[galaxy-commits] commit/galaxy-central: guerler: Charts: Save/read from backend

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e7dfb71eeb79/ Changeset: e7dfb71eeb79 User: guerler Date: 2014-03-22 18:38:48 Summary: Charts: Save/read from backend Affected #: 8 files diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -32,7 +32,7 @@ // create chart models this.types = new Types(); this.chart = new Chart(); - this.charts = new Charts(); + this.charts = new Charts(null, this); // create dataset handler this.datasets = new Datasets(this); @@ -59,9 +59,6 @@ this.setElement(this.portlet); } - // start with chart view - this.go('chart_view'); - // events var self = this; this.config.on('change:title', function() { @@ -70,6 +67,16 @@ // render this.render(); + + // load charts + this.charts.load(); + + // start with chart view + if (this.charts.length == 0) { + this.go('chart_view'); + } else { + this.go('charts_view'); + } }, // loads a view and makes sure that all others are hidden diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 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. -(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof x))return new x(e);this._wrapped=e};typeof exports!="undefined"?(typeof 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this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}};var f=t.get("dataset_id_job");f&&e.request("PUT",config.root+"api/histories/"+t.get("history_id")+"/contents/"+f,{deleted:!0}),t.state("submit","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.");else{Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/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/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(t,r){this.app=t,this.options=n.merge(r,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden"}),this.setElement(this.portlet.$el);var i=this;this.app.charts.on("remove",function(e){i._removeChart(e.id)}),this.app.charts.on("redraw",function(e){e.ready()?i._refreshChart(e):e.on("change:state",function(){e.ready()&&i._refreshChart(e)})})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=self.app.charts.get(e);this.portlet.title(n.get("title")),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_refreshChart()","Invalid attempt to refresh chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(r+" svg");this.list[n]={svg:s,$el:i},this.showChart(n),e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<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;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t.View({content:"Add charts to this table.",ondblclick:function(e){u._showChartView(e)},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.app.go("chart_view"),u.app.chart.reset()}}),edit:new n.ButtonIcon({icon:"fa-gear",tooltip:"Customize this Chart",title:"Customize",onclick:function(){var e=u.table.value();if(!e)return;u._showChartView(e)}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e)}}})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.app.charts.save(),this.table.size()==0?(this.app.go("chart_view"),this.app.chart.reset()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))},_showChartView:function(e){var t=this.app.charts.get(e);if(t.ready())this.app.go("chart_view"),this.app.chart.copy(t);else{var n=this;this.app.modal.show({title:"Please wait!",body:'The selected chart "'+t.get("title")+'" is currently being processed. Please wait...',buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),n._showChartView(e)}}})}}})}),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/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});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","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<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();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<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.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t.View({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),c.execute?this.table.add(c.title+" (requires processing)"):this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("charts_view"),o._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("charts_view")}})}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("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.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this.app.charts.get(this.chart.id);e?e.copy(this.chart):(e=this.chart.clone(),e.copy(this.chart),this.app.charts.add(e)),e.trigger("redraw",e),this.app.charts.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500,title:"Create a new chart"}})}),define("plugin/models/charts",["plugin/models/chart"],function(e){return Backbone.Collection.extend({model:e,save:function(){var e=new Visualization({type:"charts",config:{charts:[]}});e.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)})}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked 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t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div 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 n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()})}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},s.cleanup(t),t.state("submit","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.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(t,r){this.app=t,this.options=n.merge(r,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden"}),this.setElement(this.portlet.$el);var i=this;this.app.charts.on("remove",function(e){i._removeChart(e.id)}),this.app.charts.on("redraw",function(e){i._drawChart(e)})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=this.app.charts.get(e);this.portlet.title(n.get("title")),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_drawChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_drawChart()","Invalid attempt to draw chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(i.find("svg")[0]);this.list[n]={svg:s,$el:i},e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<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;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t.View({content:"Add charts to this table.",ondblclick:function(e){u._showChartView(e)},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.app.go("chart_view"),u.app.chart.reset()}}),edit:new n.ButtonIcon({icon:"fa-gear",tooltip:"Customize this Chart",title:"Customize",onclick:function(){var e=u.table.value();if(!e)return;u._showChartView(e)}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u._wait(t,function(){u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e),u.app.jobs.cleanup(t)}}})})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.app.charts.save(),this.table.size()==0?(this.app.go("chart_view"),this.app.chart.reset()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))},_showChartView:function(e){var t=this,n=this.app.charts.get(e);this._wait(n,function(){t.app.go("chart_view"),t.app.chart.copy(n)})},_wait:function(e,t){if(e.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:'The selected chart "'+e.get("title")+'" is currently being processed. Please wait...',buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$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/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});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","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_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({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.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.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(o)}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/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t.View({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),c.execute?this.table.add(c.title+" (requires processing)"):this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("charts_view"),o._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("charts_view")}})}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_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()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this.app.charts.get(this.chart.id);e?e.copy(this.chart):(e=this.chart.clone(),e.copy(this.chart),this.app.charts.add(e)),e.trigger("redraw",e),this.app.charts.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500,title:"Create a new chart"}})}),define("plugin/models/charts",["plugin/models/chart","plugin/models/group"],function(e,t){return Backbone.Collection.extend({model:e,vis:null,initialize:function(e,t){this.app=t,this.id=this.app.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.app.options.config.dataset_id,charts:[]}}),this.id&&(this.vis.id=this.id);var n=this.app.options.config.charts;n&&(this.vis.get("config").charts=n)},save:function(){this.vis.get("config").charts=[];var e=this;this.each(function(t){var n={attributes:t.attributes,settings:t.settings.attributes,groups:[]};t.groups.each(function(e){n.groups.push(e.attributes)}),e.vis.get("config").charts.push(n)});var e=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)}).then(function(t){t&&t.id&&(e.id=t.id)})},load:function(){var n=this.vis.get("config").charts;for(var r in n){var i=n[r],s=new e;s.set(i.attributes),s.settings.set(i.settings);for(var o in i.groups)s.groups.add(new t(i.groups[o]));s.state("ok","Loaded previously saved visualization."),this.add(s),s.trigger("redraw",s)}}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/views/charts","plugin/views/chart","plugin/models/config","plugin/models/chart","plugin/models/charts","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(n){this.options=n,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new a,this.jobs=new i(this),this.types=new c,this.chart=new f,this.charts=new l(null,this),this.datasets=new s(this),this.charts_view=new o(this),this.chart_view=new u(this),this.options.config.widget?this.portlet=$("<div></div>"):this.portlet=new t.View({icon:"fa-bar-chart-o"}),this.portlet.append(this.charts_view.$el),this.portlet.append(this.chart_view.$el),this.options.config.widget?this.setElement(this.portlet):this.setElement(this.portlet.$el);var r=this;this.config.on("change:title",function(){r._refreshTitle()}),this.render(),this.charts.load(),this.charts.length==0?this.go("chart_view"):this.go("charts_view")},go:function(e){switch(e){case"chart_view":this.chart_view.show(),this.charts_view.hide();break;case"charts_view":this.chart_view.hide(),this.charts_view.show()}},render:function(){this._refreshTitle()},_refreshTitle:function(){var e=this.config.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 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 @@ -65,7 +65,7 @@ nv.utils.windowResize(nvd3_model.update); // set chart state - chart.set('state', 'ok'); + chart.state('ok', 'Chart has been drawn.'); }); }); } diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/library/jobs.js --- a/config/plugins/visualizations/charts/static/library/jobs.js +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -13,6 +13,20 @@ this.options = Utils.merge(options, this.optionsDefault); }, + // clean + cleanup: function(chart) { + // cleanup previous dataset file + var previous = chart.get('dataset_id_job'); + if (previous) { + var self = this; + Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() { + // update galaxy history + self._refreshHdas(); + }); + } + + }, + // create job submit: function(chart, settings_string, columns_string, callback) { // link this @@ -39,11 +53,8 @@ } } - // cleanup previous dataset file - var previous = chart.get('dataset_id_job'); - if (previous) { - Utils.request('PUT', config.root + 'api/histories/' + chart.get('history_id') + '/contents/' + previous, { deleted: true }); - } + // cleanup + self.cleanup(chart); // set chart state chart.state('submit', 'Sending job request...'); @@ -56,9 +67,7 @@ chart.state('failed', 'Job submission failed. No response.'); } else { // update galaxy history - if (Galaxy && Galaxy.currHistoryPanel) { - Galaxy.currHistoryPanel.refreshHdas(); - } + self._refreshHdas(); // get dataset var job = response.outputs[0]; @@ -105,6 +114,14 @@ setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout')); } }); + }, + + // refresh history panel + _refreshHdas: function() { + // update galaxy history + if (Galaxy && Galaxy.currHistoryPanel) { + Galaxy.currHistoryPanel.refreshHdas(); + } } }); diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/models/charts.js --- a/config/plugins/visualizations/charts/static/models/charts.js +++ b/config/plugins/visualizations/charts/static/models/charts.js @@ -1,30 +1,113 @@ // dependencies -define(['plugin/models/chart'], function(Chart) { +define(['plugin/models/chart', 'plugin/models/group'], function(Chart, Group) { // collection return Backbone.Collection.extend( { - model: Chart, + // nested chart model contains collections + model : Chart, - // save charts - save: function() { + // viz model + vis: null, + + // initialize + initialize: function(options, app) { + // initialize parameters + this.app = app; + this.id = this.app.options.id; + // create visualization - var vis = new Visualization({ - type : 'charts', + this.vis = new Visualization({ + type : 'charts', config : { - charts : [] + dataset_id : this.app.options.config.dataset_id, + charts : [] } }); - // copy attributes - //vis.set(this.attributes); + // add visualization id + if (this.id) { + this.vis.id = this.id; + } + + // add charts + var charts_array = this.app.options.config.charts; + if (charts_array) { + this.vis.get('config').charts = charts_array; + } + }, + + // pack and save nested chart models + save: function() { + // reset + this.vis.get('config').charts = []; + + // pack nested chart models into arrays attributes + var self = this; + this.each(function(chart) { + // create chart dictionary + var chart_dict = { + attributes : chart.attributes, + settings : chart.settings.attributes, + groups : [] + }; + + // append groups + chart.groups.each(function(group) { + chart_dict.groups.push(group.attributes); + }); + + // add chart to charts array + self.vis.get('config').charts.push(chart_dict); + }); // save visualization - vis.save() - .fail( function( xhr, status, message ){ - console.error( xhr, status, message ); - alert( 'Error loading data:\n' + xhr.responseText ); + var self = this; + this.vis.save() + .fail(function(xhr, status, message) { + console.error(xhr, status, message); + alert( 'Error loading data:\n' + xhr.responseText ); + }) + .then(function(response) { + if (response && response.id) { + self.id = response.id; + } }); + }, + + // load nested models/collections from packed dictionary + load: function() { + // get charts array + var charts_array = this.vis.get('config').charts; + + // unpack chart models + for (var i in charts_array) { + // get chart details + var chart_dict = charts_array[i]; + + // construct chart model + var chart = new Chart(); + + // main + chart.set(chart_dict.attributes); + + // get settings + chart.settings.set(chart_dict.settings); + + // get groups + for (var j in chart_dict.groups) { + chart.groups.add(new Group(chart_dict.groups[j])); + } + + // reset status + chart.state('ok', 'Loaded previously saved visualization.'); + + // add to collection + this.add(chart); + + // trigger + chart.trigger('redraw', chart); + } } }); diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/views/charts.js --- a/config/plugins/visualizations/charts/static/views/charts.js +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -78,20 +78,25 @@ // title var chart = self.app.charts.get(chart_id); - // show modal - self.app.modal.show({ - title : 'Are you sure?', - body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.', - buttons : { - 'Cancel' : function() {self.app.modal.hide();}, - 'Delete' : function() { - // hide modal - self.app.modal.hide(); - - // remove chart - self.app.charts.remove(chart_id); + // make sure that chart is ready + self._wait (chart, function() { + self.app.modal.show({ + title : 'Are you sure?', + body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.', + buttons : { + 'Cancel' : function() {self.app.modal.hide();}, + 'Delete' : function() { + // hide modal + self.app.modal.hide(); + + // remove chart + self.app.charts.remove(chart_id); + + // cleanup + self.app.jobs.cleanup(chart); + } } - } + }); }); } }), @@ -185,14 +190,19 @@ // show chart editor _showChartView: function(chart_id) { + var self = this; + var chart = this.app.charts.get(chart_id); + this._wait (chart, function() { + self.app.go('chart_view'); + self.app.chart.copy(chart); + }); + }, + + // wait for chart to be ready + _wait: function(chart, callback) { // get chart - var chart = this.app.charts.get(chart_id); if (chart.ready()) { - // show chart view - this.app.go('chart_view'); - - // load chart into view - this.app.chart.copy(chart); + callback(); } else { // show modal var self = this; @@ -206,7 +216,7 @@ self.app.modal.hide(); // retry - self._showChartView(chart_id); + setTimeout(function() { self._wait(chart, callback); }, self.app.config.get('query_timeout')); } } }); diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 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 @@ -43,17 +43,7 @@ // redraw this.app.charts.on('redraw', function(chart) { - // redraw if chart is not currently processed - if (chart.ready()) { - self._refreshChart(chart); - } else { - // redraw once current drawing process has finished - chart.on('change:state', function() { - if (chart.ready()) { - self._refreshChart(chart); - } - }); - } + self._drawChart(chart); }); }, @@ -69,7 +59,7 @@ var item = this.list[chart_id]; if (item) { // get chart - var chart = self.app.charts.get(chart_id); + var chart = this.app.charts.get(chart_id); // update portlet this.portlet.title(chart.get('title')); @@ -100,13 +90,13 @@ }, // add - _refreshChart: function(chart) { + _drawChart: function(chart) { // link this var self = this; // check if (!chart.ready()) { - self.app.log('viewport:_refreshChart()', 'Invalid attempt to refresh chart before completion.'); + self.app.log('viewport:_drawChart()', 'Invalid attempt to draw chart before completion.'); return; } @@ -126,7 +116,7 @@ this.portlet.append($chart_el); // find svg element - var svg = d3.select(id + ' svg'); + var svg = d3.select($chart_el.find('svg')[0]); // add chart to list this.list[chart_id] = { @@ -134,9 +124,6 @@ $el : $chart_el } - // show chart from list - this.showChart(chart_id); - // clear all previous handlers (including redraw listeners) chart.off('change:state'); @@ -172,7 +159,7 @@ // set chart state chart.state('wait', 'Please wait...'); - + // identify chart type var chart_type = chart.get('type'); var chart_settings = this.app.types.get(chart_type); diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -71,9 +71,10 @@ require(['plugin/app'], function(App) { // load options var options = { + id : ${h.to_json_string( visualization_id )} || undefined, config : ${h.to_json_string( config )} } - console.log(options); + // create application app = new App(options); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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