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config.php
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config.php
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<?php
// Application_ID
$app_id="net_control";
// Page title
$page_title="NetControl4BioMed";
// The header HTML code
$head='
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta http-Equiv="Cache-Control" Content="no-cache">
<meta http-Equiv="Pragma" Content="no-cache">
<meta http-Equiv="Expires" Content="0">
<link rel="stylesheet" href="nc4bm.css" type="text/css" media="screen" />
';
$style='';
// The header HTML code
$header='
<header>
<h1>NetControl4BioMed: Network Controllability for Biomedicine</h1>
<a href="documentation.html" target="_new">Documentation</a>
<a href="download.html" target="_new">Download</a>
<a href="http://combio.abo.fi/research/network-controlability-project/" target="_new">The Project Page</a>
<a href="about.html" onclick="window.open(\'about.html\', \'newwindow\', \'width=700, height=520\'); return false;">About</a>
<a href=".">Home</a>
</header>
<div class=\"main-content\">
';
// The footer HTML code
$footer='
<footer class="footer-distributed">
<div class="footer-center">
<div>
<a href="http://www.tucs.fi" target="_new">
<i class="tucs logo"><img id="tucs" src="img/TUCS_logo.png"/></i>
<p><span>TUCS</span></p>
</a>
</div>
<div>
<a href="http://www.abo.fi" target="_new">
<i class="abo logo"><img id="abo" src="img/ABO_logo.png"/></i>
<p><span>Åbo Akademi</span></p>
</a>
</div>
<div>
<a href="http://www.aka.fi" target="_new">
<i class="acm logo"><img id="acm" src="img/AKA_logo.png"/></i>
<p><span>Academy of Finland</span></p>
</a>
</div>
<div>
<a href="http://www.tekes.fi" target="_new">
<i class="tekes logo"><img id="tekes" src="img/TEKES_logo.png"/></i>
<p><span>Tekes</span></p>
</a>
</div>
<div>
<a href="http://www.cimo.fi" target="_new">
<i class="cimo logo"><img id="cimo" src="img/CIMO_logo.png"/></i>
<p><span>CIMO</span></p>
</a>
</div>
</div>
<div class="footer-right">
<p class="footer-company-about">
<a href="about.html" onclick="window.open(\'about.html\', \'newwindow\', \'width=700, height=520\'); return false;"><span>About</span></a>
<a href="http://combio.abo.fi/nc/net_control/contributors.html" onclick="window.open(\'http://combio.abo.fi/nc/net_control/contributors.html\', \'newwindow\', \'width=400, height=250\'); return false;">Contributors</a>
<a href="http://combio.abo.fi/nc/net_control/references.html" onclick="window.open(\'http://combio.abo.fi/nc/net_control/references.html\', \'newwindow\', \'width=700, height=520\'); return false;">References</a>
<a href="licence.html" onclick="window.open(\'licence.html\', \'newwindow\', \'width=700, height=520\'); return false;">Licence</a>
</p>
</div>
<div class="footer-right">
<p class="footer-company-about">
<span>Contact</span>
<a href="mailto:kkanhaiy@abo.fi">Krishna Kanhaiya</a>
<a href="mailto:vrogojin@abo.fi">Vladimir Rogojin</a>
</p>
</div>
</footer>
';
// Per each key-value pair from this array, the page will contain a
// multiline text input with the name equal to the key. The input
// will be preceded by the description given by the value.
$fields = array(
"title" => array(
"desc" => "<div class=\"form-title-row\">\n
<center>\n
<h1>ANALYZE</h1>\n
</center>\n
</div>\n",
"type" => "inline"
),
"useremail" => array(
"desc" => "Please Enter a Valid Email Address (The pipeline will report its progress here):",
"type" => "email"
),
"network" => array(
"desc" => "List of Seed Proteins to Generate the Network <a href=\"help/network.html\" onclick=\"window.open('help/network.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "textarea"
),
"graphml" => array(
"desc" => "Custom network <a href=\"help/graphml.html\" onclick=\"window.open('help/graphml.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "file",
"id" => "graphml"
),
"cancers" => array(
"desc" => "Cancer Cell Lines <a href=\"help/cancers.html\" onclick=\"window.open('help/cancers.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "select",
"options" => array(
"none" => "None",
"Breast cancer" => array(
"BT-20" => "BT-20",
"BT-474" => "BT-474",
"BT-549" => "BT-549",
"CAL-51" => "CAL-51",
"CAMA-1" => "CAMA-1",
"EFM-19" => "EFM-19",
"HCC1143" => "HCC1143",
"HCC1187" => "HCC1187",
"HCC1395" => "HCC1395",
"HCC1419" => "HCC1419",
"HCC1428" => "HCC1428",
"HCC1500" => "HCC1500",
"HCC1806" => "HCC1806",
"HCC1937" => "HCC1937",
"HCC1954" => "HCC1954",
"HCC38" => "HCC38",
"Hs_578T" => "Hs_578T",
"KPL-1" => "KPL-1",
"MCF7" => "MCF7",
"MDA-MB-157" => "MDA-MB-157",
"MDA-MB-231" => "MDA-MB-231",
"MDA-MB-361" => "MDA-MB-361",
"MDA-MB-436" => "MDA-MB-436",
"MDA-MB-453" => "MDA-MB-453",
"MDA-MB-468" => "MDA-MB-468",
"SK-BR-3" => "SK-BR-3",
"SW527" => "SW527",
"T-47D" => "T-47D",
"ZR-75-1" => "ZR-75-1"
),
"Ovarian cancer" => array(
"609050M" => "609050M",
"A2780" => "A2780",
"A2780_CIS" => "A2780 CIS",
"MM_OVCAR432_Bast_1" => "MM OVCAR432 Bast 1",
"OV-1946" => "OV-1946",
"OV-90" => "OV-90",
"OVCA1369_TR" => "OVCA1369 TR",
"OVCA433_Bast" => "OVCA433 Bast",
"OVCA5" => "OVCA5",
"OVCA8" => "OVCA8",
"OVCAR-3" => "OVCAR-3",
"SK-OV-3" => "SK-OV-3",
"TOV-1946" => "TOV-1946",
"TOV-2223G" => "TOV-2223G",
"TOV-3133G" => "TOV-3133G"
),
"Pancreatic cancer" => array(
"AsPC-1" => "AsPC-1",
"BxPC-3" => "BxPC-3",
"CFPAC-1" => "CFPAC-1",
"Capan-2" => "Capan-2",
"HPAC" => "HPAC",
"HPAF-II" => "HPAF-II",
"HPDE" => "HPDE",
"Hs_766T" => "Hs 766T",
"IMIM-PC-1" => "IMIM-PC-1",
"IMIM-PC-2" => "IMIM-PC-2",
"KP-3" => "KP-3",
"KP-4" => "KP-4",
"MIA_PaCa-2" => "MIA PaCa-2",
"PANC-1" => "PANC-1",
"PL45" => "PL45",
"PaTu_8988S" => "PaTu 8988S",
"PaTu_8988T" => "PaTu 8988T",
"Panc_02.03" => "Panc 02.03",
"Panc_03.27" => "Panc 03.27",
"Panc_04.03" => "Panc 04.03",
"Panc_05.04" => "Panc 05.04",
"Panc_08.13" => "Panc 08.13",
"Panc_10.05" => "Panc 10.05"
)
)
),
"cancer_checkbox" => array(
"desc" => "Include Cancer Cell Line in Network Creation <a href=\"help/cancer_checkbox.html\" onclick=\"window.open('help/cancer_checkbox.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "checkbox",
"value" => "cancer-network"
),
"target_genes" => array(
"desc" => "List of Additional Target Proteins <a href=\"help/target_genes.html\" onclick=\"window.open('help/target_genes.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "textarea"
),
"gap" => array(
"desc" => "Gap Between Seed Proteins <a href=\"help/gap.html\" onclick=\"window.open('help/gap.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "select",
"options" => array(
"1" => "One",
"2" => "Two",
"3" => "Three",
"4" => "Four",
"5" => "Five"
)
),
"drug" => array(
"label" => "Target By Drug",
"desc" => "Include in the analysis drug target approved proteins from DrugBank <a href=\"help/drug.html\" onclick=\"window.open('help/drug.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "checkbox",
"value" => "drug"
),
"drug_targets" => array(
"desc" => "User defined drug target proteins to be included in the analysis <a href=\"help/drug_targets.html\" onclick=\"window.open('help/drug_targets.html', 'newwindow', 'width=300, height=250'); return false;\"><img src=\"q.png\" width=\"12px\" height=\"12px\"></a>",
"type" => "textarea"
)
);
$form_class="form-labels-on-top";
$form_row_class="form-row";
$form_checkbox_class="form-check-box";
//$app_dir="/var/docker/combio_docker/volumes_web_services/remote_call/".$app_id."/";
$app_dir=getcwd()."/";
// Directory at the host to place the result files online for prolonged access
$wwwdir = $app_dir.getLocalSession();
// URL of the dir to access online the result files placed for prolonged access
$resurl = getLocalSession();
// The temporary directory to store intermediate files in on local host.
$tmpdir = "/tmp/$app_id";
// The name of the file we need to show on the page.
$resultFile = "res";
// List of result files to put online
$resultFiles = array(
"html" => array(
"remote" => "result.html",
"link_text" => "Result"
)
);
// The maximal allowed size of files, in bytes.
$maxResultSize = 1 * 1024 * 1024; // 1 MB
// Remote command.
$remoteCommand = "/home/net_control/start_net_control.sh";
// The simulator will stop if task is not completed within this interval.
//$remoteTimeout = 30;
// Remote host and user
$remoteHost = "net_control@backend";
// The list of options to specify to all ssh-related commands.
#$sshOpts = "-i /var/www/html/net_control/id_rsa -o 'StrictHostKeyChecking no' -o 'UserKnownHostsFile /dev/null'";
$sshOpts = "-i ".getcwd()."/id_rsa -o 'StrictHostKeyChecking no' -o 'UserKnownHostsFile /dev/null'";
#echo $sshOpts;
#$sshOpts = "-i /home/net_control/.ssh/id_rsa -o 'StrictHostKeyChecking no' -o 'UserKnownHostsFile /dev/null'";
// Should we erase working folder at the remote host after completion of executing of the program?
$eraseRemoteDir = false;
// The submit buttons to have and the commands to run, by submit
// button.
$fullurl = full_url_base($_SERVER);
$buttons = array(
"run" => array(
"value" => "Submit",
"command" => function($workingdir) { //Script to execute set of remote bash commands
if(handleNORS()) {
return;
}
global $remoteCommand;
global $remoteTimeout;
global $app_id;
global $wwwdir;
global $fullurl;
$remotedir = $app_id."/".getLocalSession();
// echo $app_id."/".getLocalSession();
$commands = array(
"'cd $remotedir;"
. "export SESSION_ID=" . getLocalSession() . "; export SERVER_DIR=$wwwdir; export SERVER_URL=$fullurl; $remoteCommand $remotedir;"
// . "echo > res; echo --- >> res; cat output >> res; echo --- >> res; cat err >> res'"
. "touch res;'"
);
withInputOnRemoteHost($workingdir, $remotedir, $commands);
},
"prettify" => function($output) { //Generate HTML output based on the result obtained from the remote host
if(($output == "") || handleremoteError($output))
return;
// We now have to get back the parts of the output.
$parts = preg_split("/---/", $output);
// echo("<p />FIELD1:");
echo("<pre>" . $parts[0] . "</pre>");
// echo("<p />FIELD2:");
// echo("<pre>" . $parts[1] . "</pre>");
echo("<hr />");
// list_all_results($session_id);
echo("<hr />");
}
)
);
// Complains and returns 1 if invalid input is supplied.
// Otherwise returns 0.
function handleNoRS() {
/* if((!isset($_POST["target_genes"]) || (trim($_POST["target_genes"]) == ""))&&
(!isset($_POST["network"]) || (trim($_POST["network"]) == ""))) {
prettyError("Empty input supplied for target proteins or network!");
return 1;
}*/
return 0;
}
// Get the full URL of the current page
function url_origin( $s, $use_forwarded_host = false )
{
$ssl = ( ! empty( $s['HTTPS'] ) && $s['HTTPS'] == 'on' );
$sp = strtolower( $s['SERVER_PROTOCOL'] );
$protocol = substr( $sp, 0, strpos( $sp, '/' ) ) . ( ( $ssl ) ? 's' : '' );
$port = $s['SERVER_PORT'];
$port = ( ( ! $ssl && $port=='80' ) || ( $ssl && $port=='443' ) ) ? '' : ':'.$port;
$host = ( $use_forwarded_host && isset( $s['HTTP_X_FORWARDED_HOST'] ) ) ? $s['HTTP_X_FORWARDED_HOST'] : ( isset( $s['HTTP_HOST'] ) ? $s['HTTP_HOST'] : null );
$host = isset( $host ) ? $host : $s['SERVER_NAME'] . $port;
return $protocol . '://' . $host;
}
function full_url_base( $s, $use_forwarded_host = false )
{
$file_path=url_origin( $s, $use_forwarded_host ) . $s['REQUEST_URI'];
return dirname($file_path);
}
// The submit button on the form will be called like this.
$submitValue = "run";
$tooBigResError = "Result too big. Currently, the result size is limited to "
. $maxResultSize . " bytes."
?>