<commit_before><%@ page import="java.io.BufferedReader" %>
<%@ page import="java.io.ByteArrayInputStream" %>
<%@ page import="java.io.InputStream" %>
<%@ page import="java.io.InputStreamReader" %>
<%@ page import="java.util.zip.GZIPInputStream" %>
<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %>
<%@ page import="org.mskcc.cbio.portal.util.FileUploadRequestWrapper" %>
<%@ page import="org.apache.commons.lang.StringEscapeUtils" %>
<%@ page import="org.apache.commons.fileupload.FileItem" %>
<%@ page import="org.apache.commons.codec.binary.Base64" %>
<html>
<body>

    <jsp:include page="WEB-INF/jsp/global/css_include.jsp" flush="true" />

<link href="css/network/network_ui.css" type="text/css" rel="stylesheet"/>


<script type="text/javascript" src="js/lib/jquery.min.js"></script>
<script type="text/javascript" src="js/lib/jquery.tipTip.minified.js"></script>
<script type="text/javascript" src="js/lib/jquery.address.js"></script>
<script type="text/javascript" src="js/lib/jquery-ui.min.js"></script>
<script type="text/javascript" src="js/lib/jquery.popeye-2.1.min.js"></script>
<script type="text/javascript" src="js/lib/jquery.quovolver.mini.js"></script>
<script type="text/javascript" src="js/lib/cytoscape_web/AC_OETags.min.js"></script>
<script type="text/javascript" src="js/lib/cytoscape_web/cytoscapeweb.min.js"></script>

<script type="text/javascript" src="js/src/network/network-visualization.js"></script>
<script type="text/javascript" src="js/src/network/network-viz.js"></script>

<table width="100%" cellspacing="0px" cellpadding="2px" border="0px">
	<tr valign="middle">
		<td valign="middle" width="25%">
			<a href="http://www.mskcc.org"><img src="images/msk_logo.png" alt="MSKCC Logo"></a>
		</td>
		<td valign="middle" width="50%">
			<span id="header_site_name">
                            Network Visualization Service
			</span>
		</td>
		<td valign="middle" width="25%">
			Powered by:<br/><a href="http://cbioportal.org/"><%= GlobalProperties.getTitle() %></a>
		</td>
	</tr>
</table>
<script type="text/javascript">
    //alert('< %=org.mskcc.cbio.portal.util.ResponseUtil.getResponseString(request.getInputStream())%>');
</script>
                        
<%
String format = request.getParameter("format");
String graphml = null;

if (format!=null) {
    graphml = request.getParameter("graphml");
    if (graphml!=null&&!graphml.isEmpty()) {
        if (!format.equalsIgnoreCase("graphml")) {
            try {
                byte[] bytes = null;
                if (format.equalsIgnoreCase("graphml.gz")) {
                    bytes = graphml.getBytes();
                } else if (format.equalsIgnoreCase("graphml.gz.base64")) {
                    bytes = Base64.decodeBase64(graphml.getBytes());
                }

                if (bytes!=null) {
                    BufferedReader bufferedReader = new BufferedReader(
                            new InputStreamReader(new GZIPInputStream(<commit_msg>fixed outdated netviz.jsp by adding missing dependencies<commit_after><%@ page import="java.io.BufferedReader" %>
<%@ page import="java.io.ByteArrayInputStream" %>
<%@ page import="java.io.InputStream" %>
<%@ page import="java.io.InputStreamReader" %>
<%@ page import="java.util.zip.GZIPInputStream" %>
<%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %>
<%@ page import="org.mskcc.cbio.portal.util.FileUploadRequestWrapper" %>
<%@ page import="org.apache.commons.lang.StringEscapeUtils" %>
<%@ page import="org.apache.commons.fileupload.FileItem" %>
<%@ page import="org.apache.commons.codec.binary.Base64" %>
<html>
<body>

    <jsp:include page="WEB-INF/jsp/global/css_include.jsp" flush="true" />

<link href="css/network/network_ui.css" type="text/css" rel="stylesheet"/>


<script type="text/javascript" src="js/lib/jquery.min.js"></script>
<script type="text/javascript" src="js/lib/jquery.tipTip.minified.js"></script>
<script type="text/javascript" src="js/lib/jquery.address.min.js"></script>
<script type="text/javascript" src="js/lib/jquery-ui.min.js"></script>
<script type="text/javascript" src="js/lib/jquery.popeye-2.1.min.js"></script>
<script type="text/javascript" src="js/lib/jquery.quovolver.mini.js"></script>
<script type="text/javascript" src="js/lib/jquery.expander.min.js"></script>
<script type="text/javascript" src="js/lib/underscore-min.js"></script>
<script type="text/javascript" src="js/lib/backbone-min.js"></script>
<script type="text/javascript" src="js/lib/cytoscape_web/AC_OETags.min.js"></script>
<script type="text/javascript" src="js/lib/cytoscape_web/cytoscapeweb.min.js"></script>

<script type="text/javascript" src="js/src/network/network-visualization.js"></script>
<script type="text/javascript" src="js/src/network/network-viz.js"></script>

<jsp:include page="WEB-INF/jsp/network_views.jsp"/>

<table width="100%" cellspacing="0px" cellpadding="2px" border="0px">
	<tr valign="middle">
		<td valign="middle" width="25%">
			<a href="http://www.mskcc.org"><img src="images/msk_logo.png" alt="MSKCC Logo"></a>
		</td>
		<td valign="middle" width="50%">
			<span id="header_site_name">
                            Network Visualization Service
			</span>
		</td>
		<td valign="middle" width="25%">
			Powered by:<br/><a href="http://cbioportal.org/"><%= GlobalProperties.getTitle() %></a>
		</td>
	</tr>
</table>
<script type="text/javascript">
    //alert('< %=org.mskcc.cbio.portal.util.ResponseUtil.getResponseString(request.getInputStream())%>');

    // TODO duplicate code, see js_include.jsp
	// This is for the moustache-like templates
	// prevents collisions with JSP tags
	_.templateSettings = {
		interpolate : /\{\{(.+?)\}\}/g
	};

</script>
                        
<%
String format = request.getParameter("format");
String graphml = null;

if (format!=null) {
    graphml = request.getParameter("graphml");
    if (graphml!=null&&!graphml.isEmpty()) {
        if (!format.equalsIgnoreCase("graphml")) {
            try {
                byte[] bytes = null;
                if (format.equalsIgnoreCase("graphml.gz")) {
                    bytes = graphml.getBytes();
                } else if (format.equalsIgnoreCase("graphml.gz.base64")) {
                    bytes = Base64.decodeBase64(graphml.getBytes());
                }

                if (bytes!=null) {
                    BufferedReader bufferedReader = new BufferedReader(
                            new InputStreamReader(new GZIPInputStream(
{'fraction_non_alphanumeric': 0.18889578163771711, 'fraction_numerical': 0.006823821339950372, 'mean_word_length': 3.794795539033457, 'pattern_counts': {'":': 0, '<': 124, '<?xml version=': 0, '>': 122, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3725634', 'n_tokens_mistral': 2224, 'n_tokens_neox': 2083, 'n_words': 311}