getMessage()));
exit;
}
/**
* Utility function to import the required javascript for the xref panel
*/
function wpiAddXrefPanelScripts() {
XrefPanel::addXrefPanelScripts();
}
function createPathwayObject($pwTitle, $oldid) {
$pathway = Pathway::newFromTitle($pwTitle);
if($oldId) {
$pathway->setActiveRevision($oldId);
}
return $pathway;
}
function delete($title) {
global $wgUser, $wgOut;
$pathway = Pathway::newFromTitle($_GET['pwTitle']);
if($wgUser->isAllowed('delete')) {
$pathway = Pathway::newFromTitle($_GET['pwTitle']);
$pathway->delete();
echo "Deleted
";
echo "Pathway $title was deleted, return to wikipathways";
} else {
echo "
Error
";
echo "Pathway $title is not deleted, you have no delete permissions";
$wgOut->permissionRequired( 'delete' );
}
exit;
}
function revert($pwTitle, $oldId) {
$pathway = Pathway::newFromTitle($pwTitle);
$pathway->revert($oldId);
//Redirect to old page
$url = $pathway->getTitleObject()->getFullURL();
header("Location: $url");
exit;
}
function launchGenMappConverter($pathway) {
global $wgUser;
$webstart = file_get_contents(WPI_SCRIPT_PATH . "/applet/genmapp.jnlp");
$pwUrl = $pathway->getFileURL(FILETYPE_GPML);
$pwName = substr($pathway->getFileName(''), 0, -1);
$arg = "" . htmlspecialchars($pwUrl) . "";
$arg .= "" . htmlspecialchars($pwName) . "";
$webstart = str_replace("", $arg, $webstart);
$webstart = str_replace("CODE_BASE", WPI_URL . "/applet/", $webstart);
sendWebstart($webstart, $pathway->name(), "genmapp.jnlp");//This exits script
}
function launchCytoscape($pathway) {
global $wgUser;
$webstart = file_get_contents(WPI_SCRIPT_PATH . "/bin/cytoscape/cy1.jnlp");
$arg = createJnlpArg("-N", $pathway->getFileURL(FILETYPE_GPML));
$webstart = str_replace(" ", $arg, $webstart);
$webstart = str_replace("CODE_BASE", WPI_URL . "/bin/cytoscape/", $webstart);
sendWebstart($webstart, $pathway->name(), "cytoscape.jnlp");//This exits script
}
function sendWebstart($webstart, $tmpname, $filename = "wikipathways.jnlp") {
ob_start();
ob_clean();
//return webstart file directly
header("Content-type: application/x-java-jnlp-file");
header("Cache-Control: must-revalidate, post-check=0, pre-check=0");
header("Content-Disposition: attachment; filename=\"{$filename}\"");
echo $webstart;
exit;
}
function getJnlpURL($webstart, $tmpname) {
$wsFile = tempnam(getcwd() . "/tmp",$tmpname);
writeFile($wsFile, $webstart);
return 'http://' . $_SERVER['HTTP_HOST'] . '/wpi/tmp/' . basename($wsFile);
}
function createJnlpArg($flag, $value) {
//return "" . $flag . ' "' . $value . '"' . "\n";
if(!$flag || !$value) return '';
return "" . htmlspecialchars($flag) . "\n" . htmlspecialchars($value) . "\n";
}
function downloadFile($fileType, $pwTitle) {
$pathway = Pathway::newFromTitle($pwTitle);
if(!$pathway->isReadable()) {
throw new Exception("You don't have permissions to view this pathway");
}
if($fileType === 'mapp') {
launchGenMappConverter($pathway);
}
ob_start();
if($oldid = $_REQUEST['oldid']) {
$pathway->setActiveRevision($oldid);
}
//Register file type for caching
Pathway::registerFileType($fileType);
$file = $pathway->getFileLocation($fileType);
$fn = $pathway->getFileName($fileType);
$mime = MimeTypes::getMimeType($fileType);
if(!$mime) $mime = "text/plain";
ob_clean();
header("Content-type: $mime");
header("Cache-Control: must-revalidate, post-check=0, pre-check=0");
header("Content-Disposition: attachment; filename=\"$fn\"");
//header("Content-Length: " . filesize($file));
set_time_limit(0);
@readfile($file);
exit();
}
function getClientOs() {
$regex = array(
'windows' => '([^dar]win[dows]*)[\s]?([0-9a-z]*)[\w\s]?([a-z0-9.]*)',
'mac' => '(68[k0]{1,3})|(ppc mac os x)|([p\S]{1,5}pc)|(darwin)',
'linux' => 'x11|inux');
$ua = $_SERVER['HTTP_USER_AGENT'];
foreach (array_keys($regex) as $os) {
if(eregi($regex[$os], $ua)) return $os;
}
}
$spName2Code = array('Human' => 'Hs', 'Rat' => 'Rn', 'Mouse' => 'Mm');//TODO: complete
function toGlobalLink($localLink) {
if($wgScriptPath && $wgScriptPath != '') {
$wgScriptPath = "$wgScriptPath/";
}
return urlencode("http://" . $_SERVER['HTTP_HOST'] . "$wgScriptPath$localLink");
}
function writeFile($filename, $data) {
$dir = dirname($filename);
if(!file_exists($dir)) {
mkdir(dirname($filename), 0777, true); //Make sure the directory exists
}
$handle = fopen($filename, 'w');
if(!$handle) {
throw new Exception ("Couldn't open file $filename");
}
if(fwrite($handle, $data) === FALSE) {
throw new Exception ("Couldn't write file $filename");
}
if(fclose($handle) === FALSE) {
throw new Exception ("Couln't close file $filename");
}
}
function tag($name, $text, $attributes = array()) {
foreach(array_keys($attributes) as $key) {
if($value = $attributes[$key])$attr .= $key . '="' . $value . '" ';
}
return "<$name $attr>$text";
}
/**
* Modified wfShellExec for java calls. This does not include the memory limit
* on the ulimit call, since this doesn't work well with java.
* @param $cmd Command line, properly escaped for shell.
* @param &$retval optional, will receive the program's exit code.
* (non-zero is usually failure)
* @return collected stdout as a string (trailing newlines stripped)
*/
function wfJavaExec( $cmd, &$retval=null ) {
global $IP, $wgMaxShellMemory, $wgMaxShellFileSize;
if( wfIniGetBool( 'safe_mode' ) ) {
wfDebug( "wfShellExec can't run in safe_mode, PHP's exec functions are too broken.\n" );
$retval = 1;
return "Unable to run external programs in safe mode.";
}
if ( php_uname( 's' ) == 'Linux' ) {
$time = intval( ini_get( 'max_execution_time' ) );
$filesize = intval( $wgMaxShellFileSize );
if ( $time > 0) {
$script = "$IP/bin/ulimit4-nomemory.sh";
if ( is_executable( $script ) ) {
$cmd = escapeshellarg( $script ) . " $time $filesize " . escapeshellarg( $cmd );
}
}
} elseif ( php_uname( 's' ) == 'Windows NT' ) {
# This is a hack to work around PHP's flawed invocation of cmd.exe
# http://news.php.net/php.internals/21796
$cmd = '"' . $cmd . '"';
}
wfDebug( "wfJavaExec: $cmd\n" );
$retval = 1; // error by default?
ob_start();
passthru( $cmd, $retval );
$output = ob_get_contents();
ob_end_clean();
return $output;
}
?>