GUI: changed link from arc to straight line. Cleaned up javascript.
diff --git a/web/js/onos-topology.js b/web/js/onos-topology.js
index a5d84cc..61eb9da 100644
--- a/web/js/onos-topology.js
+++ b/web/js/onos-topology.js
@@ -15,279 +15,14 @@
     var path = svg.selectAll("path");
     var circle = svg.selectAll("circle");
     var text = svg.selectAll("g");
+    var node_drag = d3.behavior.drag()
+        .on("dragstart", dragstart)
+        .on("drag", dragmove)
+        .on("dragend", dragend);
 
     d3.json(data_source, init);
 
-    function init(json){
-        nodes = force.nodes();
-        links = force.links();
-
-	json.nodes.forEach(function(item) {
-            nodes.push(item);
-	});
-	json.links.forEach(function(item) {
-            links.push(item);
-	});
-	draw(nodes, links);
-    }
-    function gone_links (json, links, gone) {
-	for (var i = 0; i < links.length ; i ++){
-	    var found = 0;
-	    for (var j = 0; j < json.links.length ; j ++){
-		if (links[i].source.name == json.nodes[json.links[j].source].name && 
-		    links[i].target.name == json.nodes[json.links[j].target].name ){
-		    found = 1;
-		    break;
-		}
-	    }
-	    if ( found == 0 ){
-		gone.push(links[i]);
-	    }
-	}
-	return gone;
-    }
-    function added_links (json, links, added) {
-	for (var j = 0; j < json.links.length ; j ++){
-	    var found = 0;
-	    for (var i = 0; i < links.length ; i ++){
-		if (links[i].source.name == json.nodes[json.links[j].source].name && 
-		    links[i].target.name == json.nodes[json.links[j].target].name ){
-		    found = 1;
-		    break;
-		}
-	    }
-	    if ( found == 0 ){
-		added.push(json.links[j]);
-	    }
-	}
-	return added;
-    }
-
-    function update(json) {
-	Array.prototype.diff2 = function(arr) {
-	    return this.filter(function(i) {
-		for (var j = 0; j < arr.length ; j++) {
-		    if (arr[j].source === i.source.index && 
-			arr[j].target === i.target.index)
-			return false;
-		}
-		return true;
-	    });
-	};
-
-	Array.prototype.diff = function(arr) {
-	    return this.filter(function(i) {
-		for (var j = 0; j < arr.length ; j++) {
-		    if (arr[j].source.index === i.source && 
-			arr[j].target.index === i.target)
-			return false;
-		}
-		return true;
-	    });
-	};
-
-	Array.prototype.node_diff = function(arr) {
-	    return this.filter(function(i) {
-		for (var j = 0; j < arr.length ; j++) {
-		    if (arr[j].name === i.name)
-			return false;
-		}
-		return true;
-	    });
-	};
-
-
-//        links.sort(function(a,b) {
-//            if (a.source > b.source) {return 1;}
-//            else if (a.source < b.source) {return -1;}
-//            else {
-//                if (a.target > b.target) {return 1;}
-//                if (a.target < b.target) {return -1;}
-//                else {return 0;}
-//            }
-//        });
-//        for (var i=0; i<links.length; i++) {
-//          if (i != 0 &&
-//            links[i].source == links[i-1].source &&
-//            links[i].target == links[i-1].target) {
-//            links[i].linknum = links[i-1].linknum + 1;
-//          }
-//          else {links[i].linknum = 1;};
-//        };
-
-	function cdiff(topo) {
-            var changed = false;
-
-            var n_adds = topo.nodes.node_diff(nodes);
-            var n_rems = nodes.node_diff(topo.nodes);
-            for (var i = 0; i < n_adds.length; i++) {
-		nodes.push(n_adds[i]);
-		changed = true;
-            }
-            for (var i = 0; i < n_rems.length; i++) {
-		for (var j = 0; j < nodes.length; j++) {
-		    if ( nodes[j].name == n_rems[i].name ){
-			nodes.splice(j,1);
-			changed = true;
-			break;
-		    }
-		}
-            }
-
-            var l_adds = [];
-            var l_rems = [];
-	    l_adds = added_links(topo, links, l_adds);
-            l_rems = gone_links(topo, links, l_rems);
-
-            for (var i = 0; i < l_rems.length ; i++) {
-		for (var j = 0; j < links.length; j++) {
-                    if (links[j].source.name == l_rems[i].source.name &&
-			links[j].target.name == l_rems[i].target.name) {
-			links.splice(j,1);
-			changed = true;
-			break;
-                    }
-		}
-            }
-            for (var i = 0; i < l_adds.length; i++) {
-		var s;
-		var t;
-		for (var j = 0; j < nodes.length; j++) {
-		    if ( json.nodes[l_adds[i].source].name == nodes[j].name ){
-			s = j;
-			break;
-		    }
-		}
-		for (var j = 0; j < nodes.length; j++) {
-		    if ( json.nodes[l_adds[i].target].name == nodes[j].name ){
-			t = j;
-			break;
-		    }
-		}
-		l_adds[i].source = s;
-		l_adds[i].target = t;
-		links.push(l_adds[i]);
-		changed = true;
-            }
-	    return changed
-	}
-
-
-	var changed = cdiff(json);
-        for (var i = 0; i < nodes.length; i++) {
-            for (var j = 0; j < json.nodes.length; j++) {
-		if ( nodes[i].name == json.nodes[j].name ){
-		    nodes[i].group = json.nodes[j].group
-		}
-	    }
-	}
-
-//	console.log(nodes);
-//	console.log(links);
-
-	console.log("changed? " + changed);
-
-	if (changed){
-            path = svg.selectAll("path").data(links)
-            circle = svg.selectAll("circle").data(nodes);
-	    text = svg.selectAll("text").data(nodes);
-
-	    force.stop();
-            path.enter().append("svg:path")
-		.attr("class", function(d) { return "link"; })
-		.attr("marker-end", "url(#Triangle)");
-
-            circle.enter().append("svg:circle")
-		.attr("r", 6)
-                .call(force.drag);
-
-/*	    text.enter().append("svg:text")
-		.attr("x", 8)
-		.attr("y", ".31em")
-		.attr("class", "shadow")
-		.text(function(d) { return d.name.split(":")[7]; }); */
-
-	    text.enter().append("svg:text")
-		.attr("x", 8)
-		.attr("y", ".31em")
-		.text(function(d) { return d.name.split(":")[7]; }); 
-
-            circle.append("title")
-	      .text(function(d) { return d.name; });
-
-	    circle.attr("fill", function(d) {
-		if (d.group == 1){return "red";}
-		else if (d.group == 2){return "blue";}
-		else if (d.group == 3){return "green";}
-		else{ return "gray"; }
-	    });
-
-
-	    path.exit().remove();
-            circle.exit().remove();
-            text.exit().remove();
-
-	    console.log(nodes);
-	    console.log(links);
-
-	    force.on("tick", tick);
-            force.start();
-	}
-    }
-    function draw(nodes, links){
-        path = svg.append("svg:g").selectAll("path").data(links)
-        circle = svg.append("svg:g").selectAll("circle").data(nodes);
-	text = svg.append("svg:g").selectAll("text").data(nodes);
-
-        path.enter().append("svg:path")
-	    .attr("class", function(d) { return "link"; })
-	    .attr("marker-end", "url(#Triangle)");
-
-        circle.enter().append("svg:circle")
-            .attr("r", 8)
-            .call(force.drag);
-
-/*	text.enter().append("svg:text")
-	    .attr("x", 8)
-	    .attr("y", ".31em")
-	    .attr("class", "shadow")
-	    .text(function(d) { return d.name.split(":")[7]; }); */
-
-	text.enter().append("svg:text")
-	    .attr("x", 8)
-	    .attr("y", ".31em")
-	    .text(function(d) { return d.name.split(":")[7]; }); 
-
-	circle.append("title")
-	    .text(function(d) { return d.name; });
-
-	circle.attr("fill", function(d) {
-	    if (d.group == 1){return "red";}
-	    else if (d.group == 2){return "blue";}
-	    else if (d.group == 3){return "green";}
-	    else{ return "gray"; }
-	});
-
-	force.on("tick", tick);
-	path.exit().remove();
-        circle.exit().remove();
-//        text.exit().remove();
-
-	force.start();
-
-	setInterval(function() {
-            $.ajax({
-//		url: 'http://onosnat.onlab.us:8080/topology',
-		url: data_source,
-		success: function(json) {
-		    update(json)
-		},
-		dataType: "json"
-            });
-	}, 3000); 
-    }
-
-/*
+/* For debugging  */
     $("#more").click( function() {
         $.ajax({
 	    url: 'http://onosnat.onlab.us:8080/topology_more',
@@ -306,14 +41,271 @@
 	    dataType: "json"
         });
     });
-*/
+/**/
+
+    function compare_link (a, b){
+        if (a.source > b.source) {return 1;}
+        else if (a.source < b.source) {return -1;}
+        else {
+            if (a.target > b.target) {return 1 ;}
+            if (a.target < b.target) {return -1;}
+            else {return 0;}
+        }
+    }
+
+    function init(json){
+        nodes = force.nodes();
+        links = force.links();
+
+	json.nodes.forEach(function(item) {
+            nodes.push(item);
+	});
+	json.links.forEach(function(item) {
+            links.push(item);
+	});
+
+        links.sort(compare_link);
+        for (var i=1; i<links.length; i++) {
+          if (links[i].source == links[i-1].source &&
+            links[i].target == links[i-1].target) {
+            links[i].linknum = links[i-1].linknum + 1;
+          }
+          else {
+	      links[i].linknum = 1;
+	  };
+        };
+	init_draw(nodes, links);
+    }
+
+    /* Return nodes that is not in the current list of nodes */
+    Array.prototype.node_diff = function(arr) {
+	return this.filter(function(i) {
+	    for (var j = 0; j < arr.length ; j++) {
+		if (arr[j].name === i.name)
+		    return false;
+	    }
+	    return true;
+	});
+    };
+
+    /* Return removed links */
+    function gone_links (json, links, gone) {
+	for (var i = 0; i < links.length ; i ++){
+	    var found = 0;
+	    for (var j = 0; j < json.links.length ; j ++){
+		if (links[i].source.name == json.nodes[json.links[j].source].name && 
+		    links[i].target.name == json.nodes[json.links[j].target].name ){
+		    found = 1;
+		    break;
+		}
+	    }
+	    if ( found == 0 ){
+		gone.push(links[i]);
+	    }
+	}
+	return gone;
+    }
+
+    /* Return added links */
+    function added_links (json, links, added) {
+	for (var j = 0; j < json.links.length ; j ++){
+	    var found = 0;
+	    for (var i = 0; i < links.length ; i ++){
+		if (links[i].source.name == json.nodes[json.links[j].source].name && 
+		    links[i].target.name == json.nodes[json.links[j].target].name ){
+		    found = 1;
+		    break;
+		}
+	    }
+	    if ( found == 0 ){
+		added.push(json.links[j]);
+	    }
+	}
+	return added;
+    }
+
+    function dragstart(d, i) {
+        force.stop() // stops the force auto positioning before you start dragging
+    }
+
+    function dragmove(d, i) {
+        d.px += d3.event.dx;
+        d.py += d3.event.dy;
+        d.x += d3.event.dx;
+        d.y += d3.event.dy; 
+        tick(); // this is the key to make it work together with updating both px,py,x,y on d !
+    }
+
+    function dragend(d, i) {
+        d.fixed = true; // of course set the node to fixed so the force doesn't include the node in its auto positioning stuff
+        tick();
+        force.resume();
+    }
+
+    /* check if toplogy has changed and update node[] and link[] accordingly */
+    function cdiff(json) {
+        var changed = false;
+
+	var n_adds = json.nodes.node_diff(nodes);
+        var n_rems = nodes.node_diff(json.nodes);
+        for (var i = 0; i < n_adds.length; i++) {
+	    nodes.push(n_adds[i]);
+	    changed = true;
+        }
+        for (var i = 0; i < n_rems.length; i++) {
+	    for (var j = 0; j < nodes.length; j++) {
+		if ( nodes[j].name == n_rems[i].name ){
+		    nodes.splice(j,1);
+		    changed = true;
+		    break;
+		}
+	    }
+        }
+        var l_adds = [];
+        var l_rems = [];
+	l_adds = added_links(json, links, l_adds);
+        l_rems = gone_links(json, links, l_rems);
+        for (var i = 0; i < l_rems.length ; i++) {
+	    for (var j = 0; j < links.length; j++) {
+                if (links[j].source.name == l_rems[i].source.name &&
+		    links[j].target.name == l_rems[i].target.name) {
+		    links.splice(j,1);
+		    changed = true;
+		    break;
+                }
+	    }
+        }
+	// Sorce/target of an element of l_adds[] are corresponding to the index of json.node[]
+	// which is different from the index of node[] (new nodes are always added to the last)
+	// So update soure/target node indexes of l_add[] need to be fixed to point to the proper
+	// node in node[];
+        for (var i = 0; i < l_adds.length; i++) {
+	    for (var j = 0; j < nodes.length; j++) {
+		if ( json.nodes[l_adds[i].source].name == nodes[j].name ){
+		    l_adds[i].source = j; 
+		    break;
+		}
+	    }
+	    for (var j = 0; j < nodes.length; j++) {
+		if ( json.nodes[l_adds[i].target].name == nodes[j].name ){
+		    l_adds[i].target = j;
+		    break;
+		}
+	    }
+	    links.push(l_adds[i]);
+	    changed = true;
+        }
+
+	// Update "group" attribute of nodes
+	for (var i = 0; i < nodes.length; i++) {
+            for (var j = 0; j < json.nodes.length; j++) {
+		if ( nodes[i].name == json.nodes[j].name ){
+		    if (nodes[i].group != json.nodes[j].group){
+			nodes[i].group = json.nodes[j].group;
+			changed = true;
+		    }
+		}
+	    }
+	}
+	return changed
+    }
+
+    function draw(force, path, circle, text){
+	force.stop();
+        path.enter().append("svg:path")
+	    .attr("class", function(d) { return "link"; });
+
+        circle.enter().append("svg:circle")
+	    .attr("r", 8)
+	    .call(node_drag);
+//            .call(force.drag);
+
+	text.enter().append("svg:text")
+	    .attr("x", 8)
+	    .attr("y", ".31em")
+	    .text(function(d) { return d.name.split(":")[6] + d.name.split(":")[7] });
+
+        circle.append("title")
+	    .text(function(d) { return d.name; });
+
+	circle.attr("fill", function(d) {
+	    if (d.group == 1){return "red";}
+	    else if (d.group == 2){return "blue";}
+	    else if (d.group == 3){return "green";}
+	    else{ return "gray"; }
+	});
+
+	path.attr("stroke", function(d) {
+	    if(d.type == 1){
+		return "red"
+	    } else {
+		return "black"
+	    }
+	}).attr("stroke-width", function(d) {
+	    if(d.type == 1){
+		return "4px";
+	    } else {
+		return "1.5px";
+	    }
+	}).attr("marker-end", function(d) {
+	    if(d.type == 1){
+		return "url(#TriangleRed)";
+	    } else {
+		return "url(#Triangle)";
+	    }
+	});
+
+	
+	path.exit().remove();
+        circle.exit().remove();
+        text.exit().remove();
+	
+	force.on("tick", tick);
+        force.start();
+
+    }
+
+    function update(json) {
+	var changed = cdiff(json);
+
+	console.log("changed? " + changed);
+
+	if (changed){
+
+            path = svg.selectAll("path").data(links)
+            circle = svg.selectAll("circle").data(nodes);
+	    text = svg.selectAll("text").data(nodes);
+
+	    draw(force, path, circle, text);
+	}
+    }
+
+    function init_draw(nodes, links){
+        path = svg.append("svg:g").selectAll("path").data(links)
+        circle = svg.append("svg:g").selectAll("circle").data(nodes);
+	text = svg.append("svg:g").selectAll("text").data(nodes);
+
+	draw(force, path, circle, text);
+
+	setInterval(function() {
+            $.ajax({
+//		url: 'http://onosnat.onlab.us:8080/topology',
+		url: data_source,
+		success: function(json) {
+		    update(json)
+		},
+		dataType: "json"
+            });
+	}, 3000); 
+    }
+
 
     function tick() {
 	path.attr("d", function(d) {
 	    var dx = d.target.x - d.source.x,
 	    dy = d.target.y - d.source.y,
 	    dr = 1/d.linknum;  //linknum is defined above
-	    dr = 300;
+	    dr = 0;  // 0 for direct line
 	    return "M" + d.source.x + "," + d.source.y + "A" + dr + "," + dr + " 0 0,1 " + d.target.x + "," + d.target.y;
 	});
 //	circle.attr("cx", function(d) { return d.x; }).attr("cy", function(d) { return d.y; });
@@ -327,9 +319,9 @@
 	    else{ return "gray"; }
 	});
 //	text.attr("x", function(d) { return d.x; }).attr("y", function(d) { return d.y; });
-//	text.attr("x", function(d) { return d.x; }).attr("y", function(d) { return d.y; });
 	text.attr("transform", function(d) {
 	    return "translate(" + d.x + "," + d.y + ")";
 	});
     }
 }
+
diff --git a/web/onos-topology.html b/web/onos-topology.html
index 5297871..0b5c313 100644
--- a/web/onos-topology.html
+++ b/web/onos-topology.html
@@ -40,7 +40,7 @@
     </marker>
   </defs>
 <script type="text/javascript">
-gui("http://onosnat.onlab.us:8080/topology");
+gui("http://gui.onlab.us:8080/topology");
 </script>
 </svg>
 </body>
diff --git a/web/topology_rest.py b/web/topology_rest.py
index a91bd7c..0a6c756 100755
--- a/web/topology_rest.py
+++ b/web/topology_rest.py
@@ -99,7 +99,7 @@
 
   return id
 
-@app.route("/topology")
+@app.route('/topology', methods=['GET'])
 def topology_for_gui():
   try:
     command = "curl -s \'http://%s:%s/wm/core/topology/switches/all/json\'" % (RestIP, RestPort)
@@ -260,6 +260,7 @@
   try:
     command = "curl -s \'http://%s:%s/wm/core/topology/switches/all/json\'" % (RestIP, RestPort)
 #    http://localhost:8080/wm/core/topology/switches/active/json
+    print command
     result = os.popen(command).read()
     parsedResult = json.loads(result)
   except:
@@ -352,6 +353,7 @@
 def query_links():
   try:
     command = 'curl -s http://%s:%s/graphs/%s/vertices?key=type\&value=port' % (RestIP, RestPort, DBName)
+    print command
     result = os.popen(command).read()
     parsedResult = json.loads(result)['results']
   except:
@@ -407,5 +409,4 @@
 #    devices()
   else:
     app.debug = True
-#    app.run(host="10.0.1.29", port=9000)
-    app.run(host="0.0.0.0", port=9000)
+    app.run(threaded=True, host="0.0.0.0", port=9000)