("\n", trim($str));
$stats = array();
foreach ($value as $v) {
$v = explode("\t", $v);
$stats[$v[0]] = $v[1];
}
if (!isset($stats['type'])) {
throw new Tyrant_Exception("Unable to get database type");
}
// Get the right interface for the database type
if ($stats['type'] == 'table') {
include_once dirname(__FILE__) . '/Tyrant/RDBTable.php';
$conn = new Tyrant_RDBTable($socket);
} else {
include_once dirname(__FILE__) . '/Tyrant/RDB.php';
$conn = new Tyrant_RDB($socket);
}
self::$connections[$id] =& $conn;
self::$connection = $conn;
return $conn;
}
forbidden();
}
$db = preg_replace('/[^a-z0-9]/i', '', $db);
try {
$tt = @Tyrant::connect("/tmp/{$db}.sock", 0);
} catch (Tyrant_Exception $e) {
include "../lib/spyc.php";
if (!file_exists("../{$db}.yaml")) {
forbidden('genome does not exist');
}
$genome_config = Spyc::YAMLLoad("../{$db}.yaml");
try {
if (!is_array($genome_config['output_tch'])) {
throw new Exception("ttserver should be local");
}
$tt = @Tyrant::connect($genome_config['output_tch'][0], $genome_config['output_tch'][1]);
} catch (Exception $e) {
forbidden('Could not connect to ttserver');
}
}
header('Content-Type: ' . (substr($f, -4) == ".png" ? 'image/png' : 'application/json'));
$value = $tt[$f];
if ($value === null) {
header('HTTP/1.1 404 Not Found');
} else {
header('Expires: ' . gmdate("D, d M Y H:i:s", time() + 60 * 60 * 3) . " GMT");
header('Cache-Control: public, max-age=10800');
if ($value == '-') {
echo $tt['.null'];
} else {
echo $value;
$genome_config = Spyc::YAMLLoad("../{$db}.yaml");
$ucsc_config = Spyc::YAMLLoad("../ucsc.yaml");
$serve_tracks = array();
foreach ($genome_config['serve_tracks'] as $trk) {
$serve_tracks[$trk['n']] = true;
}
$query = "db={$db}&position={$pos}";
$tt = NULL;
if (isset($genome_config['search_tch'])) {
include '../lib/Tyrant.php';
try {
if (is_array($genome_config['search_tch'])) {
$tt = @Tyrant::connect($genome_config['search_tch'][0], $genome_config['search_tch'][1]);
} else {
$sock = preg_replace('/[^a-z0-9.]|\\.tch$/i', '', $genome_config['search_tch']);
$tt = @Tyrant::connect("/tmp/{$sock}.sock", 0);
}
$value = $tt[$query];
if ($value !== NULL) {
echo gzinflate($value);
exit;
}
} catch (Exception $e) {
$tt = NULL;
}
}
$url = "{$ucsc_config['browser_hosts']['local']}{$ucsc_config['browser_urls']['tracks']}?{$query}";
if (function_exists('curl_init')) {
$ch = curl_init($url);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch, CURLOPT_HEADER, 0);
