commit/galaxy-central: 3 new changesets

12 Sep 2012

3 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/3e41b027b184/
changeset:   3e41b027b184
user:        james_taylor
date:        2012-09-12 00:24:26
summary:     circster: moving some rendering code around to enable faster bigwig rendering, adding a Base class using Backbone style inheritence
affected #:  1 file

diff -r 72f1dcdf1c542e6d4689305f5de2077c0bfb4035 -r 3e41b027b1840bfd7f6e08b7c425c87508a19c4f static/scripts/viz/visualization.js

--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -7,7 +7,7 @@
  * changes; this is advantageous because multiple views can use the same object 
  * and models can be used without views.
  */
- 
+
 // --------- Models ---------
 
 /**
@@ -690,12 +690,58 @@
     
 });
 
+// General backbone style inheritence
+var Base = function() { this.__init__ && this.__init__.apply(this, arguments) }; Base.extend = Backbone.Model.extend;
 
-var CircsterDataLayout = Backbone.Model.extend({
-    defaults: {
-        genome: null,
-        dataset: null,
-        total_gap: null
+// ---- Circster views ----
+
+var CircsterTrackView = Base.extend( {
+
+    __init__: function( options ) {
+        this.options = options;
+    },
+
+    render: function() {
+
+        genome_arcs = this.chroms_layout(),
+        chroms_arcs = this.genome_data_layout();
+            
+        // -- Render. --
+
+        // Draw background arcs for each chromosome.
+        var svg = this.options.svg,
+            radius_start = this.options.radius_start,
+            radius_end = this.options.radius_end,
+            base_arc = svg.append("g").attr("id", "inner-arc"),
+            arc_gen = d3.svg.arc()
+                .innerRadius(radius_start)
+                .outerRadius(radius_end),
+            // Draw arcs.
+            chroms_elts = base_arc.selectAll("#inner-arc>path")
+                .data(genome_arcs).enter().append("path")
+                .attr("d", arc_gen)
+                .style("stroke", "#ccc")
+                .style("fill",  "#ccc")
+                .append("title").text(function(d) { return d.data.chrom; });
+
+        // For each chromosome, draw dataset.
+        var prefs = this.options.track.get('prefs'),
+            block_color = prefs.block_color;
+
+        _.each(chroms_arcs, function(chrom_layout) {
+            if (!chrom_layout) { return; }
+
+            var group = svg.append("g"),
+                arc_gen = d3.svg.arc().innerRadius(radius_start),
+                dataset_elts = group.selectAll("path")
+                    .data(chrom_layout).enter()
+                    ;
+                    //.style("stroke", block_color)
+                    //.style("fill",  block_color)
+            
+            dataset_elts.append("path").attr("d", arc_gen).style("stroke",  block_color)
+                
+        });
     },
 
     /**
@@ -704,10 +750,10 @@
      */
     chroms_layout: function() {
         // Setup chroms layout using pie.
-        var chroms_info = this.attributes.genome.get_chroms_info(),
+        var chroms_info = this.options.genome.get_chroms_info(),
             pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null),
             init_arcs = pie_layout(chroms_info),
-            gap_per_chrom = this.attributes.total_gap / chroms_info.length,
+            gap_per_chrom = this.options.total_gap / chroms_info.length,
             chrom_arcs = _.map(init_arcs, function(arc, index) {
                 // For short chroms, endAngle === startAngle.
                 var new_endAngle = arc.endAngle - gap_per_chrom;
@@ -726,9 +772,9 @@
     genome_data_layout: function() {
         var self = this,
             chrom_arcs = this.chroms_layout(),
-            dataset = this.get('track').get('genome_wide_data'),
-            r_start = this.get('radius_start'),
-            r_end = this.get('radius_end'),
+            dataset = this.options.track.get('genome_wide_data'),
+            r_start = this.options.radius_start,
+            r_end = this.options.radius_end,
                 
             // Merge chroms layout with data.
             layout_and_data = _.zip(chrom_arcs, dataset.get('data')),
@@ -747,7 +793,7 @@
 /**
  * Layout for summary tree data in a circster visualization.
  */
-var CircsterSummaryTreeLayout = CircsterDataLayout.extend({
+var CircsterSummaryTrackView = CircsterTrackView.extend({
     
     /**
      * Returns layouts for drawing a chromosome's data.
@@ -782,7 +828,7 @@
 /**
  * Layout for BigWig data in a circster visualization.
  */
-var CircsterBigWigLayout = CircsterDataLayout.extend({
+var CircsterBigWigTrackView = CircsterTrackView.extend({
 
     /**
      * Returns layouts for drawing a chromosome's data.
@@ -860,47 +906,19 @@
         this.model.get('tracks').each(function(track, index) {
             var dataset = track.get('genome_wide_data'),
                 radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
-                // Layout chromosome arcs.
-                layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ),
-                arcs_layout = new layout_class({
-                    track: track,
-                    radius_start: radius_start,
-                    radius_end: radius_start + dataset_arc_height,
-                    genome: self.genome,
-                    total_gap: self.total_gap
-                }),
-                genome_arcs = arcs_layout.chroms_layout(),
-                chroms_arcs = arcs_layout.genome_data_layout();
-                
-            // -- Render. --
+                track_view_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigTrackView : CircsterSummaryTreeTrackView );
 
-            // Draw background arcs for each chromosome.
-            var base_arc = svg.append("g").attr("id", "inner-arc"),
-                arc_gen = d3.svg.arc()
-                    .innerRadius(radius_start)
-                    .outerRadius(radius_start + dataset_arc_height),
-                // Draw arcs.
-                chroms_elts = base_arc.selectAll("#inner-arc>path")
-                    .data(genome_arcs).enter().append("path")
-                    .attr("d", arc_gen)
-                    .style("stroke", "#ccc")
-                    .style("fill",  "#ccc")
-                    .append("title").text(function(d) { return d.data.chrom; });
+            track_view = new track_view_class({
+                track: track,
+                radius_start: radius_start,
+                radius_end: radius_start + dataset_arc_height,
+                genome: self.genome,
+                total_gap: self.total_gap,
+                svg: svg
+            });
 
-            // For each chromosome, draw dataset.
-            var prefs = track.get('prefs'),
-                block_color = prefs.block_color;
-            _.each(chroms_arcs, function(chrom_layout) {
-                if (!chrom_layout) { return; }
+            track_view.render();
 
-                var group = svg.append("g"),
-                    arc_gen = d3.svg.arc().innerRadius(radius_start),
-                    dataset_elts = group.selectAll("path")
-                        .data(chrom_layout).enter().append("path")
-                        .attr("d", arc_gen)
-                        .style("stroke", block_color)
-                        .style("fill",  block_color);
-            });
         });
     }
 });



https://bitbucket.org/galaxy/galaxy-central/changeset/db2be15c1258/
changeset:   db2be15c1258
user:        james_taylor
date:        2012-09-12 00:43:09
summary:     circster: pull out circster code an encapsulate
affected #:  3 files

diff -r 3e41b027b1840bfd7f6e08b7c425c87508a19c4f -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 static/scripts/viz/circster.js
--- /dev/null
+++ b/static/scripts/viz/circster.js
@@ -0,0 +1,244 @@
+(function(){
+
+// General backbone style inheritence
+var Base = function() { this.initialize && this.initialize.apply(this, arguments) }; Base.extend = Backbone.Model.extend;
+
+// ---- Circster views ----
+ 
+/**
+ * -- Views --
+ */
+ 
+var CircsterView = Backbone.View.extend({
+    className: 'circster',
+    
+    initialize: function(options) {
+        this.total_gap = options.total_gap;
+        this.genome = options.genome;
+        this.dataset_arc_height = options.dataset_arc_height;
+        this.track_gap = 5;
+    },
+    
+    render: function() {
+        var self = this,
+            dataset_arc_height = this.dataset_arc_height,
+            width = self.$el.width(),
+            height = self.$el.height(),
+            // Compute radius start based on model, will be centered 
+            // and fit entirely inside element by default
+            init_radius_start = ( Math.min(width,height)/2 
+                - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) );
+
+        // Set up SVG element.
+        var svg = d3.select(self.$el[0])
+              .append("svg")
+                .attr("width", width)
+                .attr("height", height)
+                .attr("pointer-events", "all")
+              // Set up zooming, dragging.
+              .append('svg:g')
+                .call(d3.behavior.zoom().on('zoom', function() {
+                    svg.attr("transform",
+                      "translate(" + d3.event.translate + ")"
+                      + " scale(" + d3.event.scale + ")");
+                }))
+                .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
+              .append('svg:g')
+                
+
+        // -- Render each dataset in the visualization. --
+        this.model.get('tracks').each(function(track, index) {
+            var dataset = track.get('genome_wide_data'),
+                radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
+                track_view_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigTrackView : CircsterSummaryTreeTrackView );
+
+            track_view = new track_view_class({
+                track: track,
+                radius_start: radius_start,
+                radius_end: radius_start + dataset_arc_height,
+                genome: self.genome,
+                total_gap: self.total_gap,
+                svg: svg
+            });
+
+            track_view.render();
+
+        });
+    }
+});
+
+var CircsterTrackView = Base.extend( {
+
+    initialize: function( options ) {
+        this.options = options;
+    },
+
+    render: function() {
+
+        genome_arcs = this.chroms_layout(),
+        chroms_arcs = this.genome_data_layout();
+            
+        // -- Render. --
+
+        // Draw background arcs for each chromosome.
+        var svg = this.options.svg,
+            radius_start = this.options.radius_start,
+            radius_end = this.options.radius_end,
+            base_arc = svg.append("g").attr("id", "inner-arc"),
+            arc_gen = d3.svg.arc()
+                .innerRadius(radius_start)
+                .outerRadius(radius_end),
+            // Draw arcs.
+            chroms_elts = base_arc.selectAll("#inner-arc>path")
+                .data(genome_arcs).enter().append("path")
+                .attr("d", arc_gen)
+                .style("stroke", "#ccc")
+                .style("fill",  "#ccc")
+                .append("title").text(function(d) { return d.data.chrom; });
+
+        // For each chromosome, draw dataset.
+        var prefs = this.options.track.get('prefs'),
+            block_color = prefs.block_color;
+
+        _.each(chroms_arcs, function(chrom_layout) {
+            if (!chrom_layout) { return; }
+
+            var group = svg.append("g"),
+                arc_gen = d3.svg.arc().innerRadius(radius_start),
+                dataset_elts = group.selectAll("path")
+                    .data(chrom_layout).enter()
+                    ;
+                    //.style("stroke", block_color)
+                    //.style("fill",  block_color)
+            
+            dataset_elts.append("path").attr("d", arc_gen).style("stroke",  block_color)
+                
+        });
+    },
+
+    /**
+     * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle 
+     * separated by gaps.
+     */
+    chroms_layout: function() {
+        // Setup chroms layout using pie.
+        var chroms_info = this.options.genome.get_chroms_info(),
+            pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null),
+            init_arcs = pie_layout(chroms_info),
+            gap_per_chrom = this.options.total_gap / chroms_info.length,
+            chrom_arcs = _.map(init_arcs, function(arc, index) {
+                // For short chroms, endAngle === startAngle.
+                var new_endAngle = arc.endAngle - gap_per_chrom;
+                arc.endAngle = (new_endAngle > arc.startAngle ? new_endAngle : arc.startAngle);
+                return arc;
+            });
+        return chrom_arcs;
+    },
+
+    /**
+     * Returns layouts for drawing a chromosome's data.
+     */
+    chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) {
+    },
+
+    genome_data_layout: function() {
+        var self = this,
+            chrom_arcs = this.chroms_layout(),
+            dataset = this.options.track.get('genome_wide_data'),
+            r_start = this.options.radius_start,
+            r_end = this.options.radius_end,
+                
+            // Merge chroms layout with data.
+            layout_and_data = _.zip(chrom_arcs, dataset.get('data')),
+            
+            // Do dataset layout for each chromosome's data using pie layout.
+            chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
+                var chrom_arc = chrom_info[0],
+                    chrom_data = chrom_info[1];
+                return self.chrom_data_layout(chrom_arc, chrom_data, r_start, r_end, dataset.get('min'), dataset.get('max'));
+            });
+
+        return chroms_data_layout;
+    }
+});
+
+/**
+ * Layout for summary tree data in a circster visualization.
+ */
+var CircsterSummaryTrackView = CircsterTrackView.extend({
+    
+    /**
+     * Returns layouts for drawing a chromosome's data.
+     */
+    chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) {
+        // If no chrom data, return null.
+        if (!chrom_data || typeof chrom_data === "string") {
+            return null;
+        }
+        
+        var data = chrom_data[0],
+            delta = chrom_data[3],
+            scale = d3.scale.linear()
+                .domain( [min, max] )
+                .range( [inner_radius, outer_radius] ),       
+            arc_layout = d3.layout.pie().value(function(d) {
+                return delta;
+            })
+                .startAngle(chrom_arc.startAngle)
+                .endAngle(chrom_arc.endAngle),
+        arcs = arc_layout(data);
+        
+        // Use scale to assign outer radius.
+        _.each(data, function(datum, index) {
+            arcs[index].outerRadius = scale(datum[1]);
+        });
+        
+        return arcs;
+    }
+});
+
+/**
+ * Layout for BigWig data in a circster visualization.
+ */
+var CircsterBigWigTrackView = CircsterTrackView.extend({
+
+    /**
+     * Returns layouts for drawing a chromosome's data.
+     */
+    chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) {
+        var data = chrom_data.data;
+        if (data.length === 0) { return; }
+        
+        var scale = d3.scale.linear()
+                .domain( [min, max] )
+                .range( [inner_radius, outer_radius] ),
+            arc_layout = d3.layout.pie().value(function(d, i) {
+                // If at end of data, draw nothing.
+                if (i + 1 === data.length) { return 0; }
+
+                // Layout is from current position to next position.
+                return data[i+1][0] - data[i][0];
+            })
+                .startAngle(chrom_arc.startAngle)
+                .endAngle(chrom_arc.endAngle),
+        arcs = arc_layout(data);
+        
+        // Use scale to assign outer radius.
+        _.each(data, function(datum, index) {
+            arcs[index].outerRadius = scale(datum[1]);
+        });
+        
+        return arcs;
+    }
+
+});
+
+// ---- Browser or CommonJS compatible exports ----
+
+if (typeof exports === 'undefined') {
+    var exports = this;
+}
+
+exports.CircsterView = CircsterView;
+
+}).call(this);


diff -r 3e41b027b1840bfd7f6e08b7c425c87508a19c4f -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -690,239 +690,6 @@
     
 });
 
-// General backbone style inheritence
-var Base = function() { this.__init__ && this.__init__.apply(this, arguments) }; Base.extend = Backbone.Model.extend;
-
-// ---- Circster views ----
-
-var CircsterTrackView = Base.extend( {
-
-    __init__: function( options ) {
-        this.options = options;
-    },
-
-    render: function() {
-
-        genome_arcs = this.chroms_layout(),
-        chroms_arcs = this.genome_data_layout();
-            
-        // -- Render. --
-
-        // Draw background arcs for each chromosome.
-        var svg = this.options.svg,
-            radius_start = this.options.radius_start,
-            radius_end = this.options.radius_end,
-            base_arc = svg.append("g").attr("id", "inner-arc"),
-            arc_gen = d3.svg.arc()
-                .innerRadius(radius_start)
-                .outerRadius(radius_end),
-            // Draw arcs.
-            chroms_elts = base_arc.selectAll("#inner-arc>path")
-                .data(genome_arcs).enter().append("path")
-                .attr("d", arc_gen)
-                .style("stroke", "#ccc")
-                .style("fill",  "#ccc")
-                .append("title").text(function(d) { return d.data.chrom; });
-
-        // For each chromosome, draw dataset.
-        var prefs = this.options.track.get('prefs'),
-            block_color = prefs.block_color;
-
-        _.each(chroms_arcs, function(chrom_layout) {
-            if (!chrom_layout) { return; }
-
-            var group = svg.append("g"),
-                arc_gen = d3.svg.arc().innerRadius(radius_start),
-                dataset_elts = group.selectAll("path")
-                    .data(chrom_layout).enter()
-                    ;
-                    //.style("stroke", block_color)
-                    //.style("fill",  block_color)
-            
-            dataset_elts.append("path").attr("d", arc_gen).style("stroke",  block_color)
-                
-        });
-    },
-
-    /**
-     * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle 
-     * separated by gaps.
-     */
-    chroms_layout: function() {
-        // Setup chroms layout using pie.
-        var chroms_info = this.options.genome.get_chroms_info(),
-            pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null),
-            init_arcs = pie_layout(chroms_info),
-            gap_per_chrom = this.options.total_gap / chroms_info.length,
-            chrom_arcs = _.map(init_arcs, function(arc, index) {
-                // For short chroms, endAngle === startAngle.
-                var new_endAngle = arc.endAngle - gap_per_chrom;
-                arc.endAngle = (new_endAngle > arc.startAngle ? new_endAngle : arc.startAngle);
-                return arc;
-            });
-        return chrom_arcs;
-    },
-
-    /**
-     * Returns layouts for drawing a chromosome's data.
-     */
-    chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) {
-    },
-
-    genome_data_layout: function() {
-        var self = this,
-            chrom_arcs = this.chroms_layout(),
-            dataset = this.options.track.get('genome_wide_data'),
-            r_start = this.options.radius_start,
-            r_end = this.options.radius_end,
-                
-            // Merge chroms layout with data.
-            layout_and_data = _.zip(chrom_arcs, dataset.get('data')),
-            
-            // Do dataset layout for each chromosome's data using pie layout.
-            chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
-                var chrom_arc = chrom_info[0],
-                    chrom_data = chrom_info[1];
-                return self.chrom_data_layout(chrom_arc, chrom_data, r_start, r_end, dataset.get('min'), dataset.get('max'));
-            });
-
-        return chroms_data_layout;
-    }
-});
-
-/**
- * Layout for summary tree data in a circster visualization.
- */
-var CircsterSummaryTrackView = CircsterTrackView.extend({
-    
-    /**
-     * Returns layouts for drawing a chromosome's data.
-     */
-    chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) {
-        // If no chrom data, return null.
-        if (!chrom_data || typeof chrom_data === "string") {
-            return null;
-        }
-        
-        var data = chrom_data[0],
-            delta = chrom_data[3],
-            scale = d3.scale.linear()
-                .domain( [min, max] )
-                .range( [inner_radius, outer_radius] ),       
-            arc_layout = d3.layout.pie().value(function(d) {
-                return delta;
-            })
-                .startAngle(chrom_arc.startAngle)
-                .endAngle(chrom_arc.endAngle),
-        arcs = arc_layout(data);
-        
-        // Use scale to assign outer radius.
-        _.each(data, function(datum, index) {
-            arcs[index].outerRadius = scale(datum[1]);
-        });
-        
-        return arcs;
-    }
-});
-
-/**
- * Layout for BigWig data in a circster visualization.
- */
-var CircsterBigWigTrackView = CircsterTrackView.extend({
-
-    /**
-     * Returns layouts for drawing a chromosome's data.
-     */
-    chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) {
-        var data = chrom_data.data;
-        if (data.length === 0) { return; }
-        
-        var scale = d3.scale.linear()
-                .domain( [min, max] )
-                .range( [inner_radius, outer_radius] ),
-            arc_layout = d3.layout.pie().value(function(d, i) {
-                // If at end of data, draw nothing.
-                if (i + 1 === data.length) { return 0; }
-
-                // Layout is from current position to next position.
-                return data[i+1][0] - data[i][0];
-            })
-                .startAngle(chrom_arc.startAngle)
-                .endAngle(chrom_arc.endAngle),
-        arcs = arc_layout(data);
-        
-        // Use scale to assign outer radius.
-        _.each(data, function(datum, index) {
-            arcs[index].outerRadius = scale(datum[1]);
-        });
-        
-        return arcs;
-    }
-
-});
- 
-/**
- * -- Views --
- */
- 
-var CircsterView = Backbone.View.extend({
-    className: 'circster',
-    
-    initialize: function(options) {
-        this.total_gap = options.total_gap;
-        this.genome = options.genome;
-        this.dataset_arc_height = options.dataset_arc_height;
-        this.track_gap = 5;
-    },
-    
-    render: function() {
-        var self = this,
-            dataset_arc_height = this.dataset_arc_height,
-            width = self.$el.width(),
-            height = self.$el.height(),
-            // Compute radius start based on model, will be centered 
-            // and fit entirely inside element by default
-            init_radius_start = ( Math.min(width,height)/2 
-                - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) );
-
-        // Set up SVG element.
-        var svg = d3.select(self.$el[0])
-              .append("svg")
-                .attr("width", width)
-                .attr("height", height)
-                .attr("pointer-events", "all")
-              // Set up zooming, dragging.
-              .append('svg:g')
-                .call(d3.behavior.zoom().on('zoom', function() {
-                    svg.attr("transform",
-                      "translate(" + d3.event.translate + ")"
-                      + " scale(" + d3.event.scale + ")");
-                }))
-                .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
-              .append('svg:g')
-                
-
-        // -- Render each dataset in the visualization. --
-        this.model.get('tracks').each(function(track, index) {
-            var dataset = track.get('genome_wide_data'),
-                radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
-                track_view_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigTrackView : CircsterSummaryTreeTrackView );
-
-            track_view = new track_view_class({
-                track: track,
-                radius_start: radius_start,
-                radius_end: radius_start + dataset_arc_height,
-                genome: self.genome,
-                total_gap: self.total_gap,
-                svg: svg
-            });
-
-            track_view.render();
-
-        });
-    }
-});
-
 /**
  * -- Routers --
  */


diff -r 3e41b027b1840bfd7f6e08b7c425c87508a19c4f -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 templates/visualization/circster.mako
--- a/templates/visualization/circster.mako
+++ b/templates/visualization/circster.mako
@@ -16,7 +16,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
 
-    ${h.js( "libs/d3", "mvc/data", "viz/visualization" )}
+    ${h.js( "libs/d3", "mvc/data", "viz/visualization", "viz/circster" )}
 
     <script type="text/javascript">
         $(function() {



https://bitbucket.org/galaxy/galaxy-central/changeset/45ddaa89e985/
changeset:   45ddaa89e985
user:        james_taylor
date:        2012-09-12 21:38:52
summary:     js: introducing a requirejs starting with circster. circster.js is a pure AMD module. visualization.js is AMD/browser compatible
affected #:  5 files

diff -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 -r 45ddaa89e9855d21ce2f6a29a0eb90cc61abd7cd static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -13,4 +13,5 @@
 
 var DatasetCollection = Backbone.Collection.extend({
     model: Dataset
-});
\ No newline at end of file
+});
+


diff -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 -r 45ddaa89e9855d21ce2f6a29a0eb90cc61abd7cd static/scripts/require.js
--- /dev/null
+++ b/static/scripts/require.js
@@ -0,0 +1,2041 @@
+/** vim: et:ts=4:sw=4:sts=4
+ * @license RequireJS 2.0.6 Copyright (c) 2010-2012, The Dojo Foundation All Rights Reserved.
+ * Available via the MIT or new BSD license.
+ * see: http://github.com/jrburke/requirejs for details
+ */
+//Not using strict: uneven strict support in browsers, #392, and causes
+//problems with requirejs.exec()/transpiler plugins that may not be strict.
+/*jslint regexp: true, nomen: true, sloppy: true */
+/*global window, navigator, document, importScripts, jQuery, setTimeout, opera */
+
+var requirejs, require, define;
+(function (global) {
+    var req, s, head, baseElement, dataMain, src,
+        interactiveScript, currentlyAddingScript, mainScript, subPath,
+        version = '2.0.6',
+        commentRegExp = /(\/\*([\s\S]*?)\*\/|([^:]|^)\/\/(.*)$)/mg,
+        cjsRequireRegExp = /[^.]\s*require\s*\(\s*["']([^'"\s]+)["']\s*\)/g,
+        jsSuffixRegExp = /\.js$/,
+        currDirRegExp = /^\.\//,
+        op = Object.prototype,
+        ostring = op.toString,
+        hasOwn = op.hasOwnProperty,
+        ap = Array.prototype,
+        aps = ap.slice,
+        apsp = ap.splice,
+        isBrowser = !!(typeof window !== 'undefined' && navigator && document),
+        isWebWorker = !isBrowser && typeof importScripts !== 'undefined',
+        //PS3 indicates loaded and complete, but need to wait for complete
+        //specifically. Sequence is 'loading', 'loaded', execution,
+        // then 'complete'. The UA check is unfortunate, but not sure how
+        //to feature test w/o causing perf issues.
+        readyRegExp = isBrowser && navigator.platform === 'PLAYSTATION 3' ?
+                      /^complete$/ : /^(complete|loaded)$/,
+        defContextName = '_',
+        //Oh the tragedy, detecting opera. See the usage of isOpera for reason.
+        isOpera = typeof opera !== 'undefined' && opera.toString() === '[object Opera]',
+        contexts = {},
+        cfg = {},
+        globalDefQueue = [],
+        useInteractive = false;
+
+    function isFunction(it) {
+        return ostring.call(it) === '[object Function]';
+    }
+
+    function isArray(it) {
+        return ostring.call(it) === '[object Array]';
+    }
+
+    /**
+     * Helper function for iterating over an array. If the func returns
+     * a true value, it will break out of the loop.
+     */
+    function each(ary, func) {
+        if (ary) {
+            var i;
+            for (i = 0; i < ary.length; i += 1) {
+                if (ary[i] && func(ary[i], i, ary)) {
+                    break;
+                }
+            }
+        }
+    }
+
+    /**
+     * Helper function for iterating over an array backwards. If the func
+     * returns a true value, it will break out of the loop.
+     */
+    function eachReverse(ary, func) {
+        if (ary) {
+            var i;
+            for (i = ary.length - 1; i > -1; i -= 1) {
+                if (ary[i] && func(ary[i], i, ary)) {
+                    break;
+                }
+            }
+        }
+    }
+
+    function hasProp(obj, prop) {
+        return hasOwn.call(obj, prop);
+    }
+
+    /**
+     * Cycles over properties in an object and calls a function for each
+     * property value. If the function returns a truthy value, then the
+     * iteration is stopped.
+     */
+    function eachProp(obj, func) {
+        var prop;
+        for (prop in obj) {
+            if (obj.hasOwnProperty(prop)) {
+                if (func(obj[prop], prop)) {
+                    break;
+                }
+            }
+        }
+    }
+
+    /**
+     * Simple function to mix in properties from source into target,
+     * but only if target does not already have a property of the same name.
+     * This is not robust in IE for transferring methods that match
+     * Object.prototype names, but the uses of mixin here seem unlikely to
+     * trigger a problem related to that.
+     */
+    function mixin(target, source, force, deepStringMixin) {
+        if (source) {
+            eachProp(source, function (value, prop) {
+                if (force || !hasProp(target, prop)) {
+                    if (deepStringMixin && typeof value !== 'string') {
+                        if (!target[prop]) {
+                            target[prop] = {};
+                        }
+                        mixin(target[prop], value, force, deepStringMixin);
+                    } else {
+                        target[prop] = value;
+                    }
+                }
+            });
+        }
+        return target;
+    }
+
+    //Similar to Function.prototype.bind, but the 'this' object is specified
+    //first, since it is easier to read/figure out what 'this' will be.
+    function bind(obj, fn) {
+        return function () {
+            return fn.apply(obj, arguments);
+        };
+    }
+
+    function scripts() {
+        return document.getElementsByTagName('script');
+    }
+
+    //Allow getting a global that expressed in
+    //dot notation, like 'a.b.c'.
+    function getGlobal(value) {
+        if (!value) {
+            return value;
+        }
+        var g = global;
+        each(value.split('.'), function (part) {
+            g = g[part];
+        });
+        return g;
+    }
+
+    function makeContextModuleFunc(func, relMap, enableBuildCallback) {
+        return function () {
+            //A version of a require function that passes a moduleName
+            //value for items that may need to
+            //look up paths relative to the moduleName
+            var args = aps.call(arguments, 0), lastArg;
+            if (enableBuildCallback &&
+                    isFunction((lastArg = args[args.length - 1]))) {
+                lastArg.__requireJsBuild = true;
+            }
+            args.push(relMap);
+            return func.apply(null, args);
+        };
+    }
+
+    function addRequireMethods(req, context, relMap) {
+        each([
+            ['toUrl'],
+            ['undef'],
+            ['defined', 'requireDefined'],
+            ['specified', 'requireSpecified']
+        ], function (item) {
+            var prop = item[1] || item[0];
+            req[item[0]] = context ? makeContextModuleFunc(context[prop], relMap) :
+                    //If no context, then use default context. Reference from
+                    //contexts instead of early binding to default context, so
+                    //that during builds, the latest instance of the default
+                    //context with its config gets used.
+                    function () {
+                        var ctx = contexts[defContextName];
+                        return ctx[prop].apply(ctx, arguments);
+                    };
+        });
+    }
+
+    /**
+     * Constructs an error with a pointer to an URL with more information.
+     * @param {String} id the error ID that maps to an ID on a web page.
+     * @param {String} message human readable error.
+     * @param {Error} [err] the original error, if there is one.
+     *
+     * @returns {Error}
+     */
+    function makeError(id, msg, err, requireModules) {
+        var e = new Error(msg + '\nhttp://requirejs.org/docs/errors.html#' + id);
+        e.requireType = id;
+        e.requireModules = requireModules;
+        if (err) {
+            e.originalError = err;
+        }
+        return e;
+    }
+
+    if (typeof define !== 'undefined') {
+        //If a define is already in play via another AMD loader,
+        //do not overwrite.
+        return;
+    }
+
+    if (typeof requirejs !== 'undefined') {
+        if (isFunction(requirejs)) {
+            //Do not overwrite and existing requirejs instance.
+            return;
+        }
+        cfg = requirejs;
+        requirejs = undefined;
+    }
+
+    //Allow for a require config object
+    if (typeof require !== 'undefined' && !isFunction(require)) {
+        //assume it is a config object.
+        cfg = require;
+        require = undefined;
+    }
+
+    function newContext(contextName) {
+        var inCheckLoaded, Module, context, handlers,
+            checkLoadedTimeoutId,
+            config = {
+                waitSeconds: 7,
+                baseUrl: './',
+                paths: {},
+                pkgs: {},
+                shim: {}
+            },
+            registry = {},
+            undefEvents = {},
+            defQueue = [],
+            defined = {},
+            urlFetched = {},
+            requireCounter = 1,
+            unnormalizedCounter = 1,
+            //Used to track the order in which modules
+            //should be executed, by the order they
+            //load. Important for consistent cycle resolution
+            //behavior.
+            waitAry = [];
+
+        /**
+         * Trims the . and .. from an array of path segments.
+         * It will keep a leading path segment if a .. will become
+         * the first path segment, to help with module name lookups,
+         * which act like paths, but can be remapped. But the end result,
+         * all paths that use this function should look normalized.
+         * NOTE: this method MODIFIES the input array.
+         * @param {Array} ary the array of path segments.
+         */
+        function trimDots(ary) {
+            var i, part;
+            for (i = 0; ary[i]; i += 1) {
+                part = ary[i];
+                if (part === '.') {
+                    ary.splice(i, 1);
+                    i -= 1;
+                } else if (part === '..') {
+                    if (i === 1 && (ary[2] === '..' || ary[0] === '..')) {
+                        //End of the line. Keep at least one non-dot
+                        //path segment at the front so it can be mapped
+                        //correctly to disk. Otherwise, there is likely
+                        //no path mapping for a path starting with '..'.
+                        //This can still fail, but catches the most reasonable
+                        //uses of ..
+                        break;
+                    } else if (i > 0) {
+                        ary.splice(i - 1, 2);
+                        i -= 2;
+                    }
+                }
+            }
+        }
+
+        /**
+         * Given a relative module name, like ./something, normalize it to
+         * a real name that can be mapped to a path.
+         * @param {String} name the relative name
+         * @param {String} baseName a real name that the name arg is relative
+         * to.
+         * @param {Boolean} applyMap apply the map config to the value. Should
+         * only be done if this normalization is for a dependency ID.
+         * @returns {String} normalized name
+         */
+        function normalize(name, baseName, applyMap) {
+            var pkgName, pkgConfig, mapValue, nameParts, i, j, nameSegment,
+                foundMap, foundI, foundStarMap, starI,
+                baseParts = baseName && baseName.split('/'),
+                normalizedBaseParts = baseParts,
+                map = config.map,
+                starMap = map && map['*'];
+
+            //Adjust any relative paths.
+            if (name && name.charAt(0) === '.') {
+                //If have a base name, try to normalize against it,
+                //otherwise, assume it is a top-level require that will
+                //be relative to baseUrl in the end.
+                if (baseName) {
+                    if (config.pkgs[baseName]) {
+                        //If the baseName is a package name, then just treat it as one
+                        //name to concat the name with.
+                        normalizedBaseParts = baseParts = [baseName];
+                    } else {
+                        //Convert baseName to array, and lop off the last part,
+                        //so that . matches that 'directory' and not name of the baseName's
+                        //module. For instance, baseName of 'one/two/three', maps to
+                        //'one/two/three.js', but we want the directory, 'one/two' for
+                        //this normalization.
+                        normalizedBaseParts = baseParts.slice(0, baseParts.length - 1);
+                    }
+
+                    name = normalizedBaseParts.concat(name.split('/'));
+                    trimDots(name);
+
+                    //Some use of packages may use a . path to reference the
+                    //'main' module name, so normalize for that.
+                    pkgConfig = config.pkgs[(pkgName = name[0])];
+                    name = name.join('/');
+                    if (pkgConfig && name === pkgName + '/' + pkgConfig.main) {
+                        name = pkgName;
+                    }
+                } else if (name.indexOf('./') === 0) {
+                    // No baseName, so this is ID is resolved relative
+                    // to baseUrl, pull off the leading dot.
+                    name = name.substring(2);
+                }
+            }
+
+            //Apply map config if available.
+            if (applyMap && (baseParts || starMap) && map) {
+                nameParts = name.split('/');
+
+                for (i = nameParts.length; i > 0; i -= 1) {
+                    nameSegment = nameParts.slice(0, i).join('/');
+
+                    if (baseParts) {
+                        //Find the longest baseName segment match in the config.
+                        //So, do joins on the biggest to smallest lengths of baseParts.
+                        for (j = baseParts.length; j > 0; j -= 1) {
+                            mapValue = map[baseParts.slice(0, j).join('/')];
+
+                            //baseName segment has config, find if it has one for
+                            //this name.
+                            if (mapValue) {
+                                mapValue = mapValue[nameSegment];
+                                if (mapValue) {
+                                    //Match, update name to the new value.
+                                    foundMap = mapValue;
+                                    foundI = i;
+                                    break;
+                                }
+                            }
+                        }
+                    }
+
+                    if (foundMap) {
+                        break;
+                    }
+
+                    //Check for a star map match, but just hold on to it,
+                    //if there is a shorter segment match later in a matching
+                    //config, then favor over this star map.
+                    if (!foundStarMap && starMap && starMap[nameSegment]) {
+                        foundStarMap = starMap[nameSegment];
+                        starI = i;
+                    }
+                }
+
+                if (!foundMap && foundStarMap) {
+                    foundMap = foundStarMap;
+                    foundI = starI;
+                }
+
+                if (foundMap) {
+                    nameParts.splice(0, foundI, foundMap);
+                    name = nameParts.join('/');
+                }
+            }
+
+            return name;
+        }
+
+        function removeScript(name) {
+            if (isBrowser) {
+                each(scripts(), function (scriptNode) {
+                    if (scriptNode.getAttribute('data-requiremodule') === name &&
+                            scriptNode.getAttribute('data-requirecontext') === context.contextName) {
+                        scriptNode.parentNode.removeChild(scriptNode);
+                        return true;
+                    }
+                });
+            }
+        }
+
+        function hasPathFallback(id) {
+            var pathConfig = config.paths[id];
+            if (pathConfig && isArray(pathConfig) && pathConfig.length > 1) {
+                removeScript(id);
+                //Pop off the first array value, since it failed, and
+                //retry
+                pathConfig.shift();
+                context.undef(id);
+                context.require([id]);
+                return true;
+            }
+        }
+
+        /**
+         * Creates a module mapping that includes plugin prefix, module
+         * name, and path. If parentModuleMap is provided it will
+         * also normalize the name via require.normalize()
+         *
+         * @param {String} name the module name
+         * @param {String} [parentModuleMap] parent module map
+         * for the module name, used to resolve relative names.
+         * @param {Boolean} isNormalized: is the ID already normalized.
+         * This is true if this call is done for a define() module ID.
+         * @param {Boolean} applyMap: apply the map config to the ID.
+         * Should only be true if this map is for a dependency.
+         *
+         * @returns {Object}
+         */
+        function makeModuleMap(name, parentModuleMap, isNormalized, applyMap) {
+            var url, pluginModule, suffix,
+                index = name ? name.indexOf('!') : -1,
+                prefix = null,
+                parentName = parentModuleMap ? parentModuleMap.name : null,
+                originalName = name,
+                isDefine = true,
+                normalizedName = '';
+
+            //If no name, then it means it is a require call, generate an
+            //internal name.
+            if (!name) {
+                isDefine = false;
+                name = '_@r' + (requireCounter += 1);
+            }
+
+            if (index !== -1) {
+                prefix = name.substring(0, index);
+                name = name.substring(index + 1, name.length);
+            }
+
+            if (prefix) {
+                prefix = normalize(prefix, parentName, applyMap);
+                pluginModule = defined[prefix];
+            }
+
+            //Account for relative paths if there is a base name.
+            if (name) {
+                if (prefix) {
+                    if (pluginModule && pluginModule.normalize) {
+                        //Plugin is loaded, use its normalize method.
+                        normalizedName = pluginModule.normalize(name, function (name) {
+                            return normalize(name, parentName, applyMap);
+                        });
+                    } else {
+                        normalizedName = normalize(name, parentName, applyMap);
+                    }
+                } else {
+                    //A regular module.
+                    normalizedName = normalize(name, parentName, applyMap);
+                    url = context.nameToUrl(normalizedName);
+                }
+            }
+
+            //If the id is a plugin id that cannot be determined if it needs
+            //normalization, stamp it with a unique ID so two matching relative
+            //ids that may conflict can be separate.
+            suffix = prefix && !pluginModule && !isNormalized ?
+                     '_unnormalized' + (unnormalizedCounter += 1) :
+                     '';
+
+            return {
+                prefix: prefix,
+                name: normalizedName,
+                parentMap: parentModuleMap,
+                unnormalized: !!suffix,
+                url: url,
+                originalName: originalName,
+                isDefine: isDefine,
+                id: (prefix ?
+                        prefix + '!' + normalizedName :
+                        normalizedName) + suffix
+            };
+        }
+
+        function getModule(depMap) {
+            var id = depMap.id,
+                mod = registry[id];
+
+            if (!mod) {
+                mod = registry[id] = new context.Module(depMap);
+            }
+
+            return mod;
+        }
+
+        function on(depMap, name, fn) {
+            var id = depMap.id,
+                mod = registry[id];
+
+            if (hasProp(defined, id) &&
+                    (!mod || mod.defineEmitComplete)) {
+                if (name === 'defined') {
+                    fn(defined[id]);
+                }
+            } else {
+                getModule(depMap).on(name, fn);
+            }
+        }
+
+        function onError(err, errback) {
+            var ids = err.requireModules,
+                notified = false;
+
+            if (errback) {
+                errback(err);
+            } else {
+                each(ids, function (id) {
+                    var mod = registry[id];
+                    if (mod) {
+                        //Set error on module, so it skips timeout checks.
+                        mod.error = err;
+                        if (mod.events.error) {
+                            notified = true;
+                            mod.emit('error', err);
+                        }
+                    }
+                });
+
+                if (!notified) {
+                    req.onError(err);
+                }
+            }
+        }
+
+        /**
+         * Internal method to transfer globalQueue items to this context's
+         * defQueue.
+         */
+        function takeGlobalQueue() {
+            //Push all the globalDefQueue items into the context's defQueue
+            if (globalDefQueue.length) {
+                //Array splice in the values since the context code has a
+                //local var ref to defQueue, so cannot just reassign the one
+                //on context.
+                apsp.apply(defQueue,
+                           [defQueue.length - 1, 0].concat(globalDefQueue));
+                globalDefQueue = [];
+            }
+        }
+
+        /**
+         * Helper function that creates a require function object to give to
+         * modules that ask for it as a dependency. It needs to be specific
+         * per module because of the implication of path mappings that may
+         * need to be relative to the module name.
+         */
+        function makeRequire(mod, enableBuildCallback, altRequire) {
+            var relMap = mod && mod.map,
+                modRequire = makeContextModuleFunc(altRequire || context.require,
+                                                   relMap,
+                                                   enableBuildCallback);
+
+            addRequireMethods(modRequire, context, relMap);
+            modRequire.isBrowser = isBrowser;
+
+            return modRequire;
+        }
+
+        handlers = {
+            'require': function (mod) {
+                return makeRequire(mod);
+            },
+            'exports': function (mod) {
+                mod.usingExports = true;
+                if (mod.map.isDefine) {
+                    return (mod.exports = defined[mod.map.id] = {});
+                }
+            },
+            'module': function (mod) {
+                return (mod.module = {
+                    id: mod.map.id,
+                    uri: mod.map.url,
+                    config: function () {
+                        return (config.config && config.config[mod.map.id]) || {};
+                    },
+                    exports: defined[mod.map.id]
+                });
+            }
+        };
+
+        function removeWaiting(id) {
+            //Clean up machinery used for waiting modules.
+            delete registry[id];
+
+            each(waitAry, function (mod, i) {
+                if (mod.map.id === id) {
+                    waitAry.splice(i, 1);
+                    if (!mod.defined) {
+                        context.waitCount -= 1;
+                    }
+                    return true;
+                }
+            });
+        }
+
+        function findCycle(mod, traced, processed) {
+            var id = mod.map.id,
+                depArray = mod.depMaps,
+                foundModule;
+
+            //Do not bother with unitialized modules or not yet enabled
+            //modules.
+            if (!mod.inited) {
+                return;
+            }
+
+            //Found the cycle.
+            if (traced[id]) {
+                return mod;
+            }
+
+            traced[id] = true;
+
+            //Trace through the dependencies.
+            each(depArray, function (depMap) {
+                var depId = depMap.id,
+                    depMod = registry[depId];
+
+                if (!depMod || processed[depId] ||
+                        !depMod.inited || !depMod.enabled) {
+                    return;
+                }
+
+                return (foundModule = findCycle(depMod, traced, processed));
+            });
+
+            processed[id] = true;
+
+            return foundModule;
+        }
+
+        function forceExec(mod, traced, uninited) {
+            var id = mod.map.id,
+                depArray = mod.depMaps;
+
+            if (!mod.inited || !mod.map.isDefine) {
+                return;
+            }
+
+            if (traced[id]) {
+                return defined[id];
+            }
+
+            traced[id] = mod;
+
+            each(depArray, function (depMap) {
+                var depId = depMap.id,
+                    depMod = registry[depId],
+                    value;
+
+                if (handlers[depId]) {
+                    return;
+                }
+
+                if (depMod) {
+                    if (!depMod.inited || !depMod.enabled) {
+                        //Dependency is not inited,
+                        //so this module cannot be
+                        //given a forced value yet.
+                        uninited[id] = true;
+                        return;
+                    }
+
+                    //Get the value for the current dependency
+                    value = forceExec(depMod, traced, uninited);
+
+                    //Even with forcing it may not be done,
+                    //in particular if the module is waiting
+                    //on a plugin resource.
+                    if (!uninited[depId]) {
+                        mod.defineDepById(depId, value);
+                    }
+                }
+            });
+
+            mod.check(true);
+
+            return defined[id];
+        }
+
+        function modCheck(mod) {
+            mod.check();
+        }
+
+        function checkLoaded() {
+            var map, modId, err, usingPathFallback,
+                waitInterval = config.waitSeconds * 1000,
+                //It is possible to disable the wait interval by using waitSeconds of 0.
+                expired = waitInterval && (context.startTime + waitInterval) < new Date().getTime(),
+                noLoads = [],
+                stillLoading = false,
+                needCycleCheck = true;
+
+            //Do not bother if this call was a result of a cycle break.
+            if (inCheckLoaded) {
+                return;
+            }
+
+            inCheckLoaded = true;
+
+            //Figure out the state of all the modules.
+            eachProp(registry, function (mod) {
+                map = mod.map;
+                modId = map.id;
+
+                //Skip things that are not enabled or in error state.
+                if (!mod.enabled) {
+                    return;
+                }
+
+                if (!mod.error) {
+                    //If the module should be executed, and it has not
+                    //been inited and time is up, remember it.
+                    if (!mod.inited && expired) {
+                        if (hasPathFallback(modId)) {
+                            usingPathFallback = true;
+                            stillLoading = true;
+                        } else {
+                            noLoads.push(modId);
+                            removeScript(modId);
+                        }
+                    } else if (!mod.inited && mod.fetched && map.isDefine) {
+                        stillLoading = true;
+                        if (!map.prefix) {
+                            //No reason to keep looking for unfinished
+                            //loading. If the only stillLoading is a
+                            //plugin resource though, keep going,
+                            //because it may be that a plugin resource
+                            //is waiting on a non-plugin cycle.
+                            return (needCycleCheck = false);
+                        }
+                    }
+                }
+            });
+
+            if (expired && noLoads.length) {
+                //If wait time expired, throw error of unloaded modules.
+                err = makeError('timeout', 'Load timeout for modules: ' + noLoads, null, noLoads);
+                err.contextName = context.contextName;
+                return onError(err);
+            }
+
+            //Not expired, check for a cycle.
+            if (needCycleCheck) {
+
+                each(waitAry, function (mod) {
+                    if (mod.defined) {
+                        return;
+                    }
+
+                    var cycleMod = findCycle(mod, {}, {}),
+                        traced = {};
+
+                    if (cycleMod) {
+                        forceExec(cycleMod, traced, {});
+
+                        //traced modules may have been
+                        //removed from the registry, but
+                        //their listeners still need to
+                        //be called.
+                        eachProp(traced, modCheck);
+                    }
+                });
+
+                //Now that dependencies have
+                //been satisfied, trigger the
+                //completion check that then
+                //notifies listeners.
+                eachProp(registry, modCheck);
+            }
+
+            //If still waiting on loads, and the waiting load is something
+            //other than a plugin resource, or there are still outstanding
+            //scripts, then just try back later.
+            if ((!expired || usingPathFallback) && stillLoading) {
+                //Something is still waiting to load. Wait for it, but only
+                //if a timeout is not already in effect.
+                if ((isBrowser || isWebWorker) && !checkLoadedTimeoutId) {
+                    checkLoadedTimeoutId = setTimeout(function () {
+                        checkLoadedTimeoutId = 0;
+                        checkLoaded();
+                    }, 50);
+                }
+            }
+
+            inCheckLoaded = false;
+        }
+
+        Module = function (map) {
+            this.events = undefEvents[map.id] || {};
+            this.map = map;
+            this.shim = config.shim[map.id];
+            this.depExports = [];
+            this.depMaps = [];
+            this.depMatched = [];
+            this.pluginMaps = {};
+            this.depCount = 0;
+
+            /* this.exports this.factory
+               this.depMaps = [],
+               this.enabled, this.fetched
+            */
+        };
+
+        Module.prototype = {
+            init: function (depMaps, factory, errback, options) {
+                options = options || {};
+
+                //Do not do more inits if already done. Can happen if there
+                //are multiple define calls for the same module. That is not
+                //a normal, common case, but it is also not unexpected.
+                if (this.inited) {
+                    return;
+                }
+
+                this.factory = factory;
+
+                if (errback) {
+                    //Register for errors on this module.
+                    this.on('error', errback);
+                } else if (this.events.error) {
+                    //If no errback already, but there are error listeners
+                    //on this module, set up an errback to pass to the deps.
+                    errback = bind(this, function (err) {
+                        this.emit('error', err);
+                    });
+                }
+
+                //Do a copy of the dependency array, so that
+                //source inputs are not modified. For example
+                //"shim" deps are passed in here directly, and
+                //doing a direct modification of the depMaps array
+                //would affect that config.
+                this.depMaps = depMaps && depMaps.slice(0);
+                this.depMaps.rjsSkipMap = depMaps.rjsSkipMap;
+
+                this.errback = errback;
+
+                //Indicate this module has be initialized
+                this.inited = true;
+
+                this.ignore = options.ignore;
+
+                //Could have option to init this module in enabled mode,
+                //or could have been previously marked as enabled. However,
+                //the dependencies are not known until init is called. So
+                //if enabled previously, now trigger dependencies as enabled.
+                if (options.enabled || this.enabled) {
+                    //Enable this module and dependencies.
+                    //Will call this.check()
+                    this.enable();
+                } else {
+                    this.check();
+                }
+            },
+
+            defineDepById: function (id, depExports) {
+                var i;
+
+                //Find the index for this dependency.
+                each(this.depMaps, function (map, index) {
+                    if (map.id === id) {
+                        i = index;
+                        return true;
+                    }
+                });
+
+                return this.defineDep(i, depExports);
+            },
+
+            defineDep: function (i, depExports) {
+                //Because of cycles, defined callback for a given
+                //export can be called more than once.
+                if (!this.depMatched[i]) {
+                    this.depMatched[i] = true;
+                    this.depCount -= 1;
+                    this.depExports[i] = depExports;
+                }
+            },
+
+            fetch: function () {
+                if (this.fetched) {
+                    return;
+                }
+                this.fetched = true;
+
+                context.startTime = (new Date()).getTime();
+
+                var map = this.map;
+
+                //If the manager is for a plugin managed resource,
+                //ask the plugin to load it now.
+                if (this.shim) {
+                    makeRequire(this, true)(this.shim.deps || [], bind(this, function () {
+                        return map.prefix ? this.callPlugin() : this.load();
+                    }));
+                } else {
+                    //Regular dependency.
+                    return map.prefix ? this.callPlugin() : this.load();
+                }
+            },
+
+            load: function () {
+                var url = this.map.url;
+
+                //Regular dependency.
+                if (!urlFetched[url]) {
+                    urlFetched[url] = true;
+                    context.load(this.map.id, url);
+                }
+            },
+
+            /**
+             * Checks is the module is ready to define itself, and if so,
+             * define it. If the silent argument is true, then it will just
+             * define, but not notify listeners, and not ask for a context-wide
+             * check of all loaded modules. That is useful for cycle breaking.
+             */
+            check: function (silent) {
+                if (!this.enabled || this.enabling) {
+                    return;
+                }
+
+                var err, cjsModule,
+                    id = this.map.id,
+                    depExports = this.depExports,
+                    exports = this.exports,
+                    factory = this.factory;
+
+                if (!this.inited) {
+                    this.fetch();
+                } else if (this.error) {
+                    this.emit('error', this.error);
+                } else if (!this.defining) {
+                    //The factory could trigger another require call
+                    //that would result in checking this module to
+                    //define itself again. If already in the process
+                    //of doing that, skip this work.
+                    this.defining = true;
+
+                    if (this.depCount < 1 && !this.defined) {
+                        if (isFunction(factory)) {
+                            //If there is an error listener, favor passing
+                            //to that instead of throwing an error.
+                            if (this.events.error) {
+                                try {
+                                    exports = context.execCb(id, factory, depExports, exports);
+                                } catch (e) {
+                                    err = e;
+                                }
+                            } else {
+                                exports = context.execCb(id, factory, depExports, exports);
+                            }
+
+                            if (this.map.isDefine) {
+                                //If setting exports via 'module' is in play,
+                                //favor that over return value and exports. After that,
+                                //favor a non-undefined return value over exports use.
+                                cjsModule = this.module;
+                                if (cjsModule &&
+                                        cjsModule.exports !== undefined &&
+                                        //Make sure it is not already the exports value
+                                        cjsModule.exports !== this.exports) {
+                                    exports = cjsModule.exports;
+                                } else if (exports === undefined && this.usingExports) {
+                                    //exports already set the defined value.
+                                    exports = this.exports;
+                                }
+                            }
+
+                            if (err) {
+                                err.requireMap = this.map;
+                                err.requireModules = [this.map.id];
+                                err.requireType = 'define';
+                                return onError((this.error = err));
+                            }
+
+                        } else {
+                            //Just a literal value
+                            exports = factory;
+                        }
+
+                        this.exports = exports;
+
+                        if (this.map.isDefine && !this.ignore) {
+                            defined[id] = exports;
+
+                            if (req.onResourceLoad) {
+                                req.onResourceLoad(context, this.map, this.depMaps);
+                            }
+                        }
+
+                        //Clean up
+                        delete registry[id];
+
+                        this.defined = true;
+                        context.waitCount -= 1;
+                        if (context.waitCount === 0) {
+                            //Clear the wait array used for cycles.
+                            waitAry = [];
+                        }
+                    }
+
+                    //Finished the define stage. Allow calling check again
+                    //to allow define notifications below in the case of a
+                    //cycle.
+                    this.defining = false;
+
+                    if (!silent) {
+                        if (this.defined && !this.defineEmitted) {
+                            this.defineEmitted = true;
+                            this.emit('defined', this.exports);
+                            this.defineEmitComplete = true;
+                        }
+                    }
+                }
+            },
+
+            callPlugin: function () {
+                var map = this.map,
+                    id = map.id,
+                    pluginMap = makeModuleMap(map.prefix, null, false, true);
+
+                on(pluginMap, 'defined', bind(this, function (plugin) {
+                    var load, normalizedMap, normalizedMod,
+                        name = this.map.name,
+                        parentName = this.map.parentMap ? this.map.parentMap.name : null;
+
+                    //If current map is not normalized, wait for that
+                    //normalized name to load instead of continuing.
+                    if (this.map.unnormalized) {
+                        //Normalize the ID if the plugin allows it.
+                        if (plugin.normalize) {
+                            name = plugin.normalize(name, function (name) {
+                                return normalize(name, parentName, true);
+                            }) || '';
+                        }
+
+                        normalizedMap = makeModuleMap(map.prefix + '!' + name,
+                                                      this.map.parentMap,
+                                                      false,
+                                                      true);
+                        on(normalizedMap,
+                            'defined', bind(this, function (value) {
+                                this.init([], function () { return value; }, null, {
+                                    enabled: true,
+                                    ignore: true
+                                });
+                            }));
+                        normalizedMod = registry[normalizedMap.id];
+                        if (normalizedMod) {
+                            if (this.events.error) {
+                                normalizedMod.on('error', bind(this, function (err) {
+                                    this.emit('error', err);
+                                }));
+                            }
+                            normalizedMod.enable();
+                        }
+
+                        return;
+                    }
+
+                    load = bind(this, function (value) {
+                        this.init([], function () { return value; }, null, {
+                            enabled: true
+                        });
+                    });
+
+                    load.error = bind(this, function (err) {
+                        this.inited = true;
+                        this.error = err;
+                        err.requireModules = [id];
+
+                        //Remove temp unnormalized modules for this module,
+                        //since they will never be resolved otherwise now.
+                        eachProp(registry, function (mod) {
+                            if (mod.map.id.indexOf(id + '_unnormalized') === 0) {
+                                removeWaiting(mod.map.id);
+                            }
+                        });
+
+                        onError(err);
+                    });
+
+                    //Allow plugins to load other code without having to know the
+                    //context or how to 'complete' the load.
+                    load.fromText = function (moduleName, text) {
+                        /*jslint evil: true */
+                        var hasInteractive = useInteractive;
+
+                        //Turn off interactive script matching for IE for any define
+                        //calls in the text, then turn it back on at the end.
+                        if (hasInteractive) {
+                            useInteractive = false;
+                        }
+
+                        //Prime the system by creating a module instance for
+                        //it.
+                        getModule(makeModuleMap(moduleName));
+
+                        req.exec(text);
+
+                        if (hasInteractive) {
+                            useInteractive = true;
+                        }
+
+                        //Support anonymous modules.
+                        context.completeLoad(moduleName);
+                    };
+
+                    //Use parentName here since the plugin's name is not reliable,
+                    //could be some weird string with no path that actually wants to
+                    //reference the parentName's path.
+                    plugin.load(map.name, makeRequire(map.parentMap, true, function (deps, cb, er) {
+                        deps.rjsSkipMap = true;
+                        return context.require(deps, cb, er);
+                    }), load, config);
+                }));
+
+                context.enable(pluginMap, this);
+                this.pluginMaps[pluginMap.id] = pluginMap;
+            },
+
+            enable: function () {
+                this.enabled = true;
+
+                if (!this.waitPushed) {
+                    waitAry.push(this);
+                    context.waitCount += 1;
+                    this.waitPushed = true;
+                }
+
+                //Set flag mentioning that the module is enabling,
+                //so that immediate calls to the defined callbacks
+                //for dependencies do not trigger inadvertent load
+                //with the depCount still being zero.
+                this.enabling = true;
+
+                //Enable each dependency
+                each(this.depMaps, bind(this, function (depMap, i) {
+                    var id, mod, handler;
+
+                    if (typeof depMap === 'string') {
+                        //Dependency needs to be converted to a depMap
+                        //and wired up to this module.
+                        depMap = makeModuleMap(depMap,
+                                               (this.map.isDefine ? this.map : this.map.parentMap),
+                                               false,
+                                               !this.depMaps.rjsSkipMap);
+                        this.depMaps[i] = depMap;
+
+                        handler = handlers[depMap.id];
+
+                        if (handler) {
+                            this.depExports[i] = handler(this);
+                            return;
+                        }
+
+                        this.depCount += 1;
+
+                        on(depMap, 'defined', bind(this, function (depExports) {
+                            this.defineDep(i, depExports);
+                            this.check();
+                        }));
+
+                        if (this.errback) {
+                            on(depMap, 'error', this.errback);
+                        }
+                    }
+
+                    id = depMap.id;
+                    mod = registry[id];
+
+                    //Skip special modules like 'require', 'exports', 'module'
+                    //Also, don't call enable if it is already enabled,
+                    //important in circular dependency cases.
+                    if (!handlers[id] && mod && !mod.enabled) {
+                        context.enable(depMap, this);
+                    }
+                }));
+
+                //Enable each plugin that is used in
+                //a dependency
+                eachProp(this.pluginMaps, bind(this, function (pluginMap) {
+                    var mod = registry[pluginMap.id];
+                    if (mod && !mod.enabled) {
+                        context.enable(pluginMap, this);
+                    }
+                }));
+
+                this.enabling = false;
+
+                this.check();
+            },
+
+            on: function (name, cb) {
+                var cbs = this.events[name];
+                if (!cbs) {
+                    cbs = this.events[name] = [];
+                }
+                cbs.push(cb);
+            },
+
+            emit: function (name, evt) {
+                each(this.events[name], function (cb) {
+                    cb(evt);
+                });
+                if (name === 'error') {
+                    //Now that the error handler was triggered, remove
+                    //the listeners, since this broken Module instance
+                    //can stay around for a while in the registry/waitAry.
+                    delete this.events[name];
+                }
+            }
+        };
+
+        function callGetModule(args) {
+            getModule(makeModuleMap(args[0], null, true)).init(args[1], args[2]);
+        }
+
+        function removeListener(node, func, name, ieName) {
+            //Favor detachEvent because of IE9
+            //issue, see attachEvent/addEventListener comment elsewhere
+            //in this file.
+            if (node.detachEvent && !isOpera) {
+                //Probably IE. If not it will throw an error, which will be
+                //useful to know.
+                if (ieName) {
+                    node.detachEvent(ieName, func);
+                }
+            } else {
+                node.removeEventListener(name, func, false);
+            }
+        }
+
+        /**
+         * Given an event from a script node, get the requirejs info from it,
+         * and then removes the event listeners on the node.
+         * @param {Event} evt
+         * @returns {Object}
+         */
+        function getScriptData(evt) {
+            //Using currentTarget instead of target for Firefox 2.0's sake. Not
+            //all old browsers will be supported, but this one was easy enough
+            //to support and still makes sense.
+            var node = evt.currentTarget || evt.srcElement;
+
+            //Remove the listeners once here.
+            removeListener(node, context.onScriptLoad, 'load', 'onreadystatechange');
+            removeListener(node, context.onScriptError, 'error');
+
+            return {
+                node: node,
+                id: node && node.getAttribute('data-requiremodule')
+            };
+        }
+
+        return (context = {
+            config: config,
+            contextName: contextName,
+            registry: registry,
+            defined: defined,
+            urlFetched: urlFetched,
+            waitCount: 0,
+            defQueue: defQueue,
+            Module: Module,
+            makeModuleMap: makeModuleMap,
+
+            /**
+             * Set a configuration for the context.
+             * @param {Object} cfg config object to integrate.
+             */
+            configure: function (cfg) {
+                //Make sure the baseUrl ends in a slash.
+                if (cfg.baseUrl) {
+                    if (cfg.baseUrl.charAt(cfg.baseUrl.length - 1) !== '/') {
+                        cfg.baseUrl += '/';
+                    }
+                }
+
+                //Save off the paths and packages since they require special processing,
+                //they are additive.
+                var pkgs = config.pkgs,
+                    shim = config.shim,
+                    paths = config.paths,
+                    map = config.map;
+
+                //Mix in the config values, favoring the new values over
+                //existing ones in context.config.
+                mixin(config, cfg, true);
+
+                //Merge paths.
+                config.paths = mixin(paths, cfg.paths, true);
+
+                //Merge map
+                if (cfg.map) {
+                    config.map = mixin(map || {}, cfg.map, true, true);
+                }
+
+                //Merge shim
+                if (cfg.shim) {
+                    eachProp(cfg.shim, function (value, id) {
+                        //Normalize the structure
+                        if (isArray(value)) {
+                            value = {
+                                deps: value
+                            };
+                        }
+                        if (value.exports && !value.exports.__buildReady) {
+                            value.exports = context.makeShimExports(value.exports);
+                        }
+                        shim[id] = value;
+                    });
+                    config.shim = shim;
+                }
+
+                //Adjust packages if necessary.
+                if (cfg.packages) {
+                    each(cfg.packages, function (pkgObj) {
+                        var location;
+
+                        pkgObj = typeof pkgObj === 'string' ? { name: pkgObj } : pkgObj;
+                        location = pkgObj.location;
+
+                        //Create a brand new object on pkgs, since currentPackages can
+                        //be passed in again, and config.pkgs is the internal transformed
+                        //state for all package configs.
+                        pkgs[pkgObj.name] = {
+                            name: pkgObj.name,
+                            location: location || pkgObj.name,
+                            //Remove leading dot in main, so main paths are normalized,
+                            //and remove any trailing .js, since different package
+                            //envs have different conventions: some use a module name,
+                            //some use a file name.
+                            main: (pkgObj.main || 'main')
+                                  .replace(currDirRegExp, '')
+                                  .replace(jsSuffixRegExp, '')
+                        };
+                    });
+
+                    //Done with modifications, assing packages back to context config
+                    config.pkgs = pkgs;
+                }
+
+                //If there are any "waiting to execute" modules in the registry,
+                //update the maps for them, since their info, like URLs to load,
+                //may have changed.
+                eachProp(registry, function (mod, id) {
+                    //If module already has init called, since it is too
+                    //late to modify them, and ignore unnormalized ones
+                    //since they are transient.
+                    if (!mod.inited && !mod.map.unnormalized) {
+                        mod.map = makeModuleMap(id);
+                    }
+                });
+
+                //If a deps array or a config callback is specified, then call
+                //require with those args. This is useful when require is defined as a
+                //config object before require.js is loaded.
+                if (cfg.deps || cfg.callback) {
+                    context.require(cfg.deps || [], cfg.callback);
+                }
+            },
+
+            makeShimExports: function (exports) {
+                var func;
+                if (typeof exports === 'string') {
+                    func = function () {
+                        return getGlobal(exports);
+                    };
+                    //Save the exports for use in nodefine checking.
+                    func.exports = exports;
+                    return func;
+                } else {
+                    return function () {
+                        return exports.apply(global, arguments);
+                    };
+                }
+            },
+
+            requireDefined: function (id, relMap) {
+                return hasProp(defined, makeModuleMap(id, relMap, false, true).id);
+            },
+
+            requireSpecified: function (id, relMap) {
+                id = makeModuleMap(id, relMap, false, true).id;
+                return hasProp(defined, id) || hasProp(registry, id);
+            },
+
+            require: function (deps, callback, errback, relMap) {
+                var moduleName, id, map, requireMod, args;
+                if (typeof deps === 'string') {
+                    if (isFunction(callback)) {
+                        //Invalid call
+                        return onError(makeError('requireargs', 'Invalid require call'), errback);
+                    }
+
+                    //Synchronous access to one module. If require.get is
+                    //available (as in the Node adapter), prefer that.
+                    //In this case deps is the moduleName and callback is
+                    //the relMap
+                    if (req.get) {
+                        return req.get(context, deps, callback);
+                    }
+
+                    //Just return the module wanted. In this scenario, the
+                    //second arg (if passed) is just the relMap.
+                    moduleName = deps;
+                    relMap = callback;
+
+                    //Normalize module name, if it contains . or ..
+                    map = makeModuleMap(moduleName, relMap, false, true);
+                    id = map.id;
+
+                    if (!hasProp(defined, id)) {
+                        return onError(makeError('notloaded', 'Module name "' +
+                                    id +
+                                    '" has not been loaded yet for context: ' +
+                                    contextName));
+                    }
+                    return defined[id];
+                }
+
+                //Callback require. Normalize args. if callback or errback is
+                //not a function, it means it is a relMap. Test errback first.
+                if (errback && !isFunction(errback)) {
+                    relMap = errback;
+                    errback = undefined;
+                }
+                if (callback && !isFunction(callback)) {
+                    relMap = callback;
+                    callback = undefined;
+                }
+
+                //Any defined modules in the global queue, intake them now.
+                takeGlobalQueue();
+
+                //Make sure any remaining defQueue items get properly processed.
+                while (defQueue.length) {
+                    args = defQueue.shift();
+                    if (args[0] === null) {
+                        return onError(makeError('mismatch', 'Mismatched anonymous define() module: ' + args[args.length - 1]));
+                    } else {
+                        //args are id, deps, factory. Should be normalized by the
+                        //define() function.
+                        callGetModule(args);
+                    }
+                }
+
+                //Mark all the dependencies as needing to be loaded.
+                requireMod = getModule(makeModuleMap(null, relMap));
+
+                requireMod.init(deps, callback, errback, {
+                    enabled: true
+                });
+
+                checkLoaded();
+
+                return context.require;
+            },
+
+            undef: function (id) {
+                //Bind any waiting define() calls to this context,
+                //fix for #408
+                takeGlobalQueue();
+
+                var map = makeModuleMap(id, null, true),
+                    mod = registry[id];
+
+                delete defined[id];
+                delete urlFetched[map.url];
+                delete undefEvents[id];
+
+                if (mod) {
+                    //Hold on to listeners in case the
+                    //module will be attempted to be reloaded
+                    //using a different config.
+                    if (mod.events.defined) {
+                        undefEvents[id] = mod.events;
+                    }
+
+                    removeWaiting(id);
+                }
+            },
+
+            /**
+             * Called to enable a module if it is still in the registry
+             * awaiting enablement. parent module is passed in for context,
+             * used by the optimizer.
+             */
+            enable: function (depMap, parent) {
+                var mod = registry[depMap.id];
+                if (mod) {
+                    getModule(depMap).enable();
+                }
+            },
+
+            /**
+             * Internal method used by environment adapters to complete a load event.
+             * A load event could be a script load or just a load pass from a synchronous
+             * load call.
+             * @param {String} moduleName the name of the module to potentially complete.
+             */
+            completeLoad: function (moduleName) {
+                var found, args, mod,
+                    shim = config.shim[moduleName] || {},
+                    shExports = shim.exports && shim.exports.exports;
+
+                takeGlobalQueue();
+
+                while (defQueue.length) {
+                    args = defQueue.shift();
+                    if (args[0] === null) {
+                        args[0] = moduleName;
+                        //If already found an anonymous module and bound it
+                        //to this name, then this is some other anon module
+                        //waiting for its completeLoad to fire.
+                        if (found) {
+                            break;
+                        }
+                        found = true;
+                    } else if (args[0] === moduleName) {
+                        //Found matching define call for this script!
+                        found = true;
+                    }
+
+                    callGetModule(args);
+                }
+
+                //Do this after the cycle of callGetModule in case the result
+                //of those calls/init calls changes the registry.
+                mod = registry[moduleName];
+
+                if (!found && !defined[moduleName] && mod && !mod.inited) {
+                    if (config.enforceDefine && (!shExports || !getGlobal(shExports))) {
+                        if (hasPathFallback(moduleName)) {
+                            return;
+                        } else {
+                            return onError(makeError('nodefine',
+                                             'No define call for ' + moduleName,
+                                             null,
+                                             [moduleName]));
+                        }
+                    } else {
+                        //A script that does not call define(), so just simulate
+                        //the call for it.
+                        callGetModule([moduleName, (shim.deps || []), shim.exports]);
+                    }
+                }
+
+                checkLoaded();
+            },
+
+            /**
+             * Converts a module name + .extension into an URL path.
+             * *Requires* the use of a module name. It does not support using
+             * plain URLs like nameToUrl.
+             */
+            toUrl: function (moduleNamePlusExt, relModuleMap) {
+                var index = moduleNamePlusExt.lastIndexOf('.'),
+                    ext = null;
+
+                if (index !== -1) {
+                    ext = moduleNamePlusExt.substring(index, moduleNamePlusExt.length);
+                    moduleNamePlusExt = moduleNamePlusExt.substring(0, index);
+                }
+
+                return context.nameToUrl(normalize(moduleNamePlusExt, relModuleMap && relModuleMap.id, true),
+                                         ext);
+            },
+
+            /**
+             * Converts a module name to a file path. Supports cases where
+             * moduleName may actually be just an URL.
+             * Note that it **does not** call normalize on the moduleName,
+             * it is assumed to have already been normalized. This is an
+             * internal API, not a public one. Use toUrl for the public API.
+             */
+            nameToUrl: function (moduleName, ext) {
+                var paths, pkgs, pkg, pkgPath, syms, i, parentModule, url,
+                    parentPath;
+
+                //If a colon is in the URL, it indicates a protocol is used and it is just
+                //an URL to a file, or if it starts with a slash, contains a query arg (i.e. ?)
+                //or ends with .js, then assume the user meant to use an url and not a module id.
+                //The slash is important for protocol-less URLs as well as full paths.
+                if (req.jsExtRegExp.test(moduleName)) {
+                    //Just a plain path, not module name lookup, so just return it.
+                    //Add extension if it is included. This is a bit wonky, only non-.js things pass
+                    //an extension, this method probably needs to be reworked.
+                    url = moduleName + (ext || '');
+                } else {
+                    //A module that needs to be converted to a path.
+                    paths = config.paths;
+                    pkgs = config.pkgs;
+
+                    syms = moduleName.split('/');
+                    //For each module name segment, see if there is a path
+                    //registered for it. Start with most specific name
+                    //and work up from it.
+                    for (i = syms.length; i > 0; i -= 1) {
+                        parentModule = syms.slice(0, i).join('/');
+                        pkg = pkgs[parentModule];
+                        parentPath = paths[parentModule];
+                        if (parentPath) {
+                            //If an array, it means there are a few choices,
+                            //Choose the one that is desired
+                            if (isArray(parentPath)) {
+                                parentPath = parentPath[0];
+                            }
+                            syms.splice(0, i, parentPath);
+                            break;
+                        } else if (pkg) {
+                            //If module name is just the package name, then looking
+                            //for the main module.
+                            if (moduleName === pkg.name) {
+                                pkgPath = pkg.location + '/' + pkg.main;
+                            } else {
+                                pkgPath = pkg.location;
+                            }
+                            syms.splice(0, i, pkgPath);
+                            break;
+                        }
+                    }
+
+                    //Join the path parts together, then figure out if baseUrl is needed.
+                    url = syms.join('/');
+                    url += (ext || (/\?/.test(url) ? '' : '.js'));
+                    url = (url.charAt(0) === '/' || url.match(/^[\w\+\.\-]+:/) ? '' : config.baseUrl) + url;
+                }
+
+                return config.urlArgs ? url +
+                                        ((url.indexOf('?') === -1 ? '?' : '&') +
+                                         config.urlArgs) : url;
+            },
+
+            //Delegates to req.load. Broken out as a separate function to
+            //allow overriding in the optimizer.
+            load: function (id, url) {
+                req.load(context, id, url);
+            },
+
+            /**
+             * Executes a module callack function. Broken out as a separate function
+             * solely to allow the build system to sequence the files in the built
+             * layer in the right sequence.
+             *
+             * @private
+             */
+            execCb: function (name, callback, args, exports) {
+                return callback.apply(exports, args);
+            },
+
+            /**
+             * callback for script loads, used to check status of loading.
+             *
+             * @param {Event} evt the event from the browser for the script
+             * that was loaded.
+             */
+            onScriptLoad: function (evt) {
+                //Using currentTarget instead of target for Firefox 2.0's sake. Not
+                //all old browsers will be supported, but this one was easy enough
+                //to support and still makes sense.
+                if (evt.type === 'load' ||
+                        (readyRegExp.test((evt.currentTarget || evt.srcElement).readyState))) {
+                    //Reset interactive script so a script node is not held onto for
+                    //to long.
+                    interactiveScript = null;
+
+                    //Pull out the name of the module and the context.
+                    var data = getScriptData(evt);
+                    context.completeLoad(data.id);
+                }
+            },
+
+            /**
+             * Callback for script errors.
+             */
+            onScriptError: function (evt) {
+                var data = getScriptData(evt);
+                if (!hasPathFallback(data.id)) {
+                    return onError(makeError('scripterror', 'Script error', evt, [data.id]));
+                }
+            }
+        });
+    }
+
+    /**
+     * Main entry point.
+     *
+     * If the only argument to require is a string, then the module that
+     * is represented by that string is fetched for the appropriate context.
+     *
+     * If the first argument is an array, then it will be treated as an array
+     * of dependency string names to fetch. An optional function callback can
+     * be specified to execute when all of those dependencies are available.
+     *
+     * Make a local req variable to help Caja compliance (it assumes things
+     * on a require that are not standardized), and to give a short
+     * name for minification/local scope use.
+     */
+    req = requirejs = function (deps, callback, errback, optional) {
+
+        //Find the right context, use default
+        var context, config,
+            contextName = defContextName;
+
+        // Determine if have config object in the call.
+        if (!isArray(deps) && typeof deps !== 'string') {
+            // deps is a config object
+            config = deps;
+            if (isArray(callback)) {
+                // Adjust args if there are dependencies
+                deps = callback;
+                callback = errback;
+                errback = optional;
+            } else {
+                deps = [];
+            }
+        }
+
+        if (config && config.context) {
+            contextName = config.context;
+        }
+
+        context = contexts[contextName];
+        if (!context) {
+            context = contexts[contextName] = req.s.newContext(contextName);
+        }
+
+        if (config) {
+            context.configure(config);
+        }
+
+        return context.require(deps, callback, errback);
+    };
+
+    /**
+     * Support require.config() to make it easier to cooperate with other
+     * AMD loaders on globally agreed names.
+     */
+    req.config = function (config) {
+        return req(config);
+    };
+
+    /**
+     * Export require as a global, but only if it does not already exist.
+     */
+    if (!require) {
+        require = req;
+    }
+
+    req.version = version;
+
+    //Used to filter out dependencies that are already paths.
+    req.jsExtRegExp = /^\/|:|\?|\.js$/;
+    req.isBrowser = isBrowser;
+    s = req.s = {
+        contexts: contexts,
+        newContext: newContext
+    };
+
+    //Create default context.
+    req({});
+
+    //Exports some context-sensitive methods on global require, using
+    //default context if no context specified.
+    addRequireMethods(req);
+
+    if (isBrowser) {
+        head = s.head = document.getElementsByTagName('head')[0];
+        //If BASE tag is in play, using appendChild is a problem for IE6.
+        //When that browser dies, this can be removed. Details in this jQuery bug:
+        //http://dev.jquery.com/ticket/2709
+        baseElement = document.getElementsByTagName('base')[0];
+        if (baseElement) {
+            head = s.head = baseElement.parentNode;
+        }
+    }
+
+    /**
+     * Any errors that require explicitly generates will be passed to this
+     * function. Intercept/override it if you want custom error handling.
+     * @param {Error} err the error object.
+     */
+    req.onError = function (err) {
+        throw err;
+    };
+
+    /**
+     * Does the request to load a module for the browser case.
+     * Make this a separate function to allow other environments
+     * to override it.
+     *
+     * @param {Object} context the require context to find state.
+     * @param {String} moduleName the name of the module.
+     * @param {Object} url the URL to the module.
+     */
+    req.load = function (context, moduleName, url) {
+        var config = (context && context.config) || {},
+            node;
+        if (isBrowser) {
+            //In the browser so use a script tag
+            node = config.xhtml ?
+                    document.createElementNS('http://www.w3.org/1999/xhtml', 'html:script') :
+                    document.createElement('script');
+            node.type = config.scriptType || 'text/javascript';
+            node.charset = 'utf-8';
+            node.async = true;
+
+            node.setAttribute('data-requirecontext', context.contextName);
+            node.setAttribute('data-requiremodule', moduleName);
+
+            //Set up load listener. Test attachEvent first because IE9 has
+            //a subtle issue in its addEventListener and script onload firings
+            //that do not match the behavior of all other browsers with
+            //addEventListener support, which fire the onload event for a
+            //script right after the script execution. See:
+            //https://connect.microsoft.com/IE/feedback/details/648057/script-onload-event...
+            //UNFORTUNATELY Opera implements attachEvent but does not follow the script
+            //script execution mode.
+            if (node.attachEvent &&
+                    //Check if node.attachEvent is artificially added by custom script or
+                    //natively supported by browser
+                    //read https://github.com/jrburke/requirejs/issues/187
+                    //if we can NOT find [native code] then it must NOT natively supported.
+                    //in IE8, node.attachEvent does not have toString()
+                    //Note the test for "[native code" with no closing brace, see:
+                    //https://github.com/jrburke/requirejs/issues/273
+                    !(node.attachEvent.toString && node.attachEvent.toString().indexOf('[native code') < 0) &&
+                    !isOpera) {
+                //Probably IE. IE (at least 6-8) do not fire
+                //script onload right after executing the script, so
+                //we cannot tie the anonymous define call to a name.
+                //However, IE reports the script as being in 'interactive'
+                //readyState at the time of the define call.
+                useInteractive = true;
+
+                node.attachEvent('onreadystatechange', context.onScriptLoad);
+                //It would be great to add an error handler here to catch
+                //404s in IE9+. However, onreadystatechange will fire before
+                //the error handler, so that does not help. If addEvenListener
+                //is used, then IE will fire error before load, but we cannot
+                //use that pathway given the connect.microsoft.com issue
+                //mentioned above about not doing the 'script execute,
+                //then fire the script load event listener before execute
+                //next script' that other browsers do.
+                //Best hope: IE10 fixes the issues,
+                //and then destroys all installs of IE 6-9.
+                //node.attachEvent('onerror', context.onScriptError);
+            } else {
+                node.addEventListener('load', context.onScriptLoad, false);
+                node.addEventListener('error', context.onScriptError, false);
+            }
+            node.src = url;
+
+            //For some cache cases in IE 6-8, the script executes before the end
+            //of the appendChild execution, so to tie an anonymous define
+            //call to the module name (which is stored on the node), hold on
+            //to a reference to this node, but clear after the DOM insertion.
+            currentlyAddingScript = node;
+            if (baseElement) {
+                head.insertBefore(node, baseElement);
+            } else {
+                head.appendChild(node);
+            }
+            currentlyAddingScript = null;
+
+            return node;
+        } else if (isWebWorker) {
+            //In a web worker, use importScripts. This is not a very
+            //efficient use of importScripts, importScripts will block until
+            //its script is downloaded and evaluated. However, if web workers
+            //are in play, the expectation that a build has been done so that
+            //only one script needs to be loaded anyway. This may need to be
+            //reevaluated if other use cases become common.
+            importScripts(url);
+
+            //Account for anonymous modules
+            context.completeLoad(moduleName);
+        }
+    };
+
+    function getInteractiveScript() {
+        if (interactiveScript && interactiveScript.readyState === 'interactive') {
+            return interactiveScript;
+        }
+
+        eachReverse(scripts(), function (script) {
+            if (script.readyState === 'interactive') {
+                return (interactiveScript = script);
+            }
+        });
+        return interactiveScript;
+    }
+
+    //Look for a data-main script attribute, which could also adjust the baseUrl.
+    if (isBrowser) {
+        //Figure out baseUrl. Get it from the script tag with require.js in it.
+        eachReverse(scripts(), function (script) {
+            //Set the 'head' where we can append children by
+            //using the script's parent.
+            if (!head) {
+                head = script.parentNode;
+            }
+
+            //Look for a data-main attribute to set main script for the page
+            //to load. If it is there, the path to data main becomes the
+            //baseUrl, if it is not already set.
+            dataMain = script.getAttribute('data-main');
+            if (dataMain) {
+                //Set final baseUrl if there is not already an explicit one.
+                if (!cfg.baseUrl) {
+                    //Pull off the directory of data-main for use as the
+                    //baseUrl.
+                    src = dataMain.split('/');
+                    mainScript = src.pop();
+                    subPath = src.length ? src.join('/')  + '/' : './';
+
+                    cfg.baseUrl = subPath;
+                    dataMain = mainScript;
+                }
+
+                //Strip off any trailing .js since dataMain is now
+                //like a module name.
+                dataMain = dataMain.replace(jsSuffixRegExp, '');
+
+                //Put the data-main script in the files to load.
+                cfg.deps = cfg.deps ? cfg.deps.concat(dataMain) : [dataMain];
+
+                return true;
+            }
+        });
+    }
+
+    /**
+     * The function that handles definitions of modules. Differs from
+     * require() in that a string for the module should be the first argument,
+     * and the function to execute after dependencies are loaded should
+     * return a value to define the module corresponding to the first argument's
+     * name.
+     */
+    define = function (name, deps, callback) {
+        var node, context;
+
+        //Allow for anonymous functions
+        if (typeof name !== 'string') {
+            //Adjust args appropriately
+            callback = deps;
+            deps = name;
+            name = null;
+        }
+
+        //This module may not have dependencies
+        if (!isArray(deps)) {
+            callback = deps;
+            deps = [];
+        }
+
+        //If no name, and callback is a function, then figure out if it a
+        //CommonJS thing with dependencies.
+        if (!deps.length && isFunction(callback)) {
+            //Remove comments from the callback string,
+            //look for require calls, and pull them into the dependencies,
+            //but only if there are function args.
+            if (callback.length) {
+                callback
+                    .toString()
+                    .replace(commentRegExp, '')
+                    .replace(cjsRequireRegExp, function (match, dep) {
+                        deps.push(dep);
+                    });
+
+                //May be a CommonJS thing even without require calls, but still
+                //could use exports, and module. Avoid doing exports and module
+                //work though if it just needs require.
+                //REQUIRES the function to expect the CommonJS variables in the
+                //order listed below.
+                deps = (callback.length === 1 ? ['require'] : ['require', 'exports', 'module']).concat(deps);
+            }
+        }
+
+        //If in IE 6-8 and hit an anonymous define() call, do the interactive
+        //work.
+        if (useInteractive) {
+            node = currentlyAddingScript || getInteractiveScript();
+            if (node) {
+                if (!name) {
+                    name = node.getAttribute('data-requiremodule');
+                }
+                context = contexts[node.getAttribute('data-requirecontext')];
+            }
+        }
+
+        //Always save off evaluating the def call until the script onload handler.
+        //This allows multiple modules to be in a file without prematurely
+        //tracing dependencies, and allows for anonymous module support,
+        //where the module name is not known until the script onload event
+        //occurs. If no context, use the global queue, and get it processed
+        //in the onscript load callback.
+        (context ? context.defQueue : globalDefQueue).push([name, deps, callback]);
+    };
+
+    define.amd = {
+        jQuery: true
+    };
+
+
+    /**
+     * Executes the text. Normally just uses eval, but can be modified
+     * to use a better, environment-specific call. Only used for transpiling
+     * loader plugins, not for plain JS modules.
+     * @param {String} text the text to execute/evaluate.
+     */
+    req.exec = function (text) {
+        /*jslint evil: true */
+        return eval(text);
+    };
+
+    //Set up with config info.
+    req(cfg);
+}(this));


diff -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 -r 45ddaa89e9855d21ce2f6a29a0eb90cc61abd7cd static/scripts/viz/circster.js
--- a/static/scripts/viz/circster.js
+++ b/static/scripts/viz/circster.js
@@ -1,14 +1,11 @@
-(function(){
+define( ["libs/d3", "viz/visualization"], function( d3, visualization ) {
 
 // General backbone style inheritence
 var Base = function() { this.initialize && this.initialize.apply(this, arguments) }; Base.extend = Backbone.Model.extend;
 
-// ---- Circster views ----
- 
 /**
- * -- Views --
- */
- 
+ * Renders a full circster visualization
+ */ 
 var CircsterView = Backbone.View.extend({
     className: 'circster',
     
@@ -50,30 +47,29 @@
         this.model.get('tracks').each(function(track, index) {
             var dataset = track.get('genome_wide_data'),
                 radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
-                track_view_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigTrackView : CircsterSummaryTreeTrackView );
+                track_renderer_class = (dataset instanceof visualization.GenomeWideBigWigData ? CircsterBigWigTrackRenderer : CircsterSummaryTreeTrackRenderer );
 
-            track_view = new track_view_class({
+            track_renderer = new track_renderer_class({
                 track: track,
                 radius_start: radius_start,
                 radius_end: radius_start + dataset_arc_height,
                 genome: self.genome,
-                total_gap: self.total_gap,
-                svg: svg
+                total_gap: self.total_gap
             });
 
-            track_view.render();
+            track_renderer.render( svg );
 
         });
     }
 });
 
-var CircsterTrackView = Base.extend( {
+var CircsterTrackRenderer = Base.extend( {
 
     initialize: function( options ) {
         this.options = options;
     },
 
-    render: function() {
+    render: function( svg ) {
 
         genome_arcs = this.chroms_layout(),
         chroms_arcs = this.genome_data_layout();
@@ -81,8 +77,7 @@
         // -- Render. --
 
         // Draw background arcs for each chromosome.
-        var svg = this.options.svg,
-            radius_start = this.options.radius_start,
+        var radius_start = this.options.radius_start,
             radius_end = this.options.radius_end,
             base_arc = svg.append("g").attr("id", "inner-arc"),
             arc_gen = d3.svg.arc()
@@ -165,7 +160,7 @@
 /**
  * Layout for summary tree data in a circster visualization.
  */
-var CircsterSummaryTrackView = CircsterTrackView.extend({
+var CircsterSummaryTrackRenderer = CircsterTrackRenderer.extend({
     
     /**
      * Returns layouts for drawing a chromosome's data.
@@ -200,7 +195,7 @@
 /**
  * Layout for BigWig data in a circster visualization.
  */
-var CircsterBigWigTrackView = CircsterTrackView.extend({
+var CircsterBigWigTrackRenderer = CircsterTrackRenderer.extend({
 
     /**
      * Returns layouts for drawing a chromosome's data.
@@ -233,12 +228,8 @@
 
 });
 
-// ---- Browser or CommonJS compatible exports ----
-
-if (typeof exports === 'undefined') {
-    var exports = this;
+return {
+    CircsterView: CircsterView
 }
 
-exports.CircsterView = CircsterView;
-
-}).call(this);
+});


diff -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 -r 45ddaa89e9855d21ce2f6a29a0eb90cc61abd7cd static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -1,3 +1,5 @@
+(function(){
+
 /**
  * Model, view, and controller objects for Galaxy visualization framework.
  * 
@@ -551,7 +553,7 @@
         {
             type: Backbone.HasOne,
             key: 'region',
-            relatedModel: 'GenomeRegion'
+            relatedModel: GenomeRegion
         }
     ]
 });
@@ -645,7 +647,7 @@
         {
             type: Backbone.HasMany,
             key: 'tracks',
-            relatedModel: 'BackboneTrack'
+            relatedModel: BackboneTrack
         }
     ],
 
@@ -772,3 +774,40 @@
         }
     });
 };
+
+// ---- Exports ----
+
+var exports = (function() {
+    if ( typeof module !== 'undefined' && module.exports ) {
+        // CommonJS
+        return module.exports;
+    } else if ( typeof define === 'function' && define.amd ) {
+        // AMD
+        exports = {}
+        define( function() { return exports } );
+        return exports
+    } else {
+        // Browser global
+        return window;
+    }
+})();
+
+exports.BrowserBookmark = BrowserBookmark                  
+exports.BrowserBookmarkCollection = BrowserBookmarkCollection
+exports.Cache = Cache
+exports.CanvasManager = CanvasManager
+exports.Genome = Genome
+exports.GenomeDataManager = GenomeDataManager
+exports.GenomeRegion = GenomeRegion
+exports.GenomeRegionCollection = GenomeRegionCollection
+exports.GenomeVisualization = GenomeVisualization
+exports.GenomeWideBigWigData = GenomeWideBigWigData
+exports.GenomeWideSummaryTreeData = GenomeWideSummaryTreeData
+exports.ReferenceTrackDataManager = ReferenceTrackDataManager
+exports.ServerStateDeferred = ServerStateDeferred
+exports.TrackBrowserRouter = TrackBrowserRouter
+exports.TrackConfig = TrackConfig
+exports.Visualization = Visualization
+exports.add_datasets = add_datasets
+
+}).call(this);
\ No newline at end of file


diff -r db2be15c12584351ef4f58bff0069ee5a4eed5a9 -r 45ddaa89e9855d21ce2f6a29a0eb90cc61abd7cd templates/visualization/circster.mako
--- a/templates/visualization/circster.mako
+++ b/templates/visualization/circster.mako
@@ -16,71 +16,83 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
 
-    ${h.js( "libs/d3", "mvc/data", "viz/visualization", "viz/circster" )}
+    ${h.js( "require", "mvc/data" )}
 
     <script type="text/javascript">
-        $(function() {
-            // -- Visualization menu and set up.
-            var menu = create_icon_buttons_menu([
-                { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { add_tracks(); } },
-                { icon_class: 'disk--arrow', title: 'Save', on_click: function() { 
-                    // Show saving dialog box
-                    show_modal("Saving...", "progress");
 
-                    $.ajax({
-                        url: "${h.url_for( action='save' )}",
-                        type: "POST",
-                        data: {
-                            'id': view.vis_id,
-                            'title': view.name,
-                            'dbkey': view.dbkey,
-                            'type': 'trackster',
-                            'config': JSON.stringify(payload)
-                        },
-                        dataType: "json",
-                        success: function(vis_info) {
-                            hide_modal();
-                            view.vis_id = vis_info.vis_id;
-                            view.has_changes = false;
+        require.config({ 
+            baseUrl: "${h.url_for('/static/scripts')}",
+            shim: {
+                "libs/d3": { exports: "d3" }
+            }
+        });
 
-                            // Needed to set URL when first saving a visualization.
-                            window.history.pushState({}, "", vis_info.url + window.location.hash);
-                        },
-                        error: function() { 
-                            show_modal( "Could Not Save", "Could not save visualization. Please try again later.", 
-                                        { "Close" : hide_modal } );
-                        }
+        require( [ "libs/d3", "viz/visualization", "viz/circster" ], function( d3, visualization, circster ) {
+
+            $(function() {
+                
+                // -- Visualization menu and set up.
+                var menu = create_icon_buttons_menu([
+                    { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { add_tracks(); } },
+                    { icon_class: 'disk--arrow', title: 'Save', on_click: function() { 
+                        // Show saving dialog box
+                        show_modal("Saving...", "progress");
+
+                        $.ajax({
+                            url: "${h.url_for( action='save' )}",
+                            type: "POST",
+                            data: {
+                                'id': view.vis_id,
+                                'title': view.name,
+                                'dbkey': view.dbkey,
+                                'type': 'trackster',
+                                'config': JSON.stringify(payload)
+                            },
+                            dataType: "json",
+                            success: function(vis_info) {
+                                hide_modal();
+                                view.vis_id = vis_info.vis_id;
+                                view.has_changes = false;
+
+                                // Needed to set URL when first saving a visualization.
+                                window.history.pushState({}, "", vis_info.url + window.location.hash);
+                            },
+                            error: function() { 
+                                show_modal( "Could Not Save", "Could not save visualization. Please try again later.", 
+                                            { "Close" : hide_modal } );
+                            }
+                        });
+                    } },
+                    { icon_class: 'cross-circle', title: 'Close', on_click: function() { 
+                        window.location = "${h.url_for( controller='visualization', action='list' )}";
+                    } }
+                ], {
+                    tooltip_config: { placement: 'bottom' }
+                });
+
+                menu.$el.attr("style", "float: right");
+                $("#center .unified-panel-header-inner").append(menu.$el);
+                // Manual tooltip config because default gravity is S and cannot be changed.
+                $(".menu-button").tooltip( { placement: 'bottom' } );
+                
+                // -- Viz set up. --
+                
+                var genome = new visualization.Genome(JSON.parse('${ h.to_json_string( genome ) }'))
+                    vis = new visualization.GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')),
+                    viz_view = new circster.CircsterView({
+                        el: $('#vis'),
+                        // Gap is difficult to set because it very dependent on chromosome size and organization.
+                        total_gap: 2 * Math.PI * 0.1,
+                        genome: genome,
+                        model: vis,
+                        dataset_arc_height: 25
                     });
-                } },
-                { icon_class: 'cross-circle', title: 'Close', on_click: function() { 
-                    window.location = "${h.url_for( controller='visualization', action='list' )}";
-                } }
-            ], {
-                tooltip_config: { placement: 'bottom' }
+                
+                // -- Render viz. --
+                    
+                viz_view.render();
+
             });
-
-            menu.$el.attr("style", "float: right");
-            $("#center .unified-panel-header-inner").append(menu.$el);
-            // Manual tooltip config because default gravity is S and cannot be changed.
-            $(".menu-button").tooltip( { placement: 'bottom' } );
-            
-            // -- Viz set up. --
-            
-            var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }'))
-                visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')),
-                viz_view = new CircsterView({
-                    el: $('#vis'),
-                    // Gap is difficult to set because it very dependent on chromosome size and organization.
-                    total_gap: 2 * Math.PI * 0.1,
-                    genome: genome,
-                    model: visualization,
-                    dataset_arc_height: 25
-                });
-            
-            // -- Render viz. --
-                
-            viz_view.render();
-
         });
     </script></%def>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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