Initial commit.

src/app/config.js

@@ -0,0 +1,52 @@
+var visjs_options = {
+  nodes: {
+    color: {
+        border: '#bbb',
+        background: '#fff',
+      highlight: {
+        border: '#fff',
+        background: '#dd3'
+      },
+      hover: {
+        border: '#2B7CE9',
+        background: '#D2E5FF'
+      }
+    },
+  },
+
+  edges: {
+    color: {
+      color:'rgba(255, 255, 255, 0.15)',
+      highlight:'#dd3',
+      hover: '#0000FF'
+    },
+    style: "arrow",
+    width: 1.5,
+    arrowScaleFactor: 0.25
+  },
+
+  tooltip: {
+    delay: 300,
+    fontColor: "#fff",
+    fontSize: 14, // px
+    fontFace: "verdana",
+    color: {
+      border: "#000",
+      background: "rgba(0,0,0,0.5)"
+    }
+  },
+
+  physics: {
+    barnesHut: {
+        enabled: true,
+        gravitationalConstant: -2000,
+        centralGravity: 0.2,
+        springLength: 95,
+        springConstant: 0.04,
+        damping: 0.15
+    }
+  }
+};
+
+var seed_url = 'http://www.scopus.com/results/results.url?sort=plf-f&src=s&st1=urea+permeation+immobilized&sid=B0FE19FE3CFF4CCF86DD857756E90636.FZg2ODcJC9ArCe8WOZPvA%3a1400&sot=b&sdt=b&sl=34&s=TITLE%28urea+permeation+immobilized%29&origin=searchbasic&txGid=B0FE19FE3CFF4CCF86DD857756E90636.FZg2ODcJC9ArCe8WOZPvA%3a140';
+

src/app/crawler.js

@@ -0,0 +1,80 @@
+function ScholarCrawler(parser, node_ids, nodes, edges)
+{
+	this.stack = [];
+
+	this.node_ids = node_ids;
+	this.parser = parser;
+	this.nodes = nodes;
+	this.edges = edges;
+
+	this.delay = 1000;
+	this.max_depth = 2;
+	this.minimum_citations = 0;
+};
+
+ScholarCrawler.prototype.formatArticle = function(node)
+{
+	node.label = '';
+	node.shape = "dot";
+	node.original_title = node.title;
+	node.title =
+		"<span class='node_tooltip'>" + node.authors +
+		"<emph> " + node.title + ".</emph> " +
+		node.source + ", " + node.year + ".</span>";
+	node.mass = node.n_citations/2 + 1;
+	node.radius = 3*Math.pow(node.n_citations, 0.8) + 3;
+	return node;
+};
+
+ScholarCrawler.prototype.process = function(url, parent_node)
+{
+	var crawler = this;
+
+	this.parser.parse(url, function(children)
+	{
+		for(i=0; i<children.length; i++)
+		{
+			var child = crawler.formatArticle(children[i]);
+
+			if(parent_node == null)
+			{
+				child['depth'] = 0;
+			}
+			else
+			{
+				child['depth'] = parent_node['depth'] + 1;
+				crawler.edges.add({"from": child['id'], "to": parent_node['id']});
+			}
+
+			if(child['n_citations'] < crawler.minimum_citations)
+				continue;
+
+			if(crawler.node_ids.indexOf(child['id']) == -1)
+			{
+				crawler.node_ids.push(child['id']);
+				crawler.nodes.add(child);
+
+				if(child['depth'] < crawler.max_depth) {
+					crawler.push(child['citations_url'], child);
+				}
+			}
+		}
+	});
+};
+
+ScholarCrawler.prototype.push = function(url, parent_node)
+{
+	this.stack.push([url, parent_node]);
+};
+
+ScholarCrawler.prototype.start = function()
+{
+	if(this.stack.length > 0)
+	{
+		var args = this.stack.pop();
+		this.process.apply(this, args);
+	}
+
+	var crawler = this;
+	setTimeout(function() { crawler.start() }, this.delay);
+};

src/app/main.js

@@ -0,0 +1,7 @@
+var gui = require('nw.gui');
+var win = gui.Window.get();
+
+win.maximize();
+
+var view = new MainMenuView();
+view.render(document.getElementById("main"));

src/app/scopus.js

@@ -0,0 +1,58 @@
+function ScopusParser() {};
+
+ScopusParser.prototype.parse = function(url, callback)
+{
+    var iframe = document.createElement("iframe");
+    $(iframe).hide();
+    document.body.appendChild(iframe);
+    iframe.src = url;
+    $(iframe).load(function()
+    {
+        var articles = [];
+        var ibody = $(iframe).contents()[0];
+
+        var select_pages = $(ibody.getElementsByName("resultsPerPage").item(0));
+        if(select_pages.val() != 200) {
+            select_pages.val(200);
+            select_pages.change();
+        }
+
+        $(ibody).find(".resultItemLists li").each(function(index, li)
+        {
+            var article = {};
+
+            $(li).find(".docTitle a").each(function(index, tag) {
+                article['url'] = tag.href;
+                article['title'] = $(tag).text();
+            });
+
+            $(li).find("a[href*='citedby']").each(function(index, tag) {
+                article['citations_url'] = tag.href;
+                article['n_citations'] = parseInt($(tag).text());
+            });
+            
+            $(li).find('.hidden-label').each(function(index, tag) {
+                if($(tag).text().indexOf("Year") == 0)
+                    article['year'] = parseInt($.trim($(tag).next().text()));
+
+                if($(tag).text().indexOf("Authors") == 0)
+                    article['authors'] = $.trim($(tag).next().text());
+
+                if($(tag).text().indexOf("Source") == 0)
+                    article['source'] = $.trim($(tag).next().text());
+            });
+
+            if(!('n_citations' in article)) {
+                article['citations_url'] = undefined;
+                article['n_citations'] = 0;
+            }
+            
+            article['id'] = $.md5(article['title'] + article['authors']);
+
+            articles.push(article);
+        });
+
+        callback(articles);
+        document.body.removeChild(iframe);
+    });
+}

src/app/templates/main_menu.html

@@ -0,0 +1,6 @@
+<div class="frame">
+  <h1>Scholarium</h1>
+  <form action="">
+    <input name="url" autocomplete="off"></input>
+  </form>
+</div>

src/app/views/main_menu.js

@@ -0,0 +1,20 @@
+function MainMenuView() {};
+
+MainMenuView.prototype.render = function(container)
+{
+    var main_menu_div = document.createElement("div");
+    $(main_menu_div).addClass("main_menu");
+
+    $(main_menu_div).load("app/templates/main_menu.html", function() {
+        document.forms[0].onsubmit = function() {
+            var seed_url = $("input[name=url]").val();
+            var view = new ShowMapView(seed_url);
+            view.render(container);
+            return false;
+        };
+    });
+
+    $(container).empty();
+    $(container).removeClass();
+    container.appendChild(main_menu_div);
+}

src/app/views/show_map.js

@@ -0,0 +1,34 @@
+function ShowMapView(seed_url) {
+	this.seed_url = seed_url;
+};
+
+ShowMapView.prototype.render = function(container)
+{
+    var node_ids = [];
+    var edges = new vis.DataSet();
+    var nodes = new vis.DataSet();
+
+    var parser = new ScopusParser();
+    var crawler = new ScholarCrawler(parser, node_ids, nodes, edges);
+    crawler.push(this.seed_url, null);
+    crawler.start();
+
+    var network_div = document.createElement('div');
+    $(network_div).addClass("mynetwork");
+    $(container).empty();
+    container.appendChild(network_div)
+
+    var data = { nodes: nodes, edges: edges };
+    var network = new vis.Network(network_div, data, visjs_options);
+
+    network.on('doubleClick', function(params) {
+        gui.Shell.openExternal(nodes.get(params.nodes[0]).url)
+    });
+
+    network.on("resize", function(params) {
+        var height = $(window).height();
+        var width = $(window).width();
+        $(".mynetwork").css("width", width);
+        $(".mynetwork").css("height", height);
+    });
+};

src/css/main.css

@@ -0,0 +1,29 @@
+@import url(http://fonts.googleapis.com/css?family=Dosis:400,700&subset=latin,latin-ext);
+
+body {
+  background-color: #066;
+}
+
+html, body {
+  margin: 0;
+  padding: 0;
+  height: 100%;
+  overflow: hidden;
+}
+
+* {
+    font-family: 'Dosis';
+}
+
+#scopus-iframe {
+  display: none;
+}
+
+.node_tooltip {
+    color: rgba(255, 255, 255, 0.5);
+}
+
+.node_tooltip emph {
+    color: #fff;
+    font-weight: bold;
+}

src/css/main_menu.css

@@ -0,0 +1,36 @@
+.main_menu {
+    text-align: center;
+    font-size: 16px;
+    font-family: sans;
+    height: 100vh;
+}
+
+.main_menu input {
+    color: #000;
+    background-color: #fff;
+    border: 0;
+    border: 2px solid #fff;
+  
+    font-size: 20px;
+	min-width: 600px;
+    padding: 8px 12px;
+    outline: 0;
+	
+}
+
+.main_menu h1 {
+    color: #fff;
+    font-size: 60px;
+}
+
+.main_menu .frame {
+    margin: 0 auto;
+    padding: 1px 1px 50px 1px;
+    background-color: rgba(0,0,0,0);
+    box-shadow: 2px 2px 100px #388;
+    width: 800px;
+    
+    top: 50%;
+    position: relative;
+    -webkit-transform: translateY(-50%);
+}

src/index.html

@@ -0,0 +1,25 @@
+<!doctype html>
+<html>
+<head>
+    <title>Scholar Explorer</title>
+
+    <script type="text/javascript" src="lib/jquery.min.js"></script>
+    <script type="text/javascript" src="lib/vis.js"></script>
+    <script type="text/javascript" src="lib/md5.js"></script>
+
+    <script type="text/javascript" src="app/scopus.js"></script>
+    <script type="text/javascript" src="app/crawler.js"></script>
+    <script type="text/javascript" src="app/config.js"></script>
+
+	<script type="text/javascript" src="app/views/show_map.js"></script>
+    <script type="text/javascript" src="app/views/main_menu.js"></script>
+
+	<link rel="stylesheet" type="text/css" href="css/main.css">
+	<link rel="stylesheet" type="text/css" href="css/main_menu.css">
+</head>
+
+<body>
+	<div id="main"></div>
+    <script type="text/javascript" src="app/main.js"></script>
+</body>
+</html>

src/lib/md5.js

@@ -0,0 +1,269 @@
+/*
+ * jQuery MD5 Plugin 1.2.1
+ * https://github.com/blueimp/jQuery-MD5
+ *
+ * Copyright 2010, Sebastian Tschan
+ * https://blueimp.net
+ *
+ * Licensed under the MIT license:
+ * http://creativecommons.org/licenses/MIT/
+ * 
+ * Based on
+ * A JavaScript implementation of the RSA Data Security, Inc. MD5 Message
+ * Digest Algorithm, as defined in RFC 1321.
+ * Version 2.2 Copyright (C) Paul Johnston 1999 - 2009
+ * Other contributors: Greg Holt, Andrew Kepert, Ydnar, Lostinet
+ * Distributed under the BSD License
+ * See http://pajhome.org.uk/crypt/md5 for more info.
+ */
+
+/*jslint bitwise: true */
+/*global unescape, jQuery */
+
+(function ($) {
+    'use strict';
+
+    /*
+    * Add integers, wrapping at 2^32. This uses 16-bit operations internally
+    * to work around bugs in some JS interpreters.
+    */
+    function safe_add(x, y) {
+        var lsw = (x & 0xFFFF) + (y & 0xFFFF),
+            msw = (x >> 16) + (y >> 16) + (lsw >> 16);
+        return (msw << 16) | (lsw & 0xFFFF);
+    }
+
+    /*
+    * Bitwise rotate a 32-bit number to the left.
+    */
+    function bit_rol(num, cnt) {
+        return (num << cnt) | (num >>> (32 - cnt));
+    }
+
+    /*
+    * These functions implement the four basic operations the algorithm uses.
+    */
+    function md5_cmn(q, a, b, x, s, t) {
+        return safe_add(bit_rol(safe_add(safe_add(a, q), safe_add(x, t)), s), b);
+    }
+    function md5_ff(a, b, c, d, x, s, t) {
+        return md5_cmn((b & c) | ((~b) & d), a, b, x, s, t);
+    }
+    function md5_gg(a, b, c, d, x, s, t) {
+        return md5_cmn((b & d) | (c & (~d)), a, b, x, s, t);
+    }
+    function md5_hh(a, b, c, d, x, s, t) {
+        return md5_cmn(b ^ c ^ d, a, b, x, s, t);
+    }
+    function md5_ii(a, b, c, d, x, s, t) {
+        return md5_cmn(c ^ (b | (~d)), a, b, x, s, t);
+    }
+
+    /*
+    * Calculate the MD5 of an array of little-endian words, and a bit length.
+    */
+    function binl_md5(x, len) {
+        /* append padding */
+        x[len >> 5] |= 0x80 << ((len) % 32);
+        x[(((len + 64) >>> 9) << 4) + 14] = len;
+
+        var i, olda, oldb, oldc, oldd,
+            a =  1732584193,
+            b = -271733879,
+            c = -1732584194,
+            d =  271733878;
+
+        for (i = 0; i < x.length; i += 16) {
+            olda = a;
+            oldb = b;
+            oldc = c;
+            oldd = d;
+
+            a = md5_ff(a, b, c, d, x[i],       7, -680876936);
+            d = md5_ff(d, a, b, c, x[i +  1], 12, -389564586);
+            c = md5_ff(c, d, a, b, x[i +  2], 17,  606105819);
+            b = md5_ff(b, c, d, a, x[i +  3], 22, -1044525330);
+            a = md5_ff(a, b, c, d, x[i +  4],  7, -176418897);
+            d = md5_ff(d, a, b, c, x[i +  5], 12,  1200080426);
+            c = md5_ff(c, d, a, b, x[i +  6], 17, -1473231341);
+            b = md5_ff(b, c, d, a, x[i +  7], 22, -45705983);
+            a = md5_ff(a, b, c, d, x[i +  8],  7,  1770035416);
+            d = md5_ff(d, a, b, c, x[i +  9], 12, -1958414417);
+            c = md5_ff(c, d, a, b, x[i + 10], 17, -42063);
+            b = md5_ff(b, c, d, a, x[i + 11], 22, -1990404162);
+            a = md5_ff(a, b, c, d, x[i + 12],  7,  1804603682);
+            d = md5_ff(d, a, b, c, x[i + 13], 12, -40341101);
+            c = md5_ff(c, d, a, b, x[i + 14], 17, -1502002290);
+            b = md5_ff(b, c, d, a, x[i + 15], 22,  1236535329);
+
+            a = md5_gg(a, b, c, d, x[i +  1],  5, -165796510);
+            d = md5_gg(d, a, b, c, x[i +  6],  9, -1069501632);
+            c = md5_gg(c, d, a, b, x[i + 11], 14,  643717713);
+            b = md5_gg(b, c, d, a, x[i],      20, -373897302);
+            a = md5_gg(a, b, c, d, x[i +  5],  5, -701558691);
+            d = md5_gg(d, a, b, c, x[i + 10],  9,  38016083);
+            c = md5_gg(c, d, a, b, x[i + 15], 14, -660478335);
+            b = md5_gg(b, c, d, a, x[i +  4], 20, -405537848);
+            a = md5_gg(a, b, c, d, x[i +  9],  5,  568446438);
+            d = md5_gg(d, a, b, c, x[i + 14],  9, -1019803690);
+            c = md5_gg(c, d, a, b, x[i +  3], 14, -187363961);
+            b = md5_gg(b, c, d, a, x[i +  8], 20,  1163531501);
+            a = md5_gg(a, b, c, d, x[i + 13],  5, -1444681467);
+            d = md5_gg(d, a, b, c, x[i +  2],  9, -51403784);
+            c = md5_gg(c, d, a, b, x[i +  7], 14,  1735328473);
+            b = md5_gg(b, c, d, a, x[i + 12], 20, -1926607734);
+
+            a = md5_hh(a, b, c, d, x[i +  5],  4, -378558);
+            d = md5_hh(d, a, b, c, x[i +  8], 11, -2022574463);
+            c = md5_hh(c, d, a, b, x[i + 11], 16,  1839030562);
+            b = md5_hh(b, c, d, a, x[i + 14], 23, -35309556);
+            a = md5_hh(a, b, c, d, x[i +  1],  4, -1530992060);
+            d = md5_hh(d, a, b, c, x[i +  4], 11,  1272893353);
+            c = md5_hh(c, d, a, b, x[i +  7], 16, -155497632);
+            b = md5_hh(b, c, d, a, x[i + 10], 23, -1094730640);
+            a = md5_hh(a, b, c, d, x[i + 13],  4,  681279174);
+            d = md5_hh(d, a, b, c, x[i],      11, -358537222);
+            c = md5_hh(c, d, a, b, x[i +  3], 16, -722521979);
+            b = md5_hh(b, c, d, a, x[i +  6], 23,  76029189);
+            a = md5_hh(a, b, c, d, x[i +  9],  4, -640364487);
+            d = md5_hh(d, a, b, c, x[i + 12], 11, -421815835);
+            c = md5_hh(c, d, a, b, x[i + 15], 16,  530742520);
+            b = md5_hh(b, c, d, a, x[i +  2], 23, -995338651);
+
+            a = md5_ii(a, b, c, d, x[i],       6, -198630844);
+            d = md5_ii(d, a, b, c, x[i +  7], 10,  1126891415);
+            c = md5_ii(c, d, a, b, x[i + 14], 15, -1416354905);
+            b = md5_ii(b, c, d, a, x[i +  5], 21, -57434055);
+            a = md5_ii(a, b, c, d, x[i + 12],  6,  1700485571);
+            d = md5_ii(d, a, b, c, x[i +  3], 10, -1894986606);
+            c = md5_ii(c, d, a, b, x[i + 10], 15, -1051523);
+            b = md5_ii(b, c, d, a, x[i +  1], 21, -2054922799);
+            a = md5_ii(a, b, c, d, x[i +  8],  6,  1873313359);
+            d = md5_ii(d, a, b, c, x[i + 15], 10, -30611744);
+            c = md5_ii(c, d, a, b, x[i +  6], 15, -1560198380);
+            b = md5_ii(b, c, d, a, x[i + 13], 21,  1309151649);
+            a = md5_ii(a, b, c, d, x[i +  4],  6, -145523070);
+            d = md5_ii(d, a, b, c, x[i + 11], 10, -1120210379);
+            c = md5_ii(c, d, a, b, x[i +  2], 15,  718787259);
+            b = md5_ii(b, c, d, a, x[i +  9], 21, -343485551);
+
+            a = safe_add(a, olda);
+            b = safe_add(b, oldb);
+            c = safe_add(c, oldc);
+            d = safe_add(d, oldd);
+        }
+        return [a, b, c, d];
+    }
+
+    /*
+    * Convert an array of little-endian words to a string
+    */
+    function binl2rstr(input) {
+        var i,
+            output = '';
+        for (i = 0; i < input.length * 32; i += 8) {
+            output += String.fromCharCode((input[i >> 5] >>> (i % 32)) & 0xFF);
+        }
+        return output;
+    }
+
+    /*
+    * Convert a raw string to an array of little-endian words
+    * Characters >255 have their high-byte silently ignored.
+    */
+    function rstr2binl(input) {
+        var i,
+            output = [];
+        output[(input.length >> 2) - 1] = undefined;
+        for (i = 0; i < output.length; i += 1) {
+            output[i] = 0;
+        }
+        for (i = 0; i < input.length * 8; i += 8) {
+            output[i >> 5] |= (input.charCodeAt(i / 8) & 0xFF) << (i % 32);
+        }
+        return output;
+    }
+
+    /*
+    * Calculate the MD5 of a raw string
+    */
+    function rstr_md5(s) {
+        return binl2rstr(binl_md5(rstr2binl(s), s.length * 8));
+    }
+
+    /*
+    * Calculate the HMAC-MD5, of a key and some data (raw strings)
+    */
+    function rstr_hmac_md5(key, data) {
+        var i,
+            bkey = rstr2binl(key),
+            ipad = [],
+            opad = [],
+            hash;
+        ipad[15] = opad[15] = undefined;                        
+        if (bkey.length > 16) {
+            bkey = binl_md5(bkey, key.length * 8);
+        }
+        for (i = 0; i < 16; i += 1) {
+            ipad[i] = bkey[i] ^ 0x36363636;
+            opad[i] = bkey[i] ^ 0x5C5C5C5C;
+        }
+        hash = binl_md5(ipad.concat(rstr2binl(data)), 512 + data.length * 8);
+        return binl2rstr(binl_md5(opad.concat(hash), 512 + 128));
+    }
+
+    /*
+    * Convert a raw string to a hex string
+    */
+    function rstr2hex(input) {
+        var hex_tab = '0123456789abcdef',
+            output = '',
+            x,
+            i;
+        for (i = 0; i < input.length; i += 1) {
+            x = input.charCodeAt(i);
+            output += hex_tab.charAt((x >>> 4) & 0x0F) +
+                hex_tab.charAt(x & 0x0F);
+        }
+        return output;
+    }
+
+    /*
+    * Encode a string as utf-8
+    */
+    function str2rstr_utf8(input) {
+        return unescape(encodeURIComponent(input));
+    }
+
+    /*
+    * Take string arguments and return either raw or hex encoded strings
+    */
+    function raw_md5(s) {
+        return rstr_md5(str2rstr_utf8(s));
+    }
+    function hex_md5(s) {
+        return rstr2hex(raw_md5(s));
+    }
+    function raw_hmac_md5(k, d) {
+        return rstr_hmac_md5(str2rstr_utf8(k), str2rstr_utf8(d));
+    }
+    function hex_hmac_md5(k, d) {
+        return rstr2hex(raw_hmac_md5(k, d));
+    }
+    
+    $.md5 = function (string, key, raw) {
+        if (!key) {
+            if (!raw) {
+                return hex_md5(string);
+            } else {
+                return raw_md5(string);
+            }
+        }
+        if (!raw) {
+            return hex_hmac_md5(key, string);
+        } else {
+            return raw_hmac_md5(key, string);
+        }
+    };
+    
+}(typeof jQuery === 'function' ? jQuery : this));

src/package.json

@@ -0,0 +1,12 @@
+{
+  "name": "Scholarium",
+  "version": "0.1-pre",
+  "main": "index.html",
+  "window": {
+    "toolbar": false,
+    "min_width": 400,
+    "min_height": 400,
+    "width": 900,
+    "height": 600
+  }
+}