<commit_before><!DOCTYPE HTML>
<html lang="eng" class="legacy">
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">

<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css"></link>
<script src="https://cdnjs.cloudflare.com/ajax/libs/js-url/2.5.3/url.min.js"></script>

<script>

    var queryParams = url("?");

    var host = "./files";
    var apiHost;

    function validateHost(host, url){
        return RegExp("^"+window.location.protocol+"//" + host).test(url);
    }

    apiHost = "//" +  decodeURIComponent(queryParams.apiHost);

    function writeScriptTag(path) {
        document.write('<script src="' + host + "/" + path + '"></' + 'script>');
    }

    function writeLinkTag(path) {
        document.write('<link rel="stylesheet" href="' + host + "/" + path + '"></' + 'link>');
    }

    writeLinkTag("bootstrap.min.css");
    writeLinkTag("responsiveslides.css");
    writeLinkTag("tipTip.css");
    writeLinkTag("jquery.qtip.min.css");
    writeLinkTag("jquery-ui-1.10.3.custom.css");
    writeLinkTag("data_table.css");
    writeLinkTag("data_table.css");
    writeLinkTag("dataTables.tableTools.min.css");
    writeLinkTag("data_table_jui.css");
    writeLinkTag("data_table_ColVis.css");
    writeLinkTag("custom_case_set.css");
    writeLinkTag("ui.dropdownchecklist.themeroller.css");
    writeLinkTag("chosen.css");
    writeLinkTag("jstree.style.css");
    writeLinkTag("bootstrap-dialog.css");
    writeLinkTag("oncoprint.css");
    writeLinkTag("header.css");
    writeLinkTag("vc-session.css");
    writeLinkTag("global_portal.css");
    writeLinkTag("network_ui.css");
    writeLinkTag("cytoscape.js-panzoom.css");


    writeScriptTag("jquery.min.js");
    writeScriptTag("jquery-migrate.js");

</script>


<script>
    writeScriptTag("jquery.cookie.js");
    writeScriptTag("jquery.address.min.js");
    writeScriptTag("jquery.expander.min.js");
    writeScriptTag("jquery.tipTip.minified.js");
    writeScriptTag("jquery-ui.min.js");
    writeScriptTag("jquery.qtip.min.js");
    writeScriptTag("chosen.jquery.js");
    writeScriptTag("ui.tabs.paging.js");
    writeScriptTag("FileSaver.min.js");
    writeScriptTag("mailme.js");
    writeScriptTag("json2.js");
    writeScriptTag("ui.dropdownchecklist-1.4-min.js");
    writeScriptTag("underscore-min.js");
    writeScriptTag("backbone-min.js");
    writeScriptTag("d3.min.js");

    writeScriptTag("cbio-util.js");
    writeScriptTag("download-util.js");
    writeScriptTag("json2.js");
    writeScriptTag("cytoscape.js");
    writeScriptTag("cytoscape.js-panzoom.js");
    writeScriptTag("layout.cose-bilkent.js");
    writeScriptTag("network-visualization.js");
    writeScriptTag("GraphMLIO.js");
    writeScriptTag("network-viz2.js");
    writeScriptTag("cytoscape.renderer.canvas.portal-renderer.js");
    writeScriptTag("d3.min.js");

</script>

<script>
    function formSubmit(path, params, target, method) {
        // method="smart" means submit with GET iff the URL wouldn't be too long

        const form = document.createElement('form');
        let computedMethod = method;
        if (method === "smart") {
            computedMethod = buildCBioPortalPageUrl(path, params).length > 1800 ? "post" : "get"; // use POST if URL will be too large for some browsers
        }
        form.setAttribute('method', computedMethod);
        form.setAttribute('action', path);
        if (target) {
            form.setAttribute('target', target);
        }

        for (const key of Object.keys(params)) {
            const hiddenField = document.createElement('input');
            hiddenField.setAttribute('type', 'hidden');
            hiddenField.setAttribute('name', key);
            hiddenField.setAttribute('value', params[key]);
            form.appendChild(hiddenField);
        }

        document.body.appendChild(form);
        form.submit();
    }
</script>

<script type="text/javascript">
    // This is for the moustache-like templates
    // prevents collisions with JSP tags
    _.templateSettings = {
        interpolate: /\{\{(.+?)\}\}/g
    };

    // calls to network do must now include all case ids
    // so we need to hijack click and form submit
    $(document).ready(function(){
        $("body").on("click","#netmsg a",function(e){
            e.preventDefault();

            switch(this.innerText) {
                case "GraphML":
                    e.preventDefault();
                    formSubmit("http://www.cbioportal.org/beta/network.do?download=on", networkParams, "_self", "post");
                    break;
                case "SIF":
                    e.preventDefault();
                    formSubmit("http://www.cbioportal.org/beta/network.do?download=on&format=sif", networkParams, "_self", "post");<commit_msg>Fix hardcoding of download urls in network tab<commit_after><!DOCTYPE HTML>
<html lang="eng" class="legacy">
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">

<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css"></link>
<script src="https://cdnjs.cloudflare.com/ajax/libs/js-url/2.5.3/url.min.js"></script>

<script>

    var queryParams = url("?");

    var host = "./files";
    var apiHost;

    function validateHost(host, url){
        return RegExp("^"+window.location.protocol+"//" + host).test(url);
    }

    apiHost = "//" +  decodeURIComponent(queryParams.apiHost);

    function writeScriptTag(path) {
        document.write('<script src="' + host + "/" + path + '"></' + 'script>');
    }

    function writeLinkTag(path) {
        document.write('<link rel="stylesheet" href="' + host + "/" + path + '"></' + 'link>');
    }

    writeLinkTag("bootstrap.min.css");
    writeLinkTag("responsiveslides.css");
    writeLinkTag("tipTip.css");
    writeLinkTag("jquery.qtip.min.css");
    writeLinkTag("jquery-ui-1.10.3.custom.css");
    writeLinkTag("data_table.css");
    writeLinkTag("data_table.css");
    writeLinkTag("dataTables.tableTools.min.css");
    writeLinkTag("data_table_jui.css");
    writeLinkTag("data_table_ColVis.css");
    writeLinkTag("custom_case_set.css");
    writeLinkTag("ui.dropdownchecklist.themeroller.css");
    writeLinkTag("chosen.css");
    writeLinkTag("jstree.style.css");
    writeLinkTag("bootstrap-dialog.css");
    writeLinkTag("oncoprint.css");
    writeLinkTag("header.css");
    writeLinkTag("vc-session.css");
    writeLinkTag("global_portal.css");
    writeLinkTag("network_ui.css");
    writeLinkTag("cytoscape.js-panzoom.css");


    writeScriptTag("jquery.min.js");
    writeScriptTag("jquery-migrate.js");

</script>


<script>
    writeScriptTag("jquery.cookie.js");
    writeScriptTag("jquery.address.min.js");
    writeScriptTag("jquery.expander.min.js");
    writeScriptTag("jquery.tipTip.minified.js");
    writeScriptTag("jquery-ui.min.js");
    writeScriptTag("jquery.qtip.min.js");
    writeScriptTag("chosen.jquery.js");
    writeScriptTag("ui.tabs.paging.js");
    writeScriptTag("FileSaver.min.js");
    writeScriptTag("mailme.js");
    writeScriptTag("json2.js");
    writeScriptTag("ui.dropdownchecklist-1.4-min.js");
    writeScriptTag("underscore-min.js");
    writeScriptTag("backbone-min.js");
    writeScriptTag("d3.min.js");

    writeScriptTag("cbio-util.js");
    writeScriptTag("download-util.js");
    writeScriptTag("json2.js");
    writeScriptTag("cytoscape.js");
    writeScriptTag("cytoscape.js-panzoom.js");
    writeScriptTag("layout.cose-bilkent.js");
    writeScriptTag("network-visualization.js");
    writeScriptTag("GraphMLIO.js");
    writeScriptTag("network-viz2.js");
    writeScriptTag("cytoscape.renderer.canvas.portal-renderer.js");
    writeScriptTag("d3.min.js");

</script>

<script>
    function formSubmit(path, params, target, method) {
        // method="smart" means submit with GET iff the URL wouldn't be too long

        const form = document.createElement('form');
        let computedMethod = method;
        if (method === "smart") {
            computedMethod = buildCBioPortalPageUrl(path, params).length > 1800 ? "post" : "get"; // use POST if URL will be too large for some browsers
        }
        form.setAttribute('method', computedMethod);
        form.setAttribute('action', path);
        if (target) {
            form.setAttribute('target', target);
        }

        for (const key of Object.keys(params)) {
            const hiddenField = document.createElement('input');
            hiddenField.setAttribute('type', 'hidden');
            hiddenField.setAttribute('name', key);
            hiddenField.setAttribute('value', params[key]);
            form.appendChild(hiddenField);
        }

        document.body.appendChild(form);
        form.submit();
    }
</script>

<script type="text/javascript">
    // This is for the moustache-like templates
    // prevents collisions with JSP tags
    _.templateSettings = {
        interpolate: /\{\{(.+?)\}\}/g
    };

    // calls to network do must now include all case ids
    // so we need to hijack click and form submit
    $(document).ready(function(){
        $("body").on("click","#netmsg a",function(e){
            e.preventDefault();

            switch(this.innerText) {
                case "GraphML":
                    e.preventDefault();
                    formSubmit(apiHost + "network.do?download=on", networkParams, "_self", "post");
                    break;
                case "SIF":
                    e.preventDefault();
                    formSubmit(apiHost + "network.do?download=on&format=sif", networkParams, "_self", "post");
{'fraction_non_alphanumeric': 0.16627322180026685, 'fraction_numerical': 0.004516062814328235, 'mean_word_length': 3.1605465414175917, 'pattern_counts': {'":': 4, '<': 43, '<?xml version=': 0, '>': 45, 'https://': 2, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 7, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5383783', 'n_tokens_mistral': 3067, 'n_tokens_neox': 2999, 'n_words': 460}