commit/galaxy-central: 4 new changesets

14 Apr 2014

4 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/8c4e3b85aa3b/
Changeset:   8c4e3b85aa3b
Branch:      next-stable
User:        natefoo
Date:        2014-04-15 01:26:24
Summary:     Close next-stable branch.
Affected #:  0 files



https://bitbucket.org/galaxy/galaxy-central/commits/9e53251b0b7e/
Changeset:   9e53251b0b7e
Branch:      stable
User:        natefoo
Date:        2014-04-15 01:27:21
Summary:     Update stable branch from next-stable for release.
Affected #:  749 files

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc .hgignore

--- a/.hgignore
+++ b/.hgignore
@@ -77,6 +77,7 @@
 tool-data/shared/ucsc/builds.txt
 tool-data/shared/ensembl/builds.txt
 tool-data/shared/ucsc/publicbuilds.txt
+tool-data/shared/ucsc/ucsc_build_sites.txt
 tool-data/*.loc
 tool-data/genome/*
 

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc README.txt
--- a/README.txt
+++ b/README.txt
@@ -26,6 +26,6 @@
 on adding tools can be found on the Galaxy website (linked above).
 
 Not all dependencies are included for the tools provided in the sample
-tool_conf.xml.  A full list of external dependencies is available at:
+tool_conf.xml. A full list of external dependencies is available at:
 
-http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
+https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/additional_template_paths.xml
--- /dev/null
+++ b/config/plugins/visualizations/additional_template_paths.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- these relative paths can contain common templates importable by all visualization plugins -->
+<paths>
+    <path>common/templates</path>
+</paths>

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/Gruntfile.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/Gruntfile.js
@@ -0,0 +1,24 @@
+// NOTE: use 'sudo npm install .', then 'grunt' to use this file
+module.exports = function(grunt) {
+    grunt.initConfig({
+        pkg: grunt.file.readJSON('package.json'),
+        requirejs: {
+            compile: {
+                options: {
+                    baseUrl : "../../../../static/scripts/",
+                    paths   : {
+                        "plugin": "../../config/plugins/visualizations/charts/static"
+                    },
+                    shim    : {
+                        "libs/underscore": { exports: "_" },
+                        "libs/backbone/backbone": { exports: "Backbone" }
+                    },
+                    name    : "plugin/app",
+                    out     : "static/build-app.js",
+                }
+            }
+        }
+    });
+    grunt.loadNpmTasks('grunt-contrib-requirejs');
+    grunt.registerTask( 'default', [ 'requirejs' ]);
+};

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/config/charts.xml
--- a/config/plugins/visualizations/charts/config/charts.xml
+++ b/config/plugins/visualizations/charts/config/charts.xml
@@ -7,15 +7,9 @@
             <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test><to_param param_attr="id">dataset_id</to_param></data_source>
-        <data_source>
-            <model_class>Visualization</model_class>
-            <test test_attr="type">charts</test>
-            <to_param param_attr="id">visualization_id</to_param>
-        </data_source></data_sources><params><param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
-        <param type="visualization" var_name_in_template="visualization">visualization_id</param></params><template>charts.mako</template></visualization>

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/package.json
--- /dev/null
+++ b/config/plugins/visualizations/charts/package.json
@@ -0,0 +1,18 @@
+{
+  "name": "galaxy-charts",
+  "version": "0.0.0",
+  "description": "Charts visualization plugin for the Galaxy informatics framework",
+  "main": " ",
+  "keywords": [
+    "galaxy",
+    "visualization",
+    "d3"
+  ],
+  "author": "Aysam Guerler",
+  "license": "BSD",
+  "devDependencies": {
+    "grunt": "~0.4.1",
+    "grunt-cli": "~0.1.9",
+    "grunt-contrib-requirejs": "~0.4.3"
+  }
+}

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,10 +1,12 @@
 // dependencies
-define(['library/portlet', 'library/ui', 'library/utils',
-        'views/charts', 'views/viewport', 'views/chart', 'views/group',
-        'models/config', 'models/datasets', 'models/chart', 'models/charts', 'models/group', 'models/types'],
-        function(   Portlet, Ui, Utils,
-                    ChartsView, ViewportView, ChartView, GroupView,
-                    Config, Datasets, Chart, Charts, Group, Types
+define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
+        'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage',
+        'plugin/views/viewer', 'plugin/views/editor',
+        'plugin/models/config', 'plugin/models/chart',
+        'plugin/charts/types'],
+        function(   Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage,
+                    ViewerView, EditorView,
+                    Config, Chart, Types
                 ) {
 
 // widget
@@ -13,66 +15,75 @@
     // initialize
     initialize: function(options)
     {
+        // deactivate all debugs outputs
+        //window.console.debug = function() {};
+        
         // link options
         this.options = options;
     
-        // link galaxy
-        this.modal = parent.Galaxy.modal;
+        // link galaxy modal or create one
+        if (Galaxy && Galaxy.modal) {
+            this.modal = Galaxy.modal;
+        } else {
+            this.modal = new Modal.View();
+        }
         
-        // create configuration model
+        //
+        // models
+        //
         this.config = new Config();
-        
-        // create chart models
         this.types = new Types();
         this.chart = new Chart();
-        this.charts = new Charts();
-        this.group = new Group();
         
-        // create dataset handler
+        //
+        // libraries
+        //
+        this.jobs = new Jobs(this);
         this.datasets = new Datasets(this);
+        this.storage = new Storage(this);
         
-        // create views
-        this.charts_view = new ChartsView(this);
-        this.group_view = new GroupView(this);
-        this.chart_view = new ChartView(this);
-        this.viewport_view = new ViewportView(this);
-        
-        // append view port to charts viewer
-        this.charts_view.append(this.viewport_view.$el);
-            
-        // create portlet
-        if (!this.options.config.widget) {
-            this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'});
-        } else {
-            this.portlet = $('<div></div>');
-        }
+        //
+        // views
+        //
+        this.viewer_view = new ViewerView(this);
+        this.editor_view = new EditorView(this);
         
         // append views
-        this.portlet.append(this.charts_view.$el);
-        this.portlet.append(this.group_view.$el);
-        this.portlet.append(this.chart_view.$el);
-        
-        // set element
-        if (!this.options.config.widget) {
-            this.setElement(this.portlet.$el);
+        this.$el.append(this.viewer_view.$el);
+        this.$el.append(this.editor_view.$el);
+
+        // pick start screen
+        if (!this.storage.load()) {
+            // show editor
+            this.go('editor');
         } else {
-            this.setElement(this.portlet);
+            // show viewport
+            this.go('viewer');
+            
+            // draw chart
+            var self = this;
+            this.chart.deferred.execute(function() {
+                self.chart.trigger('redraw');
+            });
         }
-        
-        // hide views
-        this.group_view.$el.hide();
-        this.charts_view.$el.hide();
-        
-        // events
-        var self = this;
-        this.config.on('change:current_view', function() {
-            self._showCurrent();
-        });
     },
     
-    // current view
-    _showCurrent: function() {
+    // loads a view and makes sure that all others are hidden
+    go: function(view_id) {
+        // hide all tooltips
+        $('.tooltip').hide();
         
+        // pick view
+        switch (view_id) {
+            case 'editor' :
+                this.editor_view.show();
+                this.viewer_view.hide();
+                break;
+            case 'viewer' :
+                this.editor_view.hide();
+                this.viewer_view.show();
+                break;
+        }
     },
     
     // execute command

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/build-app.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -0,0 +1,6 @@
+//     Underscore.js 1.4.4
+//     http://underscorejs.org
+//     (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
+//     Underscore may be freely distributed under the MIT license.
+
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10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:a,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_svg();var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg_el=this.$el.find("svg"),this.svg=d3.select(this.svg_el[0])},_draw:function(e){var t=this;this._create_svg(),e.state("wait","Please wait...");var n=e.deferred.register(),r=e.get("type"),i=this.app.types.get(r);if(!i.execute||i.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var s=new r(t.app,{svg:t.svg});i.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){s.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):s.draw(n,e,t._defaultRequestDictionary(e)):s.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp"  style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/_nvd3/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/config.js
@@ -0,0 +1,218 @@
+define([], function() {
+
+return {
+    title   : '',
+    columns : {
+        y : {
+            title   : 'Values for y-axis'
+        }
+    },
+    settings  : {
+        separator_label  : {
+            title       : 'X axis',
+            type        : 'separator'
+        },
+        x_axis_label : {
+            title       : 'Axis label',
+            info        : 'Provide a label for the axis.',
+            type        : 'text',
+            init        : 'X-axis',
+            placeholder : 'Axis label'
+        },
+        x_axis_type : {
+            title       : 'Axis value type',
+            info        : 'Select the value type of the axis.',
+            type        : 'select',
+            init        : 'auto',
+            data        : [
+                {
+                    label   : '-- Do not show values --',
+                    value   : 'hide',
+                    hide    : 'x_axis_tick'
+                },
+                {
+                    label   : 'Auto',
+                    value   : 'auto',
+                    hide    : 'x_axis_tick'
+                },
+                {
+                    label   : 'Float',
+                    value   : 'f',
+                    show    : 'x_axis_tick'
+                },
+                {
+                    label   : 'Exponent',
+                    value   : 'e',
+                    show    : 'x_axis_tick'
+                },
+                {
+                    label   : 'Integer',
+                    value   : 'd',
+                    hide    : 'x_axis_tick'
+                },
+                {
+                    label   : 'Percentage',
+                    value   : 'p',
+                    show    : 'x_axis_tick'
+                },
+                {
+                    label   : 'Rounded',
+                    value   : 'r',
+                    show    : 'x_axis_tick'
+                },
+                {
+                    label   : 'SI-prefix',
+                    value   : 's',
+                    show    : 'x_axis_tick'
+                }
+            ]
+        },
+        x_axis_tick : {
+            title       : 'Axis tick format',
+            info        : 'Select the tick format for the axis.',
+            type        : 'select',
+            init        : '.1',
+            data        : [
+                {
+                    label   : '0.00001',
+                    value   : '.5'
+                },
+                {
+                    label   : '0.0001',
+                    value   : '.4'
+                },
+                {
+                    label   : '0.001',
+                    value   : '.3'
+                },
+                {
+                    label   : '0.01',
+                    value   : '.2'
+                },
+                {
+                    label   : '0.1',
+                    value   : '.1'
+                },
+                {
+                    label   : '1',
+                    value   : '1'
+                }
+            ]
+
+        },
+        separator_tick  : {
+            title       : 'Y axis',
+            type        : 'separator'
+        },
+        y_axis_label : {
+            title       : 'Axis label',
+            info        : 'Provide a label for the axis.',
+            type        : 'text',
+            init        : 'Y-axis',
+            placeholder : 'Axis label'
+        },
+        y_axis_type : {
+            title       : 'Axis value type',
+            info        : 'Select the value type of the axis.',
+            type        : 'select',
+            init        : 'auto',
+            data        : [
+                {
+                    label   : '-- Do not show values --',
+                    value   : 'hide',
+                    hide    : 'y_axis_tick'
+                },
+                {
+                    label   : 'Auto',
+                    value   : 'auto',
+                    hide    : 'y_axis_tick'
+                },
+                {
+                    label   : 'Float',
+                    value   : 'f',
+                    show    : 'y_axis_tick'
+                },
+                {
+                    label   : 'Exponent',
+                    value   : 'e',
+                    show    : 'y_axis_tick'
+                },
+                {
+                    label   : 'Integer',
+                    value   : 'd',
+                    hide    : 'y_axis_tick'
+                },
+                {
+                    label   : 'Percentage',
+                    value   : 'p',
+                    show    : 'y_axis_tick'
+                },
+                {
+                    label   : 'Rounded',
+                    value   : 'r',
+                    show    : 'y_axis_tick'
+                },
+                {
+                    label   : 'SI-prefix',
+                    value   : 's',
+                    show    : 'y_axis_tick'
+                }
+            ]
+        },
+        y_axis_tick : {
+            title       : 'Axis tick format',
+            info        : 'Select the tick format for the axis.',
+            type        : 'select',
+            init        : '.1',
+            data        : [
+                {
+                    label   : '0.00001',
+                    value   : '.5'
+                },
+                {
+                    label   : '0.0001',
+                    value   : '.4'
+                },
+                {
+                    label   : '0.001',
+                    value   : '.3'
+                },
+                {
+                    label   : '0.01',
+                    value   : '.2'
+                },
+                {
+                    label   : '0.1',
+                    value   : '.1'
+                },
+                {
+                    label   : '1',
+                    value   : '1'
+                }
+            ]
+
+        },
+        separator_legend : {
+            title       : 'Others',
+            type        : 'separator'
+        },
+        show_legend : {
+            title       : 'Show legend',
+            info        : 'Would you like to add a legend?',
+            type        : 'select',
+            init        : 'true',
+            data        : [
+                {
+                    label   : 'Yes',
+                    value   : 'true'
+                },
+                {
+                    label   : 'No',
+                    value   : 'false'
+                }
+            ]
+        },
+    }
+};
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
@@ -0,0 +1,80 @@
+// dependencies
+define([], function() {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, nvd3_model, chart, request_dictionary, callback)
+    {
+        // request data
+        var self = this;
+        this.app.datasets.request(request_dictionary, function(data) {
+            nv.addGraph(function() {
+                // x axis
+                self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick'));
+                
+                // x axis label
+                nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label'));
+                
+                // y axis
+                self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick'));
+                
+                // y axis label
+                nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label'))
+                                .axisLabelDistance(30);
+                
+                // controls
+                if (chart.groups.length == 1) {
+                    nvd3_model.options({ showControls: false });
+                }
+                
+                // legend
+                var legend_visible = true;
+                if (chart.settings.get('show_legend') == 'false') {
+                    legend_visible = false;
+                }
+                nvd3_model.showLegend(legend_visible);
+                
+                // custom callback
+                if (callback) {
+                    callback(nvd3_model);
+                }
+                
+                // parse data to svg
+                self.options.svg.datum(data)
+                                .call(nvd3_model);
+     
+                // refresh on window resize
+                nv.utils.windowResize(nvd3_model.update);
+                
+                // set chart state
+                chart.state('ok', 'Chart has been drawn.');
+                
+                // unregister process
+                chart.deferred.done(process_id);
+            });
+        });
+    },
+    
+    // make axis
+    _axis: function(axis, type, tick) {
+        switch (type) {
+            case 'hide':
+                axis.tickFormat(function() { return '' });
+                break;
+            case 'auto':
+                break;
+            default:
+                axis.tickFormat(d3.format(tick + type));
+        }
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/bardiagram.js
--- a/config/plugins/visualizations/charts/static/charts/bardiagram.js
+++ /dev/null
@@ -1,33 +0,0 @@
-// dependencies
-define([], function() {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // add graph to screen
-        var self = this;
-        nv.addGraph(function() {
-            self.d3_chart = nv.models.multiBarChart();
-                
-            self.d3_chart.xAxis.tickFormat(d3.format('.2f'))
-            self.d3_chart.yAxis.tickFormat(d3.format('.1f'))
-            
-            d3.select(self.options.svg_id)
-                .datum(data)
-                .call(self.d3_chart);
- 
-            nv.utils.windowResize(self.d3_chart.update);
-        });
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/bardiagram/bardiagram.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/bardiagram/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/bardiagram/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Bar diagram',
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/histogram/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js
@@ -0,0 +1,21 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Histogram',
+    execute : true,
+    columns : {
+        y : {
+            title   : 'Observations'
+        }
+    },
+    settings  : {
+        x_axis_label : {
+            init : 'Breaks'
+        },
+        y_axis_label : {
+            init : 'Density'
+        }
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/histogram/histogram.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/histogram/histogram.js
@@ -0,0 +1,31 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        // configure request
+        var index = 0;
+        for (var i in request_dictionary.groups) {
+            var group = request_dictionary.groups[i];
+            group.columns = {
+                x: index++,
+                y: index++
+            }
+        }
+
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/horizontal.js
--- a/config/plugins/visualizations/charts/static/charts/horizontal.js
+++ /dev/null
@@ -1,33 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-        this.chart      = options.chart;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // add graph to screen
-        var self = this;
-        nv.addGraph(function() {
-            self.d3_chart = nv.models.multiBarHorizontalChart();
-            
-            self.d3_chart.xAxis.tickFormat(function() { return ''; });
-            
-            d3.select(self.options.svg_id)
-                .datum(data)
-                .call(self.d3_chart);
- 
-            nv.utils.windowResize(self.d3_chart.update);
-        });
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/horizontal/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/horizontal/config.js
@@ -0,0 +1,12 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Bar diagram (horizontal)',
+    settings : {
+        x_axis_type : {
+            init : 'hide'
+        }
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/horizontal/horizontal.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary);
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/line.js
--- a/config/plugins/visualizations/charts/static/charts/line.js
+++ /dev/null
@@ -1,39 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-        this.chart      = options.chart;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // add graph to screen
-        var self = this;
-        nv.addGraph(function() {
-            self.chart_3d = nv.models.lineChart();
-
-            self.chart_3d.xAxis
-                .tickFormat(d3.format(',f'));
-
-            self.chart_3d.yAxis
-                .tickFormat(d3.format(',.2f'));
-            
-            d3.select(self.options.svg_id)
-                .datum(data)
-                .call(self.chart_3d);
-
-            nv.utils.windowResize(self.chart_3d.update);
-            
-            return self.chart_3d;
-        });
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/line/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/line/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Line chart',
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/line/line.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/line/line.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary);
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/linewithfocus.js
--- a/config/plugins/visualizations/charts/static/charts/linewithfocus.js
+++ /dev/null
@@ -1,37 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-        this.chart      = options.chart;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // add graph to screen
-        var self = this;
-        nv.addGraph(function() {
-            self.chart_3d = nv.models.lineWithFocusChart();
-
-            self.chart_3d.xAxis
-                .tickFormat(d3.format(',f'));
-
-            self.chart_3d.yAxis
-                .tickFormat(d3.format(',.2f'));
-            
-            d3.select(self.options.svg_id)
-                .datum(data)
-                .call(self.chart_3d);
-
-            nv.utils.windowResize(self.chart_3d.update);
-        });
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Line with focus',
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/linewithfocus/linewithfocus.js
@@ -0,0 +1,21 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary);
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/piechart.js
--- a/config/plugins/visualizations/charts/static/charts/piechart.js
+++ /dev/null
@@ -1,51 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-        this.chart      = options.chart;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // loop through data groups
-        for (var key in data) {
-            // get group
-            var group = data[key];
-            
-            // format chart data
-            var pie_data = [];
-            for (var key in group.values) {
-                var value = group.values[key];
-                pie_data.push ({
-                    key : value.x,
-                    y   : value.y
-                });
-            }
-            
-            // add graph to screen
-            var self = this;
-            nv.addGraph(function() {
-                self.chart_3d = nv.models.pieChart()
-                    .donut(true)
-                    .showLegend(false);
-                
-                d3.select(self.options.svg_id)
-                    .datum(pie_data)
-                    .call(self.chart_3d);
-
-                nv.utils.windowResize(self.chart_3d.update);
-                
-                return self.chart_3d;
-            });
-        }
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/piechart/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/piechart/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Pie chart',
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/piechart/piechart.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/piechart/piechart.js
@@ -0,0 +1,57 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        // request data
+        var self = this;
+        this.app.datasets.request(request_dictionary, function(data) {
+            
+            // loop through data groups
+            for (var key in request_dictionary.groups) {
+                // get group
+                var group = request_dictionary.groups[key];
+                
+                // format chart data
+                var pie_data = [];
+                for (var key in group.values) {
+                    var value = group.values[key];
+                    pie_data.push ({
+                        key : value.x,
+                        y   : value.y
+                    });
+                }
+                
+                // add graph to screen
+                nv.addGraph(function() {
+                    self.chart_3d = nv.models.pieChart()
+                        .donut(true)
+                        .showLegend(false);
+                    
+                    self.options.svg.datum(pie_data)
+                                    .call(self.chart_3d);
+
+                    nv.utils.windowResize(self.chart_3d.update);
+                    
+                    // set chart state
+                    chart.state('ok', 'Pie chart drawn.');
+                    
+                    // unregister process
+                    chart.deferred.done(process_id);
+                });
+            }
+        });
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/scatterplot.js
--- a/config/plugins/visualizations/charts/static/charts/scatterplot.js
+++ /dev/null
@@ -1,37 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-        this.chart      = options.chart;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // add graph to screen
-        var self = this;
-        nv.addGraph(function() {
-            self.d3_chart = nv.models.scatterChart()
-                .showDistX(true)
-                .showDistY(true)
-                .color(d3.scale.category10().range());
-                
-            self.d3_chart.xAxis.tickFormat(d3.format('.02f'))
-            self.d3_chart.yAxis.tickFormat(d3.format('.02f'))
-            
-            d3.select(self.options.svg_id)
-                .datum(data)
-                .call(self.d3_chart);
- 
-            nv.utils.windowResize(self.d3_chart.update);
-        });
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/scatterplot/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/scatterplot/config.js
@@ -0,0 +1,12 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Scatter plot',
+    columns : {
+        x : {
+            title   : 'Values for x-axis'
+        }
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/scatterplot/scatterplot.js
@@ -0,0 +1,25 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) {
+            nvd3_model.showDistX(true)
+                      .showDistY(true)
+                      .color(d3.scale.category10().range());
+        });
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/stackedarea.js
--- a/config/plugins/visualizations/charts/static/charts/stackedarea.js
+++ /dev/null
@@ -1,59 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
-    // initialize
-    initialize: function(app, options) {
-        this.app        = app;
-        this.options    = options;
-        this.chart      = options.chart;
-    },
-            
-    // render
-    refresh : function(data)
-    {
-        // add graph to screen
-        var self = this;
-        nv.addGraph(function() {
-            // check data
-            var valid = true;
-            var length = 0;
-            for (var key in data) {
-                // evalute length
-                if (length == 0) {
-                    length = data[key].values.length;
-                } else {
-                    if (length != data[key].values.length) {
-                        valid = false;
-                        break;
-                    }
-                }
-            }
-            if (!valid) {
-                return;
-            }
-            
-            // make plot
-            self.d3_chart = nv.models.stackedAreaChart()
-                .x(function(d) {
-                    return d.x
-                })
-                .y(function(d) {
-                    return d.y
-                })
-                .clipEdge(true);
-            
-            self.d3_chart.xAxis.tickFormat(function() { return ''; });
-            
-            d3.select(self.options.svg_id)
-                .datum(data)
-                .call(self.d3_chart);
- 
-            nv.utils.windowResize(self.d3_chart.update);
-        });
-    }
-});
-
-});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/stackedarea/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/stackedarea/config.js
@@ -0,0 +1,7 @@
+define(['plugin/charts/_nvd3/config'], function(nvd3_config) {
+
+return $.extend(true, {}, nvd3_config, {
+    title   : 'Stacked area'
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/stackedarea/stackedarea.js
@@ -0,0 +1,26 @@
+// dependencies
+define(['plugin/charts/_nvd3/nvd3'], function(NVD3) {
+
+// widget
+return Backbone.View.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        this.app        = app;
+        this.options    = options;
+    },
+            
+    // render
+    draw : function(process_id, chart, request_dictionary)
+    {
+        var nvd3 = new NVD3(this.app, this.options);
+        nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) {
+            // make plot
+            nvd3_model.x(function(d) { return d.x })
+                      .y(function(d) { return d.y })
+                      .clipEdge(true);
+        });
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/charts/types.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -0,0 +1,39 @@
+// dependencies
+define(['plugin/charts/bardiagram/config',
+        //'plugin/charts/boxplot/config',
+        'plugin/charts/histogram/config',
+        'plugin/charts/horizontal/config',
+        'plugin/charts/line/config',
+        'plugin/charts/linewithfocus/config',
+        'plugin/charts/piechart/config',
+        'plugin/charts/scatterplot/config',
+        'plugin/charts/stackedarea/config',
+        ], function(bardiagram,
+                    //boxplot,
+                    histogram,
+                    horizontal,
+                    line,
+                    linewithfocus,
+                    piechart,
+                    scatterplot,
+                    stackedarea
+            ) {
+
+// widget
+return Backbone.Model.extend(
+{
+    // types
+    defaults: {
+        'bardiagram' : bardiagram,
+        //'boxplot' : boxplot,
+        'horizontal' : horizontal,
+        'histogram' : histogram,
+        'line' : line,
+        'linewithfocus' : linewithfocus,
+        'piechart' : piechart,
+        'scatterplot' : scatterplot,
+        'stackedarea' : stackedarea
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/datasets.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -0,0 +1,149 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.Collection.extend(
+{
+    // list of datasets
+    list: {},
+    
+    // initialize
+    initialize: function(app, options)
+    {
+        // link app
+        this.app = app;
+        
+        // configure options
+        this.options = Utils.merge(options, this.optionsDefault);
+    },
+    
+    // wait
+    request: function(options, success, error) {
+        // link this
+        var self = this;
+        
+        // check if column data is requested
+        if (options.groups) {
+            this._fetch(options, success);
+        } else {
+            // check if dataset is available from cache
+            var dataset = this.list[options.id];
+            if (dataset) {
+                success(dataset);
+                return;
+            }
+        
+            // request dataset
+            Utils.request('GET', config.root + 'api/datasets/' + options.id, {}, function(dataset) {
+                switch (dataset.state) {
+                    case 'error':
+                        if (error) {
+                            error(dataset);
+                        }
+                        break;
+                    default:
+                        self.list[options.id] = dataset;
+                        success(dataset);
+                }
+            });
+        }
+    },
+    
+    // fetch data columns into dataset object
+    _fetch: function(options, callback) {
+        // set offset
+        var offset  = options.start ? options.start : 0;
+        
+        // set limit
+        var limit   = Math.abs(options.end - options.start);
+        var query_limit = this.app.config.get('query_limit');
+        if (!limit || limit > query_limit) {
+            limit = query_limit;
+        }
+        
+        // get column indices
+        var index_string    = '';
+        var index_map       = {};
+        var index_count     = 0;
+        for (var i in options.groups) {
+            var group = options.groups[i];
+            for (var key in group.columns) {
+                var column = group.columns[key];
+                
+                // add to index string
+                index_string += column + ',';
+                
+                // add to dictionary
+                index_map[column] = index_count;
+                
+                // increase counter
+                index_count++;
+            }
+        }
+        if (index_count == 0) {
+            callback({});
+            return;
+        }
+        index_string = index_string.substring(0, index_string.length - 1);
+
+        // initialize result dictionary
+        var result = options.groups.slice(0);
+        for (var i in result) {
+            result[i].values = [];
+        }
+        
+        // make request
+        var self = this;
+        Utils.request('GET', config.root + 'api/datasets/' + options.id, {
+                data_type   : 'raw_data',
+                provider    : 'dataset-column',
+                limit       : limit,
+                offset      : offset,
+                indeces     : index_string
+            }, function(response) {
+                
+                // loop through rows
+                for (var i in response.data) {
+                    // get row
+                    var row = response.data[i];
+                    
+                    // collect all data into the defined groups
+                    for (var j in options.groups) {
+                        // get group
+                        var group = options.groups[j];
+                        
+                        // initialize value
+                        var value = {
+                            x : parseInt(i) + offset
+                        };
+                        
+                        // fill value
+                        for (var key in group.columns) {
+                            // get column
+                            var column = group.columns[key];
+                      
+                            // identify column
+                            var index = index_map[column];
+                          
+                            // read value from row
+                            var v = row[index];
+                            if(isNaN(v) || !v) {
+                                v = 0;
+                            }
+                      
+                            // add value to dictionary
+                            value[key] = v;
+                        }
+
+                        // add to result
+                        result[j].values.push(value);
+                    }
+                }
+                
+                // callback
+                callback(result);
+            });
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/deferred.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/deferred.js
@@ -0,0 +1,85 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// deferred process handler
+return Backbone.Model.extend(
+{
+    // queue
+    queue: [],
+    
+    // list of currently registered processes
+    process: {},
+    
+    // process counter
+    counter: 0,
+    
+    // initialize
+    initialize: function()
+    {
+        // loop through queue and check states
+        this.on('refresh', function() {
+            if (this.counter == 0) {
+                for (var index in this.queue) {
+                    // execute callback
+                    this.queue[index]();
+                
+                    // remove callback
+                    this.queue.splice(index, 1);
+                }
+            }
+        });
+    },
+    
+    // executes callback once all processes are unregistered
+    execute: function(callback) {
+        // add wrapper to queue
+        this.queue.push(callback);
+        
+        // trigger change
+        this.trigger('refresh');
+    },
+    
+    // register process
+    register: function() {
+        // create unique id
+        var id = Utils.uuid();
+        
+        // add process to queue
+        this.process[id] = true;
+        
+        // increase process counter
+        this.counter++;
+        
+        // log
+        console.debug('Deferred:register() - Registering ' + id);
+        
+        // return unique id
+        return id;
+    },
+    
+    // unregister process
+    done: function(id) {
+        // delete tag
+        delete this.process[id];
+        
+        // decrease process counter
+        this.counter--;
+        
+        // log
+        console.debug('Deferred:done() - Unregistering ' + id);
+        
+        // trigger change
+        this.trigger('refresh');
+    },
+    
+    // ready
+    ready: function() {
+        if (this.counter == 0) {
+            return true;
+        } else {
+            return false;
+        }
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/jobs.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -0,0 +1,152 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// widget
+return Backbone.Model.extend(
+{
+    // initialize
+    initialize: function(app, options) {
+        // link app
+        this.app = app;
+        
+        // link options
+        this.options = Utils.merge(options, this.optionsDefault);
+    },
+    
+    // clean
+    cleanup: function(chart) {
+        // cleanup previous dataset file
+        var previous =  chart.get('dataset_id_job');
+        if (previous != '') {
+            var self = this;
+            Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() {
+                // update galaxy history
+                self._refreshHdas();
+            });
+            
+            // reset id
+            chart.set('dataset_id_job', '');
+        }
+    },
+    
+    // create job
+    submit: function(chart, settings_string, columns_string, success, error) {
+        // link this
+        var self = this;
+        
+        // backup chart details
+        var chart_id        = chart.id;
+        var chart_type      = chart.get('type');
+        
+        // get chart settings
+        var chart_settings  = this.app.types.get(chart_type);
+       
+        // configure tool
+        data = {
+            'tool_id'       : 'chartskit',
+            'inputs'        : {
+                'input'     : {
+                    'id'    : chart.get('dataset_id'),
+                    'src'   : 'hda'
+                },
+                'module'    : chart_type,
+                'columns'   : columns_string,
+                'settings'  : settings_string
+            }
+        }
+        
+        // set chart state
+        chart.state('wait', 'Sending job request...');
+        
+        // post job
+        Utils.request('POST', config.root + 'api/tools', data,
+            // success handler
+            function(response) {
+                if (!response.outputs || response.outputs.length == 0) {
+                    chart.state('failed', 'Job submission failed. No response.');
+                    
+                    // call error
+                    error && error();
+                } else {
+                    // update galaxy history
+                    self._refreshHdas();
+        
+                    // get dataset
+                    var job = response.outputs[0];
+                    
+                    // check dataset
+                    chart.state('wait', 'Job has been queued...');
+                    
+                    // backup resulting dataset id
+                    chart.set('dataset_id_job', job.id);
+                    
+                    // save
+                    this.app.storage.save();
+                      
+                    // wait for job completion
+                    self._loop(job.id, function(job) {
+                        switch (job.state) {
+                            case 'ok':
+                                // update state
+                                chart.state('wait', 'Job completed successfully...');
+                               
+                                // execute success
+                                success(job);
+                               
+                                // stop loop
+                                return true;
+                            case 'error':
+                                // update state
+                                chart.state('failed', 'Job has failed. Please check the history for details.');
+                               
+                                // call error
+                                error && error();
+                               
+                                // stop loop
+                                return true;
+                            case 'running':
+                                // wait
+                                chart.state('wait', 'Job is running...');
+                               
+                                // continue loop
+                                return false;
+                        }
+                    });
+                }
+            },
+            // error handler
+            function(response) {
+                var message = '';
+                if (response && response.message && response.message.data && response.message.data.input) {
+                    message = response.message.data.input + '.';
+                }
+                // update state
+                chart.state('failed', 'This visualization requires the Charts-Kit. Please make sure it is installed. ' + message);
+                
+                // call error
+                error && error();
+                      
+            }
+        );
+    },
+    
+    // request job details
+    _loop: function(id, callback) {
+        var self = this;
+        Utils.request('GET', config.root + 'api/datasets/' + id, {}, function(job) {
+            if (!callback(job)) {
+                setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout'));
+            }
+        });
+    },
+    
+    // refresh history panel
+    _refreshHdas: function() {
+        // update galaxy history
+        if (Galaxy && Galaxy.currHistoryPanel) {
+            Galaxy.currHistoryPanel.refreshHdas();
+        }
+    }
+});
+
+});
\ No newline at end of file

diff -r 56be13c43a4e8c1ad391eab212982659e4845d94 -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc config/plugins/visualizations/charts/static/library/portlet.js
--- a/config/plugins/visualizations/charts/static/library/portlet.js
+++ /dev/null
@@ -1,171 +0,0 @@
-// dependencies
-define(['library/utils'], function(Utils) {
-
-// return
-return Backbone.View.extend(
-{
-    // visibility
-    visible: false,
-    
-    // defaults options
-    optionsDefault: {
-        label       : '',
-        icon        : 'fa-tasks',
-        buttons     : null,
-        body        : null,
-        height      : null,
-        operations  : null,
-        placement   : 'bottom',
-        overflow    : 'auto'
-    },
-    
-    // content
-    $content : null,
-    
-    // initialize
-    initialize : function(options) {
-        // configure options
-        this.options = Utils.merge(options, this.optionsDefault);
-        
-        // create new element
-        this.setElement(this.template(this.options));
-        
-        // link content
-        this.$content = this.$el.find('#content');
-        
-        // set content height
-        if (this.options.height) {
-            this.$el.find('#body').css('height', this.options.height);
-            this.$el.find('#content').css('overflow', this.options.overflow);
-        }
-        
-        // append buttons
-        this.$buttons = $(this.el).find('#buttons');
-        if (this.options.buttons) {
-            // link functions
-            var self = this;
-            $.each(this.options.buttons, function(name, item) {
-                item.$el.prop('id', name);
-                self.$buttons.append(item.$el);
-            });
-        } else {
-            this.$buttons.remove();
-        }
-        
-        // append operations
-        this.$operations = $(this.el).find('#operations');
-        if (this.options.operations) {
-            // link functions
-            var self = this;
-            $.each(this.options.operations, function(name, item) {
-                item.$el.prop('id', name);
-                self.$operations.append(item.$el);
-            });
-        }
-        
-        // add body
-        if(this.options.body) {
-            this.append(this.options.body);
-        }
-    },
-    
-    // append
-    append: function($el) {
-        this.$content.append(Utils.wrap($el));
-    },
-    
-    // content
-    content: function() {
-        return this.$content;
-    },
-    
-    // hide modal
-    show: function(){
-        // fade in
-        this.$el.fadeIn('fast');
-        
-        // set flag
-        this.visible = true;
-    },
-    
-    // hide modal
-    hide: function(){
-        // fade out
-        this.$el.fadeOut('fast');
-        
-        // set flag
-        this.visible = false;
-    },
-
-    // enable buttons
-    enableButton: function(id) {
-        this.$buttons.find('#' + id).prop('disabled', false);
-    },
-
-    // disable buttons
-    disableButton: function(id) {
-        this.$buttons.find('#' + id).prop('disabled', true);
-    },
-    
-    // enable operation
-    hideOperation: function(id) {
-        this.$operations.find('#' + id).hide();
-    },
-
-    // disable operation
-    showOperation: function(id) {
-        this.$operations.find('#' + id).show();
-    },
-    
-    // set operation
-    setOperation: function(id, callback) {
-        var $el = this.$operations.find('#' + id);
-        $el.off('click');
-        $el.on('click', callback);
-    },
-    
-    // label
-    label: function(new_label) {
-        var $el = this.$el.find('#label');
-        if (new_label) {
-            $el.html(new_label);
-        }
-        return $el.html();
-    },
-    
-    // fill regular modal template
-    template: function(options) {
-        var tmpl =  '<div class="toolForm">';
-        
-        if (options.label || options.icon) {
-            tmpl +=     '<div id="title" class="toolFormTitle" style="overflow:hidden;">' +
-                            '<div id="operations" style="float: right;"></div>' +
-                            '<div style="overflow: hidden">';
-                            
-            if (options.icon)
-                tmpl +=         '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>';
-        
-            tmpl +=             '<div id="label" style="padding-top: 2px; float: left;">' + options.label + '</div>';
-            
-            tmpl +=         '</div>' +
-                        '</div>';
-        }
-        tmpl +=         '<div id="body" class="toolFormBody">';
-        
-        if (options.placement == 'top') {
-            tmpl +=         '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>';
-        }
-        
-        tmpl +=             '<div id="content" class="content" style="height: inherit; padding: 10px;"></div>';
-        
-        if (options.placement == 'bottom') {
-            tmpl +=         '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>';
-        }
-        
-        tmpl +=         '</div>' +
-                    '</div>';
-        return tmpl;
-    }
-});
-
-});

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/1ad62c772728/
Changeset:   1ad62c772728
Branch:      stable
User:        natefoo
Date:        2014-04-15 01:28:10
Summary:     Added tag release_2014.04.14 for changeset 9e53251b0b7e
Affected #:  1 file

diff -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc -r 1ad62c7727285084e46ee3572835483e34c551a5 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -6,3 +6,4 @@
 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12
 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04
 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
+9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14


https://bitbucket.org/galaxy/galaxy-central/commits/3b3365a39194/
Changeset:   3b3365a39194
User:        natefoo
Date:        2014-04-15 01:28:45
Summary:     Merge stable to default
Affected #:  1 file

diff -r 855b03513ca92f33be6d4da54afffadad294a9cc -r 3b3365a391944f848b403412f226ee9e5499c0d5 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -6,3 +6,4 @@
 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12
 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04
 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
+9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14

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

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