License boilerplate, formatting.

src/js/config.js

@@ -1,3 +1,21 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 var scholarius_options = {
 };
 
@@ -32,7 +50,7 @@ var visjs_options = {
     leaf: {
       color: {
         border: '#fff',
-        background: '#31ae31',
+        background: '#fff',
         highlight: {
           border: '#fff',
           background: '#dd3'

src/js/crawler.js

@@ -1,3 +1,21 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 function ScholarCrawler(parser, nodes, edges)
 {
   this.stack = [];
@@ -21,8 +39,8 @@ ScholarCrawler.prototype.article_to_node = function(article)
     shape: 'dot',
     mass: article.n_citations/2 + 1,
     radius: 3*Math.pow(article.n_citations, 0.8) + 3,
-    title: "<span class='node_tooltip'>" + article.authors +
-      "<a href='' onclick='return open_external(\"" + article.url + "\")' target='_blank'> "
+    title: "<span class='node_tooltip'>" + article.authors + 
+      ".<a href='' onclick='return open_external(\"" + article.url + "\")' target='_blank'> "
       + article.title + ".</a> " + article.source + ", " + article.year + ".</span>"
   };
 };
@@ -126,21 +144,13 @@ ScholarCrawler.prototype._add_child_article = function(child_article, parent_nod
     }
   }
 
-  if(child_node.article.n_citations == 0)
-    child_node.group = "standard";
-  else if(levels == 0)
-    child_node.group = "leaf";
-  else
+  if(child_article.n_citations > 0 && levels > 0)
     this.push(child_node, levels-1);
 
   if(this.nodes.getIds().indexOf(child_node._id) < 0)
-  {
     this.nodes.add(child_node);
-  }
   else
-  {
     this.nodes.update(child_node);
-  }
 }
 
 ScholarCrawler.prototype.push = function(parent_node, levels)
@@ -152,9 +162,7 @@ ScholarCrawler.prototype.push = function(parent_node, levels)
   {
     parent_node.group = "processing";
     if(this.nodes.getIds().indexOf(parent_node._id) >= 0)
-    {
       this.nodes.update(parent_node);
-    }
   }
 };
 

src/js/main.js

@@ -1,3 +1,21 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 var assert = require('assert');
 var gui  = require('nw.gui');
 var nedb = require('nedb');

src/js/model/map.js

@@ -1,3 +1,21 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 function ScholarMap(seed_url)
 {
   this.edges = [];

src/js/parsers/generic_parser.js

@@ -1,3 +1,21 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 function GenericParser()
 {
     this.scopus_parser = new ScopusParser();

src/js/parsers/scopus_parser.js

@@ -1,68 +1,88 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 function ScopusParser()
 {
-};
+}
 
 ScopusParser.prototype._parse_results_page = 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();
-            return;
-        }
+  var iframe = document.createElement("iframe");
+  $(iframe).hide();
+  document.body.appendChild(iframe);
+  iframe.src = url;
+  $(iframe).load(function()
+  {
+    var articles = [];
+    var ibody = $(iframe).contents()[0];
 
-        $(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();
-            });
+    var select_pages = $(ibody.getElementsByName("resultsPerPage").item(0));
+    if(select_pages.val() != 200)
+    {
+      select_pages.val(200);
+      select_pages.change();
+      return;
+    }
 
-            $(li).find("a[href*='citedby']").each(function(index, tag) {
-                article.citations_url = tag.href;
-                article.n_citations = parseInt($(tag).text());
-            });
-            
-            $(li).find('.hidden-label').each(function(index, tag) {
-                if($(tag).text().indexOf("Year") == 0)
-                    article.year = parseInt($.trim($(tag).next().text()));
+    $(ibody).find(".resultItemLists li").each(function(index, li)
+    {
+      var article = {};
 
-                if($(tag).text().indexOf("Authors") == 0)
-                    article.authors = $.trim($(tag).next().text());
+      $(li).find(".docTitle a").each(function(index, tag)
+      {
+        article.url = tag.href;
+        article.title = $(tag).text();
+      });
 
-                if($(tag).text().indexOf("Source") == 0)
-                    article.source = $.trim($(tag).next().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(!('n_citations' in article)) {
-                article.citations_url = undefined;
-                article.n_citations = 0;
-            }
-            
-            article._id = $.md5(article.title + article.authors);
+        if($(tag).text().indexOf("Authors") == 0)
+          article.authors = $.trim($(tag).next().text());
 
-            articles.push(article);
-        });
+        if($(tag).text().indexOf("Source") == 0)
+          article.source = $.trim($(tag).next().text());
+      });
 
-        callback(articles);
-        document.body.removeChild(iframe);
+      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);
+  });
 }
 
 ScopusParser.prototype.parse = function(url, callback)
 {
-    if(url === undefined) return;
-    //if(url.indexOf("/results/") > 0 || url.indexOf("/search/") > 0)
-    this._parse_results_page(url, callback);
+  if(!url) return;
+  this._parse_results_page(url, callback);
 }

src/js/parsers/web_of_science_parser.js

@@ -1,72 +1,91 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 function WebOfScienceParser()
 {
-};
+}
 
 WebOfScienceParser.prototype._parse_results_page = function(url, callback)
 {
-	console.log("parsing");
-    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("pageSize").item(0));
-        if(select_pages.val() != 50) {
-            select_pages.val(50);
-            select_pages.change();
-            return;
-        }
-
-        $(ibody).find(".search-results-content").each(function(index, li)
-        {
-            var article = {};
-
-            $(li).find("a[href^='/full_record']").each(function(index, tag) {
-                article.url = tag.href;
-                article.title = $.trim($(tag).text());
-            });
+  console.log("parsing");
+  var iframe = document.createElement("iframe");
+  $(iframe).hide();
+  document.body.appendChild(iframe);
+  iframe.src = url;
 
-            $(li).next().find("a[href^='/CitingArticles']").each(function(index, tag) {
-                article.citations_url = tag.href;
-                article.n_citations = parseInt($(tag).text());
-            });
-            
-            $(li).find('span.label').each(function(index, tag) {
-                //if($(tag).text().indexOf("By:") == 0)
-                //    article.year = parseInt($.trim($(tag).next().text()));
+  $(iframe).load(function()
+  {
+    var articles = [];
+    var ibody = $(iframe).contents()[0];
 
-                if($(tag).text().indexOf("By:") == 0) {
-                    article.authors = $.trim($(tag).parent().text()).replace(/^By: /,"");
-					var source_year = $.trim($(tag).parent().next().text());
-                    article.source = source_year.replace(/Published.*/, "").replace(/\s\s+/g, ", ").replace(/, $/, "");
-                    article.year = parseInt(source_year.substr(source_year.length-4));
-				}
-            });
+    var select_pages = $(ibody.getElementsByName("pageSize").item(0));
+    if(select_pages.val() != 50)
+    {
+      select_pages.val(50);
+      select_pages.change();
+      return;
+    }
 
-            if(!('n_citations' in article)) {
-                article.citations_url = undefined;
-                article.n_citations = 0;
-            }
-            
-            article._id = $.md5(article.title + article.authors);
+    $(ibody).find(".search-results-content").each(function(index, li)
+    {
+      var article = {};
 
-            articles.push(article);
+      $(li).find("a[href^='/full_record']").each(function(index, tag)
+      {
+        article.url = tag.href;
+        article.title = $.trim($(tag).text());
+      });
 
-			console.log(article);
-        });
+      $(li).next().find("a[href^='/CitingArticles']").each(function(index, tag)
+      {
+        article.citations_url = tag.href;
+        article.n_citations = parseInt($(tag).text());
+      });
+      
+      $(li).find('span.label').each(function(index, tag)
+      {
+        if($(tag).text().indexOf("By:") == 0)
+        {
+          article.authors = $.trim($(tag).parent().text()).replace(/^By: /,"");
+          var source_year = $.trim($(tag).parent().next().text());
+          article.source = source_year.replace(/Published.*/, "")
+              .replace(/\s\s+/g, ", ").replace(/, $/, "");
+          article.year = parseInt(source_year.substr(source_year.length-4));
+        }
+      });
 
-        callback(articles);
-        document.body.removeChild(iframe);
+      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);
+  });
 }
 
 WebOfScienceParser.prototype.parse = function(url, callback)
 {
-    if(!url) return;
-    this._parse_results_page(url, callback);
+  if(!url) return;
+  this._parse_results_page(url, callback);
 }

src/js/views/main_menu.js

@@ -1,3 +1,21 @@
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
+
 function MainMenuView() {};
 
 MainMenuView.prototype.render = function(container)
@@ -22,7 +40,8 @@ MainMenuView.prototype.render = function(container)
             var ul = document.getElementById('saved_maps_container');
             var li = document.createElement("li");
 			var a = document.createElement("a");
-            a.onclick = function() {
+            a.onclick = function()
+            {
                 new ShowMapView(map).render(container);
                 return false;
             };

src/js/views/show_map.js

@@ -1,6 +1,20 @@
-//function ShowMapView(seed_url) {
-//  this.seed_url = seed_url;
-//};
+/* Copyright (C) 2014 Alinson Xavier
+ *
+ * This file is part of Scholarium.
+ *
+ * Scholarium is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * 
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this software. If not, see <http://www.gnu.org/licenses/>.
+ */
 
 function ShowMapView(map) {
   this.map = map;
@@ -14,6 +28,9 @@ ShowMapView.prototype.render = function(container)
   this.nodes.add(this.map.nodes);
   this.edges.add(this.map.edges);
 
+  document.nodes = this.nodes;
+  document.edges = this.edges;
+
   var parser = new GenericParser();
   var crawler = new ScholarCrawler(parser, this.nodes, this.edges);
   crawler.start();
@@ -34,7 +51,8 @@ ShowMapView.prototype.render = function(container)
   var data = { nodes: this.nodes, edges: this.edges };
   this.network = new vis.Network(network_div, data, visjs_options);
 
-  this.network.on('doubleClick', function(params) {
+  this.network.on('doubleClick', function(params)
+  {
     if(params.nodes.length > 0)
     {
       crawler.push(this.nodes.get(params.nodes[0]), 1);
@@ -52,7 +70,8 @@ ShowMapView.prototype.render = function(container)
     }
   }.bind(this));
 
-  this.network.on("resize", function(params) {
+  this.network.on("resize", function(params)
+  {
     var height = $(window).height();
     var width = $(window).width();
     $(".mynetwork").css("width", width);