[galaxy-commits] commit/galaxy-central: guerler: Charts: Add new selection panel, improve modularity, activate basic heat map

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/2b4c26870efb/ Changeset: 2b4c26870efb User: guerler Date: 2014-05-15 04:11:59 Summary: Charts: Add new selection panel, improve modularity, activate basic heat map Affected #: 67 files

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/app.css --- /dev/null +++ b/config/plugins/visualizations/charts/static/app.css @@ -0,0 +1,69 @@ +.charts-grid .item { + padding: 5px; + margin: 5px; + float: left; + cursor: pointer; + border-radius:5px +} + +.charts-grid .current { + border-color:#66afe9; + background-color:#EEEEFF; + outline:0; + -webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6); + box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6); +} + +.charts-grid .image { + padding: 10px; + width: 100px; +} + +.charts-grid .title { + text-align: center; + font-size: 0.9em; + word-wrap: break-work; + font-weight: bold; + width: 100px; +} + +.charts-grid .header { + font-size: 0.9em; + font-weight: bold; +} + +.charts-viewport { + height: inherit; + min-height: 50px; +} + +.charts-viewport .info { + position: absolute; + margin-left: 10px; + margin-top: 10px; + margin-bottom: 50px; +} + +.charts-viewport .text { + position: relative; + margin-left: 5px; + top: -1px; + font-size: 1.0em; +} + +.charts-viewport .icon { + font-size: 1.2em; + display: inline-block; +} + +.charts-viewport .container { + float: left; + display: block; + height: 100%; +} + +.charts-viewport .canvas { + display: block; + width:100%; + height: inherit; +} \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license.

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- No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),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){this.process[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({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.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={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; 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>'},_templateContainer:function(e,t){return'<div class="container" style="float: left; display: block; width:'+t+'%; height: 100%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas" style="display: block; width:100%; height: inherit;">'+"</div>"}})}),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:"Editor",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=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},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.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<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.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<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.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),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.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the charts tool available in the Toolshed.",cls:"toolParamHelp"})).$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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new 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n=$(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}}),p=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:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),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)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._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:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,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","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},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' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},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._get(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)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_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=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),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){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});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({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.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={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),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:"Editor",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,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$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!=""&&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({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=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var 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--",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/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others"})}),define("plugin/charts/nvd3_line_focus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others"})}),define("plugin/charts/nvd3_pie/config",[],function(){return{title:"Pie chart",library:"nvd3.js",category:"Area charts",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},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"},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"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bar/config","plugin/charts/nvd3_bar_stacked/config","plugin/charts/nvd3_bar_horizontal/config","plugin/charts/nvd3_bar_horizontal_stacked/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:f,nvd3_stackedarea_full:l,nvd3_stackedarea_stream:c,nvd3_line:s,nvd3_line_focus:o,nvd3_scatter:a,nvd3_pie:u,nvd3_histogram:i,highcharts_boxplot:h,heatmap:p}})}),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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js @@ -2,6 +2,7 @@

return { title : 'Heatmap', + category : 'Data processing (requires 'charts' tool from Toolshed)', library : '', tag : 'div', use_panels : true,

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js +++ /dev/null @@ -1,71 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], -function(Utils, HeatmapPlugin, HeatmapParameters) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // link this - var self = this; - - // loop through data groups - var index = 0; - for (var group_index in request_dictionary.groups) { - - // configure request - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - row_label: { - index : index++, - is_label : true - }, - col_label: { - index : index++, - is_label : true - }, - value: { - index : index++ - } - } - } - - // request data - this.app.datasets.request(request_dictionary, function() { - - // get group - var group = request_dictionary.groups[group_index]; - var div = self.options.canvas[group_index]; - - // draw plot - var heatmap = new HeatmapPlugin({ - 'title' : group.key, - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : div - }); - - // check if done - if (group_index == request_dictionary.groups.length - 1) { - // set chart state - chart.state('ok', 'Heat map drawn.'); - - // unregister process - chart.deferred.done(process_id); - } - }); - } - } -}); - -}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/logo.png Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js @@ -0,0 +1,71 @@ +// dependencies +define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], +function(Utils, HeatmapPlugin, HeatmapParameters) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + }, + + // render + draw : function(process_id, chart, request_dictionary) + { + // link this + var self = this; + + // loop through data groups + var index = 0; + for (var group_index in request_dictionary.groups) { + + // configure request + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = null; + group.columns = { + row_label: { + index : index++, + is_label : true + }, + col_label: { + index : index++, + is_label : true + }, + value: { + index : index++ + } + } + } + + // request data + this.app.datasets.request(request_dictionary, function() { + + // get group + var group = request_dictionary.groups[group_index]; + var div = self.options.canvas[group_index]; + + // draw plot + var heatmap = new HeatmapPlugin({ + 'title' : group.key, + 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], + 'data' : group.values, + 'div' : div + }); + + // check if done + if (group_index == request_dictionary.groups.length - 1) { + // set chart state + chart.state('ok', 'Heat map drawn.'); + + // unregister process + chart.deferred.done(process_id); + } + }); + } + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js @@ -1,16 +1,17 @@ define([], function() {

return { - title : 'Box plot', - library : 'highcharts.js', - tag : 'div', - execute : 'boxplot', - columns : { + title : 'Box plot', + category : 'Data processing (requires 'charts' tool from Toolshed)', + library : 'highcharts.js', + tag : 'div', + execute : 'boxplot', + columns : { y : { title : 'Observations' } }, - settings : { + settings : { separator_label : { title : 'X axis', type : 'separator'

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js +++ /dev/null @@ -1,122 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // highcharts configuration - hc_config : { - chart: { - type: 'boxplot' - }, - - title: { - text: '' - }, - - legend: { - enabled: false - }, - - credits: { - enabled: false - }, - - plotOptions: { - series: { - animation: false - } - }, - - xAxis: { - categories: [], - title: { - text: '' - } - }, - - yAxis: { - title: { - text: '' - } - }, - - series: [{ - name: 'Details:', - data: [], - tooltip: { - headerFormat: '<em>{point.key}</em><br/>' - } - }] - }, - - // 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 = null; - group.columns = { - x: { - index: index++ - } - } - } - - // set axis labels - this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label'); - this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label'); - - // request data - var self = this; - this.app.datasets.request(request_dictionary, function() { - - // reset data/categories - var data = []; - var categories = []; - - // loop through data groups - for (var key in request_dictionary.groups) { - // get group - var group = request_dictionary.groups[key]; - - // add category - categories.push(group.key); - - // format chart data - var point = []; - for (var key in group.values) { - point.push(group.values[key].x); - } - - // add to data - data.push (point); - } - - // categories - self.hc_config.xAxis.categories = categories; - - // update data - self.hc_config.series[0].data = data; - - // draw plot - self.options.canvas[0].highcharts(self.hc_config); - - // set chart state - chart.state('ok', 'Box plot drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } -}); - -}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js @@ -2,6 +2,7 @@

return { title : '', + category : '', library : 'nvd3.js', tag : 'svg', columns : {

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js @@ -31,9 +31,7 @@ .axisLabelDistance(30);

// controls - if (chart.groups.length == 1) { - nvd3_model.options({ showControls: false }); - } + nvd3_model.options({showControls: false});

// legend var legend_visible = true;

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js @@ -0,0 +1,8 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Regular', + category : 'Bar diagrams' +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar/wrapper.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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js @@ -0,0 +1,13 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Horizontal', + category : 'Bar diagrams', + settings : { + x_axis_type : { + init : 'hide' + } + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/wrapper.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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js @@ -0,0 +1,13 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Stacked horizontal', + category : 'Bar diagrams', + settings : { + x_axis_type : { + init : 'hide' + } + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/wrapper.js @@ -0,0 +1,23 @@ +// 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, function(nvd3_model) { + nvd3_model.stacked(true); + }); + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/config.js +++ /dev/null @@ -1,7 +0,0 @@ -define(['plugin/charts/nvd3/config'], function(nvd3_config) { - -return $.extend(true, {}, nvd3_config, { - title : 'Bar diagram', -}); - -}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/nvd3_bardiagram.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bardiagram/nvd3_bardiagram.js +++ /dev/null @@ -1,21 +0,0 @@ -// 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/config.js @@ -1,14 +1,16 @@ + define(['plugin/charts/nvd3/config'], function(nvd3_config) {

return $.extend(true, {}, nvd3_config, { - title : 'Histogram', - execute : 'histogram', - columns : { + title : 'Histogram', + category : 'Data processing (requires 'charts' tool from Toolshed)', + execute : 'histogram', + columns : { y : { title : 'Observations' } }, - settings : { + settings : { x_axis_label : { init : 'Breaks' },

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_histogram/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/nvd3_histogram.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram/nvd3_histogram.js +++ /dev/null @@ -1,39 +0,0 @@ -// 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 = 1; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = { - x: { - index: 0 - }, - y: { - index: index++ - }, - } - } - - // link this - var self = this; - - // load nvd3 - 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram/wrapper.js @@ -0,0 +1,41 @@ +// 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 = 1; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = { + x: { + index: 0 + }, + y: { + index: index++ + }, + } + } + + // link this + var self = this; + + // load nvd3 + var nvd3 = new NVD3(this.app, this.options); + nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary, function(nvd3_model) { + nvd3_model.options({showControls: true}); + }); + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js @@ -0,0 +1,28 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Histogram', + category : 'Histograms', + execute : 'histogram_discrete', + columns : { + y : { + title : 'Observations' + } + }, + settings : { + x_axis_label : { + init : 'Breaks' + }, + y_axis_label : { + init : 'Density' + }, + y_axis_type : { + init : 'f' + }, + y_axis_tick : { + init : '.2' + } + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js @@ -0,0 +1,39 @@ +// 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 = 1; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = { + x: { + index: 0 + }, + y: { + index: index++ + }, + } + } + + // link this + var self = this; + + // load nvd3 + 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_horizontal/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_horizontal/config.js +++ /dev/null @@ -1,12 +0,0 @@ -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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_horizontal/nvd3_horizontal.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_horizontal/nvd3_horizontal.js +++ /dev/null @@ -1,21 +0,0 @@ -// 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js @@ -1,7 +1,8 @@ define(['plugin/charts/nvd3/config'], function(nvd3_config) {

return $.extend(true, {}, nvd3_config, { - title : 'Line chart', + title : 'Line chart', + category : 'Others' });

}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_line/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/nvd3_line.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_line/nvd3_line.js +++ /dev/null @@ -1,21 +0,0 @@ -// 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/wrapper.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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js @@ -0,0 +1,8 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Line with focus', + category : 'Others' +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line_focus/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_line_focus/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_line_focus/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/wrapper.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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/config.js +++ /dev/null @@ -1,7 +0,0 @@ -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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/nvd3_linewithfocus.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_linewithfocus/nvd3_linewithfocus.js +++ /dev/null @@ -1,21 +0,0 @@ -// 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js @@ -0,0 +1,115 @@ +define([], function() { + +return { + title : 'Pie chart', + library : 'nvd3.js', + category : 'Area charts', + tag : 'svg', + use_panels : true, + columns : { + label : { + title : 'Labels', + is_label : true + }, + y : { + title : 'Values' + } + }, + + settings : { + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'select', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + + donut_ratio : { + title : 'Donut ratio', + info : 'Determine how large the donut hole will be.', + type : 'select', + init : '0.5', + data : [ + { + label : '50%', + value : '0.5' + }, + { + label : '25%', + value : '0.25' + }, + { + label : '10%', + value : '0.10' + }, + { + label : '0%', + value : '0' + } + ] + }, + + label_separator : { + type : 'separator', + title : 'Label settings' + }, + + label_type : { + title : 'Donut label', + info : 'What would you like to show for each slice?', + type : 'select', + init : 'percent', + data : [ + { + label : '-- Nothing --', + value : 'hide', + hide : 'label_outside' + }, + { + label : 'Label column', + value : 'key', + show : 'label_outside' + }, + { + label : 'Value column', + value : 'value', + show : 'label_outside' + }, + { + label : 'Percentage', + value : 'percent', + show : 'label_outside' + } + ], + }, + + label_outside : { + title : 'Show outside', + info : 'Would you like to show labels outside the donut?', + type : 'select', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + } + } +}; + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_pie/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_pie/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_pie/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_pie/wrapper.js @@ -0,0 +1,115 @@ +// 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() { + + // loop through data groups + for (var group_index in request_dictionary.groups) { + // get group + var group = request_dictionary.groups[group_index]; + + // draw group + self._draw_group(chart, group, self.options.canvas[group_index]); + } + + // set chart state + chart.state('ok', 'Pie chart has been drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); + }, + + // draw group + _draw_group: function(chart, group, canvas) { + + // add title + var title = canvas.append('text'); + + // configure title attributes + this._fix_title(chart, canvas, title, group.key); + + // format chart data + var pie_data = []; + for (var key in group.values) { + var value = group.values[key]; + pie_data.push ({ + y : value.y, + x : value.label + }); + } + + // add graph to screen + var self = this; + nv.addGraph(function() { + // legend + var legend_visible = true; + if (chart.settings.get('show_legend') == 'false') { + legend_visible = false; + } + + // legend + var label_outside = true; + if (chart.settings.get('label_outside') == 'false') { + label_outside = false; + } + + // label type + var label_type = chart.settings.get('label_type'); + + // ratio + var donut_ratio = parseFloat(chart.settings.get('donut_ratio')) + + // create chart model + var chart_3d = nv.models.pieChart() + .donut(true) + .labelThreshold(.05) + .showLegend(legend_visible) + .labelType(label_type) + .donutRatio(donut_ratio) + .donutLabelsOutside(label_outside); + + // add data to canvas + canvas.datum(pie_data) + .call(chart_3d); + + // add resize trigger + nv.utils.windowResize(function() { + // update chart + chart_3d.update(); + + // fix title + self._fix_title(chart, canvas, title, group.key); + }); + }); + }, + + // fix title + _fix_title: function(chart, canvas, title_element, title_text) { + // update title + var width = parseInt(canvas.style('width')); + var height = parseInt(canvas.style('height')); + + // add title + title_element.attr('x', width / 2) + .attr('y', height - 10) + .attr('text-anchor', 'middle') + .text(title_text); + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js +++ /dev/null @@ -1,114 +0,0 @@ -define([], function() { - -return { - title : 'Pie chart', - library : 'nvd3.js', - tag : 'svg', - use_panels : true, - columns : { - label : { - title : 'Labels', - is_label : true - }, - y : { - title : 'Values' - } - }, - - settings : { - show_legend : { - title : 'Show legend', - info : 'Would you like to add a legend?', - type : 'select', - init : 'false', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] - }, - - donut_ratio : { - title : 'Donut ratio', - info : 'Determine how large the donut hole will be.', - type : 'select', - init : '0.5', - data : [ - { - label : '50%', - value : '0.5' - }, - { - label : '25%', - value : '0.25' - }, - { - label : '10%', - value : '0.10' - }, - { - label : '0%', - value : '0' - } - ] - }, - - label_separator : { - type : 'separator', - title : 'Label settings' - }, - - label_type : { - title : 'Donut label', - info : 'What would you like to show for each slice?', - type : 'select', - init : 'percent', - data : [ - { - label : '-- Nothing --', - value : 'hide', - hide : 'label_outside' - }, - { - label : 'Label column', - value : 'key', - show : 'label_outside' - }, - { - label : 'Value column', - value : 'value', - show : 'label_outside' - }, - { - label : 'Percentage', - value : 'percent', - show : 'label_outside' - } - ], - }, - - label_outside : { - title : 'Show outside', - info : 'Would you like to show labels outside the donut?', - type : 'select', - init : 'false', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] - } - } -}; - -}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js +++ /dev/null @@ -1,115 +0,0 @@ -// 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() { - - // loop through data groups - for (var group_index in request_dictionary.groups) { - // get group - var group = request_dictionary.groups[group_index]; - - // draw group - self._draw_group(chart, group, self.options.canvas[group_index]); - } - - // set chart state - chart.state('ok', 'Pie chart has been drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - }, - - // draw group - _draw_group: function(chart, group, canvas) { - - // add title - var title = canvas.append('text'); - - // configure title attributes - this._fix_title(chart, canvas, title, group.key); - - // format chart data - var pie_data = []; - for (var key in group.values) { - var value = group.values[key]; - pie_data.push ({ - y : value.y, - x : value.label - }); - } - - // add graph to screen - var self = this; - nv.addGraph(function() { - // legend - var legend_visible = true; - if (chart.settings.get('show_legend') == 'false') { - legend_visible = false; - } - - // legend - var label_outside = true; - if (chart.settings.get('label_outside') == 'false') { - label_outside = false; - } - - // label type - var label_type = chart.settings.get('label_type'); - - // ratio - var donut_ratio = parseFloat(chart.settings.get('donut_ratio')) - - // create chart model - var chart_3d = nv.models.pieChart() - .donut(true) - .labelThreshold(.05) - .showLegend(legend_visible) - .labelType(label_type) - .donutRatio(donut_ratio) - .donutLabelsOutside(label_outside); - - // add data to canvas - canvas.datum(pie_data) - .call(chart_3d); - - // add resize trigger - nv.utils.windowResize(function() { - // update chart - chart_3d.update(); - - // fix title - self._fix_title(chart, canvas, title, group.key); - }); - }); - }, - - // fix title - _fix_title: function(chart, canvas, title_element, title_text) { - // update title - var width = parseInt(canvas.style('width')); - var height = parseInt(canvas.style('height')); - - // add title - title_element.attr('x', width / 2) - .attr('y', height - 10) - .attr('text-anchor', 'middle') - .text(title_text); - } -}); - -}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js @@ -0,0 +1,13 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Scatter plot', + category : 'Others', + columns : { + x : { + title : 'Values for x-axis' + } + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatter/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_scatter/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatter/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatter/wrapper.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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/config.js +++ /dev/null @@ -1,12 +0,0 @@ -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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/nvd3_scatterplot.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_scatterplot/nvd3_scatterplot.js +++ /dev/null @@ -1,25 +0,0 @@ -// 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js @@ -1,7 +1,8 @@ define(['plugin/charts/nvd3/config'], function(nvd3_config) {

return $.extend(true, {}, nvd3_config, { - title : 'Stacked area' + title : 'Regular', + category : 'Area charts' });

}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/nvd3_stackedarea.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/nvd3_stackedarea.js +++ /dev/null @@ -1,26 +0,0 @@ -// 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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/wrapper.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 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js @@ -0,0 +1,8 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Expanded', + category : 'Area charts' +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/wrapper.js @@ -0,0 +1,27 @@ +// 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) + .style('expand'); + }); + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js @@ -0,0 +1,8 @@ +define(['plugin/charts/nvd3/config'], function(nvd3_config) { + +return $.extend(true, {}, nvd3_config, { + title : 'Stream', + category : 'Area charts' +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/logo.png has changed

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/wrapper.js @@ -0,0 +1,27 @@ +// 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) + .style('stream'); + }); + } +}); + +}); \ No newline at end of file

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/charts/types.js --- a/config/plugins/visualizations/charts/static/charts/types.js +++ b/config/plugins/visualizations/charts/static/charts/types.js @@ -1,22 +1,30 @@ // dependencies -define(['plugin/charts/nvd3_bardiagram/config', +define(['plugin/charts/nvd3_bar/config', + 'plugin/charts/nvd3_bar_stacked/config', + 'plugin/charts/nvd3_bar_horizontal/config', + 'plugin/charts/nvd3_bar_horizontal_stacked/config', 'plugin/charts/nvd3_histogram/config', - 'plugin/charts/nvd3_horizontal/config', 'plugin/charts/nvd3_line/config', - 'plugin/charts/nvd3_linewithfocus/config', - 'plugin/charts/nvd3_piechart/config', - 'plugin/charts/nvd3_scatterplot/config', + 'plugin/charts/nvd3_line_focus/config', + 'plugin/charts/nvd3_pie/config', + 'plugin/charts/nvd3_scatter/config', 'plugin/charts/nvd3_stackedarea/config', + 'plugin/charts/nvd3_stackedarea_full/config', + 'plugin/charts/nvd3_stackedarea_stream/config', 'plugin/charts/highcharts_boxplot/config', 'plugin/charts/heatmap/config', - ], function(nvd3_bardiagram, + ], function(nvd3_bar, + nvd3_bar_stacked, + nvd3_bar_horizontal, + nvd3_bar_horizontal_stacked, nvd3_histogram, - nvd3_horizontal, nvd3_line, - nvd3_linewithfocus, - nvd3_piechart, - nvd3_scatterplot, + nvd3_line_focus, + nvd3_pie, + nvd3_scatter, nvd3_stackedarea, + nvd3_stackedarea_full, + nvd3_stackedarea_stream, highcharts_boxplot, heatmap ) { @@ -26,16 +34,20 @@ { // types defaults: { - 'nvd3_bardiagram' : nvd3_bardiagram, - 'nvd3_horizontal' : nvd3_horizontal, - //'heatmap' : heatmap, - 'nvd3_histogram' : nvd3_histogram, - 'nvd3_line' : nvd3_line, - 'nvd3_linewithfocus' : nvd3_linewithfocus, - 'nvd3_piechart' : nvd3_piechart, - 'nvd3_scatterplot' : nvd3_scatterplot, - 'nvd3_stackedarea' : nvd3_stackedarea, - 'highcharts_boxplot' : highcharts_boxplot + 'nvd3_bar' : nvd3_bar, + 'nvd3_bar_stacked' : nvd3_bar_stacked, + 'nvd3_bar_horizontal' : nvd3_bar_horizontal, + 'nvd3_bar_horizontal_stacked' : nvd3_bar_horizontal_stacked, + 'nvd3_stackedarea' : nvd3_stackedarea, + 'nvd3_stackedarea_full' : nvd3_stackedarea_full, + 'nvd3_stackedarea_stream' : nvd3_stackedarea_stream, + 'nvd3_line' : nvd3_line, + 'nvd3_line_focus' : nvd3_line_focus, + 'nvd3_scatter' : nvd3_scatter, + 'nvd3_pie' : nvd3_pie, + 'nvd3_histogram' : nvd3_histogram, + 'highcharts_boxplot' : highcharts_boxplot, + 'heatmap' : heatmap } });

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/library/deferred.js --- a/config/plugins/visualizations/charts/static/library/deferred.js +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -76,11 +76,7 @@

// ready ready: function() { - if (this.counter == 0) { - return true; - } else { - return false; - } + return (this.counter == 0); } });

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/library/ui-table.js --- a/config/plugins/visualizations/charts/static/library/ui-table.js +++ b/config/plugins/visualizations/charts/static/library/ui-table.js @@ -162,13 +162,14 @@ // get values var old_value = this.value(); var new_value = $(e.target).closest('tr').attr('id'); - - // check equality - if (new_value && old_value != new_value) { - if (this.options.onconfirm) { - this.options.onconfirm(new_value); - } else { - this.value(new_value); + if (new_value != ''){ + // check equality + if (new_value && old_value != new_value) { + if (this.options.onconfirm) { + this.options.onconfirm(new_value); + } else { + this.value(new_value); + } } } },

diff -r 31e5817ba7d36a039c432205b32958e190cbabbc -r 2b4c26870efbc19441f02da19659c830cc8b591a config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -2,11 +2,35 @@ define(['utils/utils', 'plugin/library/ui-select'], function(Utils, Select) {

// plugin +var Image = Backbone.View.extend( +{ + // options + optionsDefault: { + url : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + }, + + // template + _template: function(options) { + return '<img src="' + options.url + '"/>'; + } +}); + +// plugin var Label = Backbone.View.extend( { // options optionsDefault: { - title : '' + title : '', + cls : '' },

// initialize @@ -25,7 +49,7 @@

// template _template: function(options) { - return '<label><b>' + options.title + '</b></label>'; + return '<label class="' + options.cls + '"><b>' + options.title + '</b></label>'; },

// value @@ -108,39 +132,6 @@ });

// plugin -var Icon = Backbone.View.extend( -{ - // options - optionsDefault: { - float : 'right', - icon : '', - tooltip : '', - placement : 'bottom', - title : '' - }, - - // initialize - initialize : function(options) { - // get options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // add tooltip - $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); - }, - - // element - _template: function(options) { - return '<div>' + - '<span class="fa ' + options.icon + '" style="font-size: 1.2em;"/>&nbsp;' + - options.title + - '</div>'; - } -}); - -// plugin var ButtonIcon = Backbone.View.extend( { // options @@ -194,6 +185,39 @@ });

// plugin +var Icon = Backbone.View.extend( +{ + // options + optionsDefault: { + float : 'right', + icon : '', + tooltip : '', + placement : 'bottom', + title : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // add tooltip + $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); + }, + + // element + _template: function(options) { + return '<div>' + + '<span class="fa ' + options.icon + '" style="font-size: 1.2em;"/>&nbsp;' + + options.title + + '</div>'; + } +}); + +// plugin var Anchor = Backbone.View.extend( { // options @@ -552,6 +576,7 @@ // return return { Label : Label, + Image : Image, Button : Button, Icon : Icon, ButtonIcon : ButtonIcon,

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

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