[galaxy-commits] commit/galaxy-central: guerler: ToolForm: Add data selector, dynamic column selector and checkboxes, extends json content for basic parameters

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/25804ca32d9b/ Changeset: 25804ca32d9b User: guerler Date: 2014-08-19 21:01:57 Summary: ToolForm: Add data selector, dynamic column selector and checkboxes, extends json content for basic parameters Affected #: 17 files

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license.

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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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'">&nbsp;</i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" 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class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$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="ui-message alert alert-'+e.status+'"/>'}}),c=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 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n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},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",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg%22,width:c,height:l%7D);var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/%22,display:%22none%22%7D),r.append(i)),i.empty... in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg%22,width:i*n,height:r%7D);var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).%22,buttons:%7BCancel:function()%7Bo.app.moda... n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+="&nbsp;(all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.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",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},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",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg%22,width:c,height:l%7D);var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/%22,display:%22none%22%7D),r.append(i)),i.empty... in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg%22,width:i*n,height:r%7D);var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).%22,buttons:%7BCancel:function()%7Bo.app.moda... n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,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=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),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)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),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.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<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.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+="&nbsp;(all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"&bull; "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{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:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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$.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__%22%7D%7D%7D)%7D),define(%22plugin/charts/oth... $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 config/plugins/visualizations/charts/static/library/ui-table-form.js --- a/config/plugins/visualizations/charts/static/library/ui-table-form.js +++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js @@ -88,7 +88,7 @@ break; // radiobox field case 'radiobutton' : - field = new Ui.RadioButton({ + field = new Ui.RadioButton.View({ id : 'field-' + id, data : settings_def.data, value : model.get(id),

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 config/plugins/visualizations/charts/static/views/types.js --- a/config/plugins/visualizations/charts/static/views/types.js +++ b/config/plugins/visualizations/charts/static/views/types.js @@ -35,7 +35,7 @@ $el.append(Utils.wrap((new Ui.Label({ title : 'How many data points would you like to analyze?'})).$el));

// construct chart type subset selection buttons - this.library = new Ui.RadioButton({ + this.library = new Ui.RadioButton.View({ data : [ { label: 'Few (<500)', value: 'small' }, { label: 'Some (<10k)', value: 'medium' }, { label: 'Many (>10k)', value: 'large' }],

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -991,6 +991,8 @@ # Found selected option. value = option[1] d[ 'value' ] = value + + d[ 'display' ] = self.display

return d

@@ -1230,6 +1232,8 @@ def need_late_validation( self, trans, context ): if super( ColumnListParameter, self ).need_late_validation( trans, context ): return True + if self.data_ref not in context: + return False # Get the selected dataset if selected dataset = context[ self.data_ref ] if dataset: @@ -1242,6 +1246,16 @@ # No late validation return False

+ def to_dict( self, trans, view='collection', value_mapper=None ): + # call parent to_dict + d = super( ColumnListParameter, self ).to_dict( trans ) + + # add data reference + d[ 'data_ref' ] = self.data_ref + + # return + return d +

class DrillDownSelectToolParameter( SelectToolParameter ): """

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/mvc/tools/tools-datasets.js --- /dev/null +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -0,0 +1,46 @@ +define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ + return Backbone.Model.extend({ + // initialize + initialize: function(options) { + // create history contents container + this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({}); + + // identify current history id + this.currHistoryContents.historyId = "f597429621d6eb2b";//Galaxy.currHistoryPanel.model.id; + + // make request + var self = this; + var xhr = this.currHistoryContents.fetchAllDetails() + .done( function(){ + // log request success + console.debug('tools-datasets::initialize() - Completed.'); + + // callback + options.success && options.success(); + }) + .fail( function(){ + // log request failure + console.debug('tools-datasets::initialize() - Ajax request failed.'); + }); + }, + + // filter datasets by data type + filterType: function(filter_type) { + // return matched datasets + return this.currHistoryContents.filter( function( content ){ + // link details + var history_content_type = content.get( 'history_content_type' ); + var data_type = content.get( 'data_type'); + + // apply filter + return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === ''); + }); + }, + + // filter datasets by id + filter: function(filter_id) { + // return matched datasets + return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); + } + }); +}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -1,4 +1,8 @@ -define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], function(Tools, Portlet, Table, Ui) { +define(['mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', + 'mvc/citation/citation-model', 'mvc/citation/citation-view', + 'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-datasets'], + function(Portlet, Table, Ui, CitationModel, CitationView, + Tools, ToolTemplate, ToolDatasets) {

// create tool model var Model = Backbone.Model.extend({ @@ -17,14 +21,31 @@ // link this var self = this;

+ // link options + this.options = options; + // load tool model this.model = new Model({ id : options.id });

+ // initialize datasets + this.datasets = new ToolDatasets({ + success: function() { + self._initializeToolForm(); + } + }); + }, + + // initialize tool form + _initializeToolForm: function() { // fetch model and render form + var self = this; this.model.fetch({ success: function() { + // inputs + self.inputs = self.model.get('inputs'); + // create portlet self.portlet = new Portlet.View({ icon : 'fa-wrench', @@ -41,15 +62,35 @@ } });

- // table + // create table self.table = new Table.View();

- // add message + // create message self.message = new Ui.Message(); self.portlet.append(self.message.$el);

- // append portlet + // append form $(self.main_el).append(self.portlet.$el); + + // append help + if (self.options.help != '') { + $(self.main_el).append(ToolTemplate.help(self.options.help)); + } + + // append citations + if (self.options.citations) { + // append html + $(self.main_el).append(ToolTemplate.citations()); + + // fetch citations + var citations = new CitationModel.ToolCitationCollection(); + citations.tool_id = self.options.id; + var citation_list_view = new CitationView.CitationListView({ collection: citations } ); + citation_list_view.render(); + citations.fetch(); + } + + // configure portlet and form table self.setElement(self.portlet.content()); self.portlet.append(self.table.$el); self.render(); @@ -59,9 +100,6 @@

// update render: function() { - // inputs - var settings = this.model.get('inputs'); - // reset table this.table.delAll();

@@ -72,8 +110,8 @@ var data = new Backbone.Model();

// load settings elements into table - for (var id in settings) { - this._add(settings[id], data); + for (var id in this.inputs) { + this._add(this.inputs[id], data); }

// trigger change @@ -83,53 +121,55 @@ },

// add table row - _add: function(settings_def, data) { + _add: function(inputs_def, data) { // link this var self = this;

// get id - var id = settings_def.name; - - // log - console.debug(settings_def); + var id = inputs_def.name;

// field wrapper var field = null; - + console.log(inputs_def); // create select field - var type = settings_def.type; + var type = inputs_def.type; switch(type) { // text input field case 'text' : - field = this.field_text(settings_def, data); + field = this.field_text(inputs_def, data); break;

// select field case 'select' : - field = this.field_select(settings_def, data); + field = this.field_select(inputs_def, data); break;

// radiobox field case 'radiobutton' : - field = this.field_radio(settings_def, data); + field = this.field_radio(inputs_def, data); break;

// dataset case 'data': - field = this.field_select(settings_def, data); + field = this.field_data(inputs_def, data); break;

- // slider input field + // dataset column + case 'data_column': + field = this.field_column(inputs_def, data); + break; + + // text area field case 'textarea' : - field = this.field_textarea(settings_def, data); + field = this.field_textarea(inputs_def, data); break;

// default default: field = new Ui.Input({ id : 'field-' + id, - placeholder : settings_def.placeholder, - type : settings_def.type, + placeholder : inputs_def.placeholder, + type : inputs_def.type, onchange : function() { data.set(id, field.value()); } @@ -138,7 +178,7 @@

// set value if (!data.get(id)) { - data.set(id, settings_def.value); + data.set(id, inputs_def.value); } field.value(data.get(id));

@@ -148,31 +188,26 @@ // combine field and info var $input = $('<div/>'); $input.append(field.$el); - if (settings_def.info) { - $input.append('<div class="ui-table-form-info">' + settings_def.info + '</div>'); + if (inputs_def.info) { + $input.append('<div class="ui-table-form-info">' + inputs_def.info + '</div>'); }

// add row to table - if (this.options.style == 'bold') { - this.table.add(new Ui.Label({title: settings_def.title, cls: 'form-label'}).$el); - this.table.add($input); - } else { - this.table.add('<span class="ui-table-form-title">' + settings_def.label + '</span>', '25%'); - this.table.add($input); - } - + this.table.add('<span class="ui-table-form-title">' + inputs_def.label + '</span>', '25%'); + this.table.add($input); + // add to table this.table.append(id);

// show/hide - if (settings_def.hide) { + if (inputs_def.hide) { this.table.get(id).hide(); } },

// text input field - field_text : function(settings_def, data) { - var id = settings_def.name; + field_text : function(inputs_def, data) { + var id = inputs_def.name; return new Ui.Input({ id : 'field-' + id, value : data.get(id), @@ -183,8 +218,8 @@ },

// text area - field_textarea : function(settings_def, data) { - var id = settings_def.name; + field_textarea : function(inputs_def, data) { + var id = inputs_def.name; return new Ui.Textarea({ id : 'field-' + id, onchange : function() { @@ -193,12 +228,89 @@ }); },

- // select field - field_select : function (settings_def, data) { + // data input field + field_data : function(inputs_def, data) { + // link this + var self = this; + + // get element id + var id = inputs_def.name; + + // get datasets + var datasets = this.datasets.filterType(); + // configure options fields var options = []; - for (var i in settings_def.options) { - var option = settings_def.options[i]; + for (var i in datasets) { + options.push({ + label: datasets[i].get('name'), + value: datasets[i].get('id') + }); + } + + // find referenced columns + var column_list = _.where(this.inputs, { + data_ref : id, + type : 'data_column' + }); + + // select field + return new Ui.Select.View({ + id : 'field-' + id, + data : options, + value : options[0].value, + onchange : function(value) { + // update value + data.set(id, value); + + // find selected dataset + var dataset = self.datasets.filter(value); + + // check dataset + if (dataset && column_list.length > 0) { + // log selection + console.debug('tool-form::field_data() - Selected dataset ' + value + '.'); + + // get meta data + var meta = dataset.get('metadata_column_types'); + + // check meta data + if (!meta) { + console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.'); + } + + // load column options + var columns = []; + for (var key in meta) { + // add to selection + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } + + // update referenced columns + for (var i in column_list) { + var column_field = self.list[column_list[i].name] + if (column_field) { + column_field.update(columns); + column_field.value(column_field.first()); + } + } + } else { + // log failure + console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.'); + } + } + }); + }, + + // select field + field_column : function (inputs_def, data) { + // configure options fields + var options = []; + for (var i in inputs_def.options) { + var option = inputs_def.options[i]; options.push({ label: option[0], value: option[1] @@ -206,56 +318,56 @@ }

// select field - var id = settings_def.name; + var id = inputs_def.name; return new Ui.Select.View({ id : 'field-' + id, data : options, value : data.get(id), onchange : function(value) { - // set new value data.set(id, value); - - // find selected dictionary - var dict = _.findWhere(options, {value: value}); - if (dict && dict.operations) { - var operations = dict.operations; - for (var i in operations.show) { - var target = operations.show[i]; - self.table.get(target).show(); - } - for (var i in operations.hide) { - var target = operations.hide[i]; - self.table.get(target).hide(); - } - } + } + }); + }, + + // select field + field_select : function (inputs_def, data) { + // configure options fields + var options = []; + for (var i in inputs_def.options) { + var option = inputs_def.options[i]; + options.push({ + label: option[0], + value: option[1] + }); + } + + // identify display type + var SelectClass = Ui.Select; + if (inputs_def.display == 'checkboxes') { + SelectClass = Ui.Checkbox; + } + + // select field + var id = inputs_def.name; + return new SelectClass.View({ + id : 'field-' + id, + data : options, + value : data.get(id), + onchange : function(value) { + data.set(id, value); } }); },

// radio field - field_radio : function(settings_def, data) { - var id = settings_def.name; + field_radio : function(inputs_def, data) { + var id = inputs_def.name; return new Ui.RadioButton({ id : 'field-' + id, - data : settings_def.data, + data : inputs_def.data, value : data.get(id), onchange : function(value) { - // set new value data.set(id, value); - - // find selected dictionary - var dict = _.findWhere(settings_def.data, {value: value}); - if (dict && dict.operations) { - var operations = dict.operations; - for (var i in operations.show) { - var target = operations.show[i]; - self.table.get(target).show(); - } - for (var i in operations.hide) { - var target = operations.hide[i]; - self.table.get(target).hide(); - } - } } }); }

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/mvc/tools/tools-template.js --- /dev/null +++ b/static/scripts/mvc/tools/tools-template.js @@ -0,0 +1,19 @@ +// dependencies +define([], function() { + +// tool form templates +return { + help: function(content) { + return '<div class="toolHelp">' + + '<div class="toolHelpBody">' + + content + + '</div>' + + '</div>'; + }, + + citations: function() { + return '<div id="citations"></div>'; + } +}; + +}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/mvc/ui/ui-checkbox.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-checkbox.js @@ -0,0 +1,91 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend({ + // options + optionsDefault: { + value : '', + visible : true, + cls : '', + data : [], + id : Utils.uuid() + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // current value + this.current = this.options.value; + + // onchange event handler. fires on user activity. + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + }); + }, + + // value + value : function (new_val) { + // get current value + var before = this.current; + + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.current = new_val; + } + + // check value + var after = this.current; + if (after != before && this.options.onchange) { + this.options.onchange(this.current); + } + + // get and return value + return this.current; + }, + + // get value + _getValue: function() { + var selected = this.$el.find(':checked'); + var value = null; + if (selected.length > 0) { + value = selected.val(); + } + return value; + }, + + // element + _template: function(options) { + var tmpl = '<div class="ui-checkbox">'; + for (key in options.data) { + var pair = options.data[key]; + tmpl += '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>'; + } + tmpl += '</div>'; + return tmpl; + } +}); + +return { + View : View +}; + +});

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-checkbox', 'mvc/ui/ui-radiobutton', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Checkbox, RadioButton, ButtonMenu, Modal) {

/** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -409,90 +409,6 @@ } });

-// plugin -var RadioButton = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - visible : true, - cls : '', - data : [], - id : Utils.uuid() - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // set initial value - if (this.options.value) { - this.value(this.options.value); - } - - // current value - this.current = this.options.value; - - // onchange event handler. fires on user activity. - var self = this; - this.$el.find('input').on('change', function() { - self.value(self._getValue()); - }); - }, - - // value - value : function (new_val) { - // get current value - var before = this.current; - - // set new value - if (new_val !== undefined) { - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); - this.current = new_val; - } - - // check value - var after = this.current; - if (after != before && this.options.onchange) { - this.options.onchange(this.current); - } - - // get and return value - return this.current; - }, - - // get value - _getValue: function() { - var selected = this.$el.find(':checked'); - var value = null; - if (selected.length > 0) { - value = selected.val(); - } - return value; - }, - - // element - _template: function(options) { - var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">'; - for (key in options.data) { - var pair = options.data[key]; - tmpl += '<label class="btn btn-default">' + - '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + - '</label>'; - } - tmpl += '</div>'; - return tmpl; - } -});

// return return { @@ -507,6 +423,7 @@ Message : Message, Modal : Modal, RadioButton : RadioButton, + Checkbox : Checkbox, Searchbox : Searchbox, Select : Select, Textarea : Textarea

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/mvc/ui/ui-radiobutton.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-radiobutton.js @@ -0,0 +1,93 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend({ + // options + optionsDefault: { + value : '', + visible : true, + cls : '', + data : [], + id : Utils.uuid() + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // current value + this.current = this.options.value; + + // onchange event handler. fires on user activity. + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + }); + }, + + // value + value : function (new_val) { + // get current value + var before = this.current; + + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + this.current = new_val; + } + + // check value + var after = this.current; + if (after != before && this.options.onchange) { + this.options.onchange(this.current); + } + + // get and return value + return this.current; + }, + + // get value + _getValue: function() { + var selected = this.$el.find(':checked'); + var value = null; + if (selected.length > 0) { + value = selected.val(); + } + return value; + }, + + // element + _template: function(options) { + var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">'; + for (key in options.data) { + var pair = options.data[key]; + tmpl += '<label class="btn btn-default">' + + '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + + '</label>'; + } + tmpl += '</div>'; + return tmpl; + } +}); + +return { + View : View +}; + +});

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/packed/mvc/tools/tools-datasets.js --- /dev/null +++ b/static/scripts/packed/mvc/tools/tools-datasets.js @@ -0,0 +1,1 @@ +define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId="f597429621d6eb2b";var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){return this.currHistoryContents.filter(function(c){var d=c.get("history_content_type");var e=c.get("data_type");return d==="dataset"})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/tools","mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc"],function(b,c,a,f){var e=Backbone.Model.extend({initialize:function(g){this.url=galaxy_config.root+"api/tools/"+g.id+"?io_details=true"}});var d=Backbone.View.extend({main_el:"body",initialize:function(h){var g=this;this.model=new e({id:h.id});this.model.fetch({success:function(){g.portlet=new c.View({icon:"fa-wrench",title:"<b>"+g.model.get("name")+"</b> "+g.model.get("description"),buttons:{execute:new f.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});g.table=new a.View();g.message=new f.Message();g.portlet.append(g.message.$el);$(g.main_el).append(g.portlet.$el);g.setElement(g.portlet.content());g.portlet.append(g.table.$el);g.render()}})},render:function(){var g=this.model.get("inputs");this.table.delAll();this.list=[];var h=new Backbone.Model();for(var i in g){this._add(g[i],h)}for(var i in this.list){this.list[i].trigger("change")}},_add:function(g,j){var h=this;var m=g.name;console.debug(g);var k=null;var i=g.type;switch(i){case"text":k=this.field_text(g,j);break;case"select":k=this.field_select(g,j);break;case"radiobutton":k=this.field_radio(g,j);break;case"data":k=this.field_select(g,j);break;case"textarea":k=this.field_textarea(g,j);break;default:k=new f.Input({id:"field-"+m,placeholder:g.placeholder,type:g.type,onchange:function(){j.set(m,k.value())}})}if(!j.get(m)){j.set(m,g.value)}k.value(j.get(m));this.list[m]=k;var l=$("<div/>");l.append(k.$el);if(g.info){l.append('<div class="ui-table-form-info">'+g.info+"</div>")}if(this.options.style=="bold"){this.table.add(new f.Label({title:g.title,cls:"form-label"}).$el);this.table.add(l)}else{this.table.add('<span class="ui-table-form-title">'+g.label+"</span>","25%");this.table.add(l)}this.table.append(m);if(g.hide){this.table.get(m).hide()}},field_text:function(g,h){var i=g.name;return new f.Input({id:"field-"+i,value:h.get(i),onchange:function(j){h.set(i,j)}})},field_textarea:function(g,h){var i=g.name;return new f.Textarea({id:"field-"+i,onchange:function(){h.set(i,field.value())}})},field_select:function(g,l){var h=[];for(var j in g.options){var k=g.options[j];h.push({label:k[0],value:k[1]})}var m=g.name;return new f.Select.View({id:"field-"+m,data:h,value:l.get(m),onchange:function(p){l.set(m,p);var r=_.findWhere(h,{value:p});if(r&&r.operations){var n=r.operations;for(var o in n.show){var q=n.show[o];self.table.get(q).show()}for(var o in n.hide){var q=n.hide[o];self.table.get(q).hide()}}}})},field_radio:function(g,h){var i=g.name;return new f.RadioButton({id:"field-"+i,data:g.data,value:h.get(i),onchange:function(l){h.set(i,l);var n=_.findWhere(g.data,{value:l});if(n&&n.operations){var j=n.operations;for(var k in j.show){var m=j.show[k];self.table.get(m).show()}for(var k in j.hide){var m=j.hide[k];self.table.get(m).hide()}}}})}});return{View:d}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.list=[];var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.list){this.list[l].trigger("change")}},_add:function(l,n){var k=this;var q=l.name;var o=null;console.log(l);var m=l.type;switch(m){case"text":o=this.field_text(l,n);break;case"select":o=this.field_select(l,n);break;case"radiobutton":o=this.field_radio(l,n);break;case"data":o=this.field_data(l,n);break;case"data_column":o=this.field_column(l,n);break;case"textarea":o=this.field_textarea(l,n);break;default:o=new j.Input({id:"field-"+q,placeholder:l.placeholder,type:l.type,onchange:function(){n.set(q,o.value())}})}if(!n.get(q)){n.set(q,l.value)}o.value(n.get(q));this.list[q]=o;var p=$("<div/>");p.append(o.$el);if(l.info){p.append('<div class="ui-table-form-info">'+l.info+"</div>")}this.table.add('<span class="ui-table-form-title">'+l.label+"</span>","25%");this.table.add(p);this.table.append(q);if(l.hide){this.table.get(q).hide()}},field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},field_data:function(n,q){var l=this;var r=n.name;var p=this.datasets.filterType();var m=[];for(var o in p){m.push({label:p[o].get("name"),value:p[o].get("id")})}var k=_.where(this.inputs,{data_ref:r,type:"data_column"});return new j.Select.View({id:"field-"+r,data:m,value:m[0].value,onchange:function(w){q.set(r,w);var y=l.datasets.filter(w);if(y&&k.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in k){var s=l.list[k[t].name];if(s){s.update(v);s.value(s.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/packed/mvc/tools/tools-template.js --- /dev/null +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -0,0 +1,1 @@ +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'}}}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/packed/mvc/ui/ui-checkbox.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-checkbox.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="ui-checkbox">';for(key in d.data){var e=d.data[key];c+='<input type="checkbox" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"<br>"}c+="</div>";return c}});return{View:b}}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,o,m){var c=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(p){return'<img class="ui-image '+p.cls+'" src="'+p.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options))},title:function(p){this.$el.html(p)},_template:function(p){return'<label class="ui-label '+p.cls+'">'+p.title+"</label>"},value:function(){return options.title}});var d=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){return'<div><span class="fa '+p.icon+'" class="ui-icon"/>&nbsp;'+p.title+"</div>"}});var f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick);$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){var q='<button id="'+p.id+'" type="submit" style="float: '+p.floating+';" type="button" class="ui-button '+p.cls+'">';if(p.icon){q+='<i class="icon fa '+p.icon+'"></i>&nbsp;'}q+=p.title+"</button>";return q}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick);$(this.el).tooltip({title:p.tooltip,placement:"bottom"})},_template:function(p){var q="";if(p.title){q="width: auto;"}var r='<div id="'+p.id+'" style="float: '+p.floating+"; "+q+'" class="ui-button-icon '+p.cls+'">';if(p.title){r+='<div class="button"><i class="icon fa '+p.icon+'"/>&nbsp;<span class="title">'+p.title+"</span></div>"}else{r+='<i class="icon fa '+p.icon+'"/>'}r+="</div>";return r}});var e=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",p.onclick)},_template:function(p){return'<div><a href="javascript:void(0)" class="ui-anchor '+p.cls+'">'+p.title+"</a></div>"}});var n=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(p){this.options=k.merge(p,this.optionsDefault);this.setElement("<div></div>")},update:function(q){this.options=k.merge(q,this.optionsDefault);if(q.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(q.message);this.$el.fadeIn();if(!q.persistent){var p=this;window.setTimeout(function(){if(p.$el.is(":visible")){p.$el.fadeOut()}else{p.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(p){return'<div class="ui-message alert alert-'+p.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));var p=this;if(this.options.onclick){this.$el.on("submit",function(s){var r=p.$el.find("#search");p.options.onclick(r.val())})}},_template:function(p){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+p.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var p=this;this.$el.on("input",function(){if(p.options.onchange){p.options.onchange(p.$el.val())}})},value:function(p){if(p!==undefined){this.$el.val(p)}return this.$el.val()},_template:function(p){return'<input id="'+p.id+'" type="'+p.type+'" value="'+p.value+'" placeholder="'+p.placeholder+'" class="ui-input '+p.cls+'">'}});var h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var p=this;this.$el.on("input",function(){if(p.options.onchange){p.options.onchange(p.$el.val())}})},value:function(p){if(p!==undefined){this.$el.val(p)}return this.$el.val()},_template:function(p){return'<textarea id="'+p.id+'" class="ui-textarea '+p.cls+'" rows="5"></textarea>'}});var l=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:k.uuid()},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var p=this;this.$el.find("input").on("change",function(){p.value(p._getValue())})},value:function(p){var q=this.current;if(p!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+p+'"]').closest("label").addClass("active");this.current=p}var r=this.current;if(r!=q&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var p=this.$el.find(":checked");var q=null;if(p.length>0){q=p.val()}return q},_template:function(q){var p='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in q.data){var r=q.data[key];p+='<label class="btn btn-default"><input type="radio" name="'+q.id+'" value="'+r.value+'" selected>'+r.label+"</label>"}p+="</div>";return p}});return{Anchor:e,Button:f,ButtonIcon:g,ButtonMenu:o,Icon:d,Image:c,Input:i,Label:j,Message:n,Modal:m,RadioButton:l,Searchbox:a,Select:b,Textarea:h}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,e,m,p,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/>&nbsp;'+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="ui-button '+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i>&nbsp;'}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="ui-button-icon '+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/>&nbsp;<span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=l.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'" rows="5"></textarea>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Textarea:i}}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 static/scripts/packed/mvc/ui/ui-radiobutton.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-radiobutton.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in d.data){var e=d.data[key];c+='<label class="btn btn-default"><input type="radio" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"</label>"}c+="</div>";return c}});return{View:b}}); \ No newline at end of file

diff -r 068fa60b8c2bfc7e24e684b89697abc3797a64a2 -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 templates/webapps/galaxy/tool_form.api.mako --- a/templates/webapps/galaxy/tool_form.api.mako +++ b/templates/webapps/galaxy/tool_form.api.mako @@ -1,10 +1,47 @@ <%inherit file="/base.mako"/> + +<% + # load tool help + tool_help = '' + if tool.help: + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + endif + + # check if citations exist + tool_citations = False + if tool.citations: + tool_citations = True + + # form configuration + self.form_config = { + 'id' : tool.id, + 'help' : tool_help, + 'citations' : tool_citations + } +%> +${h.js( "libs/bibtex" )} <script> require(['mvc/tools/tools-form'], function(ToolsForm){ $(function(){ - var form = new ToolsForm.View({ - id : '${tool.id}' - }); + var form = new ToolsForm.View(${ h.to_json_string(self.form_config) }); }); }); </script> + +%if tool.tool_shed_repository: + <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %> + %if tool_url: + <br/> + ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) } + %endif +%endif

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

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