Foundation for parameter sweeping visualization.

lib/galaxy/tools/__init__.py

@@ -2407,10 +2407,19 @@ class Tool:
                 if isinstance( input, DataToolParameter ):
                     param_dict.update( { 'type' : 'data', 'html' : urllib.quote( input.get_html( trans ) ) } )
                 elif isinstance( input, SelectToolParameter ):
-                    param_dict.update( { 'type' : 'select', 'html' : urllib.quote( input.get_html( trans ) ) } )
+                    param_dict.update( { 'type' : 'select', 
+                                         'html' : urllib.quote( input.get_html( trans ) ),
+                                         'options': input.static_options 
+                                         } )
                 elif isinstance( input, Conditional ):
                     # TODO.
                     pass
+                elif isinstance( input, ( IntegerToolParameter, FloatToolParameter ) ):
+                    param_dict.update( { 'type' : 'number', 'init_value' : input.value,
+                                         'html' : urllib.quote( input.get_html( trans ) ),
+                                         'min': input.min,
+                                         'max': input.max
+                                          } )
                 else:
                     param_dict.update( { 'type' : '??', 'init_value' : input.value, \
                                          'html' : urllib.quote( input.get_html( trans ) ) } )

lib/galaxy/web/controllers/tracks.py

@@ -762,6 +762,15 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryMix
                 output_dataset = joda.dataset
         
         return self.add_track_async( trans, output_dataset.id )
+        
+    @web.expose
+    @web.require_login( "use Galaxy visualizations", use_panels=True )
+    def paramamonster( self, trans, hda_ldda, dataset_id ):
+        # Get dataset.
+        dataset = self._get_dataset( trans, hda_ldda, dataset_id )
+                
+        return trans.fill_template_mako( "visualization/paramamonster.mako", dataset=dataset,
+                                          tool=self.app.toolbox.tools_by_id[ 'cufflinks' ].to_dict( trans, for_display=True ) )
     
     @web.expose
     @web.require_login( "use Galaxy visualizations", use_panels=True )

static/scripts/packed/viz/paramamonster.js

@@ -0,0 +1 @@
+var ToolParameterTree=Backbone.Model.extend({defaults:{tool:null,samples:4},initialize:function(d){var c=this.get("tool"),b=this.get("samples"),a=c.get("inputs").filter(function(h){return(["number","select"].indexOf(h.get("type"))!==-1)}),f=_.map(a,function(h){return h.get("name")});sampling=_.map(a,function(h){var i=h.get("type");if(i==="number"){return d3.scale.linear().domain([h.get("min"),h.get("max")]).ticks(b)}else{if(i==="select"){return _.map(h.get("options"),function(j){return j[0]})}}});var g=function(j,h,i){if(h.length-1===i){return _.map(h[i],function(k){return{name:k}})}return _.map(h[i],function(k){return{name:j[i]+":"+k,children:g(j,h,i+1)}})};var e={name:"Parameter Tree for "+c.get("name"),children:g(f,sampling,0)};this.set("valid_inputs",a);this.set("tree_data",e)}});var TileView=Backbone.View.extend({});var ToolParameterTreeView=Backbone.View.extend({className:"paramamonster",initialize:function(a){this.model=a.model},render:function(){var e=960,b=2000;var a=d3.layout.cluster().size([b,e-160]);var d=d3.svg.diagonal().projection(function(i){return[i.y,i.x]});var h=d3.select(this.$el[0]).append("svg").attr("width",e).attr("height",b).append("g").attr("transform","translate(80, 0)");var c=a.nodes(this.model.get("tree_data"));var g=h.selectAll("path.link").data(a.links(c)).enter().append("path").attr("class","link").attr("d",d);var f=h.selectAll("g.node").data(c).enter().append("g").attr("class","node").attr("transform",function(i){return"translate("+i.y+","+i.x+")"});f.append("circle").attr("r",4.5);f.append("text").attr("dx",function(i){return i.children?-8:8}).attr("dy",3).attr("text-anchor",function(i){return i.children?"end":"start"}).text(function(i){return i.name})}});

static/scripts/viz/paramamonster.js

@@ -0,0 +1,123 @@
+/**
+ * Visualization and components for ParamaMonster, a visualization for exploring a tool's parameter space via 
+ * genomic visualization.
+ */
+ 
+var ToolParameterTree = Backbone.Model.extend({
+    defaults: {
+        tool: null,
+        samples: 4
+    },
+    
+    
+    initialize: function(options) {
+        //
+        // -- Create tree data from tool. --
+        //
+        
+        // Valid inputs for tree are number, select parameters.
+        var tool = this.get('tool'),
+            samples = this.get('samples'),
+            inputs = tool.get('inputs').filter(function(input) {
+                return ( ['number', 'select'].indexOf(input.get('type')) !== -1 );
+            }),
+            inputs_names = _.map(inputs, function(i) { return i.get('name')});
+            // Sample from all valid inputs.
+            sampling = _.map(inputs, function(input) {
+                var type = input.get('type');
+                if (type === 'number') {
+                    return d3.scale.linear().domain([input.get('min'), input.get('max')]).ticks(samples);
+                }
+                else if (type === 'select') {
+                    return _.map(input.get('options'), function(option) {
+                        return option[0];
+                    });
+                }
+            });
+            
+        /**
+         * Returns tree data.
+         */
+        var create_tree_data = function(param_names, param_settings, index) {
+            // Terminate when last parameter setting is reached.
+            if (param_settings.length - 1 === index) {
+                return _.map(param_settings[index], function(setting) {
+                    return {
+                        name: setting
+                    }
+                });
+            }
+            
+            // Recurse to handle other parameters.
+            return _.map(param_settings[index], function(setting) {
+                 return {
+                     name: param_names[index] + ':' + setting,
+                     children: create_tree_data(param_names, param_settings, index + 1)
+                 }
+            });       
+        };
+        
+        var tree_data = {
+            name: 'Parameter Tree for ' + tool.get('name'),
+            children: create_tree_data(inputs_names, sampling, 0)
+        };
+            
+        // Set valid inputs, tree data for later use.
+        this.set('valid_inputs', inputs);
+        this.set('tree_data', tree_data);
+    }
+    
+});
+
+var TileView = Backbone.View.extend({
+    
+});
+
+var ToolParameterTreeView = Backbone.View.extend({
+    className: 'paramamonster',
+    
+    initialize: function(options) {
+        this.model = options.model;  
+    },
+    
+    render: function() {
+        var width = 960,
+            height = 2000;
+
+        var cluster = d3.layout.cluster()
+            .size([height, width - 160]);
+
+        var diagonal = d3.svg.diagonal()
+            .projection(function(d) { return [d.y, d.x]; });
+
+        var vis = d3.select(this.$el[0])
+          .append("svg")
+            .attr("width", width)
+            .attr("height", height)
+          .append("g")
+            .attr("transform", "translate(80, 0)");
+
+          var nodes = cluster.nodes(this.model.get('tree_data'));
+
+          var link = vis.selectAll("path.link")
+              .data(cluster.links(nodes))
+            .enter().append("path")
+              .attr("class", "link")
+              .attr("d", diagonal);
+
+          var node = vis.selectAll("g.node")
+              .data(nodes)
+            .enter().append("g")
+              .attr("class", "node")
+              .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; })
+
+          node.append("circle")
+              .attr("r", 4.5);
+
+          node.append("text")
+              .attr("dx", function(d) { return d.children ? -8 : 8; })
+              .attr("dy", 3)
+              .attr("text-anchor", function(d) { return d.children ? "end" : "start"; })
+              .text(function(d) { return d.name; });
+    }
+});

templates/visualization/circster.mako

@@ -16,7 +16,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
 
-    ${h.js( "libs/d3", "mvc/visualization" )}
+    ${h.js( "libs/d3", "viz/visualization" )}
 
     <script type="text/javascript">
         $(function() {
@@ -81,7 +81,7 @@
             // -- Render viz. --
                 
             circster.render();
-            $('#vis').append(circster.$el);                
+            $('#vis').append(circster.$el);
         });
     </script>
 </%def>

templates/visualization/paramamonster.mako

@@ -0,0 +1,62 @@
+<%inherit file="/webapps/galaxy/base_panels.mako"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.active_view="visualization"
+    self.message_box_visible=False
+%>
+</%def>
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    <style>
+        .unified-panel-body {
+            overflow: auto;
+        }
+        .link {
+            fill: none;
+            stroke: #ccc;
+            stroke-width: 1.5px;
+        }
+        .node {
+            font: 10px sans-serif;
+        }
+        .node circle {
+            fill: #fff;
+            stroke: steelblue;
+            stroke-width: 1.5px;
+        }
+    </style>
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+
+    ${h.templates( "tool_link", "panel_section", "tool_search" )}
+    ${h.js( "libs/d3", "viz/visualization", "viz/paramamonster", "mvc/tools" )}
+
+    <script type="text/javascript">
+        $(function() {            
+            // -- Viz set up. --
+            
+            var tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')),
+                tool_param_tree = new ToolParameterTree({ tool: tool }),
+                tool_param_tree_view = new ToolParameterTreeView({ model: tool_param_tree });
+                
+            tool_param_tree_view.render();
+            $('#vis').append(tool_param_tree_view.$el);
+        });
+    </script>
+</%def>
+
+<%def name="center_panel()">
+    <div class="unified-panel-header" unselectable="on">
+        <div class="unified-panel-header-inner">
+            <div style="float:left;" id="title"></div>
+        </div>
+        <div style="clear: both"></div>
+    </div>
+    <div id="vis" class="unified-panel-body"></div>
+</%def>