commit/galaxy-central: guerler: Charts: Added export to pdf

23 May 2014

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/f04bc600a672/
Changeset:   f04bc600a672
User:        guerler
Date:        2014-05-24 00:18:42
Summary:     Charts: Added export to pdf
Affected #:  8 files

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 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 @@
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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var 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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 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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. 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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 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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.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$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){n++;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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-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=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$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.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return 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.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(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 o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._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 s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$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(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=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]||a==="auto")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.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_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/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon 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){n++;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="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=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(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$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"},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 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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_histogram_discrete/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,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,nvd3_histogram_discrete:s,highcharts_boxplot:p,heatmap:d}})}),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 f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 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
@@ -4,10 +4,6 @@
     title       : 'Line chart',
     category    : 'Others',
     columns     : {
-        x : {
-            title   : 'Values for x-axis',
-            is_auto : true
-        },
         y : {
             title   : 'Values for y-axis'
         }

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 config/plugins/visualizations/charts/static/library/screenshot.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/screenshot.js
@@ -0,0 +1,108 @@
+/**
+ * Screenshot creator
+*/
+
+// dependencies
+define(["libs/underscore"], function(_) {
+
+    // screenshot
+    function create ($el, screenshot_url, name) {
+        var serializer = new XMLSerializer();
+        var xmlString = '';
+        var self = this;
+        var height = 0;
+        var width  = 0;
+        $el.find('svg').each(function() {
+            // get svg element
+            var $svg = $(this);
+            
+            // inline all styles
+            _inline($svg);
+            
+            // get height/width
+            height = parseInt($svg.css('height'));
+            width = parseInt($svg.css('width'));
+            
+            // configure svg
+            $svg.attr({
+                version : '1.1',
+                xmlns   : 'http://www.w3.org/2000/svg',
+                width   : width,
+                height  : height
+            });
+            xmlString += serializer.serializeToString(this);
+        });
+           
+        // do the post
+        _post($el, screenshot_url, {
+            filename    : name || 'chart',
+            type        : 'application/pdf',
+            height      : height,
+            width       : width,
+            scale       : 2,
+            svg         : xmlString
+        });
+        
+        // return string
+        return xmlString;
+    };
+    
+    // css inliner
+    function _inline ($target) {
+        for (var sheet_id in document.styleSheets) {
+            var sheet = document.styleSheets[sheet_id];
+            var rules = sheet.cssRules;
+            if (rules) {
+                for (var idx = 0, len = rules.length; idx < len; idx++) {
+                    try {
+                        $target.find(rules[idx].selectorText).each(function (i, elem) {
+                            elem.style.cssText += rules[idx].style.cssText;
+                        });
+                    } catch(err) {
+                    }
+                }
+            }
+        }
+    };
+    
+    // post operator
+    function _post ($el, url, data) {
+        // create the form
+        var form = $el.find('#viewport-form');
+        if (form.length === 0) {
+            form = $('<form>', {
+                id      : 'viewport-form',
+                method  : 'post',
+                action  : url,
+                display : 'none'
+            });
+            $el.append(form);
+        }
+
+        // reset form
+        form.empty();
+
+        // add the data
+        for (name in data) {
+            var input = $('<input/>', {
+                type    : 'hidden',
+                name    : name,
+                value   : data[name]
+            });
+            form.append(input);
+        }
+        
+        // submit
+        try {
+            form.submit();
+        } catch(err) {
+            console.log(err);
+        }
+    };
+
+// return
+return {
+    create: create
+};
+
+});

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 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
@@ -22,9 +22,6 @@
         'dblclick'  : '_ondblclick'
     },
     
-    // first
-    first: true,
-    
     // initialize
     initialize : function(options) {
         // configure options

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 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
@@ -512,7 +512,7 @@
         if (options.icon)
             tmpl +=         '<i class="fa ' + options.icon + '"></i>';
          
-                        '</button>' +
+        tmpl +=         '</button>' +
                     '</div>';
         
         // return template

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -7,7 +7,8 @@
     // options
     defaults : {
         query_limit     : 5000,
-        query_timeout   : 500
+        query_timeout   : 500,
+        screenshot_url  : 'http://export.highcharts.com/'
     }
 });
 

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 config/plugins/visualizations/charts/static/views/viewer.js
--- a/config/plugins/visualizations/charts/static/views/viewer.js
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -1,7 +1,7 @@
 // dependencies
 define(['utils/utils', 'plugin/library/ui', 'mvc/ui/ui-portlet',
-        'plugin/models/group', 'plugin/views/viewport',],
-        function(Utils, Ui, Portlet, Group, ViewportView) {
+        'plugin/models/group', 'plugin/views/viewport', 'plugin/library/screenshot'],
+        function(Utils, Ui, Portlet, Group, ViewportView, Screenshot) {
 
 // widget
 return Backbone.View.extend(
@@ -37,28 +37,17 @@
                         });
                     }
                 }),
-                /*picture_button: new Ui.ButtonIcon({
+                picture_button: new Ui.ButtonIcon({
                     icon    : 'fa-camera',
-                    tooltip : 'Download SVG-file',
+                    tooltip : 'Download PDF-file (' + self.app.config.get('screenshot_url') + ')',
                     title   : 'Screenshot',
                     onclick : function() {
                         // attempt to load chart editor
                         self._wait (self.chart, function() {
-                            self._screenshot();
+                            Screenshot.create(self.viewport_view.$el, self.app.config.get('screenshot_url'), self.chart.get('title'));
                         });
                     }
-                }),
-                settings_button: new Ui.ButtonIcon({
-                    icon    : 'fa-gear',
-                    tooltip : 'Configure this application',
-                    title   : 'Application',
-                    onclick : function() {
-                        // attempt to load chart editor
-                        self._wait (self.chart, function() {
-                            self.app.go('editor');
-                        });
-                    }
-                })*/
+                })
             }
         });
         
@@ -95,17 +84,6 @@
         this.portlet.title(title);
     },
     
-    // download svg file
-    _screenshot: function() {
-        // Encode the SVG
-        var serializer = new XMLSerializer();
-        var xmlString = serializer.serializeToString(this.viewport_view.svg.node());
-        var imgData = 'data:image/svg+xml;base64,' + btoa(xmlString);
-        //Use the download attribute (or a shim) to provide a link
-        //this.portlet.append('<a href="' + imgData + '" download>Download</a>');
-        window.location.href = 'data:application/x-download/;charset=utf-8,' + encodeURIComponent(xmlString);
-    },
-    
     // wait for chart to be ready
     _wait: function(chart, callback) {
         // get chart

diff -r f1d6f285526da8ee4c0351d2be8445f757a98d48 -r f04bc600a672c5495dc7c7356bffcf436f843a93 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -1,6 +1,6 @@
 // dependencies
-define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'],
-        function(Portlet, Ui, Utils) {
+define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'plugin/library/screenshot', 'utils/utils'],
+        function(Portlet, Ui, Screenshot, Utils) {
 
 // widget
 return Backbone.View.extend({
@@ -187,7 +187,10 @@
             }
         });
     },
-    
+
+    //
+    // REQUEST STRING FUNCTIONS
+    //
     // create default chart request
     _defaultRequestString: function(chart) {

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

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