<!-- /.navbar-top-links -->
<?php
include 'navbar-top-links.php';
?>
<!-- /.navbar-static-side -->
</nav>
<div id="page-wrapper">
<?php
include 'includes/run_check.php';
?>
<div class="row">
<div class="col-lg-12">
<h2 class="page-header">Set Alerts - run: <?php
echo cleanname($_SESSION['active_run_name']);
?>
</h1>
</div>
<!-- /.col-lg-12 -->
</div>
<div id="messages"></div>
<div class="row">
<div class="col-lg-12">
This feature will notify you of specific events occuring during the sequencing run. <br><br>This is a <strong>beta</strong> feature.<br><br> You can browse around the website once these parameters are set and notifications will appear on any page. However, these settings may not be remembered if you log out of the website.
<br>
As proof of principle we shall consider depth of coverage for the whole genome from template reads. This alert is persistent - it will remain untill dismissed (or you change pages...).
<!-- /.col-lg-12 -->
//print $value2 . "<br>";
if ($webnotify == 1) {
echo "<script type=\"text/javascript\" id=\"runscript\">\n\t\t\t\t\t\tnew PNotify({\n \t\t\t\t\t\ttitle: 'Run Finished.',\n\t\t\t\t\t \ttext: '" . cleanname($value2) . " has been completed.',\n \t\t\t\t\t\ttype: 'info',\n\t\t\t\t\t \thide: false\n\t\t\t\t\t\t});\n\n\t\t\t\t\t\t</script>";
}
if (isset($_SESSION['twittername'])) {
$message = "run finished.";
$postData = "twitteruser="******"&run=" . urlencode(cleanname($value2)) . "&message=" . urlencode($message);
//echo "alert ('".$postData."');";
// Get cURL resource
$curl = curl_init();
// Set some options - we are passing in a useragent too here
curl_setopt_array($curl, array(CURLOPT_RETURNTRANSFER => 1, CURLOPT_URL => $twiturl . 'tweet.php?' . $postData, CURLOPT_USERAGENT => 'Codular Sample cURL Request'));
// Send the request & save response to $resp
$resp = curl_exec($curl);
// Close request to clear up some resources
curl_close($curl);
}
// Get cURL resource
$curl = curl_init();
$postData = "userid=" . urlencode($_SESSION['user_name']) . "&runname=" . urlencode(cleanname($value2));
//echo $postData;
// Set some options - we are passing in a useragent too here
curl_setopt_array($curl, array(CURLOPT_RETURNTRANSFER => 1, CURLOPT_URL => 'http://www.nottingham.ac.uk/~plzloose/minoTourhome/runfinished.php?' . $postData, CURLOPT_USERAGENT => 'Codular Sample cURL Request'));
// Send the request & save response to $resp
$resp = curl_exec($curl);
// Close request to clear up some resources
curl_close($curl);
}
}
}
}
function checkuserruns()
{
if (isset($_SESSION['user_login_status']) and $_SESSION['user_login_status'] == 1) {
$db_connection = new mysqli(DB_HOST, DB_USER, DB_PASS, DB_NAME);
if (!$db_connection->connect_errno) {
$user_name = $_SESSION['user_name'];
$sql = "select users.user_name,runname, activeflag from users inner join userrun using (user_id) inner join minIONruns where userrun.runindex=minIONruns.runindex and users.user_name = '" . $user_name . "';";
$runs_available = $db_connection->query($sql);
if ($runs_available->num_rows >= 1) {
$runarray;
foreach ($runs_available as $row) {
$runarray[$row['activeflag']][$row['runname']] = $row['user_name'];
}
echo "You have " . $runs_available->num_rows . " minION runs available to view.<br>\n";
if (array_key_exists('1', $runarray)) {
echo "You have active runs available.<br>\n";
//foreach ($runarray as $runinfo) {
// if ()
//}
$_SESSION['active_run_name'] = key($runarray[1]);
echo "The currently selected active run is " . cleanname(key($runarray[1])) . ".<br>\n";
} else {
echo "You have no currently active runs.<br>\n";
unset($_SESSION['active_run_name']);
}
} else {
echo "You have no minION runs available to view.<br>\n";
}
}
return true;
}
return false;
}
?>
<!-- /.navbar-top-links -->
<?php
include 'navbar-top-links.php';
?>
<!-- /.navbar-static-side -->
</nav>
<div id="page-wrapper">
<?php
include 'includes/run_check.php';
?>
<div class="row">
<div class="col-lg-12">
<h1 class="page-header">Previous Data Summary - run: <?php
echo cleanname($_SESSION['focusrun']);
?>
</h1>
</div>
<!-- /.col-lg-12 -->
</div>
<ul class="nav nav-pills">
<li><a href="previous_summary.php">Read Summaries</a></li>
<li><a href="previous_histogram.php">Read Histograms</a></li>
<li ><a href="previous_rates.php">Sequencing Rates</a></li>
<li ><a href="previous_pores.php">Pore Activity</a></li>
<li ><a href="previous_quality.php">Read Quality</a></li>
<li class="active"><a href="previous_coverage.php">Coverage Detail</a></li>
</ul>
<div class="panel panel-default">
list($iFilteredTotal) = $rResultFilterTotal->fetch_row();
// Total data set length
$sQuery = "SELECT COUNT(*) FROM `" . $sTable . "`";
$rResultTotal = $db->query($sQuery) or die($db->error);
list($iTotal) = $rResultTotal->fetch_row();
/**
* Output
*/
$output = array("sEcho" => intval($input['sEcho']), "iTotalRecords" => $iTotal, "iTotalDisplayRecords" => $iFilteredTotal, "aaData" => array());
while ($aRow = $rResult->fetch_assoc()) {
$row = array();
for ($i = 0; $i < $iColumnCount; $i++) {
if ($aColumns[$i] == 'version') {
// Special output formatting for 'version' column
$row[] = $aRow[$aColumns[$i]] == '0' ? '-' : $aRow[$aColumns[$i]];
} elseif ($aColumns[$i] == 'runname') {
$row[] = cleanname($aRow[$aColumns[$i]]);
} elseif ($aColumns[$i] != ' ') {
// General output
$row[] = $aRow[$aColumns[$i]];
}
}
$output['aaData'][] = $row;
}
//$jsonstring = json_encode( $output );
//$callback = $_GET['callback'];
//echo $callback.'('.$jsonstring.');';
echo json_encode($output);
} else {
echo "ERROR";
}
$sqldeleteexecute = $mindb_connection->query($sqldelete);
$sqlinsert = "insert into alerts (name,reference,twitterhandle,type,threshold,start,end,control,complete) values (" . $name . "," . $reference . "," . $twitterhandle . "," . $type . "," . $threshold . "," . $start . "," . $end . "," . $control . ",0);";
$sqlinsertexecute = $mindb_connection->query($sqlinsert);
} elseif ($name === "'genbarcodecoveragedelete'") {
$sqldelete = "delete from alerts where name = 'genbarcodecoverage';";
$sqldeleteexecute = $mindb_connection->query($sqldelete);
//echo $sqldelete . "<br>";
} elseif ($name === "'barcodecoveragedelete'") {
$sqldelete = "delete from alerts where name = 'barcodecoverage';";
$sqldeleteexecute = $mindb_connection->query($sqldelete);
//echo $sqldelete . "<br>";
} elseif ($name === "'referencecoveragedelete'") {
//echo "YELLOW";
$alert_index = substr($reference, 10, -1);
$sqldelete = "delete from alerts where alert_index = " . $alert_index . ";";
//echo $sqldelete . "<br>";
$sqldeleteexecute = $mindb_connection->query($sqldelete);
//echo $sqldelete . "<br>";
} else {
$sqlinsert = "insert into alerts (name,reference,twitterhandle,type,threshold,start,end,control,complete) values (" . $name . "," . $reference . "," . $twitterhandle . "," . $type . "," . $threshold . "," . $start . "," . $end . "," . $control . ",0);";
//echo $sqlinsert;
$sqlinsertexecute = $mindb_connection->query($sqlinsert);
}
}
echo "<div class='alert alert-success alert-dismissible' role='alert'> <button type='button' class='close' data-dismiss='alert'><span aria-hidden='true'>×</span><span class='sr-only'>Close</span></button> <strong>Success!</strong> An alert has been set for the following run: " . cleanname($_SESSION['active_run_name']) . "<br> The alert is for {$name} on {$typeref} strands. </div>";
} else {
echo "<div class='alert alert-danger alert-dismissible' role='alert'> <button type='button' class='close' data-dismiss='alert'><span aria-hidden='true'>×</span><span class='sr-only'>Close</span></button> <strong>Failed!</strong> An alert has not been set. You should not normally see this message so a really unexpected error has occured.</div>";
}
} else {
echo "ERROR";
}
function nav_id_filter($id, $item)
{
return 'nav-' . cleanname($item->title);
}
<div class='modal-content'>
<div class='modal-header'>
<button type='button' class='close' data-dismiss='modal' aria-hidden='true'>×</button>
<h4 class='modal-title' id='myModalLabel'>Start your minION</h4>
</div>
<div class='modal-body'>
<div id='startminioninfo'>
<p>This will attempt to restart your minION sequencer remotely.</p>
<p>If you are sure you wish to do this select an available run script and click 'Start minION' below. Otherwise close this window.</p>
<?php
$availablescripts = "SELECT * FROM messages where message = 'runscript' order by message_index;";
$availablescriptsare = $mindb_connection->query($availablescripts);
if ($availablescriptsare->num_rows > 0) {
foreach ($availablescriptsare as $row) {
echo "\n <div class='radio'>\n <label>\n <input type='radio' name='scriptRadios' id='" . $row['param1'] . "' value='" . $row['param1'] . "' >\n " . cleanname($row['param1']) . ".py\n </label>\n </div>\n ";
}
} else {
echo "Not Available.";
}
?>
</div>
<div id='startworking'>
<p class='text-center'>We're working to restart your minION device. Please be patient and don't navigate away from this page.</p>
<p class='text-center'><img src='images/loader.gif' alt='loader'></p>
</div>
<div class='modal-footer'>
<button type='button' class='btn btn-default' data-dismiss='modal'>Close</button>
foreach ($currentbiasis as $row) {
echo $row['param1'] . " mV";
}
} else {
echo "Not Available";
}
echo "</td>\n </tr>\n <tr>\n <td>Yield</td>\n <td>";
$currentyield = "SELECT * FROM messages where message = 'yield' order by message_index desc limit 1;";
#echo $currentbias . "<br>";
$currentyieldis = $mindb_connection2->query($currentyield);
if ($currentyieldis->num_rows > 0) {
foreach ($currentyieldis as $row) {
echo $row['param1'];
}
} else {
echo "Not Available.";
}
echo "</td>\n </tr>\n\t\t\t\t</table>\n\n <em>Available scripts are:</em><br>\n ";
$availablescripts = "SELECT * FROM messages where message = 'runscript' order by message_index;";
#echo $currentbias . "<br>";
$availablescriptsare = $mindb_connection2->query($availablescripts);
if ($availablescriptsare->num_rows > 0) {
foreach ($availablescriptsare as $row) {
echo "->" . cleanname($row['param1']) . "<br>";
}
} else {
echo "Not Available.";
}
echo "\n\n\t\t\t\t</div>\n\t\t\t\t</div>\n\t\t\t</div>";
}
}
}
}
if ($index['job'] == "basenotification") {
$sql_template = "SELECT sum(length(sequence)) as bases FROM basecalled_" . $index['type'] . ";";
$mindb_connection = new mysqli(DB_HOST, DB_USER, DB_PASS, $index['database']);
$template = $mindb_connection->query($sql_template);
if ($template->num_rows >= 1) {
foreach ($template as $row) {
if (($row['bases'] - $row['bases'] % $index['threshold']) / $index['threshold'] >= 1) {
$checkrunning = $index['database'] . "basecoverage" . $index['type'];
//echo $checkrunning;
$basecoveragetemp = $memcache->get("{$checkrunning}");
if (($row['bases'] - $row['bases'] % $index['threshold']) / $index['threshold'] > $basecoveragetemp) {
if (isset($index['twittername']) && $index['threshold'] >= 500000) {
$message = "Sequenced " . $index['threshold'] * (($row['bases'] - $row['bases'] % $index['threshold']) / $index['threshold']) . " bases on " . $index['type'];
$postData = "twitteruser="******"&run=" . urlencode(cleanname($index['database'])) . "&message=" . urlencode($message);
$curl = curl_init();
// Set some options - we are passing in a useragent too here
curl_setopt_array($curl, array(CURLOPT_RETURNTRANSFER => 1, CURLOPT_URL => $twiturl . 'tweet.php?' . $postData, CURLOPT_USERAGENT => 'Codular Sample cURL Request'));
// Send the request & save response to $resp
$resp = curl_exec($curl);
// Close request to clear up some resources
curl_close($curl);
}
$memcache->set("{$checkrunning}", ($row['bases'] - $row['bases'] % $index['threshold']) / $index['threshold']);
}
}
}
}
}
}
#echo $currentbias . "<br>";
$currentsampleis = $mindb_connection2->query($currentsample);
if ($currentsampleis->num_rows > 0) {
foreach ($currentsampleis as $row) {
echo $row['param1'];
}
} else {
echo "Not Available";
}
echo "</td>\n </tr>\n <tr>\n <td>Run Name</td>\n <td>";
$currentdataset = "SELECT * FROM messages where message = 'Dataset' order by message_index desc limit 1;";
#echo $currentbias . "<br>";
$currentdatasetis = $mindb_connection2->query($currentdataset);
if ($currentdatasetis->num_rows > 0) {
foreach ($currentdatasetis as $row) {
echo cleanname($row['param1']);
}
} else {
echo "Not Available";
}
echo "</td>\n </tr>\n <tr>\n <td>Voltage Offset</td>\n <td>";
$currentbias = "SELECT * FROM messages where message = 'biasvoltage' order by message_index desc limit 1;";
$currentbiasis = $mindb_connection2->query($currentbias);
if ($currentbiasis->num_rows > 0) {
foreach ($currentbiasis as $row) {
echo $row['param1'] . " mV";
}
} else {
echo "Not Available";
}
echo "</td>\n </tr>\n <tr>\n <td>Yield</td>\n <td>";