1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0b2d939a7870/ changeset: 0b2d939a7870 user: jgoecks date: 2012-06-05 23:10:23 summary: Foundation for parameter sweeping visualization. affected #: 6 files diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2407,10 +2407,19 @@ 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 ) ) } ) diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -762,6 +762,15 @@ 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 ) diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 static/scripts/packed/viz/paramamonster.js --- /dev/null +++ b/static/scripts/packed/viz/paramamonster.js @@ -0,0 +1,1 @@ +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})}}); \ No newline at end of file diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 static/scripts/viz/paramamonster.js --- /dev/null +++ b/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; }); + } +}); \ No newline at end of file diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 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/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> diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 templates/visualization/paramamonster.mako --- /dev/null +++ b/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> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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