*****************************************************************************/
// EVERY *top-level* page must start this way:
// 1. Define it's relationship to the root of the MolProbity installation.
// Pages in subdirectories of lib/ or public_html/ will need more "/.." 's.
if (!defined('MP_BASE_DIR')) {
define('MP_BASE_DIR', realpath(dirname(__FILE__) . '/..'));
}
// 2. Include core functionality - defines constants, etc.
require_once MP_BASE_DIR . '/lib/core.php';
require_once MP_BASE_DIR . '/lib/model.php';
// 3. Restore session data. If you don't want to access the session
// data for some reason, you must call mpInitEnvirons() instead.
mpStartSession();
// 4. For pages that want to see the session but not change it, such as
// pages that are refreshing periodically to monitor a background job.
mpSessReadOnly();
#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
// Security check on filename
$file = realpath($_REQUEST['file']);
if (!$file || !startsWith($file, realpath($_SESSION['dataDir']))) {
mpLog("security:Attempt to access '{$file}' as '{$_REQUEST['file']}'");
die("Security failure: illegal file request '{$_REQUEST['file']}'");
}
/**
* Context is not used; $_SESSION[bgjob] is used instead.
*/
function display($context)
{
// Because we can't modify $_SESSION while a background job is running,
// we have to "cheat" on our contract and use display() to take action.
// This is not recommended for normal MolProbity pages!!
if (isset($_REQUEST['abort']) && $_REQUEST['abort'] == $_SESSION['bgjob']['processID']) {
// Sometimes jobs die due to seg fault or PHP syntax error.
// Thus, the isRunning flag remains set forever, causing the UI to "hang".
// However, posix_kill() will return failure, b/c the job no longer exists.
// So, we try to kill the job and proceed, with the assumption that it worked.
posix_kill($_SESSION['bgjob']['processID'], 9);
// 9 --> KILL
mpSessReadOnly(false);
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
// It no longer makes sense to continue -- needed vars may be undefined.
// All we can do is return to the main page!
//pageGoto("sitemap.php"); No, b/c we're already in display()
$_SESSION['bgjob']['whereNext'] = "welcome.php";
mpSaveSession();
}
$ellapsed = time() - $_SESSION['bgjob']['startTime'];
if ($_SESSION['bgjob']['isRunning'] && !$_SESSION['bgjob']['processID'] && $ellapsed > 5) {
$url = makeEventURL("onGoto", "welcome.php");
$refresh = "10; URL={$url}";
echo $this->pageHeader("Job failed to start");
//, "none", $refresh);
echo "<p>It appears that your background job failed to start.\n";
echo "<br>This is probably due to a syntax error in one of the PHP scripts.\n";
echo "<br>See the session error log for hints.\n";
echo "<p><a href='{$url}'>Click here</a> to continue.\n";
echo $this->pageFooter();
} elseif ($_SESSION['bgjob']['isRunning']) {
// We have to be very careful to not overwrite $_SESSION while the
// background job is running, or data could be lost!!!
mpSessReadOnly(true);
// A simple counter to make sure browsers think each reload
// is a "unique" page...
$count = $_REQUEST['count'] + 1;
// We use basename() to get "index.php" instead of the full path,
// which is subject to corruption with URL forwarding thru kinemage.
$url = basename($_SERVER['PHP_SELF']) . "?{$_SESSION['sessTag']}&count={$count}";
// Refresh once quickly to get list of tasks displayed, then at given rate
$rate = $count == 1 ? 2 : $_SESSION['bgjob']['refreshRate'];
// Slow down if this is a long job
if ($ellapsed > 30 && $rate < 5) {
$rate = 5;
} elseif ($ellapsed > 120 && $rate < 10) {
$rate = 10;
} elseif ($ellapsed > 1200 && $rate < 30) {
$rate = 30;
}
// after 20 min, refresh every 30 sec
$refresh = "{$rate}; URL={$url}";
echo $this->pageHeader("Job is running...", "none", $refresh);
echo "<p><center>\n";
echo "<table border='0'><tr><td>\n";
echo "<img src='img/2sod-anim.gif'></td><td>\n";
@readfile("{$_SESSION['dataDir']}/" . MP_DIR_SYSTEM . "/progress");
echo "</td></tr></table></center>\n";
echo "<p><small>Your job has been running for " . $this->fmtTime($ellapsed) . ".</small>\n";
echo "<br><small>If this page doesn't update after {$rate} seconds, <a href='{$url}'>click here</a>.</small>\n";
if (isset($_SESSION['bgjob']['processID'])) {
echo "<br><small>If needed, you can <a href='{$url}&abort={$_SESSION[bgjob][processID]}'>abort this job</a>.\n";
}
echo $this->pageFooter();
} elseif ($_SESSION['bgjob']['modelError']) {
$url = makeEventURL("onGoto", "welcome.php");
$pdburlMODEL = "http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#MODEL";
$pdburlENDMDL = "http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ENDMDL";
$refresh = "10; URL={$url}";
echo $this->pageHeader("CCTBX job failed");
//, "none", $refresh);
echo "<p>It appears that the PDB you provided has a formatting error.\n";
echo "<br>MolProbity believes the formatting error has to do with mismatched MODEL and ENDMDL cards.\n\n";
echo "<p>Each MODEL card must be uniquely numbered and have a matching ENDMDL card.\n";
echo "<p>The most common error is 'MODEL 1' existing with no ENDMDL card.\n";
echo "<br>For further info please see the <a href='{$pdburlMODEL}' target=\"_blank\">PDB's MODEL</a> and <a href='{$pdburlENDMDL}' target=\"_blank\">ENDMDL</a> documentation.\n";
echo "<p><strong>To fix:</strong> please check your fomatting conforms to proper PDB";
echo "<br>conventions and try again. If you continue experiencing problems please";
echo "<br>contact us using the feedback page which you can access on the left-hand";
echo "<br>navigation bar from the main page.\n";
echo "<p><a href='{$url}'>Click here</a> to return to the main page. \n";
echo $this->pageFooter();
} elseif ($_SESSION['bgjob']['elementError']) {
$url = makeEventURL("onGoto", "welcome.php");
$pdburl = "http://www.wwpdb.org/documentation/file-format/format33/sect9.html#ATOM";
$refresh = "10; URL={$url}";
echo $this->pageHeader("CCTBX job failed");
//, "none", $refresh);
echo "<p>It appears that the PDB you provided has a formatting error.\n";
echo "<br>MolProbity believes the formatting error has to do with improper chemical names (a.k.a. element symbols)\n\n";
echo "<p>Here is an example of PDB format:";
echo "<pre>\n";
echo " 1 2 3 4 5 6 7 8\n";
echo "12345678901234567890123456789012345678901234567890123456789012345678901234567890\n";
echo "ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N\n";
echo "ATOM 33 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N\n";
echo "ATOM 34 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C\n";
echo "ATOM 35 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C\n";
echo "ATOM 36 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C\n";
echo "ATOM 37 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C\n";
echo "ATOM 38 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O\n";
echo "ATOM 39 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O\n";
echo "ATOM 40 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C\n";
echo "ATOM 41 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C\n";
echo "ATOM 42 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C\n";
echo "ATOM 43 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C\n";
echo "ATOM 44 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C\n";
echo "ATOM 45 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C\n";
echo "HETATM 46 MG MG B 101 44.444 55.555 66.666 1.00 42.42 MG\n";
echo "</pre><p>Chemical names must be in columns 77-78 of the PDB file, right justified (e.g. \" C\"). ";
echo "<br>For further info please see the <a href='{$pdburl}' target=\"_blank\">PDB formatting</a> guide.\n";
echo "<p><strong>To fix:</strong> please check your fomatting conforms to proper PDB";
echo "<br>conventions and try again. If you continue experiencing problems please";
echo "<br>contact us using the feedback page which you can access on the left-hand";
echo "<br>navigation bar from the main page.\n";
echo "<p><a href='{$url}'>Click here</a> to return to the main page.\n";
echo $this->pageFooter();
} elseif ($_SESSION['bgjob']['cctbxError']) {
$url = makeEventURL("onGoto", "feedback_setup.php");
$refresh = "10; URL={$url}";
echo $this->pageHeader("CCTBX job failed");
//, "none", $refresh);
echo "<p>It appears that your CCTBX-powered job failed.\n";
echo "<br>This is probably due to a syntax error in one of the CCTBX scripts!\n";
echo "<br>See the session error log for hints, and please report the bug using the Feedback tool.\n";
echo "<p><a href='{$url}'>Click here</a> to continue.\n";
echo $this->pageFooter();
} else {
$url = makeEventURL("onGoto", $_SESSION['bgjob']['whereNext'], $_SESSION['bgjob']);
$refresh = "3; URL={$url}";
echo $this->pageHeader("Job is finished", "none", $refresh);
echo "<p><center>\n";
echo "<p><table border='0'><tr><td>\n";
@readfile("{$_SESSION['dataDir']}/" . MP_DIR_SYSTEM . "/progress");
echo "</td></tr></table></center>\n";
echo "<p><small>Your job ran for " . $this->fmtTime($_SESSION['bgjob']['endTime'] - $_SESSION['bgjob']['startTime']) . ".</small>\n";
echo "<br><small>If nothing happens after 3 seconds, <a href='{$url}'>click here</a>.<small>\n";
echo $this->pageFooter();
}
}
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
// Note that changing size breaks the "Close" button, at least in Safari, b/c the page reloads.
if (isset($_REQUEST['size'])) {
$kingSize = $_REQUEST['size'];
setcookie('viewking_kingSize', $kingSize);
// You could get in trouble if a background job was running (hence the check here)
// or if you somehow hit the size-change link while another page was loading (unlikely),
// because this update would be overwriten when the background job exited (hopefully),
// or this update would overwrite the results of the background job just as it ended (disaster).
if (!$_SESSION['bgjob']['isRunning']) {
mpSessReadOnly(false);
$_SESSION['kingSize'] = $kingSize;
}
} elseif (isset($_COOKIE['viewking_kingSize'])) {
$kingSize = $_COOKIE['viewking_kingSize'];
} elseif (isset($_SESSION['kingSize'])) {
$kingSize = $_SESSION['kingSize'];
} else {
$kingSize = 'default';
}
if ($kingSize == "tiny") {
$size = "width='600' height='400'";
} elseif ($kingSize == "small") {
$size = "width='700' height='500'";
} elseif ($kingSize == "large") {
$size = "width='1300' height='950'";
/**
* Be warned -- this function makes the current session READ ONLY.
* The session data file must not be overwritten until the job ends.
* This function ONLY makes sense in the context of a session.
*
* This command does NOT automatically do a pageGoto("job_progress.php").
* You should do that manually BEFORE calling this function, or use another
* background job monitor with equivalent functionality.
* You can't pageGoto() AFTER calling this function b/c the session is frozen!
*
* $script Absolute path to a PHP script to run.
* Command is "php -f $script ".session_id()
* $whereNext name of the next delegate script, for after the job
* $delay number of seconds to wait between refreshes
*/
function launchBackground($script, $whereNext, $delay = 5)
{
if ($_SESSION['bgjob']['isRunning']) {
return false;
}
// No! Caller probably put some data in there already for this new job!
// This has to be done in the launch functions instead.
//unset($_SESSION['bgjob']); // Clean up any old data
// Remove old progress file
$progress = "{$_SESSION['dataDir']}/" . MP_DIR_SYSTEM . "/progress";
if (file_exists($progress)) {
unlink($progress);
}
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['isRunning'] = true;
$_SESSION['bgjob']['startTime'] = time();
$_SESSION['bgjob']['refreshRate'] = $delay;
$_SESSION['bgjob']['whereNext'] = $whereNext;
$errlog = $_SESSION['dataDir'] . "/" . MP_DIR_SYSTEM . "/errors";
// Make sure session variables are written to disk.
// session_write_close() doesn't take effect until end of script
mpSaveSession();
// Otherwise, end-of-script write can truncate the file to nothing
// just as the background job is starting, leading to random failure (?)
mpSessReadOnly(true);
// Save current dir so we can exec script in it's own dir.
$pwd = getcwd();
chdir(dirname($script));
// Run the script in the background
$cmd = "php -f {$script} '" . session_id() . "' >> {$errlog} 2>&1 &";
exec($cmd);
// Restore the current dir
chdir($pwd);
}
