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commit/galaxy-central: guerler: Add tool form basics, refactor ui libraries, add alternative tool form template
by commits-noreply＠bitbucket.org 13 Aug '14
by commits-noreply＠bitbucket.org 13 Aug '14
13 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/898a172941b1/
Changeset: 898a172941b1
User: guerler
Date: 2014-08-13 19:53:07
Summary: Add tool form basics, refactor ui libraries, add alternative tool form template
Affected #: 20 files
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,5 +1,5 @@
// dependencies
-define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
+define(['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',
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
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No 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","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$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=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<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=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$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.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<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",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$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",["plugin/library/ui-table","plugin/library/ui","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",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$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 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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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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){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",width:c,height:l});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/",display:"none"}),r.append(i)),i.empty();for(name 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",width:i*n,height:r});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)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new 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+=" (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+" - "+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({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=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<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 --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_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_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",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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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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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 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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 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){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?(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 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$.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",query_limit:1e4,settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.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__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.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 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/library/ui-button-menu.js
--- a/config/plugins/visualizations/charts/static/library/ui-button-menu.js
+++ /dev/null
@@ -1,169 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-/**
- * This class creates a button with dropdown menu. It extends the functionality of the Ui.ButtonIcon class.
- */
-return Backbone.View.extend({
- // main options
- optionsDefault: {
- // same as Ui.ButtonIcon
- id : '',
- title : '',
- float : 'right',
- icon : null,
- onclick : null,
- cls : 'icon-btn',
- tooltip : '',
-
- // additional options
- target : '',
- href : '',
- onunload : null,
- visible : true,
- tag : ''
- },
-
- // optional sub menu
- $menu: null,
-
- // initialize
- initialize: function (options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // add template for tab
- this.setElement($(this._template(this.options)));
-
- // find root
- var $root = $(this.el).find('.root');
-
- // link head
- var self = this;
- $root.on('click', function(e) {
- // hide all tooltips
- $('.tooltip').hide();
-
- // prevent default
- e.preventDefault();
-
- // add click event
- if(self.options.onclick) {
- self.options.onclick();
- }
- });
-
- // visiblity
- if (!this.options.visible)
- this.hide();
-
- // add tooltip
- $root.tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // show
- show: function() {
- $(this.el).show();
- },
-
- // hide
- hide: function() {
- $(this.el).hide();
- },
-
- // add menu item
- addMenu: function (options) {
- // menu option defaults
- var menuOptions = {
- title : '',
- target : '',
- href : '',
- onclick : null,
- divider : false,
- icon : null,
- cls : 'button-menu btn-group'
- }
-
- // get options
- menuOptions = Utils.merge(options, menuOptions);
-
- // check if submenu element is available
- if (!this.$menu) {
- // insert submenu element into root
- $(this.el).append(this._templateMenu());
-
- // update element link
- this.$menu = $(this.el).find('.menu');
- }
-
- // create
- var $item = $(this._templateMenuItem(menuOptions));
-
- // add events
- $item.on('click', function(e) {
- // prevent default
- e.preventDefault();
-
- // add click event
- if(menuOptions.onclick) {
- menuOptions.onclick();
- }
- });
-
- // append menu
- this.$menu.append($item);
-
- // append divider
- if (menuOptions.divider)
- this.$menu.append($(this._templateDivider()));
- },
-
- // fill template header
- _templateMenuItem: function (options) {
- var tmpl = '<li>' +
- '<a href="' + options.href + '" target="' + options.target + '">';
-
- if (options.icon)
- tmpl += '<i class="fa ' + options.icon + '"></i>';
-
- tmpl += ' ' + options.title +
- '</a>' +
- '</li>';
- return tmpl;
- },
-
- // fill template header
- _templateMenu: function () {
- return '<ul class="menu dropdown-menu pull-right" role="menu"></ul>';
- },
-
- _templateDivider: function() {
- return '<li class="divider"></li>';
- },
-
- // element
- _template: function(options) {
- // width
- var width = '';
- if (options.title) {
- width = 'width: auto;';
- }
-
- // string
- var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">';
-
- // title
- if (options.title) {
- str += '<div class="root button dropdown-toggle" data-toggle="dropdown">' +
- '<i class="icon fa ' + options.icon + '"/> ' +
- '<span class="title">' + options.title + '</span>' +
- '</div>';
- } else {
- str += '<i class="icon fa ' + options.icon + '"/>';
- }
- str += '</div>';
- return str;
- }
-});
-
-});
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/library/ui-select.js
--- a/config/plugins/visualizations/charts/static/library/ui-select.js
+++ /dev/null
@@ -1,241 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-/**
- * This class creates/wraps a default html select field as backbone class.
- */
-var View = Backbone.View.extend({
- // options
- optionsDefault : {
- id : '',
- cls : '',
- empty : 'No data available',
- visible : true,
- wait : false
- },
-
- // value
- selected : null,
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // initial value
- this.selected = this.options.value;
-
- // create new element
- this.setElement(this._template(this.options));
-
- // link elements
- this.$select = this.$el.find('#select');
- this.$icon = this.$el.find('#icon');
-
- // add change event. fires only on user activity
- var self = this;
- this.$select.on('change', function() {
- self.value(self.$select.val());
- });
-
- // add change event. fires on trigger
- this.on('change', function() {
- if (self.options.onchange) {
- self.options.onchange(self.value());
- }
- });
-
- // refresh
- this._refresh();
-
- // show/hide
- if (!this.options.visible) {
- this.hide();
- }
-
- // wait
- if (this.options.wait) {
- this.wait();
- } else {
- this.show();
- }
- },
-
- // value
- value : function (new_value) {
-
- // get current id/value
- var before = this.selected;
-
- // check if new_value is defined
- if (new_value !== undefined) {
- this.selected = new_value;
- this.$select.val(new_value);
- }
-
- // get current id/value
- var after = this.selected;
- if (after) {
- // fire onchange
- if (after != before && this.options.onchange) {
- this.options.onchange(after);
- }
- }
-
- // return
- return after;
- },
-
- // first
- first: function() {
- var options = this.$select.find('option');
- if (options.length > 0) {
- return options.val();
- } else {
- return undefined;
- }
- },
-
- // label
- text : function () {
- return this.$select.find('option:selected').text();
- },
-
- // show
- show: function() {
- this.$icon.removeClass();
- this.$icon.addClass('fa fa-caret-down');
- this.$select.show();
- this.$el.show();
- },
-
- // hide
- hide: function() {
- this.$el.hide();
- },
-
- // wait
- wait: function() {
- this.$icon.removeClass();
- this.$icon.addClass('fa fa-spinner fa-spin');
- this.$select.hide();
- },
-
- // disabled
- disabled: function() {
- return this.$select.is(':disabled');
- },
-
- // enable
- enable: function() {
- this.$select.prop('disabled', false);
- },
-
- // disable
- disable: function() {
- this.$select.prop('disabled', true);
- },
-
- // add
- add: function(options) {
- // add options
- this.$select.append(this._templateOption(options));
-
- // refresh
- this._refresh();
- },
-
- // remove
- del: function(value) {
- // remove option
- this.$select.find('option[value=' + value + ']').remove();
- this.$select.trigger('change');
-
- // refresh
- this._refresh();
- },
-
- // render
- update: function(options) {
- // remove all options
- this.$select.find('option').remove();
-
- // add new options
- for (var key in options) {
- this.$select.append(this._templateOption(options[key]));
- }
-
- // refresh
- this._refresh();
- },
-
- // set on change event
- setOnChange: function(callback) {
- this.options.onchange = callback;
- },
-
- // check if selected value exists
- exists: function(value) {
- return this.$select.find('option[value=' + value + ']').length > 0;
- },
-
- // refresh
- _refresh: function() {
- // remove placeholder
- this.$select.find('option[value=null]').remove();
-
- // count remaining entries
- var remaining = this.$select.find('option').length;
- if (remaining == 0) {
- // disable select field
- this.disable();
-
- // append placeholder
- this.$select.append(this._templateOption({value : 'null', label : this.options.empty}));
- } else {
- // enable select field
- this.enable();
- }
-
- // update value
- if (this.selected) {
- this.$select.val(this.selected);
- }
- },
-
- // option
- _templateOption: function(options) {
- return '<option value="' + options.value + '">' + options.label + '</option>';
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div id="' + options.id + '" class="ui-select">' +
- '<div class="button">' +
- '<i id="icon"/>' +
- '</div>' +
- '<select id="select" class="select ' + options.cls + ' ' + options.id + '">';
- for (key in options.data) {
- // options
- var item = options.data[key];
-
- // identify selected value
- var tag = '';
- if (item.value == options.value || item.value == '') {
- tag = 'selected';
- }
-
- // add template string
- tmpl += '<option value="' + item.value + '" ' + tag + '>' + item.label + '</option>';
- }
- tmpl += '</select>' +
- '</div>';
- return tmpl;
- }
-});
-
-return {
- View: View
-}
-
-});
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 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
@@ -1,5 +1,5 @@
// dependencies
-define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
+define(['mvc/ui/ui-table', 'mvc/ui/ui-misc', 'utils/utils'],
function(Table, Ui, Utils) {
/**
@@ -230,10 +230,10 @@
// add to table
this.table.append(id);
- // show/hide
- if (settings_def.hide) {
- this.table.get(id).hide();
- }
+ // show/hide
+ if (settings_def.hide) {
+ this.table.get(id).hide();
+ }
}
});
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/library/ui-table.js
--- a/config/plugins/visualizations/charts/static/library/ui-table.js
+++ /dev/null
@@ -1,217 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-/**
- * This class creates a ui table element.
- */
-var View = Backbone.View.extend({
- // current row
- row: null,
-
- // count rows
- row_count: 0,
-
- // defaults options
- optionsDefault: {
- content : 'No content available.',
- onchange : null,
- ondblclick : null,
- onconfirm : null,
- cls : ''
- },
-
- // events
- events : {
- 'click' : '_onclick',
- 'dblclick' : '_ondblclick'
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- var $el = $(this._template(options));
-
- // link sub-elements
- this.$thead = $el.find('thead');
- this.$tbody = $el.find('tbody');
- this.$tmessage = $el.find('tmessage');
-
- // set element
- this.setElement($el);
-
- // initialize row
- this.row = $('<tr></tr>');
- },
-
- // add header cell
- addHeader: function($el) {
- var wrapper = $('<th></th>');
- wrapper.append($el);
- this.row.append(wrapper);
- },
-
- // header
- appendHeader: function() {
- // append header row
- this.$thead.append(this.row);
-
- // row
- this.row = $('<tr></tr>');
- },
-
- // add row cell
- add: function($el, width, align) {
- var wrapper = $('<td></td>');
- if (width) {
- wrapper.css('width', width);
- }
- if (align) {
- wrapper.css('text-align', align);
- }
- wrapper.append($el);
- this.row.append(wrapper);
- },
-
- // append
- append: function(id) {
- this._commit(id);
- },
-
- // prepend
- prepend: function(id) {
- this._commit(id, true);
- },
-
- // get element
- get: function(id) {
- return this.$el.find('#' + id);
- },
-
- // delete
- del: function(id) {
- var item = this.$tbody.find('#' + id);
- if (item.length > 0) {
- item.remove();
- this.row_count--;
- this._refresh();
- }
- },
-
- // delete all
- delAll: function() {
- this.$tbody.empty();
- this.row_count = 0;
- this._refresh();
- },
-
- // value
- value: function(new_value) {
- // get current id/value
- this.before = this.$tbody.find('.current').attr('id');
-
- // check if new_value is defined
- if (new_value !== undefined) {
- this.$tbody.find('tr').removeClass('current');
- if (new_value) {
- this.$tbody.find('#' + new_value).addClass('current');
- }
- }
-
- // get current id/value
- var after = this.$tbody.find('.current').attr('id');
- if(after === undefined) {
- return null;
- } else {
- // fire onchange
- if (after != this.before && this.options.onchange) {
- this.options.onchange(new_value);
- }
-
- // return current value
- return after;
- }
- },
-
- // size
- size: function() {
- return this.$tbody.find('tr').length;
- },
-
- // commit
- _commit: function(id, prepend) {
- // remove previous item with same id
- this.del(id);
-
- // add
- this.row.attr('id', id);
-
- // add row
- if (prepend) {
- this.$tbody.prepend(this.row);
- } else {
- this.$tbody.append(this.row);
- }
-
- // row
- this.row = $('<tr></tr>');
-
- // row count
- this.row_count++;
- this._refresh();
- },
-
- // onclick
- _onclick: function(e) {
- // get values
- var old_value = this.value();
- var new_value = $(e.target).closest('tr').attr('id');
- if (new_value != ''){
- // check equality
- if (new_value && old_value != new_value) {
- if (this.options.onconfirm) {
- this.options.onconfirm(new_value);
- } else {
- this.value(new_value);
- }
- }
- }
- },
-
- // ondblclick
- _ondblclick: function(e) {
- var value = this.value();
- if (value && this.options.ondblclick) {
- this.options.ondblclick(value);
- }
- },
-
- // refresh
- _refresh: function() {
- if (this.row_count == 0) {
- this.$tmessage.show();
- } else {
- this.$tmessage.hide();
- }
- },
-
- // load html template
- _template: function(options)
- {
- return '<div>' +
- '<table class="ui-table ' + options.cls + '">' +
- '<thead></thead>' +
- '<tbody style="cursor: pointer;"></tbody>' +
- '</table>' +
- '<tmessage>' + options.content + '</tmessage>' +
- '<div>';
- }
-});
-
-return {
- View: View
-}
-
-});
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/library/ui.js
--- a/config/plugins/visualizations/charts/static/library/ui.js
+++ /dev/null
@@ -1,514 +0,0 @@
-// dependencies
-define(['utils/utils', 'plugin/library/ui-select', 'plugin/library/ui-button-menu', 'mvc/ui/ui-modal'],
- function(Utils, Select, ButtonMenu, Modal) {
-
-/**
- * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.
- */
-
-// plugin
-var Image = Backbone.View.extend({
- // options
- optionsDefault: {
- url : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
- },
-
- // template
- _template: function(options) {
- return '<img class="ui-image ' + options.cls + '" src="' + options.url + '"/>';
- }
-});
-
-// plugin
-var Label = Backbone.View.extend({
- // options
- optionsDefault: {
- title : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
- },
-
- // title
- title: function(new_title) {
- this.$el.html(new_title);
- },
-
- // template
- _template: function(options) {
- return '<label class="ui-label ' + options.cls + '">' + options.title + '</label>';
- },
-
- // value
- value: function() {
- return options.title;
- }
-});
-
-// plugin
-var Icon = Backbone.View.extend({
- // options
- optionsDefault: {
- float : 'right',
- icon : '',
- tooltip : '',
- placement : 'bottom',
- title : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- return '<div>' +
- '<span class="fa ' + options.icon + '" class="ui-icon"/> ' +
- options.title +
- '</div>';
- }
-});
-
-// plugin
-var Button = Backbone.View.extend({
- // options
- optionsDefault: {
- id : null,
- title : '',
- float : 'right',
- cls : 'btn btn-default',
- icon : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add event
- $(this.el).on('click', options.onclick);
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- var str = '<button id="' + options.id + '" type="submit" style="float: ' + options.float + ';" type="button" class="ui-button ' + options.cls + '">';
- if (options.icon) {
- str += '<i class="icon fa ' + options.icon + '"></i> ' ;
- }
- str += options.title +
- '</button>';
- return str;
- }
-});
-
-// plugin
-var ButtonIcon = Backbone.View.extend({
- // options
- optionsDefault: {
- id : null,
- title : '',
- float : 'right',
- cls : 'icon-btn',
- icon : '',
- tooltip : '',
- onclick : null
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add event
- $(this.el).on('click', options.onclick);
-
- // add tooltip
- $(this.el).tooltip({title: options.tooltip, placement: 'bottom'});
- },
-
- // element
- _template: function(options) {
- // width
- var width = '';
- if (options.title) {
- width = 'width: auto;';
- }
-
- // string
- var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon ' + options.cls + '">';
-
- // title
- if (options.title) {
- str += '<div class="button">' +
- '<i class="icon fa ' + options.icon + '"/> ' +
- '<span class="title">' + options.title + '</span>' +
- '</div>';
- } else {
- str += '<i class="icon fa ' + options.icon + '"/>';
- }
- str += '</div>';
- return str;
- }
-});
-
-// plugin
-var Anchor = Backbone.View.extend({
- // options
- optionsDefault: {
- title : '',
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add event
- $(this.el).on('click', options.onclick);
- },
-
- // element
- _template: function(options) {
- return '<div><a href="javascript:void(0)" class="ui-anchor ' + options.cls + '">' + options.title + '</a></div>';
- }
-});
-
-// plugin
-var Message = Backbone.View.extend({
- // options
- optionsDefault: {
- message : '',
- status : 'info',
- persistent : false
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement('<div></div>');
- },
-
- // update
- update : function(options) {
- // get options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // show message
- if (options.message != '') {
- this.$el.html(this._template(this.options));
- this.$el.find('.alert').append(options.message);
- this.$el.fadeIn();
-
- // check if message is persistent
- if (!options.persistent) {
- // set timer
- var self = this;
- window.setTimeout(function() {
- if (self.$el.is(':visible')) {
- self.$el.fadeOut();
- } else {
- self.$el.hide();
- }
- }, 3000);
- }
- } else {
- this.$el.fadeOut();
- }
- },
-
- // element
- _template: function(options) {
- return '<div class="ui-message alert alert-' + options.status + '"/>';
- }
-});
-
-// plugin
-var Searchbox = Backbone.View.extend({
- // options
- optionsDefault: {
- onclick : null,
- searchword : ''
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // add click event
- var self = this;
- if (this.options.onclick) {
- this.$el.on('submit', function(e) {
- var search_field = self.$el.find('#search');
- self.options.onclick(search_field.val());
- });
- }
- },
-
- // element
- _template: function(options) {
- return '<div class="ui-search">' +
- '<form onsubmit="return false;">' +
- '<input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="' + options.searchword + '">' +
- '<button type="submit" class="btn search-btn">' +
- '<i class="fa fa-search"></i>' +
- '</button>' +
- '</form>' +
- '</div>';
- }
-});
-
-// plugin
-var Input = Backbone.View.extend({
- // options
- optionsDefault: {
- value : '',
- type : 'text',
- placeholder : '',
- disabled : false,
- visible : true,
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // disable input field
- if (this.options.disabled) {
- this.$el.prop('disabled', true);
- }
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.on('input', function() {
- if (self.options.onchange) {
- self.options.onchange(self.$el.val());
- }
- });
- },
-
- // value
- value : function (new_val) {
- if (new_val !== undefined) {
- this.$el.val(new_val);
- }
- return this.$el.val();
- },
-
- // element
- _template: function(options) {
- return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="ui-input ' + options.cls + '">';
- }
-});
-
-// plugin
-var Textarea = Backbone.View.extend({
- // options
- optionsDefault: {
- value : '',
- type : 'text',
- placeholder : '',
- disabled : false,
- visible : true,
- cls : ''
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // disable input field
- if (this.options.disabled) {
- this.$el.prop('disabled', true);
- }
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.on('input', function() {
- if (self.options.onchange) {
- self.options.onchange(self.$el.val());
- }
- });
- },
-
- // value
- value : function (new_val) {
- if (new_val !== undefined) {
- this.$el.val(new_val);
- }
- return this.$el.val();
- },
-
- // element
- _template: function(options) {
- return '<textarea id="' + options.id + '" class="ui-textarea ' + options.cls + '" rows="5"></textarea>';
- }
-});
-
-// 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 {
- Anchor : Anchor,
- Button : Button,
- ButtonIcon : ButtonIcon,
- ButtonMenu : ButtonMenu,
- Icon : Icon,
- Image : Image,
- Input : Input,
- Label : Label,
- Message : Message,
- Modal : Modal,
- RadioButton : RadioButton,
- Searchbox : Searchbox,
- Select : Select,
- Textarea : Textarea
-}
-});
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/views/editor.js
--- a/config/plugins/visualizations/charts/static/views/editor.js
+++ b/config/plugins/visualizations/charts/static/views/editor.js
@@ -1,5 +1,5 @@
// dependencies
-define(['mvc/ui/ui-tabs', 'plugin/library/ui', 'mvc/ui/ui-portlet', 'utils/utils',
+define(['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(Tabs, Ui, Portlet, Utils, Chart, Group, GroupView, SettingsView, TypesView) {
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -1,5 +1,5 @@
// dependencies
-define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
+define(['mvc/ui/ui-table', 'mvc/ui/ui-misc', 'utils/utils'],
function(Table, Ui, Utils) {
/**
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/views/settings.js
--- a/config/plugins/visualizations/charts/static/views/settings.js
+++ b/config/plugins/visualizations/charts/static/views/settings.js
@@ -1,5 +1,5 @@
// dependencies
-define(['plugin/library/ui', 'plugin/library/ui-table-form', 'utils/utils'],
+define(['mvc/ui/ui-misc', 'plugin/library/ui-table-form', 'utils/utils'],
function(Ui, TableForm, Utils) {
/**
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 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
@@ -1,5 +1,5 @@
// dependencies
-define(['utils/utils', 'plugin/library/ui'], function(Utils, Ui) {
+define(['utils/utils', 'mvc/ui/ui-misc'], function(Utils, Ui) {
/**
* This class renders the chart type selection grid.
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/views/viewer.js
--- a/config/plugins/visualizations/charts/static/views/viewer.js
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -1,5 +1,5 @@
// dependencies
-define(['utils/utils', 'plugin/library/ui', 'mvc/ui/ui-portlet',
+define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet',
'plugin/views/viewport', 'plugin/library/screenshot'],
function(Utils, Ui, Portlet, ViewportView, Screenshot) {
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -1,5 +1,5 @@
// dependencies
-define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'],
+define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils'],
function(Portlet, Ui, Utils) {
/**
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1061,6 +1061,7 @@
requires_setting_metadata = True
default_tool_action = DefaultToolAction
dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' )
+ default_template = 'tool_form.mako'
def __init__( self, config_file, root, app, guid=None, repository_id=None ):
"""Load a tool from the config named by `config_file`"""
@@ -2011,7 +2012,7 @@
return self.__no_display_interface_response()
if len(incoming):
self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {}, source=source )
- return "tool_form.mako", dict( errors={}, tool_state=state, param_values={}, incoming={} )
+ return self.default_template, dict( errors={}, tool_state=state, param_values={}, incoming={} )
all_errors = []
all_params = []
@@ -2029,7 +2030,7 @@
# error messages
if any( all_errors ):
error_message = "One or more errors were found in the input you provided. The specific errors are marked below."
- template = "tool_form.mako"
+ template = self.default_template
template_vars = dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message )
# If we've completed the last page we can execute the tool
elif all_pages or state.page == self.last_page:
@@ -2091,7 +2092,7 @@
# Just a refresh, render the form with updated state and errors.
if not self.display_interface:
return self.__no_display_interface_response()
- return 'tool_form.mako', dict( errors=errors, tool_state=state )
+ return self.default_template, dict( errors=errors, tool_state=state )
def __handle_page_advance( self, trans, state, errors ):
state.page += 1
@@ -2099,7 +2100,7 @@
self.fill_in_new_state( trans, self.inputs_by_page[ state.page ], state.inputs )
if not self.display_interface:
return self.__no_display_interface_response()
- return 'tool_form.mako', dict( errors=errors, tool_state=state )
+ return self.default_template, dict( errors=errors, tool_state=state )
def __no_display_interface_response( self ):
return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] )
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 static/scripts/mvc/tools/tools-form.js
--- /dev/null
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -0,0 +1,267 @@
+define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], function(Tools, Portlet, Table, Ui) {
+
+ // create tool model
+ var Model = Backbone.Model.extend({
+ initialize: function (options) {
+ this.url = galaxy_config.root + 'api/tools/' + options.id + '?io_details=true';
+ }
+ });
+
+ // create form view
+ var View = Backbone.View.extend({
+ // base element
+ body: 'body',
+
+ // initialize
+ initialize: function(options) {
+ // link this
+ var self = this;
+
+ // load tool model
+ this.model = new Model({
+ id : options.id
+ });
+
+ // fetch model and render form
+ this.model.fetch({
+ success: function() {
+ // create portlet
+ self.portlet = new Portlet.View({
+ icon : 'fa-wrench',
+ title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'),
+ buttons: {
+ execute: new Ui.ButtonIcon({
+ icon : 'fa-check',
+ tooltip : 'Execute the tool',
+ title : 'Execute',
+ float :'clear',
+ onclick : function() {
+ }
+ }),
+ }
+ });
+
+ // table
+ self.table = new Table.View();
+
+ // add message
+ self.message = new Ui.Message();
+ self.portlet.append(self.message.$el);
+
+ // append portlet
+ $(self.body).append(self.portlet.$el);
+ self.setElement(self.portlet.content());
+ self.portlet.append(self.table.$el);
+ self.render();
+ }
+ });
+ },
+
+ // update
+ render: function() {
+ // inputs
+ var settings = this.model.get('inputs');
+
+ // reset table
+ this.table.delAll();
+
+ // reset list
+ this.list = [];
+
+ // model
+ var data = new Backbone.Model();
+
+ // load settings elements into table
+ for (var id in settings) {
+ this._add(settings[id], data);
+ }
+
+ // trigger change
+ for (var id in this.list) {
+ this.list[id].trigger('change');
+ }
+ },
+
+ // add table row
+ _add: function(settings_def, data) {
+ // link this
+ var self = this;
+
+ // get id
+ var id = settings_def.name;
+
+ // log
+ console.debug(settings_def);
+
+ // field wrapper
+ var field = null;
+
+ // create select field
+ var type = settings_def.type;
+ switch(type) {
+ // text input field
+ case 'text' :
+ field = this.field_text(settings_def, data);
+ break;
+
+ // select field
+ case 'select' :
+ field = this.field_select(settings_def, data);
+ break;
+
+ // radiobox field
+ case 'radiobutton' :
+ field = this.field_radio(settings_def, data);
+ break;
+
+ // dataset
+ case 'data':
+ field = this.field_select(settings_def, data);
+ break;
+
+ // slider input field
+ case 'textarea' :
+ field = this.field_textarea(settings_def, data);
+ break;
+
+ // default
+ default:
+ field = new Ui.Input({
+ id : 'field-' + id,
+ placeholder : settings_def.placeholder,
+ type : settings_def.type,
+ onchange : function() {
+ data.set(id, field.value());
+ }
+ });
+ }
+
+ // set value
+ if (!data.get(id)) {
+ data.set(id, settings_def.value);
+ }
+ field.value(data.get(id));
+
+ // add list
+ this.list[id] = field;
+
+ // combine field and info
+ var $input = $('<div/>');
+ $input.append(field.$el);
+ if (settings_def.info) {
+ $input.append('<div class="ui-table-form-info">' + settings_def.info + '</div>');
+ }
+
+ // add row to table
+ if (this.options.style == 'bold') {
+ this.table.add(new Ui.Label({title: settings_def.title, cls: 'form-label'}).$el);
+ this.table.add($input);
+ } else {
+ this.table.add('<span class="ui-table-form-title">' + settings_def.label + '</span>', '25%');
+ this.table.add($input);
+ }
+
+ // add to table
+ this.table.append(id);
+
+ // show/hide
+ if (settings_def.hide) {
+ this.table.get(id).hide();
+ }
+ },
+
+ // text input field
+ field_text : function(settings_def, data) {
+ var id = settings_def.name;
+ return new Ui.Input({
+ id : 'field-' + id,
+ value : data.get(id),
+ onchange : function(value) {
+ data.set(id, value);
+ }
+ });
+ },
+
+ // text area
+ field_textarea : function(settings_def, data) {
+ var id = settings_def.name;
+ return new Ui.Textarea({
+ id : 'field-' + id,
+ onchange : function() {
+ data.set(id, field.value());
+ }
+ });
+ },
+
+ // select field
+ field_select : function (settings_def, data) {
+ // configure options fields
+ var options = [];
+ for (var i in settings_def.options) {
+ var option = settings_def.options[i];
+ options.push({
+ label: option[0],
+ value: option[1]
+ });
+ }
+
+ // select field
+ var id = settings_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();
+ }
+ }
+ }
+ });
+ },
+
+ // radio field
+ field_radio : function(settings_def, data) {
+ var id = settings_def.name;
+ return new Ui.RadioButton({
+ id : 'field-' + id,
+ data : settings_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();
+ }
+ }
+ }
+ });
+ }
+ });
+
+ return {
+ View: View
+ };
+});
diff -r 08580f127c031810c14c23e622700185ea582ccd -r 898a172941b10e435a6616c8cc04ccec6c7984d3 static/scripts/mvc/ui/ui-button-menu.js
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-button-menu.js
@@ -0,0 +1,169 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+/**
+ * This class creates a button with dropdown menu. It extends the functionality of the Ui.ButtonIcon class.
+ */
+return Backbone.View.extend({
+ // main options
+ optionsDefault: {
+ // same as Ui.ButtonIcon
+ id : '',
+ title : '',
+ float : 'right',
+ icon : null,
+ onclick : null,
+ cls : 'icon-btn',
+ tooltip : '',
+
+ // additional options
+ target : '',
+ href : '',
+ onunload : null,
+ visible : true,
+ tag : ''
+ },
+
+ // optional sub menu
+ $menu: null,
+
+ // initialize
+ initialize: function (options) {
+ // get options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // add template for tab
+ this.setElement($(this._template(this.options)));
+
+ // find root
+ var $root = $(this.el).find('.root');
+
+ // link head
+ var self = this;
+ $root.on('click', function(e) {
+ // hide all tooltips
+ $('.tooltip').hide();
+
+ // prevent default
+ e.preventDefault();
+
+ // add click event
+ if(self.options.onclick) {
+ self.options.onclick();
+ }
+ });
+
+ // visiblity
+ if (!this.options.visible)
+ this.hide();
+
+ // add tooltip
+ $root.tooltip({title: options.tooltip, placement: 'bottom'});
+ },
+
+ // show
+ show: function() {
+ $(this.el).show();
+ },
+
+ // hide
+ hide: function() {
+ $(this.el).hide();
+ },
+
+ // add menu item
+ addMenu: function (options) {
+ // menu option defaults
+ var menuOptions = {
+ title : '',
+ target : '',
+ href : '',
+ onclick : null,
+ divider : false,
+ icon : null,
+ cls : 'button-menu btn-group'
+ }
+
+ // get options
+ menuOptions = Utils.merge(options, menuOptions);
+
+ // check if submenu element is available
+ if (!this.$menu) {
+ // insert submenu element into root
+ $(this.el).append(this._templateMenu());
+
+ // update element link
+ this.$menu = $(this.el).find('.menu');
+ }
+
+ // create
+ var $item = $(this._templateMenuItem(menuOptions));
+
+ // add events
+ $item.on('click', function(e) {
+ // prevent default
+ e.preventDefault();
+
+ // add click event
+ if(menuOptions.onclick) {
+ menuOptions.onclick();
+ }
+ });
+
+ // append menu
+ this.$menu.append($item);
+
+ // append divider
+ if (menuOptions.divider)
+ this.$menu.append($(this._templateDivider()));
+ },
+
+ // fill template header
+ _templateMenuItem: function (options) {
+ var tmpl = '<li>' +
+ '<a href="' + options.href + '" target="' + options.target + '">';
+
+ if (options.icon)
+ tmpl += '<i class="fa ' + options.icon + '"></i>';
+
+ tmpl += ' ' + options.title +
+ '</a>' +
+ '</li>';
+ return tmpl;
+ },
+
+ // fill template header
+ _templateMenu: function () {
+ return '<ul class="menu dropdown-menu pull-right" role="menu"></ul>';
+ },
+
+ _templateDivider: function() {
+ return '<li class="divider"></li>';
+ },
+
+ // element
+ _template: function(options) {
+ // width
+ var width = '';
+ if (options.title) {
+ width = 'width: auto;';
+ }
+
+ // string
+ var str = '<div id="' + options.id + '" style="float: ' + options.float + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">';
+
+ // title
+ if (options.title) {
+ str += '<div class="root button dropdown-toggle" data-toggle="dropdown">' +
+ '<i class="icon fa ' + options.icon + '"/> ' +
+ '<span class="title">' + options.title + '</span>' +
+ '</div>';
+ } else {
+ str += '<i class="icon fa ' + options.icon + '"/>';
+ }
+ str += '</div>';
+ return str;
+ }
+});
+
+});
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Paired collection creator: better notifications, style tweaks
by commits-noreply＠bitbucket.org 13 Aug '14
by commits-noreply＠bitbucket.org 13 Aug '14
13 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/08580f127c03/
Changeset: 08580f127c03
User: carlfeberhard
Date: 2014-08-13 19:43:09
Summary: Paired collection creator: better notifications, style tweaks
Affected #: 6 files
diff -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 -r 08580f127c031810c14c23e622700185ea582ccd static/scripts/mvc/collection/paired-collection-creator.js
--- a/static/scripts/mvc/collection/paired-collection-creator.js
+++ b/static/scripts/mvc/collection/paired-collection-creator.js
@@ -1,7 +1,8 @@
define([
+ "utils/levenshtein",
"mvc/base-mvc",
"utils/localization"
-], function( baseMVC, _l ){
+], function( levelshteinDistance, baseMVC, _l ){
//=============================================================================
/** An interface for building collections of paired datasets.
*/
@@ -600,7 +601,10 @@
this.$( '.autopair-link' ).toggle( this.unpaired.length !== 0 );
if( this.unpaired.length === 0 ){
this._renderUnpairedEmpty();
+ //this.$( '.unpaired-columns .paired-column .column-datasets' )
+ // .append( this._renderUnpairedEmpty() );
//TODO: would be best to return here (the $columns)
+ return;
}
// create the dataset dom arrays
@@ -615,10 +619,15 @@
$fwd = split[0].map( function( dataset ){
return creator._renderUnpairedDataset( dataset );
});
+
+ if( !$fwd.length && !$rev.length ){
+ this._renderUnpairedNotShown();
+ return;
+ }
// add to appropo cols
//TODO: not the best way to render
this.$( '.unpaired-columns .column-datasets' ).empty();
- return this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd )
+ this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd )
.add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) )
.add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) );
},
@@ -652,6 +661,14 @@
this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg );
return $msg;
},
+ /** a message to display when no unpaired can be shown with the current filters */
+ _renderUnpairedNotShown : function(){
+ //console.debug( '-- renderUnpairedEmpty' );
+ var $msg = $( '<div class="empty-message"></div>' )
+ .text( '(' + _l( 'no datasets were found matching the current filters' ) + ')' );
+ this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg );
+ return $msg;
+ },
/** render the paired section and update counts of paired datasets */
_renderPaired : function( speed, callback ){
@@ -774,6 +791,7 @@
//TODO: ideally only re-render the columns (or even elements) involved
this._renderUnpaired();
this._renderPaired();
+ this.splitView();
});
this.on( 'filter-change', function(){
@@ -788,6 +806,19 @@
this.on( 'autopair', function(){
this._renderUnpaired();
this._renderPaired();
+
+ var message, msgClass = null;
+ if( this.paired.length ){
+ msgClass = 'alert-success';
+ message = this.paired.length + ' ' + _l( 'pairs created' );
+ if( !this.unpaired.length ){
+ message += ': ' + _l( 'all datasets have been successfully paired' );
+ this.hideUnpaired();
+ }
+ } else {
+ message = _l( 'Could not automatically create any pairs from the given dataset names' );
+ }
+ this._showAlert( message, msgClass );
});
//this.on( 'all', function(){
@@ -840,14 +871,12 @@
// ........................................................................ header
/** expand help */
_clickMoreHelp : function( ev ){
- this.$( '.main-help' ).css( 'max-height', 'none' );
- this.$( '.main-help .help-content p:first-child' ).css( 'white-space', 'normal' );
+ this.$( '.main-help' ).addClass( 'expanded' );
this.$( '.more-help' ).hide();
},
/** collapse help */
_clickLessHelp : function( ev ){
- this.$( '.main-help' ).css( 'max-height', '' );
- this.$( '.main-help .help-content p:first-child' ).css( 'white-space', '' );
+ this.$( '.main-help' ).removeClass( 'expanded' );
this.$( '.more-help' ).show();
},
@@ -1192,231 +1221,189 @@
//TODO: better way of localizing text-nodes in long strings
/** underscore template fns attached to class */
PairedCollectionCreator.templates = PairedCollectionCreator.templates || {
-/** the skeleton */
-main : _.template([
- '<div class="header flex-row no-flex"></div>',
- '<div class="middle flex-row flex-row-container"></div>',
- '<div class="footer flex-row no-flex">'
-].join('')),
-/** the header (not including help text) */
-header : _.template([
- '<div class="main-help well clear">',
- '<a class="more-help" href="javascript:void(0);">', _l( 'More help' ), '</a>',
- '<div class="help-content">',
- '<a class="less-help" href="javascript:void(0);">', _l( 'Less' ), '</a>',
+ /** the skeleton */
+ main : _.template([
+ '<div class="header flex-row no-flex"></div>',
+ '<div class="middle flex-row flex-row-container"></div>',
+ '<div class="footer flex-row no-flex">'
+ ].join('')),
+
+ /** the header (not including help text) */
+ header : _.template([
+ '<div class="main-help well clear">',
+ '<a class="more-help" href="javascript:void(0);">', _l( 'More help' ), '</a>',
+ '<div class="help-content">',
+ '<a class="less-help" href="javascript:void(0);">', _l( 'Less' ), '</a>',
+ '</div>',
'</div>',
- '</div>',
- '<div class="alert alert-dismissable">',
- '<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>',
- '<span class="alert-message"></span>',
- '</div>',
+ '<div class="alert alert-dismissable">',
+ '<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>',
+ '<span class="alert-message"></span>',
+ '</div>',
- '<div class="column-headers vertically-spaced flex-column-container">',
- '<div class="forward-column flex-column column">',
- '<div class="column-header">',
- '<div class="column-title">',
- '<span class="title">', _l( 'Unpaired forward' ), '</span>',
- '<span class="title-info unpaired-info"></span>',
- '</div>',
- '<div class="unpaired-filter forward-unpaired-filter pull-left">',
- '<input class="search-query" placeholder="', _l( 'Filter this list' ), '" />',
+ '<div class="column-headers vertically-spaced flex-column-container">',
+ '<div class="forward-column flex-column column">',
+ '<div class="column-header">',
+ '<div class="column-title">',
+ '<span class="title">', _l( 'Unpaired forward' ), '</span>',
+ '<span class="title-info unpaired-info"></span>',
+ '</div>',
+ '<div class="unpaired-filter forward-unpaired-filter pull-left">',
+ '<input class="search-query" placeholder="', _l( 'Filter this list' ), '" />',
+ '</div>',
'</div>',
'</div>',
+ '<div class="paired-column flex-column no-flex column">',
+ '<div class="column-header">',
+ '<a class="choose-filters-link" href="javascript:void(0)">',
+ _l( 'Choose filters' ),
+ '</a>',
+ '<a class="clear-filters-link" href="javascript:void(0);">',
+ _l( 'Clear filters' ),
+ '</a><br />',
+ '<a class="autopair-link" href="javascript:void(0);">',
+ _l( 'Auto-pair' ),
+ '</a>',
+ '</div>',
+ '</div>',
+ '<div class="reverse-column flex-column column">',
+ '<div class="column-header">',
+ '<div class="column-title">',
+ '<span class="title">', _l( 'Unpaired reverse' ), '</span>',
+ '<span class="title-info unpaired-info"></span>',
+ '</div>',
+ '<div class="unpaired-filter reverse-unpaired-filter pull-left">',
+ '<input class="search-query" placeholder="', _l( 'Filter this list' ), '" />',
+ '</div>',
+ '</div>',
+ '</div>',
+ '</div>'
+ ].join('')),
+
+ /** the middle: unpaired, divider, and paired */
+ middle : _.template([
+ // contains two flex rows (rows that fill available space) and a divider btwn
+ '<div class="unpaired-columns flex-column-container scroll-container flex-row">',
+ '<div class="forward-column flex-column column">',
+ '<ol class="column-datasets"></ol>',
+ '</div>',
+ '<div class="paired-column flex-column no-flex column">',
+ '<ol class="column-datasets"></ol>',
+ '</div>',
+ '<div class="reverse-column flex-column column">',
+ '<ol class="column-datasets"></ol>',
+ '</div>',
'</div>',
- '<div class="paired-column flex-column no-flex column">',
+ '<div class="flexible-partition">',
+ '<div class="flexible-partition-drag"></div>',
'<div class="column-header">',
- '<a class="choose-filters-link" href="javascript:void(0)">',
- _l( 'Choose filters' ),
- '</a>',
- '<a class="clear-filters-link" href="javascript:void(0);">',
- _l( 'Clear filters' ),
- '</a><br />',
- '<a class="autopair-link" href="javascript:void(0);">',
- _l( 'Auto-pair' ),
+ '<div class="column-title paired-column-title">',
+ '<span class="title"></span>',
+ '</div>',
+ '<a class="unpair-all-link" href="javascript:void(0);">',
+ _l( 'Unpair all' ),
'</a>',
'</div>',
'</div>',
- '<div class="reverse-column flex-column column">',
- '<div class="column-header">',
- '<div class="column-title">',
- '<span class="title">', _l( 'Unpaired reverse' ), '</span>',
- '<span class="title-info unpaired-info"></span>',
- '</div>',
- '<div class="unpaired-filter reverse-unpaired-filter pull-left">',
- '<input class="search-query" placeholder="', _l( 'Filter this list' ), '" />',
+ '<div class="paired-columns flex-column-container scroll-container flex-row">',
+ '<div class="forward-column flex-column column">',
+ '<ol class="column-datasets"></ol>',
+ '</div>',
+ '<div class="paired-column flex-column no-flex column">',
+ '<ol class="column-datasets"></ol>',
+ '</div>',
+ '<div class="reverse-column flex-column column">',
+ '<ol class="column-datasets"></ol>',
+ '</div>',
+ '</div>'
+ ].join('')),
+
+ /** creation and cancel controls */
+ footer : _.template([
+ '<div class="attributes clear">',
+ '<input class="collection-name form-control pull-right" ',
+ 'placeholder="', _l( 'Enter a name for your new list' ), '" />',
+ '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>',
+ '</div>',
+
+ '<div class="actions clear vertically-spaced">',
+ '<div class="other-options pull-left">',
+ '<button class="cancel-create btn" tabindex="-1">', _l( 'Cancel' ), '</button>',
+ '<div class="create-other btn-group dropup">',
+ '<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',
+ _l( 'Create a different kind of collection' ),
+ ' <span class="caret"></span>',
+ '</button>',
+ '<ul class="dropdown-menu" role="menu">',
+ '<li><a href="#">', _l( 'Create a <i>single</i> pair' ), '</a></li>',
+ '<li><a href="#">', _l( 'Create a list of <i>unpaired</i> datasets' ), '</a></li>',
+ '</ul>',
'</div>',
'</div>',
- '</div>',
- '</div>'
-].join('')),
-/** the middle: unpaired, divider, and paired */
-middle : _.template([
- // contains two flex rows (rows that fill available space) and a divider btwn
- '<div class="unpaired-columns flex-column-container scroll-container flex-row">',
- '<div class="forward-column flex-column column">',
- '<ol class="column-datasets"></ol>',
- '</div>',
- '<div class="paired-column flex-column no-flex column">',
- '<ol class="column-datasets"></ol>',
- '</div>',
- '<div class="reverse-column flex-column column">',
- '<ol class="column-datasets"></ol>',
- '</div>',
- '</div>',
- '<div class="flexible-partition">',
- '<div class="flexible-partition-drag"></div>',
- '<div class="column-header">',
- '<div class="column-title paired-column-title">',
- '<span class="title"></span>',
+ '<div class="main-options pull-right">',
+ '<button class="create-collection btn btn-primary">', _l( 'Create list' ), '</button>',
'</div>',
- '<a class="unpair-all-link" href="javascript:void(0);">',
- _l( 'Unpair all' ),
- '</a>',
- '</div>',
- '</div>',
- '<div class="paired-columns flex-column-container scroll-container flex-row">',
- '<div class="forward-column flex-column column">',
- '<ol class="column-datasets"></ol>',
- '</div>',
- '<div class="paired-column flex-column no-flex column">',
- '<ol class="column-datasets"></ol>',
- '</div>',
- '<div class="reverse-column flex-column column">',
- '<ol class="column-datasets"></ol>',
- '</div>',
- '</div>'
-].join('')),
+ '</div>'
+ ].join('')),
-/** creation and cancel controls */
-footer : _.template([
- '<div class="attributes clear">',
- '<input class="collection-name form-control pull-right" ',
- 'placeholder="', _l( 'Enter a name for your new list' ), '" />',
- '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>',
- '</div>',
-
- '<div class="actions clear vertically-spaced">',
- '<div class="other-options pull-left">',
- '<button class="cancel-create btn" tabindex="-1">', _l( 'Cancel' ), '</button>',
- '<div class="create-other btn-group dropup">',
- '<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',
- _l( 'Create a different kind of collection' ),
- ' <span class="caret"></span>',
- '</button>',
- '<ul class="dropdown-menu" role="menu">',
- '<li><a href="#">', _l( 'Create a <i>single</i> pair' ), '</a></li>',
- '<li><a href="#">', _l( 'Create a list of <i>unpaired</i> datasets' ), '</a></li>',
- '</ul>',
- '</div>',
- '</div>',
-
- '<div class="main-options pull-right">',
- '<button class="create-collection btn btn-primary">', _l( 'Create list' ), '</button>',
- '</div>',
- '</div>'
-].join('')),
-
-/** help content */
-helpContent : _.template([
- '<p>', _l([
- 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse ',
- 'reads) that can be passed to tools and workflows in order to have analyses done on the entire ',
- 'group. This interface allows you to create a collection, choose which datasets are paired, ',
- 'and re-order the final collection.'
- ].join( '' )), '</p>',
- '<p>', _l([
- 'Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',
- '(hover over the underlined words to highlight below). ',
- 'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',
- '<ul>To pair datasets, you can:',
- '<li>Click a dataset in the ',
- '<i data-target=".unpaired-columns .forward-column .column-datasets,',
- '.unpaired-columns .forward-column">forward column</i> ',
- 'to select it then click a dataset in the ',
- '<i data-target=".unpaired-columns .reverse-column .column-datasets,',
- '.unpaired-columns .reverse-column">reverse column</i>.',
- '</li>',
- '<li>Click one of the "Pair these datasets" buttons in the ',
- '<i data-target=".unpaired-columns .paired-column .column-datasets,',
- '.unpaired-columns .paired-column">middle column</i> ',
- 'to pair the datasets in a particular row.',
- '</li>',
- '<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',
- 'to have your datasets automatically paired based on name.',
- '</li>',
- '</ul>'
- ].join( '' )), '</p>',
- '<p>', _l([
- '<ul>You can filter what is shown in the unpaired sections by:',
- '<li>Entering partial dataset names in either the ',
- '<i data-target=".forward-unpaired-filter input">forward filter</i> or ',
- '<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',
- '</li>',
- '<li>Choosing from a list of preset filters by clicking the ',
- '<i data-target=".choose-filters-link">"Choose filters" link</i>.',
- '</li>',
- '<li>Clearing the filters by clicking the ',
- '<i data-target=".clear-filters-link">"Clear filters" link</i>.',
- '</li>',
- '</ul>'
- ].join( '' )), '</p>',
- '<p>', _l([
- 'To unpair individual dataset pairs, click the ',
- '<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ',
- 'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'
- ].join( '' )), '</p>',
- '<p>', _l([
- 'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ',
- 'click <i data-target=".create-collection">"Create list"</i>.',
- '(Note: you do not have to pair all unpaired datasets to finish.)'
- ].join( '' )), '</p>'
-].join(''))
-}
-
-//=============================================================================
-//TODO: to own file
-/*
-(Imported for edit distance algorith. From: https://gist.github.com/andrei-m/982927)
-Copyright (c) 2011 Andrei Mackenzie
-*/
-// Compute the edit distance between the two given strings
-//exports.getEditDistance = function(a, b){
-function levenshteinDistance(a, b){
- if(a.length === 0){ return b.length; }
- if(b.length === 0){ return a.length; }
-
- var matrix = [];
-
- // increment along the first column of each row
- var i;
- for(i = 0; i <= b.length; i++){
- matrix[i] = [i];
- }
-
- // increment each column in the first row
- var j;
- for(j = 0; j <= a.length; j++){
- matrix[0][j] = j;
- }
-
- // Fill in the rest of the matrix
- for(i = 1; i <= b.length; i++){
- for(j = 1; j <= a.length; j++){
- if(b.charAt(i-1) === a.charAt(j-1)){
- matrix[i][j] = matrix[i-1][j-1];
- } else {
- matrix[i][j] = Math.min(matrix[i-1][j-1] + 1, // substitution
- Math.min(matrix[i][j-1] + 1, // insertion
- matrix[i-1][j] + 1)); // deletion
- }
- }
- }
-
- //console.debug( '\t\t levenshteinDistance', a, b, matrix[b.length][a.length] );
- return matrix[b.length][a.length];
-}
+ /** help content */
+ helpContent : _.template([
+ '<p>', _l([
+ 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ',
+ 'These collections can be passed to tools and workflows in order to have analyses done each member of ',
+ 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ',
+ 'and re-order the final collection.'
+ ].join( '' )), '</p>',
+ '<p>', _l([
+ 'Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',
+ '(hover over the underlined words to highlight below). ',
+ 'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',
+ '<ul>To pair datasets, you can:',
+ '<li>Click a dataset in the ',
+ '<i data-target=".unpaired-columns .forward-column .column-datasets,',
+ '.unpaired-columns .forward-column">forward column</i> ',
+ 'to select it then click a dataset in the ',
+ '<i data-target=".unpaired-columns .reverse-column .column-datasets,',
+ '.unpaired-columns .reverse-column">reverse column</i>.',
+ '</li>',
+ '<li>Click one of the "Pair these datasets" buttons in the ',
+ '<i data-target=".unpaired-columns .paired-column .column-datasets,',
+ '.unpaired-columns .paired-column">middle column</i> ',
+ 'to pair the datasets in a particular row.',
+ '</li>',
+ '<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',
+ 'to have your datasets automatically paired based on name.',
+ '</li>',
+ '</ul>'
+ ].join( '' )), '</p>',
+ '<p>', _l([
+ '<ul>You can filter what is shown in the unpaired sections by:',
+ '<li>Entering partial dataset names in either the ',
+ '<i data-target=".forward-unpaired-filter input">forward filter</i> or ',
+ '<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',
+ '</li>',
+ '<li>Choosing from a list of preset filters by clicking the ',
+ '<i data-target=".choose-filters-link">"Choose filters" link</i>.',
+ '</li>',
+ '<li>Clearing the filters by clicking the ',
+ '<i data-target=".clear-filters-link">"Clear filters" link</i>.',
+ '</li>',
+ '</ul>'
+ ].join( '' )), '</p>',
+ '<p>', _l([
+ 'To unpair individual dataset pairs, click the ',
+ '<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ',
+ 'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'
+ ].join( '' )), '</p>',
+ '<p>', _l([
+ 'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ',
+ 'click <i data-target=".create-collection">"Create list"</i>. ',
+ '(Note: you do not have to pair all unpaired datasets to finish.)'
+ ].join( '' )), '</p>'
+ ].join(''))
+};
//=============================================================================
@@ -1451,7 +1438,6 @@
//=============================================================================
-//TODO: to own file
/** a modal version of the paired collection creator */
var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){
options = _.defaults( options || {}, {
@@ -1476,6 +1462,7 @@
closing_events: true
});
//TODO: remove modal header
+ window.PCC = creator;
return creator;
};
diff -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 -r 08580f127c031810c14c23e622700185ea582ccd static/scripts/packed/mvc/collection/paired-collection-creator.js
--- a/static/scripts/packed/mvc/collection/paired-collection-creator.js
+++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js
@@ -1,1 +1,1 @@
-define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(g){return g.name.indexOf(this.filters[0])>=0},_filterRevFn:function(g){return g.name.indexOf(this.filters[1])>=0},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=d(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",data:JSON.stringify(g)}).fail(function(m,j,l){console.error(m,j,l);var k=e("An error occurred while creating this collection");if(m){if(m.readyState===0&&m.status===0){k+=": "+e("Galaxy could not be reached and may be updating.")+e(" Try again in a few minutes.")}else{if(m.responseJSON){k+="<br /><pre>"+JSON.stringify(m.responseJSON)+"</pre>"}else{k+=": "+l}}}i._showAlert(k,"alert-danger")}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},render:function(g,h){this.$el.empty().html(f.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(f.templates.header()).find(".help-content").prepend($(f.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(f.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,e("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,e("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty()}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});this.$(".unpaired-columns .column-datasets").empty();return this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",e("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset unpaired").attr("draggable",true).addClass(g.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(g.name)).data("dataset",g)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(e("Pair these datasets")))},_renderUnpairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+e("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderPaired:function(j,k){var i=[],g=[],h=[];this.$(".paired-column-title .title").text([this.paired.length,e("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",e("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+e("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(f.templates.footer());if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',e("Forward"),": ",k,", ",e("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',e("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return this.$(g).popover({container:".collection-creator",placement:"bottom",html:true,content:i})},_validationWarning:function(h,g){var i="validation-warning";if(h==="name"){h=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(g){h=h||this.$("."+i);h.removeClass(i)}else{h.addClass(i)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(g){this._renderUnpaired();this._renderPaired()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired()});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .paired-column .dataset-name":"_clickPairName","click .unpair-btn":"_clickUnpair","mouseover .dataset.paired":"_hoverPaired","mouseout .dataset.paired":"_hoverOutPaired","change .collection-name":"_changeName","click .cancel-create":function(g){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(g){this.$(".main-help").css("max-height","none");this.$(".main-help .help-content p:first-child").css("white-space","normal");this.$(".more-help").hide()},_clickLessHelp:function(g){this.$(".main-help").css("max-height","");this.$(".main-help .help-content p:first-child").css("white-space","");this.$(".more-help").show()},_showAlert:function(h,g){g=g||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(g).show().find(".alert-message").html(h)},_hideAlert:function(g){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(g){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(g){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(g,h){g=g||0;this.$(".unpaired-columns").hide(g,h);this.$(".paired-columns").show(g).css("flex","1 0 auto");this.unpairedPanelHidden=true},hidePaired:function(g,h){g=g||0;this.$(".unpaired-columns").show(g).css("flex","1 0 auto");this.$(".paired-columns").hide(g,h);this.pairedPanelHidden=true},splitView:function(g,h){g=g||0;this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(g);return this},_clickUnpairAll:function(g){this.unpairAll()},_clickAutopair:function(h){var g=this.autoPair();this.trigger("autopair",g)},_clickFilterChoice:function(h){var g=$(h.currentTarget);this.$(".forward-unpaired-filter input").val(g.data("forward"));this.$(".reverse-unpaired-filter input").val(g.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(g){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(g){g.stopPropagation();return this.toggleSelectUnpaired($(g.currentTarget))},toggleSelectUnpaired:function(i,h){h=h||{};var j=i.data("dataset"),g=h.force!==undefined?h.force:!i.hasClass("selected");if(!i.size()||j===undefined){return i}if(g){i.addClass("selected");if(!h.waitToPair){this.pairAllSelected()}}else{i.removeClass("selected")}return i},pairAllSelected:function(h){h=h||{};var i=this,j=[],g=[],k=[];i.$(".unpaired-columns .forward-column .dataset.selected").each(function(){j.push($(this).data("dataset"))});i.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){g.push($(this).data("dataset"))});j.length=g.length=Math.min(j.length,g.length);j.forEach(function(m,l){try{k.push(i._pair(m,g[l],{silent:true}))}catch(n){console.error(n)}});if(k.length&&!h.silent){this.trigger("pair:new",k)}return k},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_clickPairRow:function(i){var j=$(i.currentTarget).index(),h=$(".unpaired-columns .forward-column .dataset").eq(j).data("dataset"),g=$(".unpaired-columns .reverse-column .dataset").eq(j).data("dataset");this._pair(h,g)},_startPartitionDrag:function(h){var g=this,k=h.pageY;$("body").css("cursor","ns-resize");g.$(".flexible-partition-drag").css("color","black");function j(l){g.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",i)}function i(l){var m=l.pageY-k;if(!g.adjPartition(m)){$("body").trigger("mouseup")}k+=m}$("body").mousemove(i);$("body").one("mouseup",j)},adjPartition:function(h){var g=this.$(".unpaired-columns"),i=this.$(".paired-columns"),j=parseInt(g.css("height"),10),k=parseInt(i.css("height"),10);j=Math.max(10,j+h);k=k-h;if(j<=10){this.hideUnpaired();return false}else{if(!g.is("visible")){g.show()}}if(k<=15){this.hidePaired();if(k<10){return false}}else{if(!i.is("visible")){i.show()}}g.css({height:j+"px",flex:"0 0 auto"});return true},_clickPairName:function(i){var h=$(i.currentTarget),j=this.paired[h.parent().index()],g=prompt("Enter a new name for the pair:",j.name);if(g){j.name=g;h.text(j.name)}},_clickUnpair:function(h){var g=Math.floor($(h.currentTarget).index()/2);this._unpair(this.paired[g])},_hoverPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.emphasizePair(h)},_hoverOutPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.deemphasizePair(h)},emphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).addClass("emphasized")},deemphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).removeClass("emphasized")},_changeName:function(g){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(h){var g=this._getName();if(!g){this._validationWarning("name")}else{this.createList()}},_printList:function(h){var g=this;_.each(h,function(i){if(h===g.paired){g._printPair(i)}else{}})},_printPair:function(g){console.debug(g.forward.name,g.reverse.name,": ->",g.name)},toString:function(){return"PairedCollectionCreator"}});f.templates=f.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',e("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',e("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div 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\ No newline at end of file
+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return 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m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=levenshteinDistance(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",data:JSON.stringify(g)}).fail(function(m,j,l){console.error(m,j,l);var k=d("An error occurred while creating this collection");if(m){if(m.readyState===0&&m.status===0){k+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(m.responseJSON){k+="<br /><pre>"+JSON.stringify(m.responseJSON)+"</pre>"}else{k+=": "+l}}}i._showAlert(k,"alert-danger")}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});if(!k.length&&!h.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .column-datasets").empty();this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset 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"));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",d("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(e.templates.footer());if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',d("Forward"),": ",k,", ",d("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return 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have been successfully paired");this.hideUnpaired()}}else{g=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(g,h)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .paired-column .dataset-name":"_clickPairName","click .unpair-btn":"_clickUnpair","mouseover .dataset.paired":"_hoverPaired","mouseout .dataset.paired":"_hoverOutPaired","change .collection-name":"_changeName","click .cancel-create":function(g){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(g){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(g){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(h,g){g=g||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(g).show().find(".alert-message").html(h)},_hideAlert:function(g){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(g){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(g){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(g,h){g=g||0;this.$(".unpaired-columns").hide(g,h);this.$(".paired-columns").show(g).css("flex","1 0 auto");this.unpairedPanelHidden=true},hidePaired:function(g,h){g=g||0;this.$(".unpaired-columns").show(g).css("flex","1 0 auto");this.$(".paired-columns").hide(g,h);this.pairedPanelHidden=true},splitView:function(g,h){g=g||0;this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(g);return this},_clickUnpairAll:function(g){this.unpairAll()},_clickAutopair:function(h){var g=this.autoPair();this.trigger("autopair",g)},_clickFilterChoice:function(h){var g=$(h.currentTarget);this.$(".forward-unpaired-filter input").val(g.data("forward"));this.$(".reverse-unpaired-filter input").val(g.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(g){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(g){g.stopPropagation();return this.toggleSelectUnpaired($(g.currentTarget))},toggleSelectUnpaired:function(i,h){h=h||{};var j=i.data("dataset"),g=h.force!==undefined?h.force:!i.hasClass("selected");if(!i.size()||j===undefined){return i}if(g){i.addClass("selected");if(!h.waitToPair){this.pairAllSelected()}}else{i.removeClass("selected")}return i},pairAllSelected:function(h){h=h||{};var i=this,j=[],g=[],k=[];i.$(".unpaired-columns .forward-column .dataset.selected").each(function(){j.push($(this).data("dataset"))});i.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){g.push($(this).data("dataset"))});j.length=g.length=Math.min(j.length,g.length);j.forEach(function(m,l){try{k.push(i._pair(m,g[l],{silent:true}))}catch(n){console.error(n)}});if(k.length&&!h.silent){this.trigger("pair:new",k)}return k},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_clickPairRow:function(i){var j=$(i.currentTarget).index(),h=$(".unpaired-columns .forward-column .dataset").eq(j).data("dataset"),g=$(".unpaired-columns .reverse-column .dataset").eq(j).data("dataset");this._pair(h,g)},_startPartitionDrag:function(h){var g=this,k=h.pageY;$("body").css("cursor","ns-resize");g.$(".flexible-partition-drag").css("color","black");function j(l){g.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",i)}function i(l){var m=l.pageY-k;if(!g.adjPartition(m)){$("body").trigger("mouseup")}k+=m}$("body").mousemove(i);$("body").one("mouseup",j)},adjPartition:function(h){var g=this.$(".unpaired-columns"),i=this.$(".paired-columns"),j=parseInt(g.css("height"),10),k=parseInt(i.css("height"),10);j=Math.max(10,j+h);k=k-h;if(j<=10){this.hideUnpaired();return false}else{if(!g.is("visible")){g.show()}}if(k<=15){this.hidePaired();if(k<10){return false}}else{if(!i.is("visible")){i.show()}}g.css({height:j+"px",flex:"0 0 auto"});return true},_clickPairName:function(i){var h=$(i.currentTarget),j=this.paired[h.parent().index()],g=prompt("Enter a new name for the pair:",j.name);if(g){j.name=g;h.text(j.name)}},_clickUnpair:function(h){var g=Math.floor($(h.currentTarget).index()/2);this._unpair(this.paired[g])},_hoverPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.emphasizePair(h)},_hoverOutPaired:function(i){var g=$(i.currentTarget),h=g.index();if(g.parents(".reverse-column").size()){h=Math.floor(h/2)}this.deemphasizePair(h)},emphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).addClass("emphasized")},deemphasizePair:function(g){this.$(".paired-columns .forward-column .dataset.paired").eq(g).add(this.$(".paired-columns .paired-column .dataset.paired").eq(g)).add(this.$(".paired-columns .reverse-column .dataset.paired").eq(g)).removeClass("emphasized")},_changeName:function(g){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(h){var g=this._getName();if(!g){this._validationWarning("name")}else{this.createList()}},_printList:function(h){var g=this;_.each(h,function(i){if(h===g.paired){g._printPair(i)}else{}})},_printPair:function(g){console.debug(g.forward.name,g.reverse.name,": ->",g.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',d("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>"].join("")),footer:_.template(['<div class="attributes clear">','<input class="collection-name form-control pull-right" ','placeholder="',d("Enter a name for your new list"),'" />','<div class="collection-name-prompt pull-right">',d("Name"),":</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',d("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',d("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',d("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',d("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',d("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new e(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});window.PCC=h;return h};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}});
\ No newline at end of file
diff -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 -r 08580f127c031810c14c23e622700185ea582ccd static/scripts/packed/utils/levenshtein.js
--- /dev/null
+++ b/static/scripts/packed/utils/levenshtein.js
@@ -0,0 +1,1 @@
+define([],function(){function a(d,c){if(d.length===0){return c.length}if(c.length===0){return d.length}var e=[];var g;for(g=0;g<=c.length;g++){e[g]=[g]}var f;for(f=0;f<=d.length;f++){e[0][f]=f}for(g=1;g<=c.length;g++){for(f=1;f<=d.length;f++){if(c.charAt(g-1)===d.charAt(f-1)){e[g][f]=e[g-1][f-1]}else{e[g][f]=Math.min(e[g-1][f-1]+1,Math.min(e[g][f-1]+1,e[g-1][f]+1))}}}return e[c.length][d.length]}return a});
\ No newline at end of file
diff -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 -r 08580f127c031810c14c23e622700185ea582ccd static/scripts/utils/levenshtein.js
--- /dev/null
+++ b/static/scripts/utils/levenshtein.js
@@ -0,0 +1,60 @@
+define([
+], function(){
+//=============================================================================
+/**
+(Imported for edit distance algorith. From: https://gist.github.com/andrei-m/982927)
+Copyright (c) 2011 Andrei Mackenzie
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
+rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
+persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
+Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+// Compute the edit distance between the two given strings
+//exports.getEditDistance = function(a, b){
+function levenshteinDistance(a, b){
+ if(a.length === 0){ return b.length; }
+ if(b.length === 0){ return a.length; }
+
+ var matrix = [];
+
+ // increment along the first column of each row
+ var i;
+ for(i = 0; i <= b.length; i++){
+ matrix[i] = [i];
+ }
+
+ // increment each column in the first row
+ var j;
+ for(j = 0; j <= a.length; j++){
+ matrix[0][j] = j;
+ }
+
+ // Fill in the rest of the matrix
+ for(i = 1; i <= b.length; i++){
+ for(j = 1; j <= a.length; j++){
+ if(b.charAt(i-1) === a.charAt(j-1)){
+ matrix[i][j] = matrix[i-1][j-1];
+ } else {
+ matrix[i][j] = Math.min(matrix[i-1][j-1] + 1, // substitution
+ Math.min(matrix[i][j-1] + 1, // insertion
+ matrix[i-1][j] + 1)); // deletion
+ }
+ }
+ }
+
+ //console.debug( '\t\t levenshteinDistance', a, b, matrix[b.length][a.length] );
+ return matrix[b.length][a.length];
+}
+
+//=============================================================================
+ return levenshteinDistance;
+});
diff -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 -r 08580f127c031810c14c23e622700185ea582ccd static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1821,9 +1821,11 @@
.collection-creator .column-title .title{font-weight:bold}
.collection-creator .column-title .title-info{color:grey}.collection-creator .column-title .title-info:before{content:' - '}
.collection-creator .paired-column{text-align:center;width:22%}
-.collection-creator .header{padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal}
+.collection-creator .header{padding-bottom:8px}.collection-creator .header .main-help{margin-bottom:17px;overflow:hidden;padding:15px;background:#f8f8f8}.collection-creator .header .main-help:not(.expanded){max-height:49px}.collection-creator .header .main-help:not(.expanded) .help-content p:first-child{overflow:hidden;white-space:nowrap;text-overflow:ellipsis}
+.collection-creator .header .main-help:not(.expanded) .help-content>*:not(:first-child){display:none}
+.collection-creator .header .main-help.expanded{max-height:none}
+.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal}
.collection-creator .header .main-help .help-content ul,.collection-creator .header .main-help .help-content li{list-style:circle;margin-left:16px}
-.collection-creator .header .main-help .help-content p:first-child{overflow:hidden;white-space:nowrap;text-overflow:ellipsis}
.collection-creator .header .main-help .help-content .less-help{display:inline-block;width:100%;text-align:right}
.collection-creator .header .main-help .more-help{float:right}
.collection-creator .header .column-headers .column-header .unpaired-filter{width:100%}.collection-creator .header .column-headers .column-header .unpaired-filter .search-query{width:100%;height:22px}
diff -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 -r 08580f127c031810c14c23e622700185ea582ccd static/style/src/less/ui/paired-collection-creator.less
--- a/static/style/src/less/ui/paired-collection-creator.less
+++ b/static/style/src/less/ui/paired-collection-creator.less
@@ -142,11 +142,29 @@
padding-bottom: 8px;
.main-help {
- max-height: 36px;
- margin-bottom: 16px;
+ margin-bottom: 17px;
overflow: hidden;
- padding: 8px;
+ padding: 15px;
background: #f8f8f8;
+
+ &:not(.expanded) {
+ // chosen to match alert - dependent on line height and .alert padding
+ max-height: 49px;
+ .help-content {
+ p:first-child {
+ overflow: hidden;
+ white-space: nowrap;
+ text-overflow: ellipsis;
+ }
+ > *:not(:first-child) {
+ display: none;
+ }
+ }
+ }
+ &.expanded {
+ max-height: none;
+ }
+
.help-content {
i {
cursor: help;
@@ -160,18 +178,13 @@
list-style: circle;
margin-left: 16px;
}
- p:first-child {
- overflow: hidden;
- white-space: nowrap;
- text-overflow: ellipsis;
- }
.less-help {
display: inline-block;
width: 100%;
text-align: right;
}
}
- .more-help {
+ .more-help {
//display: inline-block;
float: right;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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commit/galaxy-central: jmchilton: PEP-8 fixes for repair_repository_manager.py...
by commits-noreply＠bitbucket.org 13 Aug '14
by commits-noreply＠bitbucket.org 13 Aug '14
13 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3e7e8a3f1b70/
Changeset: 3e7e8a3f1b70
User: jmchilton
Date: 2014-08-13 17:17:29
Summary: PEP-8 fixes for repair_repository_manager.py...
... 'cause I promised @dannon.
Affected #: 1 file
diff -r 724f9ab6ba158b580b20e12545f3337144e7e886 -r 3e7e8a3f1b7085a6a1b6beea0ca40260fa7287d7 lib/tool_shed/galaxy_install/repair_repository_manager.py
--- a/lib/tool_shed/galaxy_install/repair_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py
@@ -1,4 +1,3 @@
-import os
import tempfile
import logging
@@ -109,7 +108,7 @@
tool_panel_section_dict = metadata.get( 'tool_panel_section', None )
if tool_panel_section_dict:
# The repository must be in the uninstalled state. The structure of tool_panel_section_dict is:
- # {<tool guid> :
+ # {<tool guid> :
# [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]}
# Here is an example:
# {"localhost:9009/repos/test/filter/Filter1/1.1.0":
@@ -160,7 +159,7 @@
except Exception, e:
error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) )
log.debug( error_message )
- repair_dict [ repository.name ] = error_message
+ repair_dict[ repository.name ] = error_message
elif repository.status not in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED ]:
shed_tool_conf, tool_path, relative_install_dir = \
suc.get_tool_panel_config_tool_path_install_dir( self.app, repository )
@@ -223,4 +222,4 @@
basic_util.remove_dir( work_dir )
irm.update_tool_shed_repository_status( repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLED )
- return repair_dict
\ No newline at end of file
+ return repair_dict
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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13 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/724f9ab6ba15/
Changeset: 724f9ab6ba15
User: jmchilton
Date: 2014-08-13 17:14:34
Summary: Merge latest stable.
Affected #: 7 files
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -8,7 +8,7 @@
5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14
7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02
-8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02
+7a4d321c0e38fa263ea83d29a35a608c3181fcba latest_2014.06.02
9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14
6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13
3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08
@@ -17,3 +17,5 @@
9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
+ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
+7e4d21621ce12e13ebbdf9fd3259df58c3ef124c latest_2014.08.11
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 lib/galaxy/webapps/galaxy/api/datasets.py
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -199,12 +199,12 @@
if isinstance( data_provider, (SamDataProvider, BamDataProvider ) ):
# Get reference sequence.
if dataset.dbkey:
- # FIXME: increase region 500bp each way to provide sequence for overlapping reads. As reads
- # get longer, this will need to be increased and/or a handle to the genomic data may be need
- # to be given to the data provider.
+ # FIXME: increase region 1M each way to provide sequence for
+ # spliced/gapped reads. Probably should provide refseq object
+ # directly to data provider.
region = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom,
- low=( max( 0, int( low ) - 500 ) ),
- high=( int( high ) + 500 ) )
+ low=( max( 0, int( low ) - 1000000 ) ),
+ high=( int( high ) + 1000000 ) )
# Get mean depth.
if not indexer:
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 lib/tool_shed/galaxy_install/repair_repository_manager.py
--- a/lib/tool_shed/galaxy_install/repair_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py
@@ -1,5 +1,6 @@
+import os
+import tempfile
import logging
-import os
log = logging.getLogger( __name__ )
@@ -7,6 +8,8 @@
from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
from tool_shed.galaxy_install.tools import tool_panel_manager
+from tool_shed.util import hg_util
+from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import shed_util_common as suc
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 static/scripts/packed/viz/trackster/painters.js
--- a/static/scripts/packed/viz/trackster/painters.js
+++ b/static/scripts/packed/viz/trackster/painters.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
+define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,rect_y+(draw_height-1)/2,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,draw_height=(mode==="Pack"?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;var line_height=y_start+1+(draw_height-1)/2;dashedLine(ctx,b1_end,line_height,b2_start,line_height)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=Math.floor((ac-ae.low)/af*ah);ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -907,7 +907,7 @@
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
- ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1);
+ ctx.fillRect(s_start, rect_y + (draw_height - 1)/2, s_end - s_start, 1);
// No change in seq_offset because sequence not used when skipping.
base_offset += cig_len;
break;
@@ -1017,6 +1017,7 @@
f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ),
y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
+ draw_height = (mode === 'Pack' ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT),
label_color = this.prefs.label_color;
// Draw read.
@@ -1049,7 +1050,8 @@
b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) );
if (connector && b2_start > b1_end) {
ctx.fillStyle = CONNECTOR_COLOR;
- dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5);
+ var line_height = y_start + 1 + (draw_height - 1)/2;
+ dashedLine(ctx, b1_end, line_height, b2_start, line_height);
}
} else {
// Read is single.
diff -r 9b2dc0bd882a0432809f455acce191c333b8df02 -r 724f9ab6ba158b580b20e12545f3337144e7e886 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -3242,7 +3242,7 @@
width = this.view.container.width(),
new_div = $("<div/>").addClass('label-container');
while ( position < view.high ) {
- var screenPosition = ( position - view.low ) / range * width;
+ var screenPosition = Math.floor( ( position - view.low ) / range * width );
new_div.append( $("<div/>").addClass('label').text(commatize( position )).css( {
left: screenPosition
}));
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: BjoernGruening: Adding missing imports.
by commits-noreply＠bitbucket.org 13 Aug '14
by commits-noreply＠bitbucket.org 13 Aug '14
13 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d2fc633d1bcc/
Changeset: d2fc633d1bcc
Branch: stable
User: BjoernGruening
Date: 2014-08-13 14:56:37
Summary: Adding missing imports.
Affected #: 1 file
diff -r 7e81cbc2603f0695802ab49dcd65f6dda7b42322 -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a lib/tool_shed/galaxy_install/repair_repository_manager.py
--- a/lib/tool_shed/galaxy_install/repair_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py
@@ -1,5 +1,6 @@
+import os
+import tempfile
import logging
-import os
log = logging.getLogger( __name__ )
@@ -7,6 +8,8 @@
from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
from tool_shed.galaxy_install.tools import tool_panel_manager
+from tool_shed.util import hg_util
+from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import shed_util_common as suc
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix to 264657d: make infomessage and persistent across states; Style tweaks
by commits-noreply＠bitbucket.org 13 Aug '14
by commits-noreply＠bitbucket.org 13 Aug '14
13 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9b2dc0bd882a/
Changeset: 9b2dc0bd882a
User: carlfeberhard
Date: 2014-08-13 16:03:29
Summary: Fix to 264657d: make infomessage and persistent across states; Style tweaks
Affected #: 4 files
diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/scripts/mvc/dataset/dataset-li.js
--- a/static/scripts/mvc/dataset/dataset-li.js
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -4,7 +4,13 @@
"utils/localization"
], function( STATES, BASE_MVC, _l ){
/* global Backbone */
-//==============================================================================
+/*==============================================================================
+TODO:
+ straighten out state rendering and templates used
+ inaccessible/STATES.NOT_VIEWABLE is a special case
+ simplify button rendering
+
+==============================================================================*/
var _super = BASE_MVC.ListItemView;
/** @class Read only list view for either LDDAs, HDAs, or HDADCEs.
* Roughly, any DatasetInstance (and not a raw Dataset).
@@ -196,9 +202,16 @@
*/
_renderDetails : function(){
//TODO: generalize to be allow different details for each state
+
+ // no access - render nothing but a message
+ if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){
+ return $( this.templates.noAccess( this.model.toJSON(), this ) );
+ }
+
var $details = _super.prototype._renderDetails.call( this );
$details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() );
- $details.find( '.summary' ).html( this._renderSummary() );
+ $details.find( '.summary' ).html( this._renderSummary() )
+ .prepend( this._renderDetailMessages() );
$details.find( '.display-applications' ).html( this._renderDisplayApplications() );
//TODO: double tap
@@ -214,6 +227,18 @@
return summaryRenderFn( json, this );
},
+ /** Render messages to be displayed only when the details are shown */
+ _renderDetailMessages : function(){
+ var view = this,
+ $warnings = $( '<div class="detail-messages"></div>' ),
+ json = view.model.toJSON();
+//TODO:! unordered (map)
+ _.each( view.templates.detailMessages, function( templateFn ){
+ $warnings.append( $( templateFn( json, view ) ) );
+ });
+ return $warnings;
+ },
+
/** Render the external display application links */
_renderDisplayApplications : function(){
if( this.model.isDeletedOrPurged() ){ return ''; }
@@ -369,6 +394,14 @@
'</div>'
], 'dataset' );
+ var noAccessTemplate = BASE_MVC.wrapTemplate([
+ '<div class="details">',
+ '<div class="summary">',
+ _l( 'You do not have permission to view this dataset' ),
+ '</div>',
+ '</div>'
+ ], 'dataset' );
+
//TODO: still toooooooooooooo complex - rework
var summaryTemplates = {};
summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([
@@ -410,22 +443,10 @@
'<div>', _l( 'The job creating this dataset was cancelled before completion' ), '</div>'
], 'dataset' );
summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([
- '<div>',
- '<% if( dataset.resubmitted ){ %>',
- _l( 'The job creating this dataset has been resubmitted is now waiting to run' ),
- '<% } else { %>',
- _l( 'This job is waiting to run' ),
- '<% } %>',
- '</div>'
+ '<div>', _l( 'This job is waiting to run' ), '</div>'
], 'dataset' );
summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([
- '<div>',
- '<% if( dataset.resubmitted ){ %>',
- _l( 'The job creating this dataset has been resubmitted is now running' ),
- '<% } else { %>',
- _l( 'This job is currently running' ),
- '<% } %>',
- '</div>'
+ '<div>', _l( 'This job is currently running' ), '</div>'
], 'dataset' );
summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([
'<div>', _l( 'This dataset is currently uploading' ), '</div>'
@@ -450,6 +471,18 @@
'<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'
], 'dataset' );
+ // messages to be displayed only within the details section ('below the fold')
+ var detailMessageTemplates = {
+ resubmitted : BASE_MVC.wrapTemplate([
+ // deleted not purged
+ '<% if( model.resubmitted ){ %>',
+ '<div class="resubmitted-msg infomessagesmall">',
+ _l( 'The job creating this dataset has been resubmitted' ),
+ '</div>',
+ '<% } %>'
+ ])
+ };
+
// this is applied to both old and new style display apps
var displayApplicationsTemplate = BASE_MVC.wrapTemplate([
'<% _.each( apps, function( app ){ %>',
@@ -469,7 +502,9 @@
return _.extend( {}, _super.prototype.templates, {
warnings : warnings,
details : detailsTemplate,
+ noAccess : noAccessTemplate,
summaries : summaryTemplates,
+ detailMessages : detailMessageTemplates,
displayApplications : displayApplicationsTemplate
});
}());
diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/scripts/packed/mvc/dataset/dataset-li.js
--- a/static/scripts/packed/mvc/dataset/dataset-li.js
+++ b/static/scripts/packed/mvc/dataset/dataset-li.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var g=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var h=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var i={};i[a.OK]=i[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");i[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");i[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");i[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");i[a.QUEUED]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now waiting to run"),"<% } else { %>",c("This job is waiting to run"),"<% } %>","</div>"],"dataset");i[a.RUNNING]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now running"),"<% } else { %>",c("This job is currently running"),"<% } %>","</div>"],"dataset");i[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");i[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");i[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");i[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");i[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");i.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:g,details:h,summaries:i,displayApplications:f})}());return{DatasetListItemView:d}});
\ No newline at end of file
+define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDetailMessages:function(){var f=this,h=$('<div class="detail-messages"></div>'),g=f.model.toJSON();_.each(f.templates.detailMessages,function(i){h.append($(i(g,f)))});return h},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var h=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var i=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var g=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var j={};j[a.OK]=j[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");j[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");j[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");j[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");j[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");j[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");j[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");j[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");j[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");j[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");j[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");j.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var k={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:h,details:i,noAccess:g,summaries:j,detailMessages:k,displayApplications:f})}());return{DatasetListItemView:d}});
\ No newline at end of file
diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1684,13 +1684,13 @@
.dataset .details .actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px}
.dataset .details .actions .left .icon-btn:only-child{margin:0px;border-radius:3px}
.dataset .details .actions .left .icon-btn{margin-right:2px}
-.dataset .details .actions .left:not(:empty){margin-bottom:8px}
.dataset .details .actions .left .icon-btn.visualization-btn{margin-left:0px;border-radius:0px 3px 3px 0px;border-right:1px solid #bfbfbf}
.dataset .details .actions .right{display:inline-block;float:right}.dataset .details .actions .right .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none}
.dataset .details .actions .right .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px}
.dataset .details .actions .right .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px}
.dataset .details .actions .right .icon-btn:only-child{margin:0px;border-radius:3px}
.dataset .details .actions .right .icon-btn{margin-left:2px}
+.dataset .details .actions:not(:last-child){margin-bottom:8px}
.dataset .details .tags-display{display:none;margin-bottom:8px}.dataset .details .tags-display .select2-container{min-width:0px}.dataset .details .tags-display .select2-container .select2-choices{border-radius:3px}
.dataset .details .annotation-display{display:none;margin-bottom:8px}.dataset .details .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line;overflow:auto}
.dataset .details .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'}
diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/style/src/less/history.less
--- a/static/style/src/less/history.less
+++ b/static/style/src/less/history.less
@@ -356,11 +356,6 @@
.icon-btn {
margin-right: @icon-btn-margin;
}
- &:not(:empty) {
- // can't use :empty on dataset-actions - will always have left & right, so
- // add gap to left (more likely to have children)
- .list-item .vertical-spacing;
- }
// have to reapply here - dropdown wrapped in div
.icon-btn.visualization-btn {
margin-left: 0px;
@@ -375,6 +370,9 @@
margin-left: @icon-btn-margin;
}
}
+ &:not(:last-child) {
+ .list-item .vertical-spacing;
+ }
}
//TODO: move these out
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Controller updates for the resubmitted dataset instance state (thanks Carl!)
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d301ac50aa86/
Changeset: d301ac50aa86
User: natefoo
Date: 2014-08-12 21:21:40
Summary: Controller updates for the resubmitted dataset instance state (thanks Carl!)
Affected #: 2 files
diff -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -940,10 +940,9 @@
def mark_as_resubmitted( self ):
job = self.get_job()
self.sa_session.refresh( job )
- # TODO: Enable this code once a UI for resubmitted datasets exists
- #for dataset in [ dataset_assoc.dataset for dataset_assoc in job.output_datasets + job.output_library_datasets ]:
- # dataset._state = model.Dataset.states.RESUBMITTED
- # self.sa_session.add( dataset )
+ for dataset in [ dataset_assoc.dataset for dataset_assoc in job.output_datasets + job.output_library_datasets ]:
+ dataset._state = model.Dataset.states.RESUBMITTED
+ self.sa_session.add( dataset )
job.state = model.Job.states.RESUBMITTED
self.sa_session.add( job )
self.sa_session.flush()
diff -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -131,15 +131,20 @@
"""
api_type = "file"
encoded_id = trans.security.encode_id( hda.id )
+ # TODO: handle failed_metadata here as well
+ state = hda.state
+ if state == trans.app.model.Dataset.states.RESUBMITTED:
+ state = hda.dataset.state
return {
'id' : encoded_id,
'history_id' : encoded_history_id,
'name' : hda.name,
'type' : api_type,
- 'state' : hda.state,
+ 'state' : state,
'deleted': hda.deleted,
'visible': hda.visible,
'purged': hda.purged,
+ 'resubmitted': hda._state == trans.app.model.Dataset.states.RESUBMITTED,
'hid' : hda.hid,
'history_content_type' : hda.history_content_type,
'url' : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ),
@@ -157,6 +162,9 @@
hda_dict = self.get_hda_dict( trans, hda )
hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda )
hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
+ if hda_dict[ 'state' ] == trans.app.model.Dataset.states.RESUBMITTED:
+ hda_dict[ 'state' ] = hda.dataset.state
+ hda_dict[ 'resubmitted' ] = True
return hda_dict
except Exception, exc:
# catch error here - returning a briefer hda_dict with an error attribute
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Do not include invalid tools when checking for "orphan" tool dependencies in the Tool Shed.
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d30b580ffbc5/
Changeset: d30b580ffbc5
User: greg
Date: 2014-08-12 20:15:00
Summary: Do not include invalid tools when checking for "orphan" tool dependencies in the Tool Shed.
Affected #: 1 file
diff -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 lib/tool_shed/galaxy_install/dependency_display.py
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -153,7 +153,7 @@
# Updating should cause no problems here since a tool dependency cannot be included
# in both dictionaries.
tool_dependencies.update( orphan_tool_dependencies )
- if tool_dependencies and ( tools or invalid_tools ):
+ if tool_dependencies and tools:
for td_key, requirements_dict in tool_dependencies.items():
if td_key == 'set_environment':
# "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Datset list item: add resubmitted message; pack scripts
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/264657dfe72d/
Changeset: 264657dfe72d
User: carlfeberhard
Date: 2014-08-12 19:56:26
Summary: Datset list item: add resubmitted message; pack scripts
Affected #: 3 files
diff -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 static/scripts/mvc/dataset/dataset-li.js
--- a/static/scripts/mvc/dataset/dataset-li.js
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -35,6 +35,7 @@
/** event listeners */
_setUpListeners : function(){
+//TODO:?? may want to move this to ListItemView (although this is only needed in the *narrow* panel views (current))
// hide the primary actions in the title bar when selectable
this.on( 'selectable', function( isSelectable ){
if( isSelectable ){
@@ -207,9 +208,10 @@
/** Defer to the appropo summary rendering fn based on state */
_renderSummary : function(){
- var summaryRenderFn = this.templates.summaries[ this.model.get( 'state' ) ];
+ var json = this.model.toJSON(),
+ summaryRenderFn = this.templates.summaries[ json.state ];
summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;
- return summaryRenderFn( this.model.toJSON(), this );
+ return summaryRenderFn( json, this );
},
/** Render the external display application links */
@@ -408,7 +410,22 @@
'<div>', _l( 'The job creating this dataset was cancelled before completion' ), '</div>'
], 'dataset' );
summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([
- '<div>', _l( 'This job is waiting to run' ), '</div>'
+ '<div>',
+ '<% if( dataset.resubmitted ){ %>',
+ _l( 'The job creating this dataset has been resubmitted is now waiting to run' ),
+ '<% } else { %>',
+ _l( 'This job is waiting to run' ),
+ '<% } %>',
+ '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([
+ '<div>',
+ '<% if( dataset.resubmitted ){ %>',
+ _l( 'The job creating this dataset has been resubmitted is now running' ),
+ '<% } else { %>',
+ _l( 'This job is currently running' ),
+ '<% } %>',
+ '</div>'
], 'dataset' );
summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([
'<div>', _l( 'This dataset is currently uploading' ), '</div>'
@@ -416,9 +433,6 @@
summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([
'<div>', _l( 'Metadata is being auto-detected' ), '</div>'
], 'dataset' );
- summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([
- '<div>', _l( 'This job is currently running' ), '</div>'
- ], 'dataset' );
summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([
'<div>', _l( 'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume' ), '</div>'
], 'dataset' );
diff -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 static/scripts/packed/mvc/collection/collection-li.js
--- a/static/scripts/packed/mvc/collection/collection-li.js
+++ b/static/scripts/packed/mvc/collection/collection-li.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(h,d,f){var c=d.ListItemView;var a=c.extend({className:c.prototype.className+" dataset-collection",fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+"(DCListItemView).initialize:",i);c.prototype.initialize.call(this,i)},expand:function(){var i=this;return i._fetchModelDetails().always(function(){i.trigger("expanded",i)})},_renderSubtitle:function(){var i=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return i.text(f("a list of datasets"));case"paired":return i.text(f("a pair of datasets"));case"list:paired":return i.text(f("a list of paired datasets"))}return i},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCListItemView("+i+")"}});a.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},c.prototype.templates,{titleBar:i})}());var b=c.extend({logger:console,className:c.prototype.className+" dataset-collection-element",fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DCEListItemView.initialize:",i);c.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCEListItemView("+i+")"}});b.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},c.prototype.templates,{titleBar:i})}());var e=h.DatasetListItemView.extend({className:h.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DatasetDCEListItemView.initialize:",i);h.DatasetListItemView.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DatasetDCEListItemView("+i+")"}});e.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},h.DatasetListItemView.prototype.templates,{titleBar:i})}());var g=a.extend({className:a.prototype.className+" dataset-collection-element",_swapNewRender:function(i){a.prototype._swapNewRender.call(this,i);var j=this.model.get("state")||"ok";this.$el.addClass("state-"+j);return this.$el},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"NestedDCDCEListItemView("+i+")"}});return{DCListItemView:a,DCEListItemView:b,DatasetDCEListItemView:e,NestedDCDCEListItemView:g}});
\ No newline at end of file
+define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(h,d,f){var c=d.ListItemView;var a=c.extend({className:c.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+"(DCListItemView).initialize:",i);c.prototype.initialize.call(this,i)},expand:function(){var i=this;return i._fetchModelDetails().always(function(){i.trigger("expanded",i)})},_renderSubtitle:function(){var i=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return i.text(f("a list of datasets"));case"paired":return i.text(f("a pair of datasets"));case"list:paired":return i.text(f("a list of paired datasets"))}return i},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCListItemView("+i+")"}});a.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},c.prototype.templates,{titleBar:i})}());var b=c.extend({logger:console,className:c.prototype.className+" dataset-collection-element",fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DCEListItemView.initialize:",i);c.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCEListItemView("+i+")"}});b.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},c.prototype.templates,{titleBar:i})}());var e=h.DatasetListItemView.extend({className:h.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DatasetDCEListItemView.initialize:",i);h.DatasetListItemView.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DatasetDCEListItemView("+i+")"}});e.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},h.DatasetListItemView.prototype.templates,{titleBar:i})}());var g=a.extend({className:a.prototype.className+" dataset-collection-element",_swapNewRender:function(i){a.prototype._swapNewRender.call(this,i);var j=this.model.get("state")||"ok";this.$el.addClass("state-"+j);return this.$el},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"NestedDCDCEListItemView("+i+")"}});return{DCListItemView:a,DCEListItemView:b,DatasetDCEListItemView:e,NestedDCDCEListItemView:g}});
\ No newline at end of file
diff -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 static/scripts/packed/mvc/dataset/dataset-li.js
--- a/static/scripts/packed/mvc/dataset/dataset-li.js
+++ b/static/scripts/packed/mvc/dataset/dataset-li.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.templates.summaries[this.model.get("state")];f=f||this.templates.summaries.unknown;return f(this.model.toJSON(),this)},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"dataset-params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var g=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var h=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var i={};i[a.OK]=i[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");i[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");i[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");i[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");i[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");i[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");i[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");i[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");i[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");i[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");i[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");i.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:g,details:h,summaries:i,displayApplications:f})}());return{DatasetListItemView:d}});
\ No newline at end of file
+define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var g=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var h=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var i={};i[a.OK]=i[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");i[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");i[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");i[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");i[a.QUEUED]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now waiting to run"),"<% } else { %>",c("This job is waiting to run"),"<% } %>","</div>"],"dataset");i[a.RUNNING]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now running"),"<% } else { %>",c("This job is currently running"),"<% } %>","</div>"],"dataset");i[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");i[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");i[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");i[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");i[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");i.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:g,details:h,summaries:i,displayApplications:f})}());return{DatasetListItemView:d}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: QA, qunit: update HDA, history contents tests
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/bdfef8f7d523/
Changeset: bdfef8f7d523
User: carlfeberhard
Date: 2014-08-12 18:48:28
Summary: QA, qunit: update HDA, history contents tests
Affected #: 2 files
diff -r f926988f8e0a480c09d3462002f482b5ac806682 -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 test/qunit/tests/hda-base.js
--- a/test/qunit/tests/hda-base.js
+++ b/test/qunit/tests/hda-base.js
@@ -1,14 +1,13 @@
// This file isn't really testing anything useful yet, it is just testing
// (or demonstrating) qunit+backbone interactions.
define([
- "mvc/dataset/hda-model",
- "mvc/dataset/hda-base",
+ "mvc/history/hda-model",
+ "mvc/history/hda-li",
"jquery",
- "sinon-qunit",
- "utils/localization"
+ "sinon-qunit"
], function(
- hdaModel,
- hdaBase,
+ HDA_MODEL,
+ HDA_BASE,
$,
sinon
){
@@ -18,10 +17,10 @@
module( "HDA base backbone view tests" );
test( "Base HDA view default construction, initialize", function() {
- var hda = new hdaModel.HistoryDatasetAssociation({
+ var hda = new HDA_MODEL.HistoryDatasetAssociation({
id : '123'
}),
- view = new hdaBase.HDABaseView({ model: hda });
+ view = new HDA_BASE.HDAListItemView({ model: hda });
strictEqual( view.model, hda );
@@ -30,6 +29,6 @@
equal( view.selected, false );
equal( view.expanded, false );
equal( view.draggable, false );
- equal( view.id(), 'hda-123' );
+ equal( view.id(), 'dataset-123' );
});
});
diff -r f926988f8e0a480c09d3462002f482b5ac806682 -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 test/qunit/tests/history_contents_model_tests.js
--- a/test/qunit/tests/history_contents_model_tests.js
+++ b/test/qunit/tests/history_contents_model_tests.js
@@ -1,46 +1,45 @@
// This file isn't really testing anything useful yet, it is just testing
// (or demonstrating) qunit+backbone interactions.
define([
- "mvc/dataset/hda-model",
+ "mvc/history/hda-model",
"jquery",
"sinon-qunit"
], function(
- hdaModel,
+ HDA_MODEL,
$,
sinon
){
module( "History Contents Model Tests" );
test( "HDA Constructions with Default Attributes", function() {
- var hda = new hdaModel.HistoryDatasetAssociation();
- expect( 2 );
+ var hda = new HDA_MODEL.HistoryDatasetAssociation({});
equal( hda.get( 'name' ), "(unnamed dataset)" );
equal( hda.get( 'state' ), "new" );
} );
test( "HDA Construction with Supplied Attributes", function() {
- var hda = new hdaModel.HistoryDatasetAssociation( {
- name: "my dataset",
- state: "ok",
- } );
- expect( 2 );
-
+ var hda = new HDA_MODEL.HistoryDatasetAssociation({
+ history_content_type : 'dataset',
+ name: "my dataset",
+ state: "ok"
+ });
equal( hda.get( 'name' ), "my dataset" );
equal( hda.get( 'state' ), "ok" );
} );
test( "HDA Deletion", function() {
- var hda = new hdaModel.HistoryDatasetAssociation( {
- id: "hda1",
- history_id: "h1",
- deleted: false,
- } );
-
- // Demonstrate sinon stubbing out of Ajax queries...
+ var hda = new HDA_MODEL.HistoryDatasetAssociation({
+ history_content_type : 'dataset',
+ id: "hda1",
+ history_id: "h1",
+ deleted: false
+ });
equal( hda.get( 'deleted' ), false );
sinon.stub( $, "ajax" );
- hda.delete();
+ hda[ 'delete' ]();
equal( hda.get( 'deleted' ), true );
- ok( $.ajax.calledWithMatch( { url: "/api/histories/h1/contents/hda1" } ) );
- } );
-} );
+ // to get the url sinon used:
+ //console.debug( $.ajax.lastCall.args[0].url )
+ ok( $.ajax.calledWithMatch( { url: "/api/histories/h1/contents/datasets/hda1" } ) );
+ });
+});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: QA, casperjs: fix selectors changed in 7005608
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f926988f8e0a/
Changeset: f926988f8e0a
User: carlfeberhard
Date: 2014-08-12 17:42:03
Summary: QA, casperjs: fix selectors changed in 7005608
Affected #: 5 files
diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 static/scripts/mvc/collection/collection-li.js
--- a/static/scripts/mvc/collection/collection-li.js
+++ b/static/scripts/mvc/collection/collection-li.js
@@ -16,7 +16,11 @@
//logger : console,
className : ListItemView.prototype.className + " dataset-collection",
- /** */
+ id : function(){
+ return [ 'dataset_collection', this.model.get( 'id' ) ].join( '-' );
+ },
+
+ /** jq speed for effects used */
fxSpeed : 'fast',
//TODO: ununsed
diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 static/scripts/mvc/dataset/dataset-li.js
--- a/static/scripts/mvc/dataset/dataset-li.js
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -16,6 +16,10 @@
//logger : console,
className : _super.prototype.className + " dataset",
+ //TODO:?? doesn't exactly match an hda's type_id
+ id : function(){
+ return [ 'dataset', this.model.get( 'id' ) ].join( '-' );
+ },
/** Set up: instance vars, options, and event handlers */
initialize : function( attributes ){
@@ -240,7 +244,7 @@
// gen. safe to show in all cases
return faIconButton({
title : _l( 'View details' ),
- classes : 'dataset-params-btn',
+ classes : 'params-btn',
href : this.model.urls.show_params,
target : this.linkTarget,
faIcon : 'fa-info-circle'
diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 test/casperjs/hda-state-tests.js
--- a/test/casperjs/hda-state-tests.js
+++ b/test/casperjs/hda-state-tests.js
@@ -321,7 +321,7 @@
// set state directly through model, wait for re-render
//TODO: not ideal to test this
this.evaluate( function(){
- return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'new' );
+ return Galaxy.currHistoryPanel.model.contents.at( 0 ).set( 'state', 'new' );
});
this.wait( 1000, function(){
this.test.comment( 'HDAs in the "new" state should be well formed' );
@@ -359,7 +359,7 @@
var errorString = 'Blah!';
this.evaluate( function( errorString ){
- return Galaxy.currHistoryPanel.model.hdas.getByHid( 1 ).set( 'error', errorString );
+ return Galaxy.currHistoryPanel.model.contents.getByHid( 1 ).set( 'error', errorString );
}, errorString );
// wait for re-render
@@ -382,8 +382,8 @@
this.historypanel.thenCollapseHda( uploadSelector, function(){
this.evaluate( function(){
- Galaxy.currHistoryPanel.model.hdas.getByHid( 1 ).unset( 'error' );
- return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'ok' );
+ Galaxy.currHistoryPanel.model.contents.getByHid( 1 ).unset( 'error' );
+ return Galaxy.currHistoryPanel.model.contents.at( 0 ).set( 'state', 'ok' );
});
});
this.wait( 1000 );
diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 test/casperjs/history-panel-tests.js
--- a/test/casperjs/history-panel-tests.js
+++ b/test/casperjs/history-panel-tests.js
@@ -230,6 +230,7 @@
// broken in webkit w/ jq 1.7
spaceghost.historypanel.waitForHdas( function(){
this.test.comment( 'HDAs can be expanded by clicking on the name' );
+ this.debug( this.jsonStr( testUploadInfo ) );
var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id;
this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title );
diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 test/casperjs/modules/historypanel.js
--- a/test/casperjs/modules/historypanel.js
+++ b/test/casperjs/modules/historypanel.js
@@ -63,7 +63,7 @@
* @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found
*/
HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title ){
- var wrapperXpath = xpath( '//span[@class="dataset-name" and contains(text(),"' + title + '")]/../../..' );
+ var wrapperXpath = xpath( '//span[@class="name" and contains(text(),"' + title + '")]/../../..' );
return this.spaceghost.elementInfoOrNull( wrapperXpath );
};
@@ -138,9 +138,13 @@
if( state !== 'ok' ){ return false; }
var hdaOpacity = this.evaluate( function( name ){
- return $( '.dataset-name:contains("' + name + '")' ).parents( '.hda' ).css( 'opacity' );
+ // locate the hda by name and return its opacity
+ console.debug( name );
+ console.debug( $( '.name:contains("' + name + '")' ) );
+ console.debug( $( '.name:contains("' + name + '")' ).parents( '.hda' ) );
+ return $( '.name:contains("' + name + '")' ).parents( '.dataset' ).css( 'opacity' );
}, hdaName );
- this.debug( 'fading in: ' + hdaOpacity );
+ //this.debug( 'fading in: ' + hdaOpacity );
return hdaOpacity >= 1;
},
function _then(){ then.call( this, hdaElement ); },
@@ -310,19 +314,19 @@
hdaTitleButtons : {
// mixing text and selectors here
display : {
- selector : '.icon-btn.dataset-display',
+ selector : '.icon-btn.display-btn',
tooltip : 'View data',
hrefTpl : '/datasets/%s/display',
nodeName : 'a'
},
edit : {
- selector : '.icon-btn.dataset-edit',
+ selector : '.icon-btn.edit-btn',
tooltip : 'Edit attributes',
hrefTpl : '/datasets/%s/edit',
nodeName : 'a'
},
'delete' : {
- selector : '.icon-btn.dataset-delete',
+ selector : '.icon-btn.delete-btn',
tooltip : 'Delete',
hrefTpl : 'javascript:void(0);',
nodeName : 'a'
@@ -330,19 +334,19 @@
},
hdaPrimaryActionButtons : {
download : {
- selector : '.icon-btn.dataset-download-btn',
+ selector : '.icon-btn.download-btn',
tooltip : 'Download',
hrefTpl : '/datasets/%s/display?to_ext=',
nodeName : 'a'
},
info : {
- selector : '.icon-btn.dataset-params-btn',
+ selector : '.icon-btn.params-btn',
tooltip : 'View details',
hrefTpl : '/datasets/%s/show_params',
nodeName : 'a'
},
rerun : {
- selector : '.icon-btn.dataset-rerun-btn',
+ selector : '.icon-btn.rerun-btn',
tooltip : 'Run this job again',
hrefTpl : '/tool_runner/rerun?id=%s',
nodeName : 'a'
@@ -365,7 +369,7 @@
},
hda : {
wrapper : {
- itemClass : '.hda',
+ itemClass : '.history-content.dataset',
stateClasses : {
prefix : 'state-',
ok : 'state-ok',
@@ -374,18 +378,18 @@
},
errorMessage : '.errormessagesmall',
- title : '.dataset-title',
- titleButtonArea : '.dataset-primary-actions',
- summary : '.dataset-summary',
- dbkey : '.dataset-dbkey .value',
- info : '.dataset-info',
- body : '.dataset-body',
+ title : '.title',
+ titleButtonArea : '.primary-actions',
+ summary : '.summary',
+ dbkey : '.dbkey .value',
+ info : '.info',
+ body : '.details',
- primaryActionButtons : '.dataset-actions .left',
- secondaryActionButtons : '.dataset-actions .right',
+ primaryActionButtons : '.actions .left',
+ secondaryActionButtons : '.actions .right',
- undeleteLink : '.dataset-undelete',
- purgeLink : '.dataset-purge',
+ undeleteLink : '.undelete-link',
+ purgeLink : '.purge-link',
peek : '.dataset-peek'
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Update tool_list.py to indicate the correct tool_conf.xml (not sample)
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3aad77adffba/
Changeset: 3aad77adffba
User: dannon
Date: 2014-08-12 17:28:08
Summary: Update tool_list.py to indicate the correct tool_conf.xml (not sample)
Affected #: 1 file
diff -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 -r 3aad77adffba5e3cbb8910ca21387c3effefc429 tool_list.py
--- a/tool_list.py
+++ b/tool_list.py
@@ -1,6 +1,6 @@
import os,sys
-#--------read tool_conf.xml.sample to get all the tool xml file names-----------
+#--------read tool_conf.xml to get all the tool xml file names-----------
onoff = 1
tool_list = []
for line in open("tool_conf.xml", "r"):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456)
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/18e8ddfb9c3c/
Changeset: 18e8ddfb9c3c
User: dannon
Date: 2014-08-12 17:25:22
Summary: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456)
tool_list.py should now use tool_conf.xml not tool_conf.xml.sample
Affected #: 1 file
diff -r a94473459ebb4749a375420492d6da9a948ccd3a -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 tool_list.py
--- a/tool_list.py
+++ b/tool_list.py
@@ -3,7 +3,7 @@
#--------read tool_conf.xml.sample to get all the tool xml file names-----------
onoff = 1
tool_list = []
-for line in open("tool_conf.xml.sample", "r"):
+for line in open("tool_conf.xml", "r"):
if line.find("<!--") != -1:
onoff = 0
if line.find("file") != -1 and onoff==1:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/82a9821e0fbb/
Changeset: 82a9821e0fbb
Branch: tool_list_fix
User: peterjc
Date: 2014-08-12 17:13:05
Summary: Created new branch tool_list_fix
Affected #: 0 files
https://bitbucket.org/galaxy/galaxy-central/commits/24d8995c3568/
Changeset: 24d8995c3568
Branch: tool_list_fix
User: peterjc
Date: 2014-08-12 17:15:04
Summary: tool_list.py should now use tool_conf.xml not tool_conf.xml.sample
See a94473459ebb4749a375420492d6da9a948ccd3a where the rest of the run_functional_tests.sh system was updated.
Affected #: 1 file
diff -r 82a9821e0fbb3b4c9387152e48be189cc2829a45 -r 24d8995c35689fc42e96d6f02dc222cbf75531ed tool_list.py
--- a/tool_list.py
+++ b/tool_list.py
@@ -3,7 +3,7 @@
#--------read tool_conf.xml.sample to get all the tool xml file names-----------
onoff = 1
tool_list = []
-for line in open("tool_conf.xml.sample", "r"):
+for line in open("tool_conf.xml", "r"):
if line.find("<!--") != -1:
onoff = 0
if line.find("file") != -1 and onoff==1:
https://bitbucket.org/galaxy/galaxy-central/commits/18e8ddfb9c3c/
Changeset: 18e8ddfb9c3c
User: dannon
Date: 2014-08-12 17:25:22
Summary: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456)
tool_list.py should now use tool_conf.xml not tool_conf.xml.sample
Affected #: 1 file
diff -r a94473459ebb4749a375420492d6da9a948ccd3a -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 tool_list.py
--- a/tool_list.py
+++ b/tool_list.py
@@ -3,7 +3,7 @@
#--------read tool_conf.xml.sample to get all the tool xml file names-----------
onoff = 1
tool_list = []
-for line in open("tool_conf.xml.sample", "r"):
+for line in open("tool_conf.xml", "r"):
if line.find("<!--") != -1:
onoff = 0
if line.find("file") != -1 and onoff==1:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: History panel: clean up and documentation
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a94473459ebb/
Changeset: a94473459ebb
User: carlfeberhard
Date: 2014-08-12 16:45:26
Summary: History panel: clean up and documentation
Affected #: 19 files
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-li-edit.js
--- a/static/scripts/mvc/collection/collection-li-edit.js
+++ b/static/scripts/mvc/collection/collection-li-edit.js
@@ -13,7 +13,8 @@
var _super = DC_LI.DCListItemView;
/** @class Editing view for DatasetCollectionElement.
*/
-var DCEListItemEdit = _super.extend({
+var DCEListItemEdit = _super.extend(
+/** @lends DCEListItemEdit.prototype */{
/** logger used to record this.log messages, commonly set to console */
//logger : console,
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-li.js
--- a/static/scripts/mvc/collection/collection-li.js
+++ b/static/scripts/mvc/collection/collection-li.js
@@ -8,7 +8,8 @@
var ListItemView = BASE_MVC.ListItemView;
/** @class Read only view for DatasetCollection.
*/
-var DCListItemView = ListItemView.extend({
+var DCListItemView = ListItemView.extend(
+/** @lends DCListItemView.prototype */{
//TODO: may not be needed
/** logger used to record this.log messages, commonly set to console */
@@ -26,7 +27,7 @@
ListItemView.prototype.initialize.call( this, attributes );
},
- /** In this override, don't show`or render any details (no need to do anything here)
+ /** In this override, don't show or render any details (no need to do anything here)
* - currently the parent control will load a panel for this collection over itself
* @fires expanded when a body has been expanded
*/
@@ -87,7 +88,8 @@
//==============================================================================
/** @class Read only view for DatasetCollectionElement.
*/
-var DCEListItemView = ListItemView.extend({
+var DCEListItemView = ListItemView.extend(
+/** @lends DCEListItemView.prototype */{
//TODO: this might be expendable - compacted with HDAListItemView
/** logger used to record this.log messages, commonly set to console */
@@ -99,7 +101,7 @@
/** jq fx speed for this view */
fxSpeed : 'fast',
- /** */
+ /** set up */
initialize : function( attributes ){
if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
this.log( 'DCEListItemView.initialize:', attributes );
@@ -138,14 +140,15 @@
/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation
* (a dataset contained in a dataset collection).
*/
-var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend({
+var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(
+/** @lends DatasetDCEListItemView.prototype */{
className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element",
/** logger used to record this.log messages, commonly set to console */
//logger : console,
- /** */
+ /** set up */
initialize : function( attributes ){
if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
this.log( 'DatasetDCEListItemView.initialize:', attributes );
@@ -185,7 +188,8 @@
/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection
* (a nested DC).
*/
-var NestedDCDCEListItemView = DCListItemView.extend({
+var NestedDCDCEListItemView = DCListItemView.extend(
+/** @lends NestedDCDCEListItemView.prototype */{
className : DCListItemView.prototype.className + " dataset-collection-element",
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-model.js
--- a/static/scripts/mvc/collection/collection-model.js
+++ b/static/scripts/mvc/collection/collection-model.js
@@ -47,7 +47,7 @@
* When collection elements are passed from the API, the underlying element is
* in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).
* This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues
- * effectively changing a DCE from a container to a subclass.
+ * effectively changing a DCE from a container to a subclass (has a --> is a).
*/
var DatasetCollectionElementMixin = {
@@ -82,7 +82,7 @@
};
//TODO: unused?
-/** Concrete class of Generic DatasetCollectionElement */
+/** @class Concrete class of Generic DatasetCollectionElement */
var DatasetCollectionElement = Backbone.Model
.extend( BASE_MVC.LoggableMixin )
.extend( DatasetCollectionElementMixin );
@@ -94,7 +94,6 @@
/** @lends DCECollection.prototype */{
model: DatasetCollectionElement,
- // comment this out to suppress log output
/** logger used to record this.log messages, commonly set to console */
//logger : console,
@@ -124,7 +123,10 @@
/** logger used to record this.log messages, commonly set to console */
//logger : console,
- defaults : _.extend( {}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ),
+ defaults : _.extend( {},
+ DATASET_MODEL.DatasetAssociation.prototype.defaults,
+ DatasetCollectionElementMixin.defaults
+ ),
// because all objects have constructors (as this hashmap would even if this next line wasn't present)
// the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
@@ -162,7 +164,7 @@
//logger : console,
//TODO: unused?
- /** */
+ /** set up */
initialize : function( attributes, options ){
this.debug( this + '(DatasetDCECollection).initialize:', attributes, options );
DCECollection.prototype.initialize.call( this, attributes, options );
@@ -203,7 +205,7 @@
/** Which class to use for elements */
collectionClass : DCECollection,
- /** */
+ /** set up: create elements instance var and (on changes to elements) update them */
initialize : function( model, options ){
this.debug( this + '(DatasetCollection).initialize:', model, options, this );
//historyContent.HistoryContent.prototype.initialize.call( this, attrs, options );
@@ -269,6 +271,7 @@
},
// ........................................................................ searchable
+ /** searchable attributes for collections */
searchAttributes : [
'name'
],
@@ -291,6 +294,7 @@
/** logger used to record this.log messages, commonly set to console */
//logger : console,
+ /** override since we know the collection will only contain datasets */
collectionClass : DatasetDCECollection,
//TODO: unused?
@@ -368,10 +372,11 @@
/** logger used to record this.log messages, commonly set to console */
//logger : console,
+ /** This is a collection of nested collections */
model: NestedDCDCE,
//TODO: unused?
- /** */
+ /** set up */
initialize : function( attrs, options ){
this.debug( this + '(NestedDCDCECollection).initialize:', attrs, options );
DCECollection.prototype.initialize.call( this, attrs, options );
@@ -394,7 +399,10 @@
/** logger used to record this.log messages, commonly set to console */
//logger : console,
- /** */
+ // because all objects have constructors (as this hashmap would even if this next line wasn't present)
+ // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
+ // - re-apply manually it now
+ /** This is both a collection and a collection element - call the constructor */
constructor : function( attributes, options ){
this.debug( '\t NestedPairDCDCE.constructor:', attributes, options );
//DatasetCollection.constructor.call( this, attributes, options );
@@ -418,10 +426,11 @@
/** logger used to record this.log messages, commonly set to console */
//logger : console,
+ /** We know this collection is composed of only nested pair collections */
model: NestedPairDCDCE,
//TODO: unused?
- /** */
+ /** set up */
initialize : function( attrs, options ){
this.debug( this + '(NestedPairDCDCECollection).initialize:', attrs, options );
NestedDCDCECollection.prototype.initialize.call( this, attrs, options );
@@ -443,11 +452,11 @@
/** logger used to record this.log messages, commonly set to console */
//logger : console,
- // list:paired is the only collection that itself contains collections
+ /** list:paired is the only collection that itself contains collections */
collectionClass : NestedPairDCDCECollection,
//TODO: unused?
- /** */
+ /** set up */
initialize : function( attributes, options ){
this.debug( this + '(ListPairedDatasetCollection).initialize:', attributes, options );
DatasetCollection.prototype.initialize.call( this, attributes, options );
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-panel.js
--- a/static/scripts/mvc/collection/collection-panel.js
+++ b/static/scripts/mvc/collection/collection-panel.js
@@ -24,7 +24,9 @@
/** (in ms) that jquery effects will use */
fxSpeed : 'fast',
+ /** sub view class used for datasets */
DatasetDCEViewClass : DC_LI.DatasetDCEListItemView,
+ /** sub view class used for nested collections */
NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView,
// ......................................................................... SET UP
@@ -229,7 +231,7 @@
}
},
- /** */
+ /** When a sub-collection is clicked, hide the current panel and render the sub-collection in its own panel */
_addCollectionPanel : function( collectionView ){
//TODO: a bit hackish
var currPanel = this,
@@ -333,9 +335,11 @@
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection. */
-var ListCollectionPanel = CollectionPanel.extend({
+var ListCollectionPanel = CollectionPanel.extend(
+/** @lends ListCollectionPanel.prototype */{
//TODO: not strictly needed - due to switch in CollectionPanel._getContentClass
+ /** sub view class used for datasets */
DatasetDCEViewClass : DC_LI.DatasetDCEListItemView,
// ........................................................................ misc
@@ -348,7 +352,8 @@
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection. */
-var PairCollectionPanel = ListCollectionPanel.extend({
+var PairCollectionPanel = ListCollectionPanel.extend(
+/** @lends PairCollectionPanel.prototype */{
// ........................................................................ misc
/** string rep */
@@ -360,9 +365,11 @@
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection. */
-var ListOfPairsCollectionPanel = CollectionPanel.extend({
+var ListOfPairsCollectionPanel = CollectionPanel.extend(
+/** @lends ListOfPairsCollectionPanel.prototype */{
//TODO: not strictly needed - due to switch in CollectionPanel._getContentClass
+ /** sub view class used for nested collections */
NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView,
// ........................................................................ misc
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/dataset/dataset-model.js
--- a/static/scripts/mvc/dataset/dataset-model.js
+++ b/static/scripts/mvc/dataset/dataset-model.js
@@ -10,7 +10,7 @@
* The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.
*/
var DatasetAssociation = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend(
- BASE_MVC.mixin( searchableMixin, {
+ BASE_MVC.mixin( searchableMixin, /** @lends DatasetAssociation.prototype */{
/** default attributes for a model */
defaults : {
@@ -43,8 +43,10 @@
//annotation : ''
},
- initialize : function( attrs, options ){
- this.debug( 'Dataset.initialize', attrs, options );
+ /** instance vars and listeners */
+ initialize : function( attributes, options ){
+ this.debug( this + '(Dataset).initialize', attributes, options );
+
//!! this state is not in trans.app.model.Dataset.states - set it here -
if( !this.get( 'accessible' ) ){
this.set( 'state', STATES.NOT_VIEWABLE );
@@ -62,7 +64,6 @@
var id = this.get( 'id' );
if( !id ){ return {}; }
var urls = {
-//TODO: how many of these are still used?
'purge' : 'datasets/' + id + '/purge_async',
'display' : 'datasets/' + id + '/display/?preview=True',
'edit' : 'datasets/' + id + '/edit',
@@ -146,6 +147,7 @@
return this.save( { deleted: false }, options );
},
+ /** remove the file behind this dataset from the filesystem (if permitted) */
purge : function _purge( options ){
//TODO: use, override model.destroy, HDA.delete({ purge: true })
if( this.get( 'purged' ) ){ return jQuery.when(); }
@@ -160,7 +162,7 @@
// }, options ));
//
//xhr.done( function( response ){
- // console.debug( 'response', response );
+ // hda.debug( 'response', response );
// //hda.set({ deleted: true, purged: true });
// hda.set( response );
//});
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/dataset/states.js
--- a/static/scripts/mvc/dataset/states.js
+++ b/static/scripts/mvc/dataset/states.js
@@ -27,8 +27,9 @@
PAUSED : 'paused',
/** metadata discovery/setting failed or errored (but otherwise ok) */
FAILED_METADATA : 'failed_metadata',
+//TODO: not in trans.app.model.Dataset.states - is in database
/** not accessible to the current user (i.e. due to permissions) */
- NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states
+ NOT_VIEWABLE : 'noPermission',
/** deleted while uploading */
DISCARDED : 'discarded',
/** the tool producing this dataset failed */
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-li-edit.js
--- a/static/scripts/mvc/history/hdca-li-edit.js
+++ b/static/scripts/mvc/history/hdca-li-edit.js
@@ -7,7 +7,8 @@
var _super = HDCA_LI.HDCAListItemView;
/** @class Editing view for HistoryDatasetCollectionAssociation.
*/
-var HDCAListItemEdit = _super.extend({
+var HDCAListItemEdit = _super.extend(
+/** @lends HDCAListItemEdit.prototype */{
/** logger used to record this.log messages, commonly set to console */
//logger : console,
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-li.js
--- a/static/scripts/mvc/history/hdca-li.js
+++ b/static/scripts/mvc/history/hdca-li.js
@@ -9,13 +9,12 @@
var _super = DC_LI.DCListItemView;
/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).
*/
-var HDCAListItemView = _super.extend({
+var HDCAListItemView = _super.extend(
+/** @lends HDCAListItemView.prototype */{
/** logger used to record this.log messages, commonly set to console */
//logger : console,
-//TODO: not a dataset
- /** */
className : _super.prototype.className + " history-content",
/** In this override, add the state as a class for use with state-based CSS */
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-model.js
--- a/static/scripts/mvc/history/hdca-model.js
+++ b/static/scripts/mvc/history/hdca-model.js
@@ -19,7 +19,6 @@
//==============================================================================
/** @class Backbone model for List Dataset Collection within a History.
- * @constructs
*/
var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend(
/** @lends HistoryListDatasetCollection.prototype */{
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-content-model.js
--- a/static/scripts/mvc/history/history-content-model.js
+++ b/static/scripts/mvc/history/history-content-model.js
@@ -34,20 +34,24 @@
// Build a new id (type_id) that prefixes the history_content_type so the bbone collection can differentiate
idAttribute : 'type_id',
+ /** override constructor to build type_id and insert into original attributes */
constructor : function( attrs, options ){
attrs.type_id = typeIdStr( attrs.history_content_type, attrs.id );
this.debug( 'HistoryContentMixin.constructor:', attrs.type_id );
Backbone.Model.apply( this, arguments );
},
+ /** object level fn for building the type_id string */
_typeIdStr : function(){
return typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) );
},
+ /** add listener to re-create type_id when the id changes */
initialize : function( attrs, options ){
this.on( 'change:id', this._createTypeId );
},
+ /** set the type_id in the model attributes */
_createTypeId : function(){
this.set( 'type_id', this._typeIdStr() );
},
@@ -90,12 +94,12 @@
return url;
},
- /** save this HDA as not visible */
+ /** save this content as not visible */
hide : function( options ){
if( !this.get( 'visible' ) ){ return jQuery.when(); }
return this.save( { visible: false }, options );
},
- /** save this HDA as visible */
+ /** save this content as visible */
unhide : function( options ){
if( this.get( 'visible' ) ){ return jQuery.when(); }
return this.save( { visible: true }, options );
@@ -114,6 +118,7 @@
//==============================================================================
+//TODO: needed?
/** @class (Concrete/non-mixin) base model for content items.
*/
var HistoryContent = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( HistoryContentMixin );
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-contents.js
--- a/static/scripts/mvc/history/history-contents.js
+++ b/static/scripts/mvc/history/history-contents.js
@@ -26,7 +26,6 @@
/** since history content is a mix, override model fn into a factory, creating based on history_content_type */
model : function( attrs, options ) {
- //console.debug( 'HistoryContents.model:', attrs, options );
//TODO: can we move the type_id stuff here?
//attrs.type_id = typeIdStr( attrs );
@@ -70,24 +69,25 @@
},
// ........................................................................ common queries
- /** Get the ids of every hda in this collection
+ /** Get the ids of every item in this collection
* @returns array of encoded ids
*/
ids : function(){
- return this.map( function( hda ){ return hda.get('id'); });
+//TODO: is this still useful since type_id
+ return this.map( function( item ){ return item.get('id'); });
},
- /** Get hdas that are not ready
- * @returns array of HDAs
+ /** Get contents that are not ready
+ * @returns array of content models
*/
notReady : function(){
- return this.filter( function( hda ){
- return !hda.inReadyState();
+ return this.filter( function( content ){
+ return !content.inReadyState();
});
},
- /** Get the id of every hda in this collection not in a 'ready' state (running).
- * @returns an array of hda ids
+ /** Get the id of every model in this collection not in a 'ready' state (running).
+ * @returns an array of model ids
* @see HistoryDatasetAssociation#inReadyState
*/
running : function(){
@@ -95,24 +95,26 @@
this.each( function( item ){
var isRunning = !item.inReadyState();
if( isRunning ){
+//TODO: is this still correct since type_id
idList.push( item.get( 'id' ) );
}
});
return idList;
},
- /** Get the hda with the given hid
+ /** Get the model with the given hid
* @param {Int} hid the hid to search for
- * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found
+ * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found
*/
getByHid : function( hid ){
- return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) );
+ return _.first( this.filter( function( content ){ return content.get( 'hid' ) === hid; }) );
},
- /** Get every 'shown' hda in this collection based on show_deleted/hidden
- * @param {Boolean} show_deleted are we showing deleted hdas?
- * @param {Boolean} show_hidden are we showing hidden hdas?
- * @returns array of hda models
+ //TODO:?? this may belong in the containing view
+ /** Get every 'shown' model in this collection based on show_deleted/hidden
+ * @param {Boolean} show_deleted are we showing deleted content?
+ * @param {Boolean} show_hidden are we showing hidden content?
+ * @returns array of content models
* @see HistoryDatasetAssociation#isVisible
*/
getVisible : function( show_deleted, show_hidden, filters ){
@@ -131,13 +133,13 @@
return filteredHdas;
},
- /** return true if any hdas don't have details */
+ /** return true if any contents don't have details */
haveDetails : function(){
- return this.all( function( hda ){ return hda.hasDetails(); });
+ return this.all( function( content ){ return content.hasDetails(); });
},
// ........................................................................ ajax
- /** fetch detailed model data for all HDAs in this collection */
+ /** fetch detailed model data for all contents in this collection */
fetchAllDetails : function( options ){
options = options || {};
var detailsFlag = { details: 'all' };
@@ -145,8 +147,8 @@
return this.fetch( options );
},
- /** using a queue, perform hdaAjaxFn on each of the hdas in this collection */
- ajaxQueue : function( hdaAjaxFn, options ){
+ /** using a queue, perform ajaxFn on each of the models in this collection */
+ ajaxQueue : function( ajaxFn, options ){
var deferred = jQuery.Deferred(),
startingLength = this.length,
responses = [];
@@ -157,12 +159,12 @@
}
// use reverse order (stylistic choice)
- var ajaxFns = this.chain().reverse().map( function( hda, i ){
+ var ajaxFns = this.chain().reverse().map( function( content, i ){
return function(){
- var xhr = hdaAjaxFn.call( hda, options );
+ var xhr = ajaxFn.call( content, options );
// if successful, notify using the deferred to allow tracking progress
xhr.done( function( response ){
- deferred.notify({ curr: i, total: startingLength, response: response, model: hda });
+ deferred.notify({ curr: i, total: startingLength, response: response, model: content });
});
// (regardless of previous error or success) if not last ajax call, shift and call the next
// if last fn, resolve deferred
@@ -183,17 +185,18 @@
},
// ........................................................................ sorting/filtering
- /** return a new collection of HDAs whose attributes contain the substring matchesWhat */
+ /** return a new collection of contents whose attributes contain the substring matchesWhat */
matches : function( matchesWhat ){
- return this.filter( function( hda ){
- return hda.matches( matchesWhat );
+ return this.filter( function( content ){
+ return content.matches( matchesWhat );
});
},
// ........................................................................ misc
+ /** override to get a correct/smarter merge when incoming data is partial */
set : function( models, options ){
// arrrrrrrrrrrrrrrrrg...
- // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone)
+ // (e.g. stupid backbone)
// w/o this partial models from the server will fill in missing data with model defaults
// and overwrite existing data on the client
// see Backbone.Collection.set and _prepareModel
@@ -213,7 +216,7 @@
Backbone.Collection.prototype.set.call( this, models, options );
},
- /** Convert this ad-hoc collection of HDAs to a formal collection tracked
+ /** Convert this ad-hoc collection of hdas to a formal collection tracked
by the server.
**/
promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-annotated.js
--- a/static/scripts/mvc/history/history-panel-annotated.js
+++ b/static/scripts/mvc/history/history-panel-annotated.js
@@ -23,7 +23,7 @@
* @constructs
*/
var AnnotatedHistoryPanel = _super.extend(
-/** @lends HistoryPanel.prototype */{
+/** @lends AnnotatedHistoryPanel.prototype */{
/** logger used to record this.log messages, commonly set to console */
// comment this out to suppress log output
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-edit-current.js
--- a/static/scripts/mvc/history/history-panel-edit-current.js
+++ b/static/scripts/mvc/history/history-panel-edit-current.js
@@ -7,7 +7,8 @@
// ============================================================================
/** session storage for history panel preferences (and to maintain state)
*/
-var HistoryPanelPrefs = BASE_MVC.SessionStorageModel.extend({
+var HistoryPanelPrefs = BASE_MVC.SessionStorageModel.extend(
+/** @lends HistoryPanelPrefs.prototype */{
defaults : {
/** is the panel currently showing the search/filter controls? */
searching : false,
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-edit.js
--- a/static/scripts/mvc/history/history-panel-edit.js
+++ b/static/scripts/mvc/history/history-panel-edit.js
@@ -333,9 +333,9 @@
// maintain a list of hdas that are selected
hdaView.on( 'selected', function( hdaView, event ){
if( !event ){ return; }
- //console.debug( 'selected', event );
+ //this.debug( 'selected', event );
var selectedIds = [];
- //console.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] );
+ //this.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] );
// shift will select a range, but not set lastSelectedViewId
if( ( event.shiftKey )
@@ -348,19 +348,19 @@
} else {
var id = hdaView.model.id;
historyView.lastSelectedViewId = id;
- //console.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId );
+ //this.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId );
selectedIds = [ id ];
}
- //console.debug( 'selectedIds:', selectedIds );
+ //this.debug( 'selectedIds:', selectedIds );
historyView.selectedHdaIds = _.union( historyView.selectedHdaIds, selectedIds );
//TODO: might want to use getSelectedHdaViews instead managing these lists with ops
- //console.debug( 'selected', historyView.selectedHdaIds );
+ //this.debug( 'selected', historyView.selectedHdaIds );
});
hdaView.on( 'de-selected', function( hdaView, event ){
- //console.debug( 'de-selected', event );
+ //this.debug( 'de-selected', event );
var id = hdaView.model.id;
historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id );
- //console.debug( 'de-selected', historyView.selectedHdaIds );
+ //this.debug( 'de-selected', historyView.selectedHdaIds );
});
},
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -8,7 +8,9 @@
], function( HISTORY_MODEL, HDA_LI, HDCA_LI, USER, BASE_MVC, _l ){
// ============================================================================
/** session storage for individual history preferences */
-var HistoryPrefs = BASE_MVC.SessionStorageModel.extend({
+var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(
+/** @lends HistoryPrefs.prototype */{
+
defaults : {
//TODO:?? expandedHdas to array?
expandedHdas : {},
@@ -85,6 +87,7 @@
/** class to use for constructing the HDA views */
HDAViewClass : HDA_LI.HDAListItemView,
+ /** class to use for constructing the HDCA views */
HDCAViewClass : HDCA_LI.HDCAListItemView,
tagName : 'div',
@@ -753,17 +756,17 @@
this.storage.get( 'show_hidden' ),
this.filters
).each( function( hda ){
- //console.debug( 'checking: ', hda.get( 'name' ) );
+ //panel.debug( 'checking: ', hda.get( 'name' ) );
if( withinSet ){
- //console.debug( '\t\t adding: ', hda.get( 'name' ) );
+ //panel.debug( '\t\t adding: ', hda.get( 'name' ) );
set.push( panel.hdaViews[ hda.id ] );
if( hda === viewA.model || hda === viewB.model ){
- //console.debug( '\t found last: ', hda.get( 'name' ) );
+ //panel.debug( '\t found last: ', hda.get( 'name' ) );
withinSet = false;
}
} else {
if( hda === viewA.model || hda === viewB.model ){
- //console.debug( 'found first: ', hda.get( 'name' ) );
+ //panel.debug( 'found first: ', hda.get( 'name' ) );
withinSet = true;
set.push( panel.hdaViews[ hda.id ] );
}
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/collection/collection-panel.js
--- a/static/scripts/packed/mvc/collection/collection-panel.js
+++ b/static/scripts/packed/mvc/collection/collection-panel.js
@@ -1,1 +1,1 @@
-define(["mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(h,f,a,e){var d=Backbone.View.extend(a.LoggableMixin).extend({tagName:"div",className:"dataset-collection-panel",fxSpeed:"fast",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.hasUser=i.hasUser;this.panelStack=[];this.parentName=i.parentName;window.collectionPanel=this},_setUpListeners:function(){this.on("all",function(i){this.log(this+"",arguments)},this);return this},_setUpModelEventHandlers:function(){return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(!this.model){return this}j=this.renderModel();$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderModel:function(){var k=this.model.get("collection_type")||this.model.object.get("collection_type"),j=_.extend(this.model.toJSON(),{parentName:this.parentName,type:k}),i=$("<div/>").append(this.templates.panel(j));this._setUpBehaviours(i);this.renderContents(i);return i},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},renderContents:function(j){j=j||this.$el;this.warn(this+".renderContents:, model:",this.model);var i=this,l={},k=this.model.getVisibleContents();this.$datasetsList(j).empty();if(k&&k.length){k.each(function(n){var o=n.id,m=i._createContentView(n);l[o]=m;i._attachContentView(m.render(),j)})}this.contentViews=l;return this.contentViews},_createContentView:function(k){var j=null,i=this._getContentClass(k);j=new i({model:k,linkTarget:this.linkTarget,hasUser:this.hasUser,logger:this.logger});this._setUpContentListeners(j);return j},_getContentClass:function(i){switch(i.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",i.get("element_type"))},_setUpContentListeners:function(j){var i=this;if(j.model.get("element_type")==="dataset_collection"){j.on("expanded",function(k){i.info("expanded",k);i._addCollectionPanel(k)})}},_addCollectionPanel:function(k){var l=this,i=k.model;var j=new c({model:i,parentName:this.model.get("name"),linkTarget:this.linkTarget});l.panelStack.push(j);l.$(".controls").add(".datasets-list").hide();l.$el.append(j.$el);j.on("close",function(){l.render();k.collapse();l.panelStack.pop()});if(!j.model.hasDetails()){var m=j.model.fetch();m.done(function(){j.render()})}else{j.render()}},_attachContentView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.append(k.$el);return this},events:{"click .navigation .back":"close"},close:function(i){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates=d.prototype.templates=(function(){var i=_.template(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- collection.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>",'<div class="datasets-list"></div>'].join(""));return{panel:function(j){return i({_l:e,collection:j})}}}());var b=d.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=b.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var g=d.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:d,ListCollectionPanel:b,PairCollectionPanel:c,ListOfPairsCollectionPanel:g}});
\ No newline at end of file
+define(["mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(h,f,a,e){var d=Backbone.View.extend(a.LoggableMixin).extend({tagName:"div",className:"dataset-collection-panel",fxSpeed:"fast",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.hasUser=i.hasUser;this.panelStack=[];this.parentName=i.parentName},_setUpListeners:function(){this.on("all",function(i){this.log(this+"",arguments)},this);return this},_setUpModelEventHandlers:function(){return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(!this.model){return this}j=this.renderModel();$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderModel:function(){var k=this.model.get("collection_type")||this.model.object.get("collection_type"),j=_.extend(this.model.toJSON(),{parentName:this.parentName,type:k}),i=$("<div/>").append(this.templates.panel(j));this._setUpBehaviours(i);this.renderContents(i);return i},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},renderContents:function(j){j=j||this.$el;this.warn(this+".renderContents:, model:",this.model);var i=this,l={},k=this.model.getVisibleContents();this.$datasetsList(j).empty();if(k&&k.length){k.each(function(n){var o=n.id,m=i._createContentView(n);l[o]=m;i._attachContentView(m.render(),j)})}this.contentViews=l;return this.contentViews},_createContentView:function(k){var j=null,i=this._getContentClass(k);j=new i({model:k,linkTarget:this.linkTarget,hasUser:this.hasUser,logger:this.logger});this._setUpContentListeners(j);return j},_getContentClass:function(i){switch(i.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",i.get("element_type"))},_setUpContentListeners:function(j){var i=this;if(j.model.get("element_type")==="dataset_collection"){j.on("expanded",function(k){i.info("expanded",k);i._addCollectionPanel(k)})}},_addCollectionPanel:function(k){var l=this,i=k.model;var j=new c({model:i,parentName:this.model.get("name"),linkTarget:this.linkTarget});l.panelStack.push(j);l.$(".controls").add(".datasets-list").hide();l.$el.append(j.$el);j.on("close",function(){l.render();k.collapse();l.panelStack.pop()});if(!j.model.hasDetails()){var m=j.model.fetch();m.done(function(){j.render()})}else{j.render()}},_attachContentView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.append(k.$el);return this},events:{"click .navigation .back":"close"},close:function(i){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates=d.prototype.templates=(function(){var i=_.template(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- collection.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>",'<div class="datasets-list"></div>'].join(""));return{panel:function(j){return i({_l:e,collection:j})}}}());var b=d.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=b.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var g=d.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:d,ListCollectionPanel:b,PairCollectionPanel:c,ListOfPairsCollectionPanel:g}});
\ No newline at end of file
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/dataset/dataset-model.js
--- a/static/scripts/packed/mvc/dataset/dataset-model.js
+++ b/static/scripts/packed/mvc/dataset/dataset-model.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var f=b.SearchableModelMixin;var e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(f,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,g){this.debug("Dataset.initialize",h,g);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var i=this.get("id");if(!i){return{}}var h={purge:"datasets/"+i+"/purge_async",display:"datasets/"+i+"/display/?preview=True",edit:"datasets/"+i+"/edit",download:"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+i,rerun:"tool_runner/rerun?id="+i,show_params:"datasets/"+i+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};var g=(galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(h,function(k,j){h[j]=g+k});this.urls=h;return h},_setUpListeners:function(){this.on("change:state",function(h,g){this.log(this+" has changed state:",h,g);if(this.inReadyState()){this.trigger("state:ready",h,g,this.previous("state"))}});this.on("change:id change:file_ext",function(g){this._generateUrls()})},toJSON:function(){var g=Backbone.Model.prototype.toJSON.call(this);return _.extend(g,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var g=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||g)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(g){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},g)},undelete:function(g){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},g)},purge:function d(g){if(this.get("purged")){return jQuery.when()}g=g||{};g.url=this.urls.purge;var h=this,i=jQuery.ajax(g);i.done(function(l,j,k){h.set({deleted:true,purged:true})});i.fail(function(n,j,m){var k=c("Unable to purge dataset");var l=("Removal of datasets by users is not allowed in this Galaxy instance");if(n.responseJSON&&n.responseJSON.error){k=n.responseJSON.error}else{if(n.responseText.indexOf(l)!==-1){k=l}}n.responseText=k;h.trigger("error",h,n,g,c(k),{error:k})});return i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var g=this.get("id")||"";if(this.get("name")){g='"'+this.get("name")+'",'+g}return"Dataset("+g+")"}}));return{DatasetAssociation:e}});
\ No newline at end of file
+define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var f=b.SearchableModelMixin;var e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(f,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(g,h){this.debug(this+"(Dataset).initialize",g,h);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var i=this.get("id");if(!i){return{}}var h={purge:"datasets/"+i+"/purge_async",display:"datasets/"+i+"/display/?preview=True",edit:"datasets/"+i+"/edit",download:"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+i,rerun:"tool_runner/rerun?id="+i,show_params:"datasets/"+i+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};var g=(galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(h,function(k,j){h[j]=g+k});this.urls=h;return h},_setUpListeners:function(){this.on("change:state",function(h,g){this.log(this+" has changed state:",h,g);if(this.inReadyState()){this.trigger("state:ready",h,g,this.previous("state"))}});this.on("change:id change:file_ext",function(g){this._generateUrls()})},toJSON:function(){var g=Backbone.Model.prototype.toJSON.call(this);return _.extend(g,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var g=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||g)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(g){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},g)},undelete:function(g){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},g)},purge:function d(g){if(this.get("purged")){return jQuery.when()}g=g||{};g.url=this.urls.purge;var h=this,i=jQuery.ajax(g);i.done(function(l,j,k){h.set({deleted:true,purged:true})});i.fail(function(n,j,m){var k=c("Unable to purge dataset");var l=("Removal of datasets by users is not allowed in this Galaxy instance");if(n.responseJSON&&n.responseJSON.error){k=n.responseJSON.error}else{if(n.responseText.indexOf(l)!==-1){k=l}}n.responseText=k;h.trigger("error",h,n,g,c(k),{error:k})});return i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var g=this.get("id")||"";if(this.get("name")){g='"'+this.get("name")+'",'+g}return"Dataset("+g+")"}}));return{DatasetAssociation:e}});
\ No newline at end of file
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/history/history-contents.js
--- a/static/scripts/packed/mvc/history/history-contents.js
+++ b/static/scripts/packed/mvc/history/history-contents.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}});
\ No newline at end of file
+define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}});
\ No newline at end of file
diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/history/history-panel-annotated.js
--- a/static/scripts/packed/mvc/history/history-panel-annotated.js
+++ b/static/scripts/packed/mvc/history/history-panel-annotated.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-panel","mvc/history/hda-li","utils/localization"],function(e,b,a){var d=e.ReadOnlyHistoryPanel;var c=d.extend({className:"annotated-history-panel",HDAViewClass:b.HDAReadonlyListItemView,renderModel:function(){this.$el.addClass(this.className);var h=d.prototype.renderModel.call(this),f=this.$datasetsList(h),g=$("<table/>").addClass("datasets-list datasets-table");g.append(f.children());f.replaceWith(g);h.find(".history-subtitle").after(this.renderHistoryAnnotation());h.find(".history-search-btn").hide();h.find(".history-controls").after(h.find(".history-search-controls").show());return h},renderHistoryAnnotation:function(){var f=this.model.get("annotation");if(!f){return null}return $(['<div class="history-annotation">',f,"</div>"].join(""))},renderHdas:function(g){g=g||this.$el;var f=d.prototype.renderHdas.call(this,g);this.$datasetsList(g).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(a("Dataset")),$("<th/>").text(a("Annotation"))]));return f},attachContentView:function(i,g){g=g||this.$el;var j=_.find(i.el.classList,function(k){return(/^state\-/).test(k)}),f=i.model.get("annotation")||"",h=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(i.$el).addClass(j?j.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(f)]);this.$datasetsList(g).append(h)},events:_.extend(_.clone(d.prototype.events),{"click tr":function(f){$(f.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(f){f.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:c}});
\ No newline at end of file
+define(["mvc/history/history-panel","mvc/history/hda-li","utils/localization"],function(e,b,a){var d=e.ReadOnlyHistoryPanel;var c=d.extend({className:"annotated-history-panel",renderModel:function(){this.$el.addClass(this.className);var h=d.prototype.renderModel.call(this),f=this.$datasetsList(h),g=$("<table/>").addClass("datasets-list datasets-table");g.append(f.children());f.replaceWith(g);h.find(".history-subtitle").after(this.renderHistoryAnnotation());h.find(".history-search-btn").hide();h.find(".history-controls").after(h.find(".history-search-controls").show());return h},renderHistoryAnnotation:function(){var f=this.model.get("annotation");if(!f){return null}return $(['<div class="history-annotation">',f,"</div>"].join(""))},renderHdas:function(g){g=g||this.$el;var f=d.prototype.renderHdas.call(this,g);this.$datasetsList(g).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(a("Dataset")),$("<th/>").text(a("Annotation"))]));return f},attachContentView:function(i,g){g=g||this.$el;var j=_.find(i.el.classList,function(k){return(/^state\-/).test(k)}),f=i.model.get("annotation")||"",h=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(i.$el).addClass(j?j.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(f)]);this.$datasetsList(g).append(h)},events:_.extend(_.clone(d.prototype.events),{"click tr":function(f){$(f.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(f){f.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:c}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Updated tag latest_2014.08.11 for changeset 7e4d21621ce1
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7e81cbc2603f/
Changeset: 7e81cbc2603f
Branch: stable
User: natefoo
Date: 2014-08-12 15:58:36
Summary: Updated tag latest_2014.08.11 for changeset 7e4d21621ce1
Affected #: 1 file
diff -r 7e4d21621ce12e13ebbdf9fd3259df58c3ef124c -r 7e81cbc2603f0695802ab49dcd65f6dda7b42322 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-52b5cc75a1757eddfb94ee373193c9d8fa2ec442 latest_2014.08.11
+7e4d21621ce12e13ebbdf9fd3259df58c3ef124c latest_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e30d65cf25e8/
Changeset: e30d65cf25e8
Branch: stable
User: BjoernGruening
Date: 2014-08-12 10:33:27
Summary: install_repository_manager do not need trans.app anymore.
Affected #: 1 file
diff -r b6d2c77d8bce44cdaba188ce949ed69f94be6bc4 -r e30d65cf25e8e28677d971c19faaae0eb390e6af lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -239,8 +239,7 @@
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
self.__ensure_can_install_repos( trans )
install_repository_manager = InstallRepositoryManager( trans.app )
- installed_tool_shed_repositories = install_repository_manager.install( trans.app,
- tool_shed_url,
+ installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url,
name,
owner,
changeset_revision,
https://bitbucket.org/galaxy/galaxy-central/commits/fa1a6a494166/
Changeset: fa1a6a494166
Branch: stable
User: BjoernGruening
Date: 2014-08-12 10:38:24
Summary: First argument to __install_repositories is the Tool Shed URL (tool_shed_url)
Affected #: 1 file
diff -r e30d65cf25e8e28677d971c19faaae0eb390e6af -r fa1a6a4941664d9f2cf6dfbb816911778b7c9dcb lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -694,7 +694,8 @@
name,
owner,
changeset_revision )
- installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict,
+ installed_tool_shed_repositories = self.__install_repositories( tool_shed_url,
+ repository_revision_dict,
repo_info_dicts,
install_options )
return installed_tool_shed_repositories
https://bitbucket.org/galaxy/galaxy-central/commits/7e4d21621ce1/
Changeset: 7e4d21621ce1
Branch: stable
User: BjoernGruening
Date: 2014-08-12 10:41:45
Summary: initiate_repository_installation was not updated in the recent code restructuring efforts
Affected #: 1 file
diff -r fa1a6a4941664d9f2cf6dfbb816911778b7c9dcb -r 7e4d21621ce12e13ebbdf9fd3259df58c3ef124c lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -789,7 +789,7 @@
# at this point because repository dependencies may have added additional repositories for installation
# along with the single specified repository.
encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
- initiate_repository_installation( self.app, installation_dict )
+ self.initiate_repository_installation( installation_dict )
# Some repositories may have repository dependencies that are required to be installed before the
# dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in
# the required order.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: History & collections: client-side file and class renaming: - li: readonly list item view, - li-edit: editable list item view, - primary identity first (eg. hda-*), - moved hda/hdca into history directory; Fix bug for dataset URLs
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/588c52157560/
Changeset: 588c52157560
User: carlfeberhard
Date: 2014-08-12 15:38:08
Summary: History & collections: client-side file and class renaming: - li: readonly list item view, - li-edit: editable list item view, - primary identity first (eg. hda-*), - moved hda/hdca into history directory; Fix bug for dataset URLs
Affected #: 74 files
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-li-edit.js
--- /dev/null
+++ b/static/scripts/mvc/collection/collection-li-edit.js
@@ -0,0 +1,33 @@
+define([
+ "mvc/collection/collection-li",
+ "utils/localization"
+], function( DC_LI, _l ){
+//==============================================================================
+/*
+
+NOTE: not much going on here. Until we find out what operations a user will need
+ to perform on their own DC's, we'll leave this empty.
+
+*/
+//==============================================================================
+var _super = DC_LI.DCListItemView;
+/** @class Editing view for DatasetCollectionElement.
+ */
+var DCEListItemEdit = _super.extend({
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ // ......................................................................... misc
+ /** string rep */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'DCEListItemEdit(' + modelString + ')';
+ }
+});
+
+//==============================================================================
+ return {
+ DCEListItemEdit : DCEListItemEdit
+ };
+});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-li.js
--- /dev/null
+++ b/static/scripts/mvc/collection/collection-li.js
@@ -0,0 +1,223 @@
+define([
+ "mvc/dataset/dataset-li",
+ "mvc/base-mvc",
+ "utils/localization"
+], function( DATASET_LI, BASE_MVC, _l ){
+/* global Backbone, LoggableMixin */
+//==============================================================================
+var ListItemView = BASE_MVC.ListItemView;
+/** @class Read only view for DatasetCollection.
+ */
+var DCListItemView = ListItemView.extend({
+//TODO: may not be needed
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ className : ListItemView.prototype.className + " dataset-collection",
+ /** */
+ fxSpeed : 'fast',
+
+//TODO: ununsed
+ /** set up */
+ initialize : function( attributes ){
+ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
+ this.log( this + '(DCListItemView).initialize:', attributes );
+ ListItemView.prototype.initialize.call( this, attributes );
+ },
+
+ /** In this override, don't show`or render any details (no need to do anything here)
+ * - currently the parent control will load a panel for this collection over itself
+ * @fires expanded when a body has been expanded
+ */
+ expand : function(){
+ var view = this;
+ return view._fetchModelDetails()
+ .always(function(){
+ view.trigger( 'expanded', view );
+ });
+ },
+
+ // ......................................................................... rendering
+ //TODO:?? possibly move to listItem
+ /** render a subtitle to show the user what sort of collection this is */
+ _renderSubtitle : function(){
+ var $subtitle = $( '<div class="subtitle"></div>' );
+ //TODO: would be good to get this in the subtitle
+ //var len = this.model.elements.length;
+ switch( this.model.get( 'collection_type' ) ){
+ case 'list':
+ return $subtitle.text( _l( 'a list of datasets' ) );
+ case 'paired':
+ return $subtitle.text( _l( 'a pair of datasets' ) );
+ case 'list:paired':
+ return $subtitle.text( _l( 'a list of paired datasets' ) );
+ }
+ return $subtitle;
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'DCListItemView(' + modelString + ')';
+ }
+});
+
+// ............................................................................ TEMPLATES
+/** underscore templates */
+DCListItemView.prototype.templates = (function(){
+
+ // use element identifier
+ var titleBarTemplate = BASE_MVC.wrapTemplate([
+ '<div class="title-bar clear" tabindex="0">',
+ '<div class="title">',
+ '<span class="name"><%- collection.element_identifier || collection.name %></span>',
+ '</div>',
+ '<div class="subtitle"></div>',
+ '</div>'
+ ], 'collection' );
+
+ return _.extend( {}, ListItemView.prototype.templates, {
+ titleBar : titleBarTemplate
+ });
+}());
+
+
+//==============================================================================
+/** @class Read only view for DatasetCollectionElement.
+ */
+var DCEListItemView = ListItemView.extend({
+//TODO: this might be expendable - compacted with HDAListItemView
+
+ /** logger used to record this.log messages, commonly set to console */
+ // comment this out to suppress log output
+ logger : console,
+
+ /** add the DCE class to the list item */
+ className : ListItemView.prototype.className + " dataset-collection-element",
+ /** jq fx speed for this view */
+ fxSpeed : 'fast',
+
+ /** */
+ initialize : function( attributes ){
+ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
+ this.log( 'DCEListItemView.initialize:', attributes );
+ ListItemView.prototype.initialize.call( this, attributes );
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'DCEListItemView(' + modelString + ')';
+ }
+});
+
+// ............................................................................ TEMPLATES
+/** underscore templates */
+DCEListItemView.prototype.templates = (function(){
+
+ // use the element identifier here - since that will persist and the user will need it
+ var titleBarTemplate = BASE_MVC.wrapTemplate([
+ '<div class="title-bar clear" tabindex="0">',
+ '<div class="title">',
+ '<span class="name"><%- element.element_identifier %></span>',
+ '</div>',
+ '<div class="subtitle"></div>',
+ '</div>'
+ ], 'element' );
+
+ return _.extend( {}, ListItemView.prototype.templates, {
+ titleBar : titleBarTemplate
+ });
+}());
+
+
+//==============================================================================
+/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation
+ * (a dataset contained in a dataset collection).
+ */
+var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend({
+
+ className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element",
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ /** */
+ initialize : function( attributes ){
+ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
+ this.log( 'DatasetDCEListItemView.initialize:', attributes );
+ DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes );
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'DatasetDCEListItemView(' + modelString + ')';
+ }
+});
+
+// ............................................................................ TEMPLATES
+/** underscore templates */
+DatasetDCEListItemView.prototype.templates = (function(){
+
+ // use the element identifier here and not the dataset name
+ //TODO:?? can we steal the DCE titlebar?
+ var titleBarTemplate = BASE_MVC.wrapTemplate([
+ '<div class="title-bar clear" tabindex="0">',
+ '<span class="state-icon"></span>',
+ '<div class="title">',
+ '<span class="name"><%- element.element_identifier %></span>',
+ '</div>',
+ '</div>'
+ ], 'element' );
+
+ return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, {
+ titleBar : titleBarTemplate
+ });
+}());
+
+
+//==============================================================================
+/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection
+ * (a nested DC).
+ */
+var NestedDCDCEListItemView = DCListItemView.extend({
+
+ className : DCListItemView.prototype.className + " dataset-collection-element",
+
+ /** logger used to record this.log messages, commonly set to console */
+ // comment this out to suppress log output
+ //logger : console,
+
+ /** In this override, add the state as a class for use with state-based CSS */
+ _swapNewRender : function( $newRender ){
+ DCListItemView.prototype._swapNewRender.call( this, $newRender );
+//TODO: model currently has no state
+ var state = this.model.get( 'state' ) || 'ok';
+ //if( this.model.has( 'state' ) ){
+ this.$el.addClass( 'state-' + state );
+ //}
+ return this.$el;
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'NestedDCDCEListItemView(' + modelString + ')';
+ }
+});
+
+
+//==============================================================================
+ return {
+ DCListItemView : DCListItemView,
+ DCEListItemView : DCEListItemView,
+ DatasetDCEListItemView : DatasetDCEListItemView,
+ NestedDCDCEListItemView : NestedDCDCEListItemView
+ };
+});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-model.js
--- a/static/scripts/mvc/collection/collection-model.js
+++ b/static/scripts/mvc/collection/collection-model.js
@@ -2,7 +2,7 @@
"mvc/dataset/dataset-model",
"mvc/base-mvc",
"utils/localization"
-], function( DATASET, BASE_MVC, _l ){
+], function( DATASET_MODEL, BASE_MVC, _l ){
//==============================================================================
/*
Notes:
@@ -118,13 +118,13 @@
//==============================================================================
/** @class Backbone model for a dataset collection element that is a dataset (HDA).
*/
-var DatasetDCE = DATASET.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,
+var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,
/** @lends DatasetDCE.prototype */{
/** logger used to record this.log messages, commonly set to console */
//logger : console,
- defaults : _.extend( {}, DATASET.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ),
+ defaults : _.extend( {}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ),
// because all objects have constructors (as this hashmap would even if this next line wasn't present)
// the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
@@ -132,7 +132,7 @@
/** call the mixin constructor */
constructor : function( attributes, options ){
this.debug( '\t DatasetDCE.constructor:', attributes, options );
- //DATASET.DatasetAssociation.prototype.constructor.call( this, attributes, options );
+ //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );
DatasetCollectionElementMixin.constructor.call( this, attributes, options );
},
@@ -140,7 +140,7 @@
/** set up */
initialize : function( attributes, options ){
this.debug( this + '(DatasetDCE).initialize:', attributes, options );
- DATASET.DatasetAssociation.prototype.initialize.call( this, attributes, options );
+ DATASET_MODEL.DatasetAssociation.prototype.initialize.call( this, attributes, options );
},
/** String representation. */
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-panel.js
--- a/static/scripts/mvc/collection/collection-panel.js
+++ b/static/scripts/mvc/collection/collection-panel.js
@@ -1,20 +1,15 @@
define([
- "mvc/collection/dataset-collection-base",
+ "mvc/collection/collection-model",
+ "mvc/collection/collection-li",
"mvc/base-mvc",
"utils/localization"
-], function( DC_BASE, BASE_MVC, _l ){
+], function( DC_MODEL, DC_LI, BASE_MVC, _l ){
/* =============================================================================
TODO:
============================================================================= */
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection.
- * @name CollectionPanel
- *
- * @augments Backbone.View
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
*/
var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(
/** @lends CollectionPanel.prototype */{
@@ -29,8 +24,8 @@
/** (in ms) that jquery effects will use */
fxSpeed : 'fast',
- DatasetDCEViewClass : DC_BASE.DatasetDCEBaseView,
- NestedDCEViewClass : DC_BASE.NestedDCEBaseView,
+ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView,
+ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView,
// ......................................................................... SET UP
/** Set up the view, set up storage, bind listeners to HistoryContents events
@@ -44,9 +39,13 @@
}
this.log( this + '.initialize:', attributes );
+ this.linkTarget = attributes.linkTarget || '_blank';
+
this.hasUser = attributes.hasUser;
this.panelStack = [];
this.parentName = attributes.parentName;
+
+ //window.collectionPanel = this;
},
/** create any event listeners for the panel
@@ -70,7 +69,7 @@
},
// ------------------------------------------------------------------------ panel rendering
- /** Render urls, historyPanel body, and hdas (if any are shown)
+ /** Render panel
* @fires: rendered when the panel is attached and fully visible
* @see Backbone.View#render
*/
@@ -122,7 +121,7 @@
return this;
},
- /** render with history data
+ /** render with collection data
* @returns {jQuery} dom fragment as temporary container to be swapped out later
*/
renderModel : function( ){
@@ -139,7 +138,7 @@
return $newRender;
},
- /** Set up HistoryPanel js/widget behaviours */
+ /** Set up js/widget behaviours */
_setUpBehaviours : function( $where ){
//TODO: these should be either sub-MVs, or handled by events
$where = $where || this.$el;
@@ -152,16 +151,16 @@
$container : function(){
return ( this.findContainerFn )?( this.findContainerFn.call( this ) ):( this.$el.parent() );
},
- /** where hdaViews are attached */
+ /** where list content views are attached */
$datasetsList : function( $where ){
return ( $where || this.$el ).find( '.datasets-list' );
},
// ------------------------------------------------------------------------ sub-views
- /** Set up/render a view for each HDA to be shown, init with model and listeners.
- * HDA views are cached to the map this.hdaViews (using the model.id as key).
- * @param {jQuery} $whereTo what dom element to prepend the HDA views to
- * @returns the number of visible hda views
+ /** Set up/render a view for each DCE to be shown, init with model and listeners.
+ * DCE views are cached to the map this.contentViews (using the model.id as key).
+ * @param {jQuery} $whereTo what dom element to prepend the DCE views to
+ * @returns the number of visible DCE views
*/
renderContents : function( $whereTo ){
//this.debug( 'renderContents, elements:', this.model.elements );
@@ -172,7 +171,7 @@
contentViews = {},
//NOTE: no filtering here
visibleContents = this.model.getVisibleContents();
- this.log( 'renderContents, visibleContents:', visibleContents, $whereTo );
+ //this.debug( 'renderContents, visibleContents:', visibleContents, $whereTo );
this.$datasetsList( $whereTo ).empty();
if( visibleContents && visibleContents.length ){
@@ -192,8 +191,8 @@
//this.debug( 'content json:', JSON.stringify( content, null, ' ' ) );
var contentView = null,
ContentClass = this._getContentClass( content );
- this.debug( 'ContentClass:', ContentClass );
- this.debug( 'content:', content );
+ //this.debug( 'content:', content );
+ //this.debug( 'ContentClass:', ContentClass );
contentView = new ContentClass({
model : content,
linkTarget : this.linkTarget,
@@ -201,20 +200,20 @@
hasUser : this.hasUser,
logger : this.logger
});
- this.debug( 'contentView:', contentView );
+ //this.debug( 'contentView:', contentView );
this._setUpContentListeners( contentView );
return contentView;
},
/** */
_getContentClass : function( content ){
- this.debug( this + '._getContentClass:', content );
- this.debug( 'DCEViewClass:', this.DCEViewClass );
+ //this.debug( this + '._getContentClass:', content );
+//TODO: subclasses use DCEViewClass - but are currently unused - decide
switch( content.get( 'element_type' ) ){
case 'hda':
- return this.DCEViewClass;
+ return this.DatasetDCEViewClass;
case 'dataset_collection':
- return this.DCEViewClass;
+ return this.NestedDCDCEViewClass;
}
throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) );
},
@@ -232,14 +231,16 @@
/** */
_addCollectionPanel : function( collectionView ){
+//TODO: a bit hackish
var currPanel = this,
collectionModel = collectionView.model;
- this.debug( 'collection panel (stack), collectionView:', collectionView );
- this.debug( 'collection panel (stack), collectionModel:', collectionModel );
+ //this.debug( 'collection panel (stack), collectionView:', collectionView );
+ //this.debug( 'collection panel (stack), collectionModel:', collectionModel );
var panel = new PairCollectionPanel({
model : collectionModel,
- parentName : this.model.get( 'name' )
+ parentName : this.model.get( 'name' ),
+ linkTarget : this.linkTarget
});
currPanel.panelStack.push( panel );
@@ -277,7 +278,7 @@
'click .navigation .back' : 'close'
},
- /** */
+ /** close/remove this collection panel */
close : function( event ){
this.$el.remove();
this.trigger( 'close' );
@@ -334,7 +335,8 @@
/** @class non-editable, read-only View/Controller for a dataset collection. */
var ListCollectionPanel = CollectionPanel.extend({
- DCEViewClass : DC_BASE.DatasetDCEBaseView,
+ //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass
+ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView,
// ........................................................................ misc
/** string rep */
@@ -360,7 +362,8 @@
/** @class non-editable, read-only View/Controller for a dataset collection. */
var ListOfPairsCollectionPanel = CollectionPanel.extend({
- DCEViewClass : DC_BASE.NestedDCDCEBaseView,
+ //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass
+ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView,
// ........................................................................ misc
/** string rep */
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/dataset-collection-base.js
--- a/static/scripts/mvc/collection/dataset-collection-base.js
+++ /dev/null
@@ -1,222 +0,0 @@
-define([
- "mvc/dataset/dataset-list-element",
- "mvc/base-mvc",
- "utils/localization"
-], function( DATASET_LI, BASE_MVC, _l ){
-/* global Backbone, LoggableMixin */
-//==============================================================================
-var ListItemView = BASE_MVC.ListItemView;
-/** @class Read only view for DatasetCollection.
- */
-var DCBaseView = ListItemView.extend({
-//TODO: may not be needed
-
- /** logger used to record this.log messages, commonly set to console */
- //logger : console,
-
- className : ListItemView.prototype.className + " dataset-collection",
- /** */
- fxSpeed : 'fast',
-
-//TODO: ununsed
- /** set up */
- initialize : function( attributes ){
- if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
- this.log( 'DCBaseView.initialize:', attributes );
- ListItemView.prototype.initialize.call( this, attributes );
- },
-
- /** In this override, don't show`or render any details (no need to do anything here)
- * - currently the parent control will load a panel for this collection over itself
- * @fires expanded when a body has been expanded
- */
- expand : function(){
- var view = this;
- return view._fetchModelDetails()
- .always(function(){
- view.trigger( 'expanded', view );
- });
- },
-
- // ......................................................................... rendering
- //TODO:?? possibly move to listItem
- /** render a subtitle to show the user what sort of collection this is */
- _renderSubtitle : function(){
- var $subtitle = $( '<div class="subtitle"></div>' );
- //TODO: would be good to get this in the subtitle
- //var len = this.model.elements.length;
- switch( this.model.get( 'collection_type' ) ){
- case 'list':
- return $subtitle.text( _l( 'a list of datasets' ) );
- case 'paired':
- return $subtitle.text( _l( 'a pair of datasets' ) );
- case 'list:paired':
- return $subtitle.text( _l( 'a list of paired datasets' ) );
- }
- return $subtitle;
- },
-
- // ......................................................................... misc
- /** String representation */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'DCBaseView(' + modelString + ')';
- }
-});
-
-// ............................................................................ TEMPLATES
-/** underscore templates */
-DCBaseView.prototype.templates = (function(){
-
- // use element identifier
- var titleBarTemplate = BASE_MVC.wrapTemplate([
- '<div class="title-bar clear" tabindex="0">',
- '<div class="title">',
- '<span class="name"><%- collection.element_identifier || collection.name %></span>',
- '</div>',
- '<div class="subtitle"></div>',
- '</div>'
- ], 'collection' );
-
- return _.extend( {}, ListItemView.prototype.templates, {
- titleBar : titleBarTemplate
- });
-}());
-
-
-//==============================================================================
-/** @class Read only view for DatasetCollectionElement.
- */
-var DCEBaseView = ListItemView.extend({
-//TODO: this might be expendable - compacted with HDADCEBaseView
-
- /** logger used to record this.log messages, commonly set to console */
- // comment this out to suppress log output
- logger : console,
-
- /** add the DCE class to the list item */
- className : ListItemView.prototype.className + " dataset-collection-element",
- /** jq fx speed for this view */
- fxSpeed : 'fast',
-
- /** */
- initialize : function( attributes ){
- if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
- this.log( 'DCEBaseView.initialize:', attributes );
- ListItemView.prototype.initialize.call( this, attributes );
- },
-
- // ......................................................................... misc
- /** String representation */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'DCEBaseView(' + modelString + ')';
- }
-});
-
-// ............................................................................ TEMPLATES
-/** underscore templates */
-DCEBaseView.prototype.templates = (function(){
-
- // use the element identifier here - since that will persist and the user will need it
- var titleBarTemplate = BASE_MVC.wrapTemplate([
- '<div class="title-bar clear" tabindex="0">',
- '<div class="title">',
- '<span class="name"><%- element.element_identifier %></span>',
- '</div>',
- '<div class="subtitle"></div>',
- '</div>'
- ], 'element' );
-
- return _.extend( {}, ListItemView.prototype.templates, {
- titleBar : titleBarTemplate
- });
-}());
-
-
-//==============================================================================
-/** @class Read only view for a DatasetCollectionElement that is also an HDA.
- */
-var DatasetDCEBaseView = DATASET_LI.DatasetListItemView.extend({
-
- className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element",
-
- /** logger used to record this.log messages, commonly set to console */
- // comment this out to suppress log output
- //logger : console,
-
- /** */
- initialize : function( attributes ){
- if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
- this.log( 'DatasetDCEBaseView.initialize:', attributes );
- DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes );
- },
-
- // ......................................................................... misc
- /** String representation */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'DatasetDCEBaseView(' + modelString + ')';
- }
-});
-
-// ............................................................................ TEMPLATES
-/** underscore templates */
-DatasetDCEBaseView.prototype.templates = (function(){
-
- // use the element identifier here and not the dataset name
- //TODO:?? can we steal the DCE titlebar?
- var titleBarTemplate = BASE_MVC.wrapTemplate([
- '<div class="title-bar clear" tabindex="0">',
- '<span class="state-icon"></span>',
- '<div class="title">',
- '<span class="name"><%- element.element_identifier %></span>',
- '</div>',
- '</div>'
- ], 'element' );
-
- return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, {
- titleBar : titleBarTemplate
- });
-}());
-
-//==============================================================================
-/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection
- * (a nested DC).
- */
-var NestedDCDCEBaseView = DCBaseView.extend({
-
- className : DCBaseView.prototype.className + " dataset-collection-element",
-
- /** logger used to record this.log messages, commonly set to console */
- // comment this out to suppress log output
- //logger : console,
-
- /** In this override, add the state as a class for use with state-based CSS */
- _swapNewRender : function( $newRender ){
- DATASET_LI.DatasetListItemView.prototype._swapNewRender.call( this, $newRender );
-//TODO: model currently has no state
- var state = this.model.get( 'state' ) || 'ok';
- //if( this.model.has( 'state' ) ){
- this.$el.addClass( 'state-' + state );
- //}
- return this.$el;
- },
-
- // ......................................................................... misc
- /** String representation */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'NestedDCDCEBaseView(' + modelString + ')';
- }
-});
-
-
-//==============================================================================
- return {
- DCBaseView : DCBaseView,
- DCEBaseView : DCEBaseView,
- DatasetDCEBaseView : DatasetDCEBaseView,
- NestedDCDCEBaseView : NestedDCDCEBaseView
- };
-});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/dataset-collection-edit.js
--- a/static/scripts/mvc/collection/dataset-collection-edit.js
+++ /dev/null
@@ -1,39 +0,0 @@
-define([
- "mvc/dataset/states",
- "mvc/collection/dataset-collection-base",
- "utils/localization"
-], function( STATES, DC_BASE_VIEW, _l ){
-//==============================================================================
-/*
-
-NOTE: not much going on here. Until we find out what operations a user will need
- to perform on their own DC's, we'll leave this empty.
-
-*/
-//==============================================================================
-var _super = DC_BASE_VIEW.DCBaseView;
-/** @class Editing view for DatasetCollection.
- * @name DatasetCollectionEditView
- *
- * @augments DCBaseView
- * @constructs
- */
-var DCEditView = _super.extend({
-
- /** logger used to record this.log messages, commonly set to console */
- // comment this out to suppress log output
- //logger : console,
-
- // ......................................................................... misc
- /** string rep */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'DCEditView(' + modelString + ')';
- }
-});
-
-//==============================================================================
- return {
- DCEditView : DCEditView
- };
-});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/hdca-base.js
--- a/static/scripts/mvc/collection/hdca-base.js
+++ /dev/null
@@ -1,67 +0,0 @@
-define([
- "mvc/dataset/states",
- "mvc/collection/dataset-collection-base",
- "mvc/base-mvc",
- "utils/localization"
-], function( STATES, DC_BASE, BASE_MVC, _l ){
-/* global Backbone */
-//==============================================================================
-var _super = DC_BASE.DCBaseView;
-/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).
- */
-var HDCABaseView = _super.extend({
-
- /** logger used to record this.log messages, commonly set to console */
- //logger : console,
-
-//TODO: not a dataset
- /** */
- className : _super.prototype.className + " history-content",
-
- /** In this override, add the state as a class for use with state-based CSS */
- _swapNewRender : function( $newRender ){
- _super.prototype._swapNewRender.call( this, $newRender );
-//TODO: model currently has no state
- var state = this.model.get( 'state' ) || STATES.OK;
- //if( this.model.has( 'state' ) ){
- this.$el.addClass( 'state-' + state );
- //}
- return this.$el;
- },
-
- // ......................................................................... misc
- /** String representation */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'HDCABaseView(' + modelString + ')';
- }
-});
-
-/** underscore templates */
-HDCABaseView.prototype.templates = (function(){
-
-// could steal this from hda-base (or use mixed content)
- var titleBarTemplate = BASE_MVC.wrapTemplate([
- // adding the hid display to the title
- '<div class="title-bar clear" tabindex="0">',
- '<span class="state-icon"></span>',
- '<div class="title">',
- //TODO: remove whitespace and use margin-right
- '<span class="hid"><%- collection.hid %></span> ',
- '<span class="name"><%- collection.name %></span>',
- '</div>',
- '<div class="subtitle"></div>',
- '</div>'
- ], 'collection' );
-
- return _.extend( {}, _super.prototype.templates, {
- titleBar : titleBarTemplate
- });
-}());
-
-
-//==============================================================================
- return {
- HDCABaseView : HDCABaseView
- };
-});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/hdca-edit.js
--- a/static/scripts/mvc/collection/hdca-edit.js
+++ /dev/null
@@ -1,55 +0,0 @@
-define([
- "mvc/dataset/states",
- "mvc/collection/hdca-base",
- "utils/localization"
-], function( STATES, HDCA_BASE, _l ){
-//==============================================================================
-var _super = HDCA_BASE.HDCABaseView;
-/** @class Editing view for HistoryDatasetCollectionAssociation.
- */
-var HDCAEditView = _super.extend({
-
- /** logger used to record this.log messages, commonly set to console */
- //logger : console,
-
- // ......................................................................... delete
- /** In this override, add the delete button. */
- _renderPrimaryActions : function(){
- this.log( this + '._renderPrimaryActions' );
- // render the display, edit attr and delete icon-buttons
- return _super.prototype._renderPrimaryActions.call( this )
- .concat([
- this._renderDeleteButton()
- ]);
- },
-
- /** Render icon-button to delete this collection. */
- _renderDeleteButton : function(){
- var self = this,
- deleted = this.model.get( 'deleted' );
- return faIconButton({
- title : deleted? _l( 'Dataset collection is already deleted' ): _l( 'Delete' ),
- classes : 'delete-btn',
- faIcon : 'fa-times',
- disabled : deleted,
- onclick : function() {
- // ...bler... tooltips being left behind in DOM (hover out never called on deletion)
- self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' );
- self.model[ 'delete' ]();
- }
- });
- },
-
- // ......................................................................... misc
- /** string rep */
- toString : function(){
- var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'HDCAEditView(' + modelString + ')';
- }
-});
-
-//==============================================================================
- return {
- HDCAEditView : HDCAEditView
- };
-});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/hdca-model.js
--- a/static/scripts/mvc/collection/hdca-model.js
+++ /dev/null
@@ -1,83 +0,0 @@
-define([
- "mvc/history/history-content-base",
- "mvc/collection/collection-model",
- "utils/localization"
-], function( HISTORY_CONTENT, DC_MODEL, _l ){
-/*==============================================================================
-
-Models for DatasetCollections contained within a history.
-
-TODO:
- these might be compactable to one class if some duplication with
- collection-model is used.
-
-==============================================================================*/
-var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,
- ListDC = DC_MODEL.ListDatasetCollection,
- PairDC = DC_MODEL.PairDatasetCollection,
- ListPairedDC = DC_MODEL.ListPairedDatasetCollection;
-
-//==============================================================================
-/** @class Backbone model for List Dataset Collection within a History.
- * @constructs
- */
-var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend(
-/** @lends HistoryListDatasetCollection.prototype */{
-
- initialize : function( model, options ){
- ListDC.prototype.initialize.call( this, model, options );
- hcontentMixin.initialize.call( this, model, options );
- },
-
- /** String representation. */
- toString : function(){
- return ([ 'HistoryListDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));
- }
-});
-
-
-//==============================================================================
-/** @class Backbone model for Pair Dataset Collection within a History.
- * @constructs
- */
-var HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend(
-/** @lends HistoryPairDatasetCollection.prototype */{
-
- initialize : function( model, options ){
- PairDC.prototype.initialize.call( this, model, options );
- hcontentMixin.initialize.call( this, model, options );
- },
-
- /** String representation. */
- toString : function(){
- return ([ 'HistoryPairDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));
- }
-});
-
-
-//==============================================================================
-/** @class Backbone model for List of Pairs Dataset Collection within a History.
- * @constructs
- */
-var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend(
-/** @lends HistoryListPairedDatasetCollection.prototype */{
-
- initialize : function( model, options ){
- ListPairedDC.prototype.initialize.call( this, model, options );
- hcontentMixin.initialize.call( this, model, options );
- },
-
- /** String representation. */
- toString : function(){
- return ([ 'HistoryListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));
- }
-});
-
-
-//==============================================================================
- return {
- HistoryListDatasetCollection : HistoryListDatasetCollection,
- HistoryPairDatasetCollection : HistoryPairDatasetCollection,
- HistoryListPairedDatasetCollection : HistoryListPairedDatasetCollection
- };
-});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/dataset/dataset-li-edit.js
--- /dev/null
+++ b/static/scripts/mvc/dataset/dataset-li-edit.js
@@ -0,0 +1,351 @@
+define([
+ "mvc/dataset/states",
+ "mvc/dataset/dataset-li",
+ "mvc/tags",
+ "mvc/annotations",
+ "mvc/base-mvc",
+ "utils/localization"
+], function( STATES, DATASET_LI, TAGS, ANNOTATIONS, BASE_MVC, _l ){
+//==============================================================================
+var _super = DATASET_LI.DatasetListItemView;
+/** @class Editing view for DatasetAssociation.
+ */
+var DatasetListItemEdit = _super.extend(
+/** @lends DatasetListItemEdit.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ /** set up: options */
+ initialize : function( attributes ){
+ _super.prototype.initialize.call( this, attributes );
+//TODO: shouldn't this err if false?
+ this.hasUser = attributes.hasUser;
+
+ /** allow user purge of dataset files? */
+ this.purgeAllowed = attributes.purgeAllowed || false;
+
+ //TODO: move to HiddenUntilActivatedViewMixin
+ /** should the tags editor be shown or hidden initially? */
+ this.tagsEditorShown = attributes.tagsEditorShown || false;
+ /** should the tags editor be shown or hidden initially? */
+ this.annotationEditorShown = attributes.annotationEditorShown || false;
+ },
+
+ // ......................................................................... titlebar actions
+ /** In this override, add the other two primary actions: edit and delete */
+ _renderPrimaryActions : function(){
+ var actions = _super.prototype._renderPrimaryActions.call( this );
+ if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){
+ return actions;
+ }
+ // render the display, edit attr and delete icon-buttons
+ return _super.prototype._renderPrimaryActions.call( this ).concat([
+ this._renderEditButton(),
+ this._renderDeleteButton()
+ ]);
+ },
+
+//TODO: move titleButtons into state renderers, remove state checks in the buttons
+
+ /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */
+ _renderEditButton : function(){
+ // don't show edit while uploading, in-accessible
+ // DO show if in error (ala previous history panel)
+ if( ( this.model.get( 'state' ) === STATES.DISCARDED )
+ || ( !this.model.get( 'accessible' ) ) ){
+ return null;
+ }
+
+ var purged = this.model.get( 'purged' ),
+ deleted = this.model.get( 'deleted' ),
+ editBtnData = {
+ title : _l( 'Edit attributes' ),
+ href : this.model.urls.edit,
+ target : this.linkTarget,
+ faIcon : 'fa-pencil',
+ classes : 'edit-btn'
+ };
+
+ // disable if purged or deleted and explain why in the tooltip
+ if( deleted || purged ){
+ editBtnData.disabled = true;
+ if( purged ){
+ editBtnData.title = _l( 'Cannot edit attributes of datasets removed from disk' );
+ } else if( deleted ){
+ editBtnData.title = _l( 'Undelete dataset to edit attributes' );
+ }
+
+ // disable if still uploading or new
+ } else if( _.contains( [ STATES.UPLOAD, STATES.NEW ], this.model.get( 'state' ) ) ){
+ editBtnData.disabled = true;
+ editBtnData.title = _l( 'This dataset is not yet editable' );
+ }
+ return faIconButton( editBtnData );
+ },
+
+ /** Render icon-button to delete this hda. */
+ _renderDeleteButton : function(){
+ // don't show delete if...
+ if( ( !this.model.get( 'accessible' ) ) ){
+ return null;
+ }
+
+ var self = this,
+ deletedAlready = this.model.isDeletedOrPurged();
+ return faIconButton({
+ title : !deletedAlready? _l( 'Delete' ) : _l( 'Dataset is already deleted' ),
+ disabled : deletedAlready,
+ faIcon : 'fa-times',
+ classes : 'delete-btn',
+ onclick : function() {
+ // ...bler... tooltips being left behind in DOM (hover out never called on deletion)
+ self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' );
+ self.model[ 'delete' ]();
+ }
+ });
+ },
+
+ // ......................................................................... details
+ /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */
+ _renderDetails : function(){
+ //TODO: generalize to be allow different details for each state
+ var $details = _super.prototype._renderDetails.call( this ),
+ state = this.model.get( 'state' );
+
+ if( !this.model.isDeletedOrPurged() && _.contains([ STATES.OK, STATES.FAILED_METADATA ], state ) ){
+ this._renderTags( $details );
+ this._renderAnnotation( $details );
+ this._makeDbkeyEditLink( $details );
+ }
+
+//TODO: TRIPLE tap, ugh.
+ this._setUpBehaviors( $details );
+ return $details;
+ },
+
+ /** Add less commonly used actions in the details section based on state */
+ _renderSecondaryActions : function(){
+ var actions = _super.prototype._renderSecondaryActions.call( this );
+ switch( this.model.get( 'state' ) ){
+ case STATES.UPLOAD:
+ case STATES.NEW:
+ case STATES.NOT_VIEWABLE:
+ return actions;
+ case STATES.ERROR:
+ // error button comes first
+ actions.unshift( this._renderErrButton() );
+ return actions.concat([ this._renderRerunButton() ]);
+ case STATES.OK:
+ case STATES.FAILED_METADATA:
+ return actions.concat([ this._renderRerunButton(), this._renderVisualizationsButton() ]);
+ }
+ return actions.concat([ this._renderRerunButton() ]);
+ },
+
+ /** Render icon-button to report an error on this dataset to the galaxy admin. */
+ _renderErrButton : function(){
+ return faIconButton({
+ title : _l( 'View or report this error' ),
+ href : this.model.urls.report_error,
+ classes : 'report-error-btn',
+ target : this.linkTarget,
+ faIcon : 'fa-bug'
+ });
+ },
+
+ /** Render icon-button to re-run the job that created this dataset. */
+ _renderRerunButton : function(){
+ return faIconButton({
+ title : _l( 'Run this job again' ),
+ href : this.model.urls.rerun,
+ classes : 'rerun-btn',
+ target : this.linkTarget,
+ faIcon : 'fa-refresh'
+ });
+ },
+
+ /** Render an icon-button or popupmenu of links based on the applicable visualizations */
+ _renderVisualizationsButton : function(){
+ //TODO: someday - lazyload visualizations
+ var visualizations = this.model.get( 'visualizations' );
+ if( ( this.model.isDeletedOrPurged() )
+ || ( !this.hasUser )
+ || ( !this.model.hasData() )
+ || ( _.isEmpty( visualizations ) ) ){
+ return null;
+ }
+ if( !_.isObject( visualizations[0] ) ){
+ this.warn( 'Visualizations have been switched off' );
+ return null;
+ }
+
+ var $visualizations = $( this.templates.visualizations( visualizations, this ) );
+ // use addBack here to include the root $visualizations elem (for the case of 1 visualization)
+ this._addScratchBookFn( $visualizations.find( '.visualization-link' ).addBack( '.visualization-link' ) );
+ return $visualizations;
+ },
+
+ /** add scratchbook functionality to visualization links */
+ _addScratchBookFn : function( $links ){
+ $links.click( function( ev ){
+ if( Galaxy.frame && Galaxy.frame.active ){
+ Galaxy.frame.add({
+ title : "Visualization",
+ type : "url",
+ content : $( this ).attr( 'href' )
+ });
+ ev.preventDefault();
+ ev.stopPropagation();
+ }
+ });
+ },
+
+//TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)
+ /** Render the tags list/control */
+ _renderTags : function( $where ){
+ if( !this.hasUser ){ return; }
+ var view = this;
+ this.tagsEditor = new TAGS.TagsEditor({
+ model : this.model,
+ el : $where.find( '.tags-display' ),
+ onshowFirstTime : function(){ this.render(); },
+ // persist state on the hda view (and not the editor) since these are currently re-created each time
+ onshow : function(){ view.tagsEditorShown = true; },
+ onhide : function(){ view.tagsEditorShown = false; },
+ $activator : faIconButton({
+ title : _l( 'Edit dataset tags' ),
+ classes : 'tag-btn',
+ faIcon : 'fa-tags'
+ }).appendTo( $where.find( '.actions .right' ) )
+ });
+ if( this.tagsEditorShown ){ this.tagsEditor.toggle( true ); }
+ },
+
+ /** Render the annotation display/control */
+ _renderAnnotation : function( $where ){
+ if( !this.hasUser ){ return; }
+ var view = this;
+ this.annotationEditor = new ANNOTATIONS.AnnotationEditor({
+ model : this.model,
+ el : $where.find( '.annotation-display' ),
+ onshowFirstTime : function(){ this.render(); },
+ // persist state on the hda view (and not the editor) since these are currently re-created each time
+ onshow : function(){ view.annotationEditorShown = true; },
+ onhide : function(){ view.annotationEditorShown = false; },
+ $activator : faIconButton({
+ title : _l( 'Edit dataset annotation' ),
+ classes : 'annotate-btn',
+ faIcon : 'fa-comment'
+ }).appendTo( $where.find( '.actions .right' ) )
+ });
+ if( this.annotationEditorShown ){ this.annotationEditor.toggle( true ); }
+ },
+
+ /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */
+ _makeDbkeyEditLink : function( $details ){
+ // make the dbkey a link to editing
+ if( this.model.get( 'metadata_dbkey' ) === '?'
+ && !this.model.isDeletedOrPurged() ){
+ var editableDbkey = $( '<a class="value">?</a>' )
+ .attr( 'href', this.model.urls.edit )
+ .attr( 'target', this.linkTarget );
+ $details.find( '.dbkey .value' ).replaceWith( editableDbkey );
+ }
+ },
+
+ // ......................................................................... events
+ /** event map */
+ events : _.extend( _.clone( _super.prototype.events ), {
+ 'click .undelete-link' : function( ev ){ this.model.undelete(); return false; },
+ 'click .purge-link' : '_confirmPurge'
+ }),
+
+ /** listener for item purge */
+ _confirmPurge : function _confirmPurge( ev ){
+//TODO: confirm dialog
+ this.model.purge();
+ return false;
+ },
+
+ // ......................................................................... misc
+ /** string rep */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'HDAEditView(' + modelString + ')';
+ }
+});
+
+
+// ............................................................................ TEMPLATES
+/** underscore templates */
+DatasetListItemEdit.prototype.templates = (function(){
+//TODO: move to require text! plugin
+
+ var warnings = _.extend( {}, _super.prototype.templates.warnings, {
+ failed_metadata : BASE_MVC.wrapTemplate([
+ // in this override, provide a link to the edit page
+ '<% if( dataset.state === "failed_metadata" ){ %>',
+ '<div class="failed_metadata-warning warningmessagesmall">',
+ _l( 'An error occurred setting the metadata for this dataset' ),
+ '<br /><a href="<%= dataset.urls.edit %>" target="<%= view.linkTarget %>">',
+ _l( 'Set it manually or retry auto-detection' ),
+ '</a>',
+ '</div>',
+ '<% } %>'
+ ], 'dataset' ),
+
+ deleted : BASE_MVC.wrapTemplate([
+ // in this override, provide links to undelete or purge the dataset
+ '<% if( dataset.deleted && !dataset.purged ){ %>',
+ // deleted not purged
+ '<div class="deleted-msg warningmessagesmall">',
+ _l( 'This dataset has been deleted' ),
+ '<br /><a class="undelete-link" href="javascript:void(0);">', _l( 'Undelete it' ), '</a>',
+ '<% if( view.purgeAllowed ){ %>',
+ '<br /><a class="purge-link" href="javascript:void(0);">',
+ _l( 'Permanently remove it from disk' ),
+ '</a>',
+ '<% } %>',
+ '</div>',
+ '<% } %>'
+ ], 'dataset' )
+ });
+
+ var visualizationsTemplate = BASE_MVC.wrapTemplate([
+ '<% if( visualizations.length === 1 ){ %>',
+ '<a class="visualization-btn visualization-link icon-btn" href="<%= visualizations[0].href %>"',
+ ' target="<%= visualizations[0].target %>" title="', _l( 'Visualize in' ),
+ ' <%= visualizations[0].html %>">',
+ '<span class="fa fa-bar-chart-o"></span>',
+ '</a>',
+
+ '<% } else { %>',
+ '<div class="visualizations-dropdown dropdown">',
+ '<a class="visualization-btn icon-btn" data-toggle="dropdown" title="', _l( 'Visualize' ), '">',
+ '<span class="fa fa-bar-chart-o"></span>',
+ '</a>',
+ '<ul class="dropdown-menu" role="menu">',
+ '<% _.each( visualizations, function( visualization ){ %>',
+ '<li><a class="visualization-link" href="<%= visualization.href %>"',
+ ' target="<%= visualization.target %>">',
+ '<%= visualization.html %>',
+ '</a></li>',
+ '<% }); %>',
+ '</ul>',
+ '</div>',
+ '<% } %>'
+ ], 'visualizations' );
+
+ return _.extend( {}, _super.prototype.templates, {
+ warnings : warnings,
+ visualizations : visualizationsTemplate
+ });
+}());
+
+
+//==============================================================================
+ return {
+ DatasetListItemEdit : DatasetListItemEdit
+ };
+});
diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/dataset/dataset-li.js
--- /dev/null
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -0,0 +1,464 @@
+define([
+ "mvc/dataset/states",
+ "mvc/base-mvc",
+ "utils/localization"
+], function( STATES, BASE_MVC, _l ){
+/* global Backbone */
+//==============================================================================
+var _super = BASE_MVC.ListItemView;
+/** @class Read only list view for either LDDAs, HDAs, or HDADCEs.
+ * Roughly, any DatasetInstance (and not a raw Dataset).
+ */
+var DatasetListItemView = _super.extend(
+/** @lends DatasetListItemView.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ className : _super.prototype.className + " dataset",
+
+ /** Set up: instance vars, options, and event handlers */
+ initialize : function( attributes ){
+ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
+ this.log( this + '.initialize:', attributes );
+ _super.prototype.initialize.call( this, attributes );
+
+ /** where should pages from links be displayed? (default to new tab/window) */
+ this.linkTarget = attributes.linkTarget || '_blank';
+
+ this._setUpListeners();
+ },
+
+ /** event listeners */
+ _setUpListeners : function(){
+ // hide the primary actions in the title bar when selectable
+ this.on( 'selectable', function( isSelectable ){
+ if( isSelectable ){
+ this.$( '.primary-actions' ).hide();
+ } else {
+ this.$( '.primary-actions' ).show();
+ }
+ });
+
+ // re-rendering on any model changes
+ this.model.on( 'change', function( model, options ){
+ // if the model moved into the ready state and is expanded without details, fetch those details now
+ if( this.model.changedAttributes().state && this.model.inReadyState()
+ && this.expanded && !this.model.hasDetails() ){
+ // will render automatically (due to fetch -> change)
+ this.model.fetch();
+
+ } else {
+ this.render();
+ }
+ }, this );
+
+ this.on( 'all', function( event ){
+ this.log( event );
+ }, this );
+ },
+
+ // ......................................................................... expandable
+ /** In this override, only get details if in the ready state.
+ * Note: fetch with no 'change' event triggering to prevent automatic rendering.
+ */
+ _fetchModelDetails : function(){
+ var view = this;
+ if( view.model.inReadyState() && !view.model.hasDetails() ){
+ return view.model.fetch({ silent: true });
+ }
+ return jQuery.when();
+ },
+
+ // ......................................................................... removal
+ /** Remove this view's html from the DOM and remove all event listeners.
+ * @param {Number or String} speed jq effect speed
+ * @param {Function} callback an optional function called when removal is done (scoped to this view)
+ */
+ remove : function( speed, callback ){
+ var view = this;
+ speed = speed || this.fxSpeed;
+ this.$el.fadeOut( speed, function(){
+ Backbone.View.prototype.remove.call( view );
+ if( callback ){ callback.call( view ); }
+ });
+ },
+
+ // ......................................................................... rendering
+ /* TODO:
+ dataset states are the issue primarily making dataset rendering complex
+ each state should have it's own way of displaying/set of details
+ often with different actions that can be applied
+ throw in deleted/purged/visible and things get complicated easily
+ I've considered (a couple of times) - creating a view for each state
+ - but recreating the view during an update...seems wrong
+ */
+ /** Render this HDA, set up ui.
+ * @param {Number or String} speed jq fx speed
+ * @returns {Object} this
+ */
+ render : function( speed ){
+ //HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide
+ // handle that here by removing previous view's tooltips
+ //this.$el.find("[title]").tooltip( "destroy" );
+ return _super.prototype.render.call( this, speed );
+ },
+
+ /** In this override, add the dataset state as a class for use with state-based CSS */
+ _swapNewRender : function( $newRender ){
+ _super.prototype._swapNewRender.call( this, $newRender );
+ if( this.model.has( 'state' ) ){
+ this.$el.addClass( 'state-' + this.model.get( 'state' ) );
+ }
+ return this.$el;
+ },
+
+ // ................................................................................ titlebar
+ /** In this override, add the dataset display button. */
+ _renderPrimaryActions : function(){
+ // render just the display for read-only
+ return [ this._renderDisplayButton() ];
+ },
+
+ /** Render icon-button to display dataset data */
+ _renderDisplayButton : function(){
+//TODO:?? too complex - possibly move into template
+ // don't show display if not viewable or not accessible
+ var state = this.model.get( 'state' );
+ if( ( state === STATES.NOT_VIEWABLE )
+ || ( state === STATES.DISCARDED )
+ || ( !this.model.get( 'accessible' ) ) ){
+ return null;
+ }
+
+ var displayBtnData = {
+ target : this.linkTarget,
+ classes : 'display-btn'
+ };
+
+ // show a disabled display if the data's been purged
+ if( this.model.get( 'purged' ) ){
+ displayBtnData.disabled = true;
+ displayBtnData.title = _l( 'Cannot display datasets removed from disk' );
+
+ // disable if still uploading
+ } else if( state === STATES.UPLOAD ){
+ displayBtnData.disabled = true;
+ displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' );
+
+ // disable if still new
+ } else if( state === STATES.NEW ){
+ displayBtnData.disabled = true;
+ displayBtnData.title = _l( 'This dataset is not yet viewable' );
+
+ } else {
+ displayBtnData.title = _l( 'View data' );
+
+ // default link for dataset
+ displayBtnData.href = this.model.urls.display;
+
+ // add frame manager option onclick event
+ var self = this;
+ displayBtnData.onclick = function( ev ){
+ if( Galaxy.frame && Galaxy.frame.active ){
+ // Create frame with TabularChunkedView.
+ Galaxy.frame.add({
+ title : "Data Viewer: " + self.model.get( 'name' ),
+ type : "other",
+ content : function( parent_elt ){
+ var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) });
+ $.when( new_dataset.fetch() ).then( function(){
+ DATA.createTabularDatasetChunkedView({
+ model: new_dataset,
+ parent_elt: parent_elt,
+ embedded: true,
+ height: '100%'
+ });
+ });
+ }
+ });
+ ev.preventDefault();
+ }
+ };
+ }
+ displayBtnData.faIcon = 'fa-eye';
+ return faIconButton( displayBtnData );
+ },
+
+ // ......................................................................... rendering details
+ /** Render the enclosing div of the hda body and, if expanded, the html in the body
+ * @returns {jQuery} rendered DOM
+ */
+ _renderDetails : function(){
+ //TODO: generalize to be allow different details for each state
+ var $details = _super.prototype._renderDetails.call( this );
+ $details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() );
+ $details.find( '.summary' ).html( this._renderSummary() );
+ $details.find( '.display-applications' ).html( this._renderDisplayApplications() );
+
+//TODO: double tap
+ this._setUpBehaviors( $details );
+ return $details;
+ },
+
+ /** Defer to the appropo summary rendering fn based on state */
+ _renderSummary : function(){
+ var summaryRenderFn = this.templates.summaries[ this.model.get( 'state' ) ];
+ summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;
+ return summaryRenderFn( this.model.toJSON(), this );
+ },
+
+ /** Render the external display application links */
+ _renderDisplayApplications : function(){
+ if( this.model.isDeletedOrPurged() ){ return ''; }
+ // render both old and new display apps using the same template
+ return [
+ this.templates.displayApplications( this.model.get( 'display_apps' ), this ),
+ this.templates.displayApplications( this.model.get( 'display_types' ), this )
+ ].join( '' );
+ },
+
+ // ......................................................................... secondary/details actions
+ /** A series of links/buttons for less commonly used actions: re-run, info, etc. */
+ _renderSecondaryActions : function(){
+ this.debug( '_renderSecondaryActions' );
+ switch( this.model.get( 'state' ) ){
+ case STATES.NOT_VIEWABLE:
+ return [];
+ case STATES.OK:
+ case STATES.FAILED_METADATA:
+ case STATES.ERROR:
+ return [ this._renderDownloadButton(), this._renderShowParamsButton() ];
+ }
+ return [ this._renderShowParamsButton() ];
+ },
+
+ /** Render icon-button to show the input and output (stdout/err) for the job that created this.
+ * @returns {jQuery} rendered DOM
+ */
+ _renderShowParamsButton : function(){
+ // gen. safe to show in all cases
+ return faIconButton({
+ title : _l( 'View details' ),
+ classes : 'dataset-params-btn',
+ href : this.model.urls.show_params,
+ target : this.linkTarget,
+ faIcon : 'fa-info-circle'
+ });
+ },
+
+ /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.
+ * @returns {jQuery} rendered DOM
+ */
+ _renderDownloadButton : function(){
+//TODO: to (its own) template fn
+ // don't show anything if the data's been purged
+ if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; }
+
+ // return either: a popupmenu with links to download assoc. meta files (if there are meta files)
+ // or a single download icon-button (if there are no meta files)
+ if( !_.isEmpty( this.model.get( 'meta_files' ) ) ){
+ return this._renderMetaFileDownloadButton();
+ }
+
+ return $([
+ '<a class="download-btn icon-btn" href="', this.model.urls.download, '" title="' + _l( 'Download' ) + '">',
+ '<span class="fa fa-floppy-o"></span>',
+ '</a>'
+ ].join( '' ));
+ },
+
+ /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */
+ _renderMetaFileDownloadButton : function(){
+ var urls = this.model.urls;
+ return $([
+ '<div class="metafile-dropdown dropdown">',
+ '<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',
+ ' title="' + _l( 'Download' ) + '">',
+ '<span class="fa fa-floppy-o"></span>',
+ '</a>',
+ '<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">',
+ '<li><a href="' + urls.download + '">', _l( 'Download dataset' ), '</a></li>',
+ _.map( this.model.get( 'meta_files' ), function( meta_file ){
+ return [
+ '<li><a href="', urls.meta_download + meta_file.file_type, '">',
+ _l( 'Download' ), ' ', meta_file.file_type,
+ '</a></li>'
+ ].join( '' );
+ }).join( '\n' ),
+ '</ul>',
+ '</div>'
+ ].join( '\n' ));
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'DatasetListItemView(' + modelString + ')';
+ }
+});
+
+// ............................................................................ TEMPLATES
+/** underscore templates */
+DatasetListItemView.prototype.templates = (function(){
+//TODO: move to require text! plugin
+
+ var warnings = _.extend( {}, _super.prototype.templates.warnings, {
+ failed_metadata : BASE_MVC.wrapTemplate([
+ // failed metadata is rendered as a warning on an otherwise ok dataset view
+ '<% if( model.state === "failed_metadata" ){ %>',
+ '<div class="warningmessagesmall">',
+ _l( 'An error occurred setting the metadata for this dataset' ),
+ '</div>',
+ '<% } %>'
+ ]),
+ error : BASE_MVC.wrapTemplate([
+ // error during index fetch - show error on dataset
+ '<% if( model.error ){ %>',
+ '<div class="errormessagesmall">',
+ _l( 'There was an error getting the data for this dataset' ), ': <%- model.error %>',
+ '</div>',
+ '<% } %>'
+ ]),
+ purged : BASE_MVC.wrapTemplate([
+ '<% if( model.purged ){ %>',
+ '<div class="purged-msg warningmessagesmall">',
+ _l( 'This dataset has been deleted and removed from disk' ),
+ '</div>',
+ '<% } %>'
+ ]),
+ deleted : BASE_MVC.wrapTemplate([
+ // deleted not purged
+ '<% if( model.deleted && !model.purged ){ %>',
+ '<div class="deleted-msg warningmessagesmall">',
+ _l( 'This dataset has been deleted' ),
+ '</div>',
+ '<% } %>'
+ ])
+
+ //NOTE: hidden warning is only needed for HDAs
+ });
+
+ var detailsTemplate = BASE_MVC.wrapTemplate([
+ '<div class="details">',
+ '<div class="summary"></div>',
+
+ '<div class="actions clear">',
+ '<div class="left"></div>',
+ '<div class="right"></div>',
+ '</div>',
+
+ // do not display tags, annotation, display apps, or peek when deleted
+ '<% if( !dataset.deleted && !dataset.purged ){ %>',
+ '<div class="tags-display"></div>',
+ '<div class="annotation-display"></div>',
+
+ '<div class="display-applications"></div>',
+
+ '<% if( dataset.peek ){ %>',
+ '<pre class="dataset-peek"><%= dataset.peek %></pre>',
+ '<% } %>',
+ '<% } %>',
+ '</div>'
+ ], 'dataset' );
+
+//TODO: still toooooooooooooo complex - rework
+ var summaryTemplates = {};
+ summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([
+ '<% if( dataset.misc_blurb ){ %>',
+ '<div class="blurb">',
+ '<span class="value"><%- dataset.misc_blurb %></span>',
+ '</div>',
+ '<% } %>',
+
+ '<% if( dataset.data_type ){ %>',
+ '<div class="datatype">',
+ '<label class="prompt">', _l( 'format' ), '</label>',
+ '<span class="value"><%- dataset.data_type %></span>',
+ '</div>',
+ '<% } %>',
+
+ '<% if( dataset.metadata_dbkey ){ %>',
+ '<div class="dbkey">',
+ '<label class="prompt">', _l( 'database' ), '</label>',
+ '<span class="value">',
+ '<%- dataset.metadata_dbkey %>',
+ '</span>',
+ '</div>',
+ '<% } %>',
+
+ '<% if( dataset.misc_info ){ %>',
+ '<div class="info">',
+ '<span class="value"><%- dataset.misc_info %></span>',
+ '</div>',
+ '<% } %>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.NEW ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'This is a new dataset and not all of its data are available yet' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.NOT_VIEWABLE ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'You do not have permission to view this dataset' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.DISCARDED ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'The job creating this dataset was cancelled before completion' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'This job is waiting to run' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'This dataset is currently uploading' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'Metadata is being auto-detected' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'This job is currently running' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume' ), '</div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.ERROR ] = BASE_MVC.wrapTemplate([
+ '<% if( !dataset.purged ){ %>',
+ '<div><%- dataset.misc_blurb %></div>',
+ '<% } %>',
+ '<span class="help-text">', _l( 'An error occurred with this dataset' ), ':</span>',
+ '<div class="job-error-text"><%- dataset.misc_info %></div>'
+ ], 'dataset' );
+ summaryTemplates[ STATES.EMPTY ] = BASE_MVC.wrapTemplate([
+ '<div>', _l( 'No data' ), ': <i><%- dataset.misc_blurb %></i></div>'
+ ], 'dataset' );
+ summaryTemplates.unknown = BASE_MVC.wrapTemplate([
+ '<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'
+ ], 'dataset' );
+
+ // this is applied to both old and new style display apps
+ var displayApplicationsTemplate = BASE_MVC.wrapTemplate([
+ '<% _.each( apps, function( app ){ %>',
+ '<div class="display-application">',
+ '<span class="display-application-location"><%- app.label %></span> ',
+ '<span class="display-application-links">',
+ '<% _.each( app.links, function( link ){ %>',
+ '<a target="<%= link.target %>" href="<%= link.href %>">',
+ '<% print( _l( link.text ) ); %>',
+ '</a> ',
+ '<% }); %>',
+ '</span>',
+ '</div>',
+ '<% }); %>'
+ ], 'apps' );
+
+ return _.extend( {}, _super.prototype.templates, {
+ warnings : warnings,
+ details : detailsTemplate,
+ summaries : summaryTemplates,
+ displayApplications : displayApplicationsTemplate
+ });
+}());
+
+
+// ============================================================================
+ return {
+ DatasetListItemView : DatasetListItemView
+ };
+});
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Merged in BjoernGruening/galaxy-central-4 (pull request #454)
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2f300953ad98/
Changeset: 2f300953ad98
User: jmchilton
Date: 2014-08-12 15:04:01
Summary: Merged in BjoernGruening/galaxy-central-4 (pull request #454)
Fixes for recent Tool Shed code cleanups
Affected #: 2 files
diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -239,8 +239,7 @@
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
self.__ensure_can_install_repos( trans )
install_repository_manager = InstallRepositoryManager( trans.app )
- installed_tool_shed_repositories = install_repository_manager.install( trans.app,
- tool_shed_url,
+ installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url,
name,
owner,
changeset_revision,
diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -694,7 +694,8 @@
name,
owner,
changeset_revision )
- installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict,
+ installed_tool_shed_repositories = self.__install_repositories( tool_shed_url,
+ repository_revision_dict,
repo_info_dicts,
install_options )
return installed_tool_shed_repositories
@@ -788,7 +789,7 @@
# at this point because repository dependencies may have added additional repositories for installation
# along with the single specified repository.
encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
- initiate_repository_installation( self.app, installation_dict )
+ self.initiate_repository_installation( installation_dict )
# Some repositories may have repository dependencies that are required to be installed before the
# dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in
# the required order.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/382b019fcdc1/
Changeset: 382b019fcdc1
User: BjoernGruening
Date: 2014-08-12 10:33:27
Summary: install_repository_manager do not need trans.app anymore.
Affected #: 1 file
diff -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f -r 382b019fcdc10b72fc77a9284d7adcfeb3170cd8 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -239,8 +239,7 @@
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
self.__ensure_can_install_repos( trans )
install_repository_manager = InstallRepositoryManager( trans.app )
- installed_tool_shed_repositories = install_repository_manager.install( trans.app,
- tool_shed_url,
+ installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url,
name,
owner,
changeset_revision,
https://bitbucket.org/galaxy/galaxy-central/commits/0df3fe8e9945/
Changeset: 0df3fe8e9945
User: BjoernGruening
Date: 2014-08-12 10:38:24
Summary: First argument to __install_repositories is the Tool Shed URL (tool_shed_url)
Affected #: 1 file
diff -r 382b019fcdc10b72fc77a9284d7adcfeb3170cd8 -r 0df3fe8e99457c75cefeab162dac3e90f948d764 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -694,7 +694,8 @@
name,
owner,
changeset_revision )
- installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict,
+ installed_tool_shed_repositories = self.__install_repositories( tool_shed_url,
+ repository_revision_dict,
repo_info_dicts,
install_options )
return installed_tool_shed_repositories
https://bitbucket.org/galaxy/galaxy-central/commits/f3c84cf5296f/
Changeset: f3c84cf5296f
User: BjoernGruening
Date: 2014-08-12 10:41:45
Summary: initiate_repository_installation was not updated in the recent code restructuring efforts
Affected #: 1 file
diff -r 0df3fe8e99457c75cefeab162dac3e90f948d764 -r f3c84cf5296f6b9bed917f71693ff32dd92188f4 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -789,7 +789,7 @@
# at this point because repository dependencies may have added additional repositories for installation
# along with the single specified repository.
encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
- initiate_repository_installation( self.app, installation_dict )
+ self.initiate_repository_installation( installation_dict )
# Some repositories may have repository dependencies that are required to be installed before the
# dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in
# the required order.
https://bitbucket.org/galaxy/galaxy-central/commits/2f300953ad98/
Changeset: 2f300953ad98
User: jmchilton
Date: 2014-08-12 15:04:01
Summary: Merged in BjoernGruening/galaxy-central-4 (pull request #454)
Fixes for recent Tool Shed code cleanups
Affected #: 2 files
diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -239,8 +239,7 @@
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
self.__ensure_can_install_repos( trans )
install_repository_manager = InstallRepositoryManager( trans.app )
- installed_tool_shed_repositories = install_repository_manager.install( trans.app,
- tool_shed_url,
+ installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url,
name,
owner,
changeset_revision,
diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -694,7 +694,8 @@
name,
owner,
changeset_revision )
- installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict,
+ installed_tool_shed_repositories = self.__install_repositories( tool_shed_url,
+ repository_revision_dict,
repo_info_dicts,
install_options )
return installed_tool_shed_repositories
@@ -788,7 +789,7 @@
# at this point because repository dependencies may have added additional repositories for installation
# along with the single specified repository.
encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
- initiate_repository_installation( self.app, installation_dict )
+ self.initiate_repository_installation( installation_dict )
# Some repositories may have repository dependencies that are required to be installed before the
# dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in
# the required order.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Fix multi-page tool help parsing.
by commits-noreply＠bitbucket.org 12 Aug '14
by commits-noreply＠bitbucket.org 12 Aug '14
12 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/19309418c864/
Changeset: 19309418c864
User: jmchilton
Date: 2014-08-12 14:19:04
Summary: Fix multi-page tool help parsing.
Patch thanks to Hans-Philipp Brachvogel.
Affected #: 2 files
diff -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f -r 19309418c86450b7f39691460eb430e100883cb4 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1482,10 +1482,10 @@
help_footer = help_footer + help_page.tail
# Each page has to rendered all-together because of backreferences allowed by rst
try:
- self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer,
+ self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer ),
input_encoding='utf-8', output_encoding='utf-8',
default_filters=[ 'decode.utf8' ],
- encoding_errors='replace' ) )
+ encoding_errors='replace' )
for x in self.help_by_page ]
except:
log.exception( "error in multi-page help for tool %s" % self.name )
diff -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f -r 19309418c86450b7f39691460eb430e100883cb4 test/functional/tools/multi_page.xml
--- a/test/functional/tools/multi_page.xml
+++ b/test/functional/tools/multi_page.xml
@@ -14,6 +14,10 @@
<outputs><data format="txt" name="output" /></outputs>
+ <help>
+ <page>Page 1 Help.</page>
+ <page>Page 2 Help.</page>
+ </help><tests><test><param name="p1" value="3" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Added tag latest_2014.08.11 for changeset 52b5cc75a175
by commits-noreply＠bitbucket.org 11 Aug '14
by commits-noreply＠bitbucket.org 11 Aug '14
11 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b6d2c77d8bce/
Changeset: b6d2c77d8bce
Branch: stable
User: natefoo
Date: 2014-08-11 23:22:49
Summary: Added tag latest_2014.08.11 for changeset 52b5cc75a175
Affected #: 1 file
diff -r 52b5cc75a1757eddfb94ee373193c9d8fa2ec442 -r b6d2c77d8bce44cdaba188ce949ed69f94be6bc4 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,3 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
+52b5cc75a1757eddfb94ee373193c9d8fa2ec442 latest_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f2a70e7bac29/
Changeset: f2a70e7bac29
Branch: next-stable
User: natefoo
Date: 2014-08-11 22:46:18
Summary: Close next-stable for upcoming release_2014.08.11
Affected #: 0 files
https://bitbucket.org/galaxy/galaxy-central/commits/2a2fcdf2af77/
Changeset: 2a2fcdf2af77
Branch: stable
User: natefoo
Date: 2014-08-11 22:46:48
Summary: Updated tag latest_2014.06.02 for changeset 7a4d321c0e38
Affected #: 1 file
diff -r 7a4d321c0e38fa263ea83d29a35a608c3181fcba -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -8,7 +8,7 @@
5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10
9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14
7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02
-8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02
+7a4d321c0e38fa263ea83d29a35a608c3181fcba latest_2014.06.02
9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14
6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13
3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08
https://bitbucket.org/galaxy/galaxy-central/commits/ca45b78adb41/
Changeset: ca45b78adb41
Branch: stable
User: natefoo
Date: 2014-08-11 22:47:21
Summary: Merge next-stable branch for release_2014.08.11
Affected #: 624 files
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -11,8 +11,12 @@
scripts/scramble/lib
scripts/scramble/archives
+# Python virtualenv
+.venv
+
# Database stuff
database/beaker_sessions
+database/citations
database/community_files
database/compiled_templates
database/files
@@ -35,6 +39,7 @@
tool_shed_webapp.log
tool_shed_webapp.pid
hgweb.config*
+lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml
# Reports Runtime Files
reports_webapp.lock
@@ -61,6 +66,7 @@
data_manager_conf.xml
shed_data_manager_conf.xml
object_store_conf.xml
+job_metrics_conf.xml
config/*
static/welcome.html.*
static/welcome.html
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 buildbot_setup.sh
--- a/buildbot_setup.sh
+++ b/buildbot_setup.sh
@@ -58,6 +58,7 @@
tool-data/shared/rviewer/rviewer_build_sites.txt.sample
tool-data/shared/ucsc/builds.txt.sample
tool-data/shared/ucsc/publicbuilds.txt.sample
+tool-data/shared/ucsc/ucsc_build_sites.txt.sample
"
DIRS="
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,26 +1,26 @@
// dependencies
define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
- 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage',
+ '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( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage,
+ function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, Deferred,
ViewerView, EditorView,
Config, Chart, Types
) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * Main application class.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(options)
- {
+ initialize: function(options){
// deactivate all debugs outputs
//window.console.debug = function() {};
// link options
this.options = options;
-
+
// link galaxy modal or create one
if (Galaxy && Galaxy.modal) {
this.modal = Galaxy.modal;
@@ -41,6 +41,7 @@
this.jobs = new Jobs(this);
this.datasets = new Datasets(this);
this.storage = new Storage(this);
+ this.deferred = new Deferred();
//
// views
@@ -62,7 +63,7 @@
// draw chart
var self = this;
- this.chart.deferred.execute(function() {
+ this.deferred.execute(function() {
self.chart.trigger('redraw');
});
}
@@ -100,19 +101,6 @@
console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type);
}
return undefined;
- },
-
- // execute command
- execute: function(options) {
- },
-
- // unload
- onunload: function() {
- },
-
- // log
- log: function(location, message) {
- console.log(location + ' ' + message);
}
});
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 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.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.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/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}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;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/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,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=e.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(){e.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",width:c,height:l});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/",display:"none"}),r.append(i)),i.empty();for(name 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",width:i*n,height:r});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","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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(){s.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(){s.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)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new 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){e.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("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var 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.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<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+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<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($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$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","plugin/library/ui"],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({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=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<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.chart.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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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){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","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$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=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<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=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$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.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<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",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(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.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$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",["plugin/library/ui-table","plugin/library/ui","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",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$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 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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 --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_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_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",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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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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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 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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 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){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?(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 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charts",zoomable:!0,keywords:"default small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",query_limit:1e4,settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.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__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.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","plugin/library/ui","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 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
@@ -1,9 +1,10 @@
// dependencies
define(['plugin/charts/jqplot/common/plot-config', 'plugin/charts/tools'], function(configmaker, Tools) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This is the common wrapper for jqplot based visualizations.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// get parameters
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -1,9 +1,10 @@
// dependencies
define(['plugin/charts/tools'], function(Tools) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This is the common wrapper for nvd3 based visualizations.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// get parameters
@@ -97,6 +98,7 @@
}
});
+ // return
return true;
},
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
@@ -28,7 +28,7 @@
chart.state('ok', 'Pie chart has been drawn.');
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
}
// request data
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/charts/tools.js
--- a/config/plugins/visualizations/charts/static/charts/tools.js
+++ b/config/plugins/visualizations/charts/static/charts/tools.js
@@ -2,8 +2,7 @@
define(['utils/utils'], function(Utils) {
// render
-function panelHelper (app, options)
-{
+function panelHelper (app, options) {
// link this
var self = this;
@@ -42,7 +41,7 @@
}
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
} catch (err) {
// log
console.debug('FAILED: Tools::panelHelper() - ' + err);
@@ -51,7 +50,7 @@
chart.state('failed', err);
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
}
};
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -1,7 +1,9 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// widget
+/**
+ * This class handles, formats and caches datasets.
+ */
return Backbone.Collection.extend(
{
// list of datasets
@@ -11,8 +13,7 @@
cache: {},
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link app
this.app = app;
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/deferred.js
--- a/config/plugins/visualizations/charts/static/library/deferred.js
+++ b/config/plugins/visualizations/charts/static/library/deferred.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// deferred process handler
-return Backbone.Model.extend(
-{
+/**
+ * This class handles deferred processes. It makes it easy to handle multiple and overlapping sets of deferred processes.
+ */
+return Backbone.Model.extend({
// queue
queue: [],
@@ -14,8 +15,7 @@
counter: 0,
// initialize
- initialize: function()
- {
+ initialize: function(){
// loop through queue and check states
this.on('refresh', function() {
for (var index in this.queue) {
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// widget
-return Backbone.Model.extend(
-{
+/**
+ * This class handles job submissions to the charts tool.
+ */
+return Backbone.Model.extend({
// initialize
initialize: function(app, options) {
// link app
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/screenshot.js
--- a/config/plugins/visualizations/charts/static/library/screenshot.js
+++ b/config/plugins/visualizations/charts/static/library/screenshot.js
@@ -1,4 +1,6 @@
-// dependencies
+/**
+ * This class enables users to export/download a chart as PNG, SVG or PDF.
+ */
define(["libs/underscore"], function(_) {
//
// PNG export
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/storage.js
--- a/config/plugins/visualizations/charts/static/library/storage.js
+++ b/config/plugins/visualizations/charts/static/library/storage.js
@@ -1,9 +1,10 @@
// dependencies
-define(['utils/utils', 'plugin/models/chart', 'plugin/models/group'], function(Utils, Chart, Group) {
+define(['utils/utils', 'plugin/models/chart', 'plugin/models/group', 'mvc/visualization/visualization-model'], function(Utils, Chart, Group) {
-// collection
-return Backbone.Model.extend(
-{
+/**
+ * This class saves and loads a chart through the api.
+ */
+return Backbone.Model.extend({
// viz model
vis: null,
@@ -44,7 +45,6 @@
// pack and save nested chart model
save: function() {
-
// link chart
var chart = this.app.chart;
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/ui-button-menu.js
--- a/config/plugins/visualizations/charts/static/library/ui-button-menu.js
+++ b/config/plugins/visualizations/charts/static/library/ui-button-menu.js
@@ -1,8 +1,9 @@
// dependencies
-define(['utils/utils'],
- function(Utils) {
+define(['utils/utils'], function(Utils) {
-// return button menu
+/**
+ * This class creates a button with dropdown menu. It extends the functionality of the Ui.ButtonIcon class.
+ */
return Backbone.View.extend({
// main options
optionsDefault: {
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/ui-select.js
--- a/config/plugins/visualizations/charts/static/library/ui-select.js
+++ b/config/plugins/visualizations/charts/static/library/ui-select.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// plugin
-var View = Backbone.View.extend(
-{
+/**
+ * This class creates/wraps a default html select field as backbone class.
+ */
+var View = Backbone.View.extend({
// options
optionsDefault : {
id : '',
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 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
@@ -2,9 +2,10 @@
define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
function(Table, Ui, Utils) {
-// widget
-var View = Backbone.View.extend(
-{
+/**
+ * This class takes a dictionary as input an creates an input form. It uses the Ui.Table element to organize and format the form elements.
+ */
+var View = Backbone.View.extend({
// options
optionsDefault: {
title : '',
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/ui-table.js
--- a/config/plugins/visualizations/charts/static/library/ui-table.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table.js
@@ -1,7 +1,10 @@
+// dependencies
define(['utils/utils'], function(Utils) {
-var View = Backbone.View.extend(
-{
+/**
+ * This class creates a ui table element.
+ */
+var View = Backbone.View.extend({
// current row
row: null,
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/library/ui.js
--- a/config/plugins/visualizations/charts/static/library/ui.js
+++ b/config/plugins/visualizations/charts/static/library/ui.js
@@ -2,9 +2,12 @@
define(['utils/utils', 'plugin/library/ui-select', 'plugin/library/ui-button-menu', 'mvc/ui/ui-modal'],
function(Utils, Select, ButtonMenu, Modal) {
+/**
+ * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.
+ */
+
// plugin
-var Image = Backbone.View.extend(
-{
+var Image = Backbone.View.extend({
// options
optionsDefault: {
url : '',
@@ -27,8 +30,7 @@
});
// plugin
-var Label = Backbone.View.extend(
-{
+var Label = Backbone.View.extend({
// options
optionsDefault: {
title : '',
@@ -61,8 +63,7 @@
});
// plugin
-var Icon = Backbone.View.extend(
-{
+var Icon = Backbone.View.extend({
// options
optionsDefault: {
float : 'right',
@@ -95,8 +96,7 @@
});
// plugin
-var Button = Backbone.View.extend(
-{
+var Button = Backbone.View.extend({
// options
optionsDefault: {
id : null,
@@ -134,8 +134,7 @@
});
// plugin
-var ButtonIcon = Backbone.View.extend(
-{
+var ButtonIcon = Backbone.View.extend({
// options
optionsDefault: {
id : null,
@@ -188,8 +187,7 @@
});
// plugin
-var Anchor = Backbone.View.extend(
-{
+var Anchor = Backbone.View.extend({
// options
optionsDefault: {
title : '',
@@ -215,8 +213,7 @@
});
// plugin
-var Message = Backbone.View.extend(
-{
+var Message = Backbone.View.extend({
// options
optionsDefault: {
message : '',
@@ -268,8 +265,7 @@
});
// plugin
-var Searchbox = Backbone.View.extend(
-{
+var Searchbox = Backbone.View.extend({
// options
optionsDefault: {
onclick : null,
@@ -308,8 +304,7 @@
});
// plugin
-var Input = Backbone.View.extend(
-{
+var Input = Backbone.View.extend({
// options
optionsDefault: {
value : '',
@@ -362,8 +357,7 @@
});
// plugin
-var Textarea = Backbone.View.extend(
-{
+var Textarea = Backbone.View.extend({
// options
optionsDefault: {
value : '',
@@ -416,8 +410,7 @@
});
// plugin
-var RadioButton = Backbone.View.extend(
-{
+var RadioButton = Backbone.View.extend({
// options
optionsDefault: {
value : '',
@@ -503,19 +496,19 @@
// return
return {
- Label : Label,
- Button : Button,
- Icon : Icon,
- ButtonIcon : ButtonIcon,
- Input : Input,
- Anchor : Anchor,
- Message : Message,
- Searchbox : Searchbox,
- Select : Select,
- ButtonMenu : ButtonMenu,
- Modal: Modal,
- Textarea: Textarea,
- Image: Image,
- RadioButton: RadioButton
+ Anchor : Anchor,
+ Button : Button,
+ ButtonIcon : ButtonIcon,
+ ButtonMenu : ButtonMenu,
+ Icon : Icon,
+ Image : Image,
+ Input : Input,
+ Label : Label,
+ Message : Message,
+ Modal : Modal,
+ RadioButton : RadioButton,
+ Searchbox : Searchbox,
+ Select : Select,
+ Textarea : Textarea
}
});
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/models/chart.js
--- a/config/plugins/visualizations/charts/static/models/chart.js
+++ b/config/plugins/visualizations/charts/static/models/chart.js
@@ -1,11 +1,8 @@
// dependencies
-define(['plugin/models/groups', 'plugin/library/deferred', 'mvc/visualization/visualization-model'],
- function(Groups, Deferred) {
-
+define(['plugin/models/groups'], function(Groups) {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// defaults
defaults : {
id : null,
@@ -23,7 +20,6 @@
initialize: function(options) {
this.groups = new Groups();
this.settings = new Backbone.Model();
- this.deferred = new Deferred();
},
// reset
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -2,8 +2,7 @@
define([], function() {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// options
defaults : {
query_limit : 500,
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/models/group.js
--- a/config/plugins/visualizations/charts/static/models/group.js
+++ b/config/plugins/visualizations/charts/static/models/group.js
@@ -2,8 +2,7 @@
define([], function() {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// options
defaults : {
key : 'Data label',
@@ -11,8 +10,7 @@
},
// reset
- reset: function()
- {
+ reset: function(){
this.clear({silent: true}).set(this.defaults);
this.trigger('reset', this);
}
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/models/groups.js
--- a/config/plugins/visualizations/charts/static/models/groups.js
+++ b/config/plugins/visualizations/charts/static/models/groups.js
@@ -2,8 +2,7 @@
define(['plugin/models/group'], function(Group) {
// collection
-return Backbone.Collection.extend(
-{
+return Backbone.Collection.extend({
model: Group
});
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
@@ -0,0 +1,1 @@
+!function(r){function n(r){return r}function t(r,n){for(var t=0,e=n.length,u=Array(e);e>t;++t)u[t]=r[n[t]];return u}function e(r){function n(n,t,e,u){for(;u>e;){var f=e+u>>>1;r(n[f])<t?e=f+1:u=f}return e}function t(n,t,e,u){for(;u>e;){var f=e+u>>>1;t<r(n[f])?u=f:e=f+1}return e}return t.right=t,t.left=n,t}function u(r){function n(r,n,t){for(var u=t-n,f=(u>>>1)+1;--f>0;)e(r,f,u,n);return r}function t(r,n,t){for(var u,f=t-n;--f>0;)u=r[n],r[n]=r[n+f],r[n+f]=u,e(r,1,f,n);return r}function e(n,t,e,u){for(var f,o=n[--u+t],i=r(o);(f=t<<1)<=e&&(e>f&&r(n[u+f])>r(n[u+f+1])&&f++,!(i<=r(n[u+f])));)n[u+t]=n[u+f],t=f;n[u+t]=o}return n.sort=t,n}function f(r){function n(n,e,u,f){var o,i,a,c,l=Array(f=Math.min(u-e,f));for(i=0;f>i;++i)l[i]=n[e++];if(t(l,0,f),u>e){o=r(l[0]);do(a=r(c=n[e])>o)&&(l[0]=c,o=r(t(l,0,f)[0]));while(++e<u)}return l}var t=u(r);return n}function o(r){function n(n,t,e){for(var u=t+1;e>u;++u){for(var f=u,o=n[u],i=r(o);f>t&&r(n[f-1])>i;--f)n[f]=n[f-1];n[f]=o}return n}return n}function 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G.sort(n,0,n.length)}function s(r,n,t){return H=r,I=n,J=t,X=!0,S}function h(){return s(g,y,p)}function k(r){return s(m(r),x(r),p)}function w(r){function n(n){return r(n.value)}return D=f(n),G=u(n),S}function M(){return w(n)}function U(){return T}function C(){var r=N.indexOf(V);return r>=0&&N.splice(r,1),r=rn.indexOf(t),r>=0&&rn.splice(r,1),r=q.indexOf(e),r>=0&&q.splice(r,1),S}var S={top:v,all:l,reduce:s,reduceCount:h,reduceSum:k,order:w,orderNatural:M,size:U,dispose:C,remove:C};nn.push(S);var j,B,D,G,H,I,J,K=8,L=O(K),T=0,V=d,W=d,X=!0;return arguments.length<1&&(r=n),N.push(V),rn.push(t),q.push(e),t(P,Q,0,E),h().orderNatural()}function K(){var r=J(d),n=r.all;return delete r.all,delete r.top,delete r.order,delete r.orderNatural,delete r.size,r.value=function(){return n()[0].value},r}function L(){nn.forEach(function(r){r.dispose()});var r=S.indexOf(e);for(r>=0&&S.splice(r,1),r=S.indexOf(o),r>=0&&S.splice(r,1),r=q.indexOf(a),r>=0&&q.splice(r,1),r=0;E>r;++r)z[r]&=Z;return M&=Z,X}var P,Q,T,V,W,X={filter:l,filterExact:C,filterRange:j,filterFunction:D,filterAll:B,top:H,bottom:I,group:J,groupAll:K,dispose:L,remove:L},Y=~M&-~M,Z=~Y,$=i(function(r){return T[r]}),_=h,rn=[],nn=[],tn=0,en=0;return S.unshift(e),S.push(o),q.push(a),M|=Y,(U>=32?!Y:M&(1<<U)-1)&&(z=R(z,U<<=1)),e(b,0,E),o(b,0,E),X}function a(){function r(r,n){var t;if(!h)for(t=n;E>t;++t)z[t]||(a=c(a,b[t]))}function n(r,n,t){var e,u,f;if(!h){for(e=0,f=n.length;f>e;++e)z[u=n[e]]||(a=c(a,b[u]));for(e=0,f=t.length;f>e;++e)z[u=t[e]]===r&&(a=l(a,b[u]))}}function t(){var r;for(a=v(),r=0;E>r;++r)z[r]||(a=c(a,b[r]))}function e(r,n,t){return c=r,l=n,v=t,h=!0,s}function u(){return e(g,y,p)}function f(r){return e(m(r),x(r),p)}function o(){return h&&(t(),h=!1),a}function i(){var t=N.indexOf(n);return t>=0&&N.splice(t),t=S.indexOf(r),t>=0&&S.splice(t),s}var a,c,l,v,s={reduce:e,reduceCount:u,reduceSum:f,value:o,dispose:i,remove:i},h=!0;return N.push(n),S.push(r),r(b,0,E),u()}function c(){return E}var l={add:r,remove:e,dimension:o,groupAll:a,size:c},b=[],E=0,M=0,U=8,z=C(0),N=[],S=[],q=[];return arguments.length?r(arguments[0]):l}function A(r,n){return(257>n?C:65537>n?S:q)(r)}function k(r){for(var n=A(r,r),t=-1;++t<r;)n[t]=t;return n}function O(r){return 8===r?256:16===r?65536:4294967296}b.version="1.3.7",b.permute=t;var w=b.bisect=e(n);w.by=e;var E=b.heap=u(n);E.by=u;var M=b.heapselect=f(n);M.by=f;var U=b.insertionsort=o(n);U.by=o;var z=b.quicksort=i(n);z.by=i;var N=32,C=a,S=a,q=a,F=c,R=l;"undefined"!=typeof Uint8Array&&(C=function(r){return new Uint8Array(r)},S=function(r){return new Uint16Array(r)},q=function(r){return new Uint32Array(r)},F=function(r,n){if(r.length>=n)return r;var t=new r.constructor(n);return t.set(r),t},R=function(r,n){var t;switch(n){case 16:t=S(r.length);break;case 32:t=q(r.length);break;default:throw Error("invalid array width!")}return t.set(r),t}),r.crossfilter=b}("undefined"!=typeof exports&&exports||this);
\ No newline at end of file
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/views/editor.js
--- a/config/plugins/visualizations/charts/static/views/editor.js
+++ b/config/plugins/visualizations/charts/static/views/editor.js
@@ -4,18 +4,13 @@
'plugin/views/group', 'plugin/views/settings', 'plugin/views/types'],
function(Tabs, Ui, Portlet, Utils, Chart, Group, GroupView, SettingsView, TypesView) {
-// widget
-return Backbone.View.extend(
-{
- // defaults options
- optionsDefault: {
- header : true,
- content : 'No content available.'
- },
-
+/**
+ * The charts editor holds the tabs for selecting chart types, chart configuration
+ * and data group selections.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link this
var self = this;
@@ -25,9 +20,6 @@
// get current chart object
this.chart = this.app.chart;
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
// message element
this.message = new Ui.Message();
@@ -49,7 +41,7 @@
tooltip : 'Return to Viewer',
title : 'Cancel',
onclick : function() {
- // show viewport
+ // show viewer/viewport
self.app.go('viewer');
// reset chart
@@ -200,7 +192,7 @@
this.title.value(title);
},
- // update
+ // refresh group
_refreshGroupKey: function() {
var self = this;
var counter = 0;
@@ -213,7 +205,7 @@
});
},
- // new group
+ // add group model
_addGroupModel: function() {
var group = new Group({
id : Utils.uuid()
@@ -222,7 +214,7 @@
return group;
},
- // add group
+ // add group tab
_addGroup: function(group) {
// link this
var self = this;
@@ -319,7 +311,7 @@
// wait until chart is ready
var self = this;
- this.chart.deferred.execute(function() {
+ this.app.deferred.execute(function() {
// save
self.app.storage.save();
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -2,9 +2,10 @@
define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
function(Table, Ui, Utils) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the data group selection fields.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// link app
@@ -59,7 +60,7 @@
this._refreshGroup();
},
- // update dataset
+ // update group selection table
_refreshTable: function() {
// identify datasets
var dataset_id = this.chart.get('dataset_id');
@@ -116,7 +117,7 @@
this.chart.state('wait', 'Loading metadata...');
// register process
- var process_id = this.chart.deferred.register();
+ var process_id = this.app.deferred.register();
// request dictionary
var request_dictionary = {
@@ -131,7 +132,7 @@
self.chart.state('ok', 'Metadata initialized...');
// unregister
- self.chart.deferred.done(process_id);
+ self.app.deferred.done(process_id);
}
};
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/views/settings.js
--- a/config/plugins/visualizations/charts/static/views/settings.js
+++ b/config/plugins/visualizations/charts/static/views/settings.js
@@ -2,9 +2,10 @@
define(['plugin/library/ui', 'plugin/library/ui-table-form', 'utils/utils'],
function(Ui, TableForm, Utils) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart configuration form.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// link app
@@ -18,6 +19,7 @@
// create settings
this.form = new TableForm.View(app, {
+ title : 'Configuration',
content : 'This chart type does not provide any options.'
});
@@ -36,7 +38,7 @@
// get settings
var chart_definition = this.chart.definition;
- // check if dataset is available
+ // check if chart definition is available
if (!chart_definition) {
return;
}
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 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
@@ -1,7 +1,10 @@
+// dependencies
define(['utils/utils', 'plugin/library/ui'], function(Utils, Ui) {
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart type selection grid.
+ */
+return Backbone.View.extend({
// defaults options
optionsDefault: {
onchange : null,
@@ -16,7 +19,6 @@
// initialize
initialize : function(app, options) {
-
// link this
var self = this;
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/views/viewer.js
--- a/config/plugins/visualizations/charts/static/views/viewer.js
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -1,14 +1,14 @@
// dependencies
define(['utils/utils', 'plugin/library/ui', 'mvc/ui/ui-portlet',
- 'plugin/models/group', 'plugin/views/viewport', 'plugin/library/screenshot'],
- function(Utils, Ui, Portlet, Group, ViewportView, Screenshot) {
+ 'plugin/views/viewport', 'plugin/library/screenshot'],
+ function(Utils, Ui, Portlet, ViewportView, Screenshot) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart viewer which encapsulates the chart viewport.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link app
this.app = app;
@@ -152,7 +152,7 @@
// wait for chart to be ready
_wait: function(chart, callback) {
// get chart
- if (chart.deferred.ready()) {
+ if (this.app.deferred.ready()) {
callback();
} else {
this.message.update({message: 'Your chart is currently being processed. Please wait and try again.'});
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -2,7 +2,11 @@
define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'],
function(Portlet, Ui, Utils) {
-// widget
+/**
+ * The viewport creates and manages the dom elements used by the visualization plugins to draw the chart.
+ * Additionally, this class creates default request strings and request dictionaries parsed to the visualization plugins.
+ * This is the last class of the charts core classes before handing control over to the visualization plugins.
+ */
return Backbone.View.extend({
// list of canvas elements
@@ -26,7 +30,7 @@
// use full screen for viewer
this._fullscreen(this.$el, 100);
- // create canvas element
+ // create container element
this._createContainer('div');
// events
@@ -126,7 +130,7 @@
var self = this;
// register process
- var process_id = chart.deferred.register();
+ var process_id = this.app.deferred.register();
// identify chart type
var chart_type = chart.get('type');
@@ -171,7 +175,7 @@
});
},
function() {
- chart.deferred.done(process_id);
+ this.app.deferred.done(process_id);
}
);
} else {
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 config/plugins/visualizations/charts/templates/charts.mako
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -21,6 +21,9 @@
## shared css
${h.css( 'base' )}
+ ## crossfilter
+ ${h.javascript_link( app_root + "plugins/crossfilter/crossfilter.js" )}
+
## canvg
${h.javascript_link( app_root + "plugins/canvg/rgbcolor.js" )}
${h.javascript_link( app_root + "plugins/canvg/canvg.js" )}
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -177,6 +177,7 @@
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+ <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
@@ -262,6 +263,7 @@
--><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/>
+ <sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/>
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/bam.xml
--- a/display_applications/igb/bam.xml
+++ b/display_applications/igb/bam.xml
@@ -7,8 +7,8 @@
#set nm=$bam_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" strip_https="True" />
- <param type="data" name="bam_file" url="${niceName}.bam" strip_https="True" />
+ <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" />
+ <param type="data" name="bam_file" url="${niceName}.bam" /></link></display>
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/bb.xml
--- a/display_applications/igb/bb.xml
+++ b/display_applications/igb/bb.xml
@@ -8,7 +8,7 @@
#set nm=$bigbed_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="bigbed_file" url="${niceName}.bigbed" strip_https="True" />
+ <param type="data" name="bigbed_file" url="${niceName}.bigbed" /></link></display>
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/bed.xml
--- a/display_applications/igb/bed.xml
+++ b/display_applications/igb/bed.xml
@@ -8,7 +8,7 @@
#set nm=$bed_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="bed_file" url="${niceName}.bed" strip_https="True" />
+ <param type="data" name="bed_file" url="${niceName}.bed" /><param type="template" name="bioviz" strip="True" >
http://bioviz.org/igb/galaxy.html?version=${bed_file.dbkey}&loadresidue…
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/bedgraph.xml
--- a/display_applications/igb/bedgraph.xml
+++ b/display_applications/igb/bedgraph.xml
@@ -8,7 +8,7 @@
#set nm=$bedgraph_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" strip_https="True" />
+ <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" /><param type="template" name="bioviz" strip="True" >
http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadre…
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/bigwig.xml
--- a/display_applications/igb/bigwig.xml
+++ b/display_applications/igb/bigwig.xml
@@ -8,7 +8,7 @@
#set nm=$bigwig_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="bigwig_file" url="${niceName}.bigwig" strip_https="True" />
+ <param type="data" name="bigwig_file" url="${niceName}.bigwig" /><!--<param type="template" name="position" strip="True" >
#set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file )
#if $chrom is not None:
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/gtf.xml
--- a/display_applications/igb/gtf.xml
+++ b/display_applications/igb/gtf.xml
@@ -8,7 +8,7 @@
#set nm=$gtf_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" />
+ <param type="data" name="gtf_file" url="${niceName}.gtf" /><param type="template" name="bioviz" strip="True" >
http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue…
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 display_applications/igb/wig.xml
--- a/display_applications/igb/wig.xml
+++ b/display_applications/igb/wig.xml
@@ -8,7 +8,7 @@
#set nm=$wig_file_for_name.name
${re.sub('\W',"_",nm)}
</param>
- <param type="data" name="wig_file" url="${niceName}.wig" strip_https="True" />
+ <param type="data" name="wig_file" url="${niceName}.wig" /><param type="template" name="position" strip="True" >
#set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file )
#if $chrom is not None:
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -26,25 +26,24 @@
pysqlite = 2.5.6
python_lzo = 1.08_2.03_static
PyYAML = 3.10
-threadframe = 0.2
guppy = 0.1.10
SQLAlchemy = 0.7.9
; msgpack_python = 0.2.4
[eggs:noplatform]
-amqp = 1.4.3
+amqp = 1.4.5
anyjson = 0.3.3
Beaker = 1.4
bioblend = 0.4.2
boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
-drmaa = 0.6
+drmaa = 0.7.6
elementtree = 1.2.6_20050316
Fabric = 1.7.0
GeneTrack = 2.0.0_beta_1
importlib = 1.0.3
-kombu = 3.0.12
+kombu = 3.0.13
lrucache = 0.2
Mako = 0.4.1
mock = 1.0.1
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -19,27 +19,30 @@
<!-- Override the $DRMAA_LIBRARY_PATH environment variable --><param id="drmaa_library_path">/sge/lib/libdrmaa.so</param></plugin>
- <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner">
- <!-- More information on LWR can be found at https://lwr.readthedocs.org -->
- <!-- Uncomment following line to use libcurl to perform HTTP calls (defaults to urllib) -->
+ <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" />
+ <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" />
+ <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" />
+ <!-- Pulsar runners (see more at https://pulsar.readthedocs.org) -->
+ <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner">
+ <!-- Allow optimized HTTP calls with libcurl (defaults to urllib) --><!-- <param id="transport">curl</param> -->
- <!-- *Experimental Caching*: Uncomment next parameters to enable
- caching and specify the number of caching threads to enable on Galaxy
- side. Likely will not work with newer features such as MQ support.
- If this is enabled be sure to specify a `file_cache_dir` in the remote
- LWR's main configuration file.
+
+ <!-- *Experimental Caching*: Next parameter enables caching.
+ Likely will not work with newer features such as MQ support.
+
+ If this is enabled be sure to specify a `file_cache_dir` in
+ the remote Pulsar's servers main configuration file.
--><!-- <param id="cache">True</param> -->
- <!-- <param id="transfer_threads">2</param> --></plugin>
- <plugin id="amqp_lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner">
- <param id="url">amqp://guest:guest@localhost:5672//</param>
- <!-- If using message queue driven LWR - the LWR will generally
- initiate file transfers so a the URL of this Galaxy instance
- must be configured. -->
- <param id="galaxy_url">http://localhost:8080/</param>
- <!-- If multiple managers configured on the LWR, specify which one
- this plugin targets. -->
+ <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner">
+ <!-- AMQP URL to connect to. -->
+ <param id="amqp_url">amqp://guest:guest@localhost:5672//</param>
+ <!-- URL remote Pulsar apps should transfer files to this Galaxy
+ instance to/from. -->
+ <param id="galaxy_url">http://localhost:8080</param>
+ <!-- Pulsar job manager to communicate with (see Pulsar
+ docs for information on job managers). --><!-- <param id="manager">_default_</param> --><!-- The AMQP client can provide an SSL client certificate (e.g. for
validation), the following options configure that certificate
@@ -58,9 +61,17 @@
higher value (in seconds) (or `None` to use blocking connections). --><!-- <param id="amqp_consumer_timeout">None</param> --></plugin>
- <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" />
- <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" />
- <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" />
+ <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner">
+ <!-- Pulsar job runner with default parameters matching those
+ of old LWR job runner. If your Pulsar server is running on a
+ Windows machine for instance this runner should still be used.
+
+ These destinations still needs to target a Pulsar server,
+ older LWR plugins and destinations still work in Galaxy can
+ target LWR servers, but this support should be considered
+ deprecated and will disappear with a future release of Galaxy.
+ -->
+ </plugin></plugins><handlers default="handlers"><!-- Additional job handlers - the id should match the name of a
@@ -91,12 +102,107 @@
<!-- Warning: Local slot count doesn't tie up additional worker threads, to prevent over
allocating machine define a second local runner with different name and fewer workers
to run this destination. -->
+ <param id="embed_metadata_in_job">True</param>
+ <!-- Above parameter will be default (with no option to set
+ to False) in an upcoming release of Galaxy, but you can
+ try it early - it will slightly speed up local jobs by
+ embedding metadata calculation in job script itself.
+ --><job_metrics /><!-- Above element demonstrates embedded job metrics definition - see
job_metrics_conf.xml.sample for full documentation on possible nested
elements. This empty block will simply disable job metrics for the
corresponding destination. --></destination>
+ <destination id="docker_local" runner="local">
+ <param id="docker_enabled">true</param>
+ <!-- docker_volumes can be used to configure volumes to expose to docker,
+ For added isolation append :ro to the path to mount it read only.
+ Galaxy will attempt to infer a reasonable set of defaults which
+ volumes should be exposed how based on Galaxy's settings and the
+ destination - but be sure to add any library paths or data incides
+ that may be needed read-only.
+ -->
+ <!--
+ <param id="docker_volumes">$defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro</param>
+ -->
+ <!-- For a stock Galaxy instance and traditional job runner $defaults will
+ expand out as:
+
+ $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw
+
+ This assumes most of what is needed is available under Galaxy's root directory,
+ the tool directory, and the Galaxy's file_path (if using object store creatively
+ you will definitely need to expand defaults).
+
+ This configuration allows any docker instance to write to any Galaxy
+ file - for greater isolation set outputs_to_working_directory in
+ universe_wsgi.ini. This will cause $defaults to allow writing to much
+ less. It will then expand as follows:
+
+ $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro
+
+ If using the Pulsar, defaults will be even further restricted because the
+ Pulsar will (by default) stage all needed inputs into the job's job_directory
+ (so there is not need to allow the docker container to read all the
+ files - let alone write over them). Defaults in this case becomes:
+
+ $job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw
+
+ Python string.Template is used to expand volumes and values $defaults,
+ $galaxy_root, $default_file_path, $tool_directory, $working_directory,
+ are available to all jobs and $job_directory is also available for
+ Pulsar jobs.
+ -->
+ <!-- One can run docker using volumes-from tag by setting the following
+ parameter. For more information on volumes-from check out the following
+ docker tutorial. https://docs.docker.com/userguide/dockervolumes/
+ -->
+ <!-- <param id="docker_volumes_from">parent_container_name</param> -->
+ <!-- Control memory allocatable by docker container with following option:
+ -->
+ <!-- <param id="docker_memory">24G</param> -->
+ <!-- By default Docker will need to runnable by Galaxy using
+ password-less sudo - this can be configured by adding the
+ following line to the sudoers file of all compute nodes
+ with docker enabled:
+
+ galaxy ALL = (root) NOPASSWD: SETENV: /usr/bin/docker
+
+ The follow option is set to false to disable sudo (docker
+ must likewise be configured to allow this).
+ -->
+ <!-- <param id="docker_sudo">false</param> -->
+ <!-- Following option can be used to tweak sudo command used by
+ default. -->
+ <!-- <param id="docker_sudo_cmd">/usr/bin/sudo -extra_param</param> -->
+ <!-- By default, docker container will not have any networking
+ enabled. host networking can be bridged by uncommenting next option
+ http://docs.docker.io/reference/run/#network-settings
+ -->
+ <!-- <param id="docker_net">bridge</param> -->
+ <!-- Following command can be used to tweak docker command. -->
+ <!-- <param id="docker_cmd">/usr/local/custom_docker/docker</param> -->
+ <!-- Following can be used to connect to docke server in different
+ ways (translated as -H argument to docker client). -->
+ <!-- <param id="docker_host">unix:///var/run/docker.sock</param> -->
+ <!-- <param id="docker_host">:5555</param> -->
+ <!-- <param id="docker_host">:5555</param> -->
+ <!-- <param id="docker_host">tcp://127.0.0.1:4243</param> -->
+
+ <!-- If deployer wants to use docker for isolation, but does not
+ trust tool's specified container - a destination wide override
+ can be set. This will cause all jobs on this destination to use
+ that docker image. -->
+ <!-- <param id="docker_container_id_override">busybox:ubuntu-14.04</param> -->
+
+ <!-- Likewise, if deployer wants to use docker for isolation and
+ does trust tool's specified container - but also wants tool's not
+ configured to run in a container the following option can provide
+ a fallback. -->
+ <!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
+
+ </destination><destination id="pbs" runner="pbs" tags="mycluster"/><destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"><!-- Define parameters that are native to the job runner plugin. -->
@@ -129,87 +235,71 @@
<!-- A destination that represents a method in the dynamic runner. --><param id="function">foo</param></destination>
- <destination id="secure_lwr" runner="lwr">
- <param id="url">https://windowshost.examle.com:8913/</param>
- <!-- If set, private_token must match token remote LWR server configured with. -->
+ <destination id="secure_pulsar_rest_dest" runner="pulsar_rest">
+ <param id="url">https://examle.com:8913/</param>
+ <!-- If set, private_token must match token in remote Pulsar's
+ configuration. --><param id="private_token">123456789changeme</param><!-- Uncomment the following statement to disable file staging (e.g.
- if there is a shared file system between Galaxy and the LWR
+ if there is a shared file system between Galaxy and the Pulsar
server). Alternatively action can be set to 'copy' - to replace
http transfers with file system copies, 'remote_transfer' to cause
- the lwr to initiate HTTP transfers instead of Galaxy, or
- 'remote_copy' to cause lwr to initiate file system copies.
+ the Pulsar to initiate HTTP transfers instead of Galaxy, or
+ 'remote_copy' to cause Pulsar to initiate file system copies.
If setting this to 'remote_transfer' be sure to specify a
'galaxy_url' attribute on the runner plugin above. --><!-- <param id="default_file_action">none</param> --><!-- The above option is just the default, the transfer behavior
none|copy|http can be configured on a per path basis via the
- following file. See lib/galaxy/jobs/runners/lwr_client/action_mapper.py
- for examples of how to configure this file. This is very beta
- and nature of file will likely change.
+ following file. See Pulsar documentation for more details and
+ examples.
-->
- <!-- <param id="file_action_config">file_actions.json</param> -->
- <!-- Uncomment following option to disable Galaxy tool dependency
- resolution and utilize remote LWR's configuraiton of tool
- dependency resolution instead (same options as Galaxy for
- dependency resolution are available in LWR). At a minimum
- the remote LWR server should define a tool_dependencies_dir in
- its `server.ini` configuration. The LWR will not attempt to
- stage dependencies - so ensure the the required galaxy or tool
- shed packages are available remotely (exact same tool shed
- installed changesets are required).
+ <!-- <param id="file_action_config">file_actions.yaml</param> -->
+ <!-- The non-legacy Pulsar runners will attempt to resolve Galaxy
+ dependencies remotely - to enable this set a tool_dependency_dir
+ in Pulsar's configuration (can work with all the same dependency
+ resolutions mechanisms as Galaxy - tool Shed installs, Galaxy
+ packages, etc...). To disable this behavior, set the follow parameter
+ to none. To generate the dependency resolution command locally
+ set the following parameter local.
-->
- <!-- <param id="dependency_resolution">remote</params> -->
- <!-- Traditionally, the LWR allow Galaxy to generate a command line
- as if it were going to run the command locally and then the
- LWR client rewrites it after the fact using regular
- expressions. Setting the following value to true causes the
- LWR runner to insert itself into the command line generation
- process and generate the correct command line from the get go.
- This will likely be the default someday - but requires a newer
- LWR version and is less well tested. -->
- <!-- <param id="rewrite_parameters">true</params> -->
+ <!-- <param id="dependency_resolution">none</params> --><!-- Uncomment following option to enable setting metadata on remote
- LWR server. The 'use_remote_datatypes' option is available for
+ Pulsar server. The 'use_remote_datatypes' option is available for
determining whether to use remotely configured datatypes or local
ones (both alternatives are a little brittle). --><!-- <param id="remote_metadata">true</param> --><!-- <param id="use_remote_datatypes">false</param> --><!-- <param id="remote_property_galaxy_home">/path/to/remote/galaxy-central</param> -->
- <!-- If remote LWR server is configured to run jobs as the real user,
+ <!-- If remote Pulsar server is configured to run jobs as the real user,
uncomment the following line to pass the current Galaxy user
along. --><!-- <param id="submit_user">$__user_name__</param> -->
- <!-- Various other submission parameters can be passed along to the LWR
- whose use will depend on the remote LWR's configured job manager.
+ <!-- Various other submission parameters can be passed along to the Pulsar
+ whose use will depend on the remote Pulsar's configured job manager.
For instance:
-->
- <!-- <param id="submit_native_specification">-P bignodes -R y -pe threads 8</param> -->
+ <!-- <param id="submit_native_specification">-P bignodes -R y -pe threads 8</param> -->
+ <!-- Disable parameter rewriting and rewrite generated commands
+ instead. This may be required if remote host is Windows machine
+ but probably not otherwise.
+ -->
+ <!-- <param id="rewrite_parameters">false</params> --></destination>
- <destination id="amqp_lwr_dest" runner="amqp_lwr" >
- <!-- url and private_token are not valid when using MQ driven LWR. The plugin above
- determines which queue/manager to target and the underlying MQ server should be
- used to configure security.
- -->
- <!-- Traditionally, the LWR client sends request to LWR
- server to populate various system properties. This
+ <destination id="pulsar_mq_dest" runner="amqp_pulsar" >
+ <!-- The RESTful Pulsar client sends a request to Pulsar
+ to populate various system properties. This
extra step can be disabled and these calculated here
on client by uncommenting jobs_directory and
specifying any additional remote_property_ of
interest, this is not optional when using message
queues.
-->
- <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param>
- <!-- Default the LWR send files to and pull files from Galaxy when
- using message queues (in the more traditional mode Galaxy sends
- files to and pull files from the LWR - this is obviously less
- appropriate when using a message queue).
-
- The default_file_action currently requires pycurl be available
- to Galaxy (presumably in its virtualenv). Making this dependency
- optional is an open task.
+ <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param>
+ <!-- Otherwise MQ and Legacy pulsar destinations can be supplied
+ all the same destination parameters as the RESTful client documented
+ above (though url and private_token are ignored when using a MQ).
-->
- <param id="default_file_action">remote_transfer</param></destination><destination id="ssh_torque" runner="cli"><param id="shell_plugin">SecureShell</param>
@@ -239,7 +329,40 @@
--><param id="request_cpus">8</param></destination>
+
+ <!-- Jobs that hit the walltime on one destination can be automatically
+ resubmitted to another destination. Walltime detection is
+ currently only implemented in the slurm runner.
+
+ Multiple resubmit tags can be defined, the first resubmit matching
+ the terminal condition of a job will be used.
+
+ The 'condition' attribute is optional, if not present, the
+ resubmit destination will be used for all conditions. Currently,
+ only the "walltime_reached" condition is implemented.
+
+ The 'handler' tag is optional, if not present, the job's original
+ handler will be reused for the resubmitted job.
+ -->
+ <destination id="short_fast" runner="slurm">
+ <param id="nativeSpecification">--time=00:05:00 --nodes=1</param>
+ <resubmit condition="walltime_reached" destination="long_slow" handler="sge_handler" />
+ </destination>
+ <destination id="long_slow" runner="sge">
+ <!-- The destination that you resubmit jobs to can be any runner type -->
+ <param id="nativeSpecification">-l h_rt=96:00:00</param>
+ </destination>
+
</destinations>
+ <resources default="default">
+ <!-- Group different parameters defined in job_resource_params_conf.xml
+ together and assign these groups ids. Tool section below can map
+ tools to different groups. This is experimental functionality!
+ -->
+ <group id="default"></group>
+ <group id="memoryonly">memory</group>
+ <group id="all">processors,memory,time,project</group>
+ </resources><tools><!-- Tools can be configured to use specific destinations or handlers,
identified by either the "id" or "tags" attribute. If assigned to
@@ -250,15 +373,57 @@
<param id="source">trackster</param></tool><tool id="bar" destination="dynamic"/>
+ <!-- Next example defines resource group to insert into tool interface
+ and pass to dynamic destination (as resource_params argument). -->
+ <tool id="longbar" destination="dynamic" resources="all" /><tool id="baz" handler="special_handlers" destination="bigmem"/></tools><limits>
- <!-- Certain limits can be defined. -->
+ <!-- Certain limits can be defined. The 'concurrent_jobs' limits all
+ control the number of jobs that can be "active" at a time, that
+ is, dispatched to a runner and in the 'queued' or 'running'
+ states.
+
+ A race condition exists that will allow destination_* concurrency
+ limits to be surpassed when multiple handlers are allowed to
+ handle jobs for the same destination. To prevent this, assign all
+ jobs for a specific destination to a single handler.
+ -->
+ <!-- registered_user_concurrent_jobs:
+ Limit on the number of jobs a user with a registered Galaxy
+ account can have active across all destinations.
+ --><limit type="registered_user_concurrent_jobs">2</limit>
+ <!-- anonymous_user_concurrent_jobs:
+ Likewise, but for unregistered/anonymous users.
+ --><limit type="anonymous_user_concurrent_jobs">1</limit>
+ <!-- destination_user_concurrent_jobs:
+ The number of jobs a user can have active in the specified
+ destination, or across all destinations identified by the
+ specified tag. (formerly: concurrent_jobs)
+ -->
+ <limit type="destination_user_concurrent_jobs" id="local">1</limit>
+ <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit>
+ <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit>
+ <!-- destination_total_concurrent_jobs:
+ The number of jobs that can be active in the specified
+ destination (or across all destinations identified by the
+ specified tag) by any/all users.
+ -->
+ <limit type="destination_total_concurrent_jobs" id="local">16</limit>
+ <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit>
+ <!-- walltime:
+ Amount of time a job can run (in any destination) before it
+ will be terminated by Galaxy.
+ --><limit type="walltime">24:00:00</limit>
- <limit type="concurrent_jobs" id="local">1</limit>
- <limit type="concurrent_jobs" tag="mycluster">2</limit>
- <limit type="concurrent_jobs" tag="longjobs">1</limit>
+ <!-- output_size:
+ Size that any defined tool output can grow to before the job
+ will be terminated. This does not include temporary files
+ created by the job. Format is flexible, e.g.:
+ '10GB' = '10g' = '10240 Mb' = '10737418240'
+ -->
+ <limit type="output_size">10GB</limit></limits></job_conf>
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 job_resource_params_conf.xml.sample
--- /dev/null
+++ b/job_resource_params_conf.xml.sample
@@ -0,0 +1,6 @@
+<parameters>
+ <param label="Processors" name="processors" type="integer" size="2" min="1" max="64" value="" help="Number of processing cores, 'ppn' value (1-64). Leave blank to use default value." />
+ <param label="Memory" name="memory" type="integer" size="3" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." />
+ <param label="Time" name="time" type="integer" size="3" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." />
+ <param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." />
+</parameters>
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -12,13 +12,13 @@
from galaxy.visualization.data_providers.registry import DataProviderRegistry
from galaxy.visualization.registry import VisualizationsRegistry
from galaxy.tools.imp_exp import load_history_imp_exp_tools
-from galaxy.tools.genome_index import load_genome_index_tools
from galaxy.sample_tracking import external_service_types
from galaxy.openid.providers import OpenIDProviders
from galaxy.tools.data_manager.manager import DataManagers
from galaxy.jobs import metrics as job_metrics
from galaxy.web.base import pluginframework
from galaxy.queue_worker import GalaxyQueueWorker
+from tool_shed.galaxy_install import update_repository_manager
import logging
log = logging.getLogger( __name__ )
@@ -80,12 +80,8 @@
# Load Data Manager
self.data_managers = DataManagers( self )
- # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories.
- if self.config.get_bool( 'enable_tool_shed_check', False ):
- from tool_shed.galaxy_install import update_manager
- self.update_manager = update_manager.UpdateManager( self )
- else:
- self.update_manager = None
+ # Load the update repository manager.
+ self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self )
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
@@ -96,8 +92,6 @@
self.datatypes_registry.load_external_metadata_tool( self.toolbox )
# Load history import/export tools.
load_history_imp_exp_tools( self.toolbox )
- # Load genome indexer tool.
- load_genome_index_tools( self.toolbox )
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = None
if self.config.visualization_plugins_directory:
@@ -159,8 +153,7 @@
self.object_store.shutdown()
if self.heartbeat:
self.heartbeat.shutdown()
- if self.update_manager:
- self.update_manager.shutdown()
+ self.update_repository_manager.shutdown()
if self.control_worker:
self.control_worker.shutdown()
try:
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -15,13 +15,12 @@
from galaxy.web.formatting import expand_pretty_datetime_format
from galaxy.util import string_as_bool
from galaxy.util import listify
-from galaxy.util import parse_xml
from galaxy.util.dbkeys import GenomeBuilds
from galaxy import eggs
-import pkg_resources
log = logging.getLogger( __name__ )
+
def resolve_path( path, root ):
"""If 'path' is relative make absolute by prepending 'root'"""
if not( os.path.isabs( path ) ):
@@ -40,9 +39,9 @@
self.config_dict = kwargs
self.root = kwargs.get( 'root_dir', '.' )
# Collect the umask and primary gid from the environment
- self.umask = os.umask( 077 ) # get the current umask
- os.umask( self.umask ) # can't get w/o set, so set it back
- self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
+ self.umask = os.umask( 077 ) # get the current umask
+ os.umask( self.umask ) # can't get w/o set, so set it back
+ self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
# Database related configuration
self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root )
@@ -65,8 +64,6 @@
tempfile.tempdir = self.new_file_path
self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root )
self.cookie_path = kwargs.get( "cookie_path", "/" )
- self.genome_data_path = kwargs.get( "genome_data_path", "tool-data/genome" )
- self.rsync_url = kwargs.get( "rsync_url", "rsync://datacache.galaxyproject.org/indexes" )
# Galaxy OpenID settings
self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' )
@@ -75,7 +72,7 @@
self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) )
self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
- self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root )
+ self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'chrom') ), self.root )
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
# The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
# and moved to the tool shed.
@@ -105,7 +102,6 @@
self.shed_tool_data_path = self.tool_data_path
self.tool_data_table_config_path = [ resolve_path( x, self.root ) for x in kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ).split( ',' ) ]
self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
- self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) )
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
self.hours_between_check = kwargs.get( 'hours_between_check', 12 )
@@ -152,6 +148,7 @@
self.dependency_resolvers_config_file = resolve_path( kwargs.get( 'dependency_resolvers_config_file', 'dependency_resolvers_conf.xml' ), self.root )
self.job_metrics_config_file = resolve_path( kwargs.get( 'job_metrics_config_file', 'job_metrics_conf.xml' ), self.root )
self.job_config_file = resolve_path( kwargs.get( 'job_config_file', 'job_conf.xml' ), self.root )
+ self.job_resource_params_file = resolve_path( kwargs.get( 'job_resource_params_file', 'job_resource_params_conf.xml' ), self.root )
self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) )
self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) )
self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
@@ -167,8 +164,9 @@
h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ]
self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h )
self.admin_users = kwargs.get( "admin_users", "" )
+ self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u]
self.reset_password_length = int( kwargs.get('reset_password_length', '15') )
- self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu")
+ self.mailing_join_addr = kwargs.get('mailing_join_addr', 'galaxy-announce-join(a)bx.psu.edu')
self.error_email_to = kwargs.get( 'error_email_to', None )
self.activation_email = kwargs.get( 'activation_email', None )
self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) )
@@ -270,9 +268,9 @@
self.object_store_cache_path = resolve_path( kwargs.get( "object_store_cache_path", "database/object_store_cache" ), self.root )
# Handle AWS-specific config options for backward compatibility
if kwargs.get( 'aws_access_key', None) is not None:
- self.os_access_key= kwargs.get( 'aws_access_key', None )
- self.os_secret_key= kwargs.get( 'aws_secret_key', None )
- self.os_bucket_name= kwargs.get( 's3_bucket', None )
+ self.os_access_key = kwargs.get( 'aws_access_key', None )
+ self.os_secret_key = kwargs.get( 'aws_secret_key', None )
+ self.os_bucket_name = kwargs.get( 's3_bucket', None )
self.os_use_reduced_redundancy = kwargs.get( 'use_reduced_redundancy', False )
else:
self.os_access_key = kwargs.get( 'os_access_key', None )
@@ -375,6 +373,12 @@
self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) )
# visualization plugin framework
self.visualization_plugins_directory = kwargs.get( 'visualization_plugins_directory', None )
+ # Default chunk size for chunkable datatypes -- 64k
+ self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
+
+ self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
+ self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) )
+ self.citation_cache_lock_dir = self.resolve_path( kwargs.get( "citation_cache_lock_dir", "database/citations/locks" ) )
@property
def sentry_dsn_public( self ):
@@ -451,19 +455,13 @@
except Exception, e:
raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) )
# Create the directories that it makes sense to create
- for path in self.file_path, \
- self.new_file_path, \
- self.job_working_directory, \
- self.cluster_files_directory, \
- self.template_cache, \
- self.ftp_upload_dir, \
- self.library_import_dir, \
- self.user_library_import_dir, \
- self.nginx_upload_store, \
- './static/genetrack/plots', \
- self.whoosh_index_dir, \
- self.object_store_cache_path, \
- os.path.join( self.tool_data_path, 'shared', 'jars' ):
+ for path in (self.file_path, self.new_file_path,
+ self.job_working_directory, self.cluster_files_directory,
+ self.template_cache, self.ftp_upload_dir,
+ self.library_import_dir, self.user_library_import_dir,
+ self.nginx_upload_store, './static/genetrack/plots',
+ self.whoosh_index_dir, self.object_store_cache_path,
+ os.path.join( self.tool_data_path, 'shared', 'jars' )):
self._ensure_directory( path )
# Check that required files exist
tool_configs = self.tool_configs
@@ -479,7 +477,7 @@
if key in self.deprecated_options:
log.warning( "Config option '%s' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." % key )
- def is_admin_user( self,user ):
+ def is_admin_user( self, user ):
"""
Determine if the provided user is listed in `admin_users`.
@@ -494,12 +492,13 @@
"""
return resolve_path( path, self.root )
+
def get_database_engine_options( kwargs, model_prefix='' ):
"""
Allow options for the SQLAlchemy database engine to be passed by using
the prefix "database_engine_option".
"""
- conversions = {
+ conversions = {
'convert_unicode': string_as_bool,
'pool_timeout': int,
'echo': string_as_bool,
@@ -521,6 +520,7 @@
rval[ key ] = value
return rval
+
def configure_logging( config ):
"""
Allow some basic logging configuration to be read from ini file.
@@ -555,7 +555,7 @@
root.addHandler( handler )
# If sentry is configured, also log to it
if config.sentry_dsn:
- pkg_resources.require( "raven" )
+ eggs.require( "raven" )
from raven.handlers.logging import SentryHandler
sentry_handler = SentryHandler( config.sentry_dsn )
sentry_handler.setLevel( logging.WARN )
@@ -574,12 +574,26 @@
tool_configs = self.config.tool_configs
if self.config.migrated_tools_config not in tool_configs:
tool_configs.append( self.config.migrated_tools_config )
+
+ from galaxy.managers.citations import CitationsManager
+ self.citations_manager = CitationsManager( self )
+
from galaxy import tools
self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
# Search support for tools
import galaxy.tools.search
self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox )
+ from galaxy.tools.deps import containers
+ galaxy_root_dir = os.path.abspath(self.config.root)
+ file_path = os.path.abspath(getattr(self.config, "file_path"))
+ app_info = containers.AppInfo(
+ galaxy_root_dir,
+ default_file_path=file_path,
+ outputs_to_working_directory=self.config.outputs_to_working_directory
+ )
+ self.container_finder = galaxy.tools.deps.containers.ContainerFinder(app_info)
+
def _configure_tool_data_tables( self, from_shed_config ):
from galaxy.tools.data import ToolDataTableManager
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/dataset_collections/__init__.py
--- a/lib/galaxy/dataset_collections/__init__.py
+++ b/lib/galaxy/dataset_collections/__init__.py
@@ -138,6 +138,21 @@
changed = self._set_from_dict( trans, dataset_collection_instance, payload )
return changed
+ def copy(
+ self,
+ trans,
+ parent, # PRECONDITION: security checks on ability to add to parent occurred during load.
+ source,
+ encoded_source_id,
+ ):
+ assert source == "hdca" # for now
+ source_hdca = self.__get_history_collection_instance( trans, encoded_source_id )
+ new_hdca = source_hdca.copy()
+ parent.add_dataset_collection( new_hdca )
+ trans.sa_session.add( new_hdca )
+ trans.sa_session.flush()
+ return source_hdca
+
def _set_from_dict( self, trans, dataset_collection_instance, new_data ):
# Blatantly stolen from UsesHistoryDatasetAssociationMixin.set_hda_from_dict.
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/dataset_collections/util.py
--- a/lib/galaxy/dataset_collections/util.py
+++ b/lib/galaxy/dataset_collections/util.py
@@ -70,7 +70,7 @@
encoded_id = security.encode_id( dataset_colleciton_instance.id )
if isinstance( parent, model.History ):
encoded_history_id = security.encode_id( parent.id )
- dict_value[ 'url' ] = web.url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" )
+ dict_value[ 'url' ] = web.url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" )
elif isinstance( parent, model.LibraryFolder ):
encoded_library_id = security.encode_id( parent.library.id )
encoded_folder_id = security.encode_id( parent.id )
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@
import subprocess
import tempfile
import zipfile
+import sqlite3
from urllib import urlencode, quote_plus
from galaxy import eggs
@@ -545,3 +546,45 @@
return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size()))
Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit)
+
+
+(a)dataproviders.decorators.has_dataproviders
+class SQlite ( Binary ):
+ file_ext = "sqlite"
+
+ # Connects and runs a query that should work on any real database
+ # If the file is not sqlite, an exception will be thrown and the sniffer will return false
+ def sniff( self, filename ):
+ try:
+ conn = sqlite3.connect(filename)
+ schema_version=conn.cursor().execute("pragma schema_version").fetchone()
+ conn.close()
+ if schema_version is not None:
+ return True
+ return False
+ except:
+ return False
+
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ dataset.peek = "SQLite Database"
+ dataset.blurb = data.nice_size( dataset.get_size() )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def display_peek( self, dataset ):
+ try:
+ return dataset.peek
+ except:
+ return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+
+ @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
+ def sqlite_dataprovider( self, dataset, **settings ):
+ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
+ return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
+
+
+Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/datatypes/dataproviders/dataset.py
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -11,6 +11,8 @@
import line
import column
import external
+from galaxy.util import sqlite
+import re
from galaxy import eggs
eggs.require( 'bx-python' )
@@ -700,3 +702,27 @@
#TODO: as samtools - need more info on output format
raise NotImplementedError()
super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs )
+
+
+class SQliteDataProvider( base.DataProvider ):
+ """
+ Data provider that uses a sqlite database file as its source.
+
+ Allows any query to be run and returns the resulting rows as sqlite3 row objects
+ """
+ settings = {
+ 'query': 'str'
+ }
+
+ def __init__( self, source, query=None, **kwargs ):
+ self.query = query
+ self.connection = sqlite.connect(source.dataset.file_name)
+ super( SQliteDataProvider, self ).__init__( source, **kwargs )
+
+ def __iter__( self ):
+ if (self.query is not None) and sqlite.is_read_only_query(self.query):
+ for row in self.connection.cursor().execute(self.query):
+ yield row
+ else:
+ yield
+
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -126,25 +126,43 @@
rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy )
return rval
- def from_JSON_dict( self, filename ):
+ def from_JSON_dict( self, filename=None, path_rewriter=None, json_dict=None ):
dataset = self.parent
- log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
- JSONified_dict = json.load( open( filename ) )
+ if filename is not None:
+ log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ JSONified_dict = json.load( open( filename ) )
+ elif json_dict is not None:
+ log.debug( 'loading metadata from dict for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ if isinstance( json_dict, basestring ):
+ JSONified_dict = json.loads( json_dict )
+ elif isinstance( json_dict, dict ):
+ JSONified_dict = json_dict
+ else:
+ raise ValueError( "json_dict must be either a dictionary or a string, got %s." % ( type( json_dict ) ) )
+ else:
+ raise ValueError( "You must provide either a filename or a json_dict" )
for name, spec in self.spec.items():
if name in JSONified_dict:
- dataset._metadata[ name ] = spec.param.from_external_value( JSONified_dict[ name ], dataset )
+ from_ext_kwds = {}
+ external_value = JSONified_dict[ name ]
+ param = spec.param
+ if isinstance( param, FileParameter ):
+ from_ext_kwds[ 'path_rewriter' ] = path_rewriter
+ dataset._metadata[ name ] = param.from_external_value( external_value, dataset, **from_ext_kwds )
elif name in dataset._metadata:
#if the metadata value is not found in our externally set metadata but it has a value in the 'old'
#metadata associated with our dataset, we'll delete it from our dataset's metadata dict
del dataset._metadata[ name ]
- def to_JSON_dict( self, filename ):
+ def to_JSON_dict( self, filename=None ):
#galaxy.model.customtypes.json_encoder.encode()
meta_dict = {}
dataset_meta_dict = self.parent._metadata
for name, spec in self.spec.items():
if name in dataset_meta_dict:
meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] )
+ if filename is None:
+ return json.dumps( meta_dict )
json.dump( meta_dict, open( filename, 'wb+' ) )
def __getstate__( self ):
@@ -521,7 +539,7 @@
value = value.id
return value
- def from_external_value( self, value, parent ):
+ def from_external_value( self, value, parent, path_rewriter=None ):
"""
Turns a value read from a external dict into its value to be pushed directly into the metadata dict.
"""
@@ -532,8 +550,13 @@
if mf is None:
mf = self.new_file( dataset = parent, **value.kwds )
# Ensure the metadata file gets updated with content
- parent.dataset.object_store.update_from_file( mf, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) )
- os.unlink( value.file_name )
+ file_name = value.file_name
+ if path_rewriter:
+ # Job may have run with a different (non-local) tmp/working
+ # directory. Correct.
+ file_name = path_rewriter( file_name )
+ parent.dataset.object_store.update_from_file( mf, file_name=file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) )
+ os.unlink( file_name )
value = mf.id
return value
@@ -722,7 +745,7 @@
sa_session.flush()
metadata_files_list.append( metadata_files )
#return command required to build
- return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
+ return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, compute_tmp_dir or tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
def external_metadata_set_successfully( self, dataset, sa_session ):
metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/datatypes/sniff.py
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -90,19 +90,19 @@
f.close()
return False
-def convert_newlines( fname, in_place=True ):
+def convert_newlines( fname, in_place=True, tmp_dir=None, tmp_prefix=None ):
"""
Converts in place a file from universal line endings
to Posix line endings.
>>> fname = get_test_fname('temp.txt')
>>> file(fname, 'wt').write("1 2\\r3 4")
- >>> convert_newlines(fname)
+ >>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
(2, None)
>>> file(fname).read()
'1 2\\n3 4\\n'
"""
- fd, temp_name = tempfile.mkstemp()
+ fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir )
fp = os.fdopen( fd, "wt" )
i = None
for i, line in enumerate( file( fname, "U" ) ):
@@ -150,20 +150,20 @@
else:
return ( i, temp_name )
-def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ):
+def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix=None ):
"""
Combines above methods: convert_newlines() and sep2tabs()
so that files do not need to be read twice
>>> fname = get_test_fname('temp.txt')
>>> file(fname, 'wt').write("1 2\\r3 4")
- >>> convert_newlines_sep2tabs(fname)
+ >>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
(2, None)
>>> file(fname).read()
'1\\t2\\n3\\t4\\n'
"""
regexp = re.compile( patt )
- fd, temp_name = tempfile.mkstemp()
+ fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir )
fp = os.fdopen( fd, "wt" )
for i, line in enumerate( file( fname, "U" ) ):
line = line.rstrip( '\r\n' )
diff -r 2a2fcdf2af7797c5288c0ae68081097a27a92dd2 -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -25,7 +25,6 @@
# All tabular data is chunkable.
CHUNKABLE = True
- CHUNK_SIZE = 50000
"""Add metadata elements"""
MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 )
@@ -262,13 +261,13 @@
def get_chunk(self, trans, dataset, chunk):
ck_index = int(chunk)
f = open(dataset.file_name)
- f.seek(ck_index * self.CHUNK_SIZE)
+ f.seek(ck_index * trans.app.config.display_chunk_size)
# If we aren't at the start of the file, seek to next newline. Do this better eventually.
if f.tell() != 0:
cursor = f.read(1)
while cursor and cursor != '\n':
cursor = f.read(1)
- ck_data = f.read(self.CHUNK_SIZE)
+ ck_data = f.read(trans.app.config.display_chunk_size)
cursor = f.read(1)
while cursor and ck_data[-1] != '\n':
ck_data += cursor
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/52b5cc75a175/
Changeset: 52b5cc75a175
Branch: stable
User: natefoo
Date: 2014-08-11 22:47:34
Summary: Added tag release_2014.08.11 for changeset ca45b78adb41
Affected #: 1 file
diff -r ca45b78adb4152fc6e7395514d46eba6b7d0b838 -r 52b5cc75a1757eddfb94ee373193c9d8fa2ec442 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -17,3 +17,4 @@
9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
+ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dd2d3e453ed0/
Changeset: dd2d3e453ed0
Branch: next-stable
User: jgoecks
Date: 2014-08-11 17:05:07
Summary: Increase reference sequence size to data provider to support reference-based compression of spliced reads.
Affected #: 1 file
diff -r d85ae37476a17205c9869d633f3aafd104b48a98 -r dd2d3e453ed074f152751bf5d9ea281ed60abc80 lib/galaxy/webapps/galaxy/api/datasets.py
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -199,12 +199,12 @@
if isinstance( data_provider, (SamDataProvider, BamDataProvider ) ):
# Get reference sequence.
if dataset.dbkey:
- # FIXME: increase region 500bp each way to provide sequence for overlapping reads. As reads
- # get longer, this will need to be increased and/or a handle to the genomic data may be need
- # to be given to the data provider.
+ # FIXME: increase region 1M each way to provide sequence for
+ # spliced/gapped reads. Probably should provide refseq object
+ # directly to data provider.
region = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom,
- low=( max( 0, int( low ) - 500 ) ),
- high=( int( high ) + 500 ) )
+ low=( max( 0, int( low ) - 1000000 ) ),
+ high=( int( high ) + 1000000 ) )
# Get mean depth.
if not indexer:
https://bitbucket.org/galaxy/galaxy-central/commits/2d9628d776a2/
Changeset: 2d9628d776a2
Branch: next-stable
User: jgoecks
Date: 2014-08-11 17:18:46
Summary: Trackster: fix location of gap line and read-pair connector line.
Affected #: 2 files
diff -r dd2d3e453ed074f152751bf5d9ea281ed60abc80 -r 2d9628d776a22cc6f0a3629176c0ee04de8be422 static/scripts/packed/viz/trackster/painters.js
--- a/static/scripts/packed/viz/trackster/painters.js
+++ b/static/scripts/packed/viz/trackster/painters.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
+define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,rect_y+(draw_height-1)/2,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,draw_height=(mode==="Pack"?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;var line_height=y_start+1+(draw_height-1)/2;dashedLine(ctx,b1_end,line_height,b2_start,line_height)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
diff -r dd2d3e453ed074f152751bf5d9ea281ed60abc80 -r 2d9628d776a22cc6f0a3629176c0ee04de8be422 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -907,7 +907,7 @@
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
- ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1);
+ ctx.fillRect(s_start, rect_y + (draw_height - 1)/2, s_end - s_start, 1);
// No change in seq_offset because sequence not used when skipping.
base_offset += cig_len;
break;
@@ -1017,6 +1017,7 @@
f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ),
y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
+ draw_height = (mode === 'Pack' ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT),
label_color = this.prefs.label_color;
// Draw read.
@@ -1049,7 +1050,8 @@
b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) );
if (connector && b2_start > b1_end) {
ctx.fillStyle = CONNECTOR_COLOR;
- dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5);
+ var line_height = y_start + 1 + (draw_height - 1)/2;
+ dashedLine(ctx, b1_end, line_height, b2_start, line_height);
}
} else {
// Read is single.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: HDA/Collections client-side refactoring for drill down view
by commits-noreply＠bitbucket.org 11 Aug '14
by commits-noreply＠bitbucket.org 11 Aug '14
11 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/700560884da7/
Changeset: 700560884da7
User: carlfeberhard
Date: 2014-08-11 17:07:34
Summary: HDA/Collections client-side refactoring for drill down view
Affected #: 48 files
diff -r bdc4017c2e7e9ecb5dfa3d36798f535402ec80aa -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f static/scripts/mvc/base-mvc.js
--- a/static/scripts/mvc/base-mvc.js
+++ b/static/scripts/mvc/base-mvc.js
@@ -53,6 +53,7 @@
//==============================================================================
/** Backbone model that syncs to the browser's sessionStorage API.
+ * This all largely happens behind the scenes and no special calls are required.
*/
var SessionStorageModel = Backbone.Model.extend({
initialize : function( initialAttrs ){
@@ -147,13 +148,128 @@
//==============================================================================
+/** A mixin for models that allow T/F/Matching to their attributes - useful when
+ * searching or filtering collections of models.
+ * @example:
+ * see hda-model for searchAttribute and searchAliases definition examples.
+ * see history-contents.matches for how collections are filtered
+ * and see readonly-history-panel.searchHdas for how user input is connected to the filtering
+ */
+var SearchableModelMixin = {
+
+ /** what attributes of an HDA will be used in a text search */
+ searchAttributes : [
+ // override
+ ],
+
+ /** our attr keys don't often match the labels we display to the user - so, when using
+ * attribute specifiers ('name="bler"') in a term, allow passing in aliases for the
+ * following attr keys.
+ */
+ searchAliases : {
+ // override
+ },
+
+ /** search the attribute with key attrKey for the string searchFor; T/F if found */
+ searchAttribute : function( attrKey, searchFor ){
+ var attrVal = this.get( attrKey );
+ //this.debug( 'searchAttribute', attrKey, attrVal, searchFor );
+ // bail if empty searchFor or unsearchable values
+ if( !searchFor
+ || ( attrVal === undefined || attrVal === null ) ){
+ return false;
+ }
+ // pass to sep. fn for deep search of array attributes
+ if( _.isArray( attrVal ) ){ return this._searchArrayAttribute( attrVal, searchFor ); }
+ return ( attrVal.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 );
+ },
+
+ /** deep(er) search for array attributes; T/F if found */
+ _searchArrayAttribute : function( array, searchFor ){
+ //this.debug( '_searchArrayAttribute', array, searchFor );
+ searchFor = searchFor.toLowerCase();
+ //precondition: searchFor has already been validated as non-empty string
+ //precondition: assumes only 1 level array
+ //TODO: could possibly break up searchFor more (CSV...)
+ return _.any( array, function( elem ){
+ return ( elem.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 );
+ });
+ },
+
+ /** search all searchAttributes for the string searchFor,
+ * returning a list of keys of attributes that contain searchFor
+ */
+ search : function( searchFor ){
+ var model = this;
+ return _.filter( this.searchAttributes, function( key ){
+ return model.searchAttribute( key, searchFor );
+ });
+ },
+
+ /** alias of search, but returns a boolean; accepts attribute specifiers where
+ * the attributes searched can be narrowed to a single attribute using
+ * the form: matches( 'genome_build=hg19' )
+ * (the attribute keys allowed can also be aliases to the true attribute key;
+ * see searchAliases above)
+ * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair
+ * @returns {Boolean} was term found in (any) attribute(s)
+ */
+ matches : function( term ){
+ var ATTR_SPECIFIER = '=',
+ split = term.split( ATTR_SPECIFIER );
+ // attribute is specified - search only that
+ if( split.length >= 2 ){
+ var attrKey = split[0];
+ attrKey = this.searchAliases[ attrKey ] || attrKey;
+ return this.searchAttribute( attrKey, split[1] );
+ }
+ // no attribute is specified - search all attributes in searchAttributes
+ return !!this.search( term ).length;
+ },
+
+ /** an implicit AND search for all terms; IOW, a model must match all terms given
+ * where terms is a whitespace separated value string.
+ * e.g. given terms of: 'blah bler database=hg19'
+ * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19
+ * To include whitespace in terms: wrap the term in double quotations (name="blah bler").
+ */
+ matchesAll : function( terms ){
+ var model = this;
+ // break the terms up by whitespace and filter out the empty strings
+ terms = terms.match( /(".*"|\w*=".*"|\S*)/g ).filter( function( s ){ return !!s; });
+ return _.all( terms, function( term ){
+ term = term.replace( /"/g, '' );
+ return model.matches( term );
+ });
+ }
+};
+
+
+//==============================================================================
+/** A view that renders hidden and shows when some activator is clicked.
+ * options:
+ * showFn: the effect used to show/hide the View (defaults to jq.toggle)
+ * $elementShown: some jqObject (defaults to this.$el) to be shown/hidden
+ * onShowFirstTime: fn called the first time the view is shown
+ * onshow: fn called every time the view is shown
+ * onhide: fn called every time the view is hidden
+ * events:
+ * hiddenUntilActivated:shown (the view is passed as an arg)
+ * hiddenUntilActivated:hidden (the view is passed as an arg)
+ * instance vars:
+ * view.hidden {boolean} is the view in the hidden state
+ */
var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */{
//TODO: since this is a mixin, consider moving toggle, hidden into HUAVOptions
- /** */
+ /** call this in your initialize to set up the mixin
+ * @param {jQuery} $activator the 'button' that's clicked to show/hide the view
+ * @param {Object} hash with mixin options
+ */
hiddenUntilActivated : function( $activator, options ){
// call this in your view's initialize fn
options = options || {};
+//TODO: flesh out options - show them all here
this.HUAVOptions = {
$elementShown : this.$el,
showFn : jQuery.prototype.toggle,
@@ -172,12 +288,15 @@
}
},
+//TODO:?? remove? use .hidden?
+ /** returns T/F if the view is hidden */
isHidden : function(){
return ( this.HUAVOptions.$elementShown.is( ':hidden' ) );
},
- /** */
+ /** toggle the hidden state, show/hide $elementShown, call onshow/hide, trigger events */
toggle : function(){
+//TODO: more specific name - toggle is too general
// can be called manually as well with normal toggle arguments
//TODO: better as a callback (when the show/hide is actually done)
// show
@@ -207,60 +326,101 @@
}
};
+
//==============================================================================
+/** Function that allows mixing of hashs into bbone MVC while showing the mixins first
+ * (before the more local class overrides/hash).
+ * Basically, a simple reversal of param order on _.defaults() - to show mixins in top of definition.
+ * @example:
+ * var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... myVars : ... }) );
+ *
+ * NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that
+ */
function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){
- // usage: var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... }) );
- //NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that
-
- // simple reversal of param order on _.defaults() - to show mixins in top of definition
var args = Array.prototype.slice.call( arguments, 0 ),
lastArg = args.pop();
args.unshift( lastArg );
return _.defaults.apply( _, args );
}
+//==============================================================================
+/** Return an underscore template fn from an array of strings.
+ * @param {String[]} template the template strings to compile into the underscore template fn
+ * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model')
+ * @returns {Function} the (wrapped) underscore template fn
+ * The function accepts:
+ *
+ * The template strings can access:
+ * the json/model hash using model ("<%- model.myAttr %>) using the jsonNamespace above
+ * _l: the localizer function
+ * view (if passed): ostensibly, the view using the template (handy for view instance vars)
+ * Because they're namespaced, undefined attributes will not throw an error.
+ *
+ * @example:
+ * templateBler : BASE_MVC.wrapTemplate([
+ * '<div class="myclass <%- mynamespace.modelClass %>">',
+ * '<span><% print( _l( mynamespace.message ) ); %>:<%= view.status %></span>'
+ * '</div>'
+ * ], 'mynamespace' )
+ *
+ * Meant to be called in a View's definition in order to compile only once.
+ *
+ */
+function wrapTemplate( template, jsonNamespace ){
+ jsonNamespace = jsonNamespace || 'model';
+ var templateFn = _.template( template.join( '' ) );
+ return function( json, view ){
+ var templateVars = { view : view || {}, _l : _l };
+ templateVars[ jsonNamespace ] = json || {};
+ return templateFn( templateVars );
+ };
+}
//==============================================================================
+/** A view which, when first rendered, shows only summary data/attributes, but
+ * can be expanded to show further details (and optionally fetch those
+ * details from the server).
+ */
var ExpandableView = Backbone.View.extend( LoggableMixin ).extend({
//TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them
//PRECONDITION: model must have method hasDetails
+ //PRECONDITION: subclasses must have templates.el and templates.details
initialize : function( attributes ){
/** are the details of this view expanded/shown or not? */
this.expanded = attributes.expanded || false;
- this.log( '\t expanded:', this.expanded );
+ //this.log( '\t expanded:', this.expanded );
},
// ........................................................................ render main
-//TODO: for lack of a better place, add rendering logic here
+ /** jq fx speed */
fxSpeed : 'fast',
/** Render this content, set up ui.
- * @param {Integer} speed the speed of the render
- * @fires rendered when rendered
- * @fires rendered:ready when first rendered and NO running HDAs
- * @returns {Object} this HDABaseView
+ * @param {Number or String} speed the speed of the render
*/
render : function( speed ){
var $newRender = this._buildNewRender();
+ this._setUpBehaviors( $newRender );
this._queueNewRender( $newRender, speed );
return this;
},
+ /** Build a temp div containing the new children for the view's $el.
+ * If the view is already expanded, build the details as well.
+ */
_buildNewRender : function(){
// create a new render using a skeleton template, render title buttons, render body, and set up events, etc.
- var $newRender = $( this.templates.skeleton( this.model.toJSON() ) );
+ var $newRender = $( this.templates.el( this.model.toJSON(), this ) );
if( this.expanded ){
- $newRender.children( '.details' ).replaceWith( this._renderDetails() );
+ this.$details( $newRender ).replaceWith( this._renderDetails().show() );
}
- this._setUpBehaviors( $newRender );
return $newRender;
},
- /** Fade out the old el, replace with new dom, then fade in.
- * @param {Boolean} fade whether or not to fade out/in when re-rendering
+ /** Fade out the old el, swap in the new contents, then fade in.
+ * @param {Number or String} speed jq speed to use for rendering effects
* @fires rendered when rendered
- * @fires rendered:ready when first rendered and NO running HDAs
*/
_queueNewRender : function( $newRender, speed ) {
speed = ( speed === undefined )?( this.fxSpeed ):( speed );
@@ -280,6 +440,7 @@
]);
},
+ /** empty out the current el, move the $newRender's children in */
_swapNewRender : function( $newRender ){
return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() );
},
@@ -287,21 +448,29 @@
/** set up js behaviors, event handlers for elements within the given container
* @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)
*/
- _setUpBehaviors : function( $container ){
- $container = $container || this.$el;
+ _setUpBehaviors : function( $where ){
+ $where = $where || this.$el;
// set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)
- make_popup_menus( $container );
- $container.find( '[title]' ).tooltip({ placement : 'bottom' });
+ make_popup_menus( $where );
+ $where.find( '[title]' ).tooltip({ placement : 'bottom' });
},
// ......................................................................... details
+ /** shortcut to details DOM (as jQ) */
+ $details : function( $where ){
+ $where = $where || this.$el;
+ return $where.find( '.details' );
+ },
+
+ /** build the DOM for the details and set up behaviors on it */
_renderDetails : function(){
- // override this
- return null;
+ var $newDetails = $( this.templates.details( this.model.toJSON(), this ) );
+ this._setUpBehaviors( $newDetails );
+ return $newDetails;
},
// ......................................................................... expansion/details
- /** Show or hide the body/details of history content.
+ /** Show or hide the details
* @param {Boolean} expand if true, expand; if false, collapse
*/
toggleExpanded : function( expand ){
@@ -320,26 +489,26 @@
*/
expand : function(){
var view = this;
-
- function _renderDetailsAndExpand(){
- view.$( '.details' ).replaceWith( view._renderDetails() );
- // needs to be set after the above or the slide will not show
- view.expanded = true;
- view.$( '.details' ).slideDown( view.fxSpeed, function(){
+ return view._fetchModelDetails()
+ .always(function(){
+ var $newDetails = view._renderDetails();
+ view.$details().replaceWith( $newDetails );
+ // needs to be set after the above or the slide will not show
+ view.expanded = true;
+ $newDetails.slideDown( view.fxSpeed, function(){
view.trigger( 'expanded', view );
});
+ });
+ },
+
+ /** Check for model details and, if none, fetch them.
+ * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not
+ */
+ _fetchModelDetails : function(){
+ if( !this.model.hasDetails() ){
+ return this.model.fetch();
}
-//TODO:?? remove
- // fetch first if no details in the model
- if( !view.model.hasDetails() ){
- // we need the change event on HDCA's for the elements to be processed - so silent == false
- view.model.fetch().always( function( model ){
- _renderDetailsAndExpand();
- });
-//TODO: no error handling
- } else {
- _renderDetailsAndExpand();
- }
+ return jQuery.when();
},
/** Hide the body/details of an HDA.
@@ -348,19 +517,378 @@
collapse : function(){
var view = this;
view.expanded = false;
- this.$( '.details' ).slideUp( view.fxSpeed, function(){
+ this.$details().slideUp( view.fxSpeed, function(){
view.trigger( 'collapsed', view );
});
}
});
+
+//==============================================================================
+/** Mixin for views that can be dragged and dropped
+ * Allows for the drag behavior to be turned on/off, setting/removing jQuery event
+ * handlers each time.
+ * dataTransfer data is set to the JSON string of the view's model.toJSON
+ * Override '$dragHandle' to define the draggable DOM sub-element.
+ */
+var DraggableViewMixin = {
+
+ /** set up instance vars to track whether this view is currently draggable */
+ initialize : function( attributes ){
+ /** is the body of this hda view expanded/not? */
+ this.draggable = attributes.draggable || false;
+ },
+
+ /** what part of the view's DOM triggers the dragging */
+ $dragHandle : function(){
+//TODO: make abstract/general - move this to listItem
+ // override to the element you want to be your view's handle
+ return this.$( '.title-bar' );
+ },
+
+ /** toggle whether this view is draggable */
+ toggleDraggable : function(){
+ if( this.draggable ){
+ this.draggableOff();
+ } else {
+ this.draggableOn();
+ }
+ },
+
+ /** allow the view to be dragged, set up event handlers */
+ draggableOn : function(){
+ this.draggable = true;
+ //TODO: I have no idea why this doesn't work with the events hash or jq.on()...
+ //this.$el.find( '.title-bar' )
+ // .attr( 'draggable', true )
+ // .bind( 'dragstart', this.dragStartHandler, false )
+ // .bind( 'dragend', this.dragEndHandler, false );
+ this.dragStartHandler = _.bind( this._dragStartHandler, this );
+ this.dragEndHandler = _.bind( this._dragEndHandler, this );
+
+ var handle = this.$dragHandle().attr( 'draggable', true ).get(0);
+ handle.addEventListener( 'dragstart', this.dragStartHandler, false );
+ handle.addEventListener( 'dragend', this.dragEndHandler, false );
+ },
+
+ /** turn of view dragging and remove event listeners */
+ draggableOff : function(){
+ this.draggable = false;
+ var handle = this.$dragHandle().attr( 'draggable', false ).get(0);
+ handle.removeEventListener( 'dragstart', this.dragStartHandler, false );
+ handle.removeEventListener( 'dragend', this.dragEndHandler, false );
+ },
+
+ /** sets the dataTransfer data to the model's toJSON
+ * @fires dragstart (bbone event) which is passed this view
+ */
+ _dragStartHandler : function( event ){
+ //this.debug( 'dragStartHandler:', this, event, arguments )
+ this.trigger( 'dragstart', this );
+ event.dataTransfer.effectAllowed = 'move';
+ //TODO: all except IE: should be 'application/json', IE: must be 'text'
+ event.dataTransfer.setData( 'text', JSON.stringify( this.model.toJSON() ) );
+ return false;
+ },
+
+ /** handle the dragend
+ * @fires dragend (bbone event) which is passed this view
+ */
+ _dragEndHandler : function( event ){
+ this.trigger( 'dragend', this );
+ //this.debug( 'dragEndHandler:', event )
+ return false;
+ }
+};
+
+
+//==============================================================================
+/** Mixin that allows a view to be selected (gen. from a list).
+ * Selection controls ($selector) may be hidden/shown/toggled.
+ * The bbone event 'selectable' is fired when the controls are shown/hidden (passed T/F).
+ * Default rendering is a font-awesome checkbox.
+ * Default selector is '.selector' within the view's $el.
+ * The bbone events 'selected' and 'de-selected' are fired when the $selector is clicked.
+ * Both events are passed the view and the (jQuery) event.
+ */
+var SelectableViewMixin = {
+
+ /** Set up instance state vars for whether the selector is shown and whether the view has been selected */
+ initialize : function( attributes ){
+ /** is the view currently in selection mode? */
+ this.selectable = attributes.selectable || false;
+ /** is the view currently selected? */
+ this.selected = attributes.selected || false;
+ },
+
+ /** $el sub-element where the selector is rendered and what can be clicked to select. */
+ $selector : function(){
+ return this.$( '.selector' );
+ },
+
+ /** How the selector is rendered - defaults to font-awesome checkbox */
+ _renderSelected : function(){
+ // override
+ this.$selector().find( 'span' )
+ .toggleClass( 'fa-check-square-o', this.selected ).toggleClass( 'fa-square-o', !this.selected );
+ },
+
+ /** Toggle whether the selector is shown */
+ toggleSelector : function(){
+//TODO: use this.selectable
+ if( !this.$selector().is( ':visible' ) ){
+ this.showSelector();
+ } else {
+ this.hideSelector();
+ }
+ },
+
+ /** Display the selector control.
+ * @param {Number} a jQuery fx speed
+ * @fires: selectable which is passed true (IOW, the selector is shown) and the view
+ */
+ showSelector : function( speed ){
+ speed = speed !== undefined? speed : this.fxSpeed;
+ // make sure selected state is represented properly
+ this.selectable = true;
+ this.trigger( 'selectable', true, this );
+ this._renderSelected();
+ this.$selector().show( speed );
+ },
+
+ /** remove the selector control
+ * @param {Number} a jQuery fx speed
+ * @fires: selectable which is passed false (IOW, the selector is not shown) and the view
+ */
+ hideSelector : function( speed ){
+ speed = speed !== undefined? speed : this.fxSpeed;
+ // reverse the process from showSelect
+ this.selectable = false;
+ this.trigger( 'selectable', false, this );
+ this.$selector().hide( speed );
+ },
+
+ /** Toggle whether the view is selected */
+ toggleSelect : function( event ){
+ if( this.selected ){
+ this.deselect( event );
+ } else {
+ this.select( event );
+ }
+ },
+
+ /** Select this view and re-render the selector control to show it
+ * @param {Event} a jQuery event that caused the selection
+ * @fires: selected which is passed the view and the DOM event that triggered it (optionally)
+ */
+ select : function( event ){
+ // switch icon, set selected, and trigger event
+ if( !this.selected ){
+ this.trigger( 'selected', this, event );
+ this.selected = true;
+ this._renderSelected();
+ }
+ return false;
+ },
+
+ /** De-select this view and re-render the selector control to show it
+ * @param {Event} a jQuery event that caused the selection
+ * @fires: de-selected which is passed the view and the DOM event that triggered it (optionally)
+ */
+ deselect : function( event ){
+ // switch icon, set selected, and trigger event
+ if( this.selected ){
+ this.trigger( 'de-selected', this, event );
+ this.selected = false;
+ this._renderSelected();
+ }
+ return false;
+ }
+};
+
+
+//==============================================================================
+/** A view that is displayed in some larger list/grid/collection.
+ * Inherits from Expandable, Selectable, Draggable.
+ * The DOM contains warnings, a title bar, and a series of primary action controls.
+ * Primary actions are meant to be easily accessible item functions (such as delete)
+ * that are rendered in the title bar.
+ *
+ * Details are rendered when the user clicks the title bar or presses enter/space when
+ * the title bar is in focus.
+ *
+ * Designed as a base class for history panel contents - but usable elsewhere (I hope).
+ */
+var ListItemView = ExpandableView.extend( mixin( SelectableViewMixin, DraggableViewMixin, {
+
+//TODO: that's a little contradictory
+ tagName : 'div',
+ className : 'list-item',
+
+ /** Set up the base class and all mixins */
+ initialize : function( attributes ){
+ ExpandableView.prototype.initialize.call( this, attributes );
+ SelectableViewMixin.initialize.call( this, attributes );
+ DraggableViewMixin.initialize.call( this, attributes );
+ },
+
+ // ........................................................................ rendering
+ /** In this override, call methods to build warnings, titlebar and primary actions */
+ _buildNewRender : function(){
+ var $newRender = ExpandableView.prototype._buildNewRender.call( this );
+ $newRender.find( '.warnings' ).replaceWith( this._renderWarnings() );
+ $newRender.find( '.title-bar' ).replaceWith( this._renderTitleBar() );
+ $newRender.find( '.primary-actions' ).append( this._renderPrimaryActions() );
+ $newRender.find( '.subtitle' ).replaceWith( this._renderSubtitle() );
+ return $newRender;
+ },
+
+ /** In this override, render the selector controls and set up dragging before the swap */
+ _swapNewRender : function( $newRender ){
+ ExpandableView.prototype._swapNewRender.call( this, $newRender );
+ if( this.selectable ){ this.showSelector( 0 ); }
+ if( this.draggable ){ this.draggableOn(); }
+ return this.$el;
+ },
+
+ /** Render any warnings the item may need to show (e.g. "I'm deleted") */
+ _renderWarnings : function(){
+ var view = this,
+ $warnings = $( '<div class="warnings"></div>' ),
+ json = view.model.toJSON();
+//TODO:! unordered (map)
+ _.each( view.templates.warnings, function( templateFn ){
+ $warnings.append( $( templateFn( json, view ) ) );
+ });
+ return $warnings;
+ },
+
+ /** Render the title bar (the main/exposed SUMMARY dom element) */
+ _renderTitleBar : function(){
+ return $( this.templates.titleBar( this.model.toJSON(), this ) );
+ },
+
+ /** Return an array of jQ objects containing common/easily-accessible item controls */
+ _renderPrimaryActions : function(){
+ // override this
+ return [];
+ },
+
+ /** Render the title bar (the main/exposed SUMMARY dom element) */
+ _renderSubtitle : function(){
+ return $( this.templates.subtitle( this.model.toJSON(), this ) );
+ },
+
+ // ......................................................................... events
+ /** event map */
+ events : {
+ // expand the body when the title is clicked or when in focus and space or enter is pressed
+ 'click .title-bar' : '_clickTitleBar',
+ 'keydown .title-bar' : '_keyDownTitleBar',
+
+ // dragging - don't work, originalEvent === null
+ //'dragstart .dataset-title-bar' : 'dragStartHandler',
+ //'dragend .dataset-title-bar' : 'dragEndHandler'
+
+ 'click .selector' : 'toggleSelect'
+ },
+
+ /** expand when the title bar is clicked */
+ _clickTitleBar : function( event ){
+ event.stopPropagation();
+ this.toggleExpanded();
+ },
+
+ /** expand when the title bar is in focus and enter or space is pressed */
+ _keyDownTitleBar : function( event ){
+ // bail (with propagation) if keydown and not space or enter
+ var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13;
+ if( event && ( event.type === 'keydown' )
+ &&( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){
+ this.toggleExpanded();
+ event.stopPropagation();
+ return false;
+ }
+ return true;
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'ListItemView(' + modelString + ')';
+ }
+}));
+
+// ............................................................................ TEMPLATES
+/** underscore templates */
+ListItemView.prototype.templates = (function(){
+//TODO: move to require text! plugin
+
+ var elTemplato = wrapTemplate([
+ '<div class="list-element">',
+ // errors, messages, etc.
+ '<div class="warnings"></div>',
+
+ // multi-select checkbox
+ '<div class="selector">',
+ '<span class="fa fa-2x fa-square-o"></span>',
+ '</div>',
+ // space for title bar buttons - gen. floated to the right
+ '<div class="primary-actions"></div>',
+ '<div class="title-bar"></div>',
+
+ // expandable area for more details
+ '<div class="details"></div>',
+ '</div>'
+ ]);
+
+ var warnings = {};
+
+ var titleBarTemplate = wrapTemplate([
+ // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display
+ '<div class="title-bar clear" tabindex="0">',
+//TODO: prob. belongs in dataset-list-item
+ '<span class="state-icon"></span>',
+ '<div class="title">',
+ '<span class="name"><%- element.name %></span>',
+ '</div>',
+ '<div class="subtitle"></div>',
+ '</div>'
+ ], 'element' );
+
+ var subtitleTemplate = wrapTemplate([
+ // override this
+ '<div class="subtitle"></div>'
+ ]);
+
+ var detailsTemplate = wrapTemplate([
+ // override this
+ '<div class="details"></div>'
+ ]);
+
+ return {
+ el : elTemplato,
+ warnings : warnings,
+ titleBar : titleBarTemplate,
+ subtitle : subtitleTemplate,
+ details : detailsTemplate
+ };
+}());
+
+
//==============================================================================
return {
LoggableMixin : LoggableMixin,
SessionStorageModel : SessionStorageModel,
+ SearchableModelMixin : SearchableModelMixin,
HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin,
mixin : mixin,
- ExpandableView : ExpandableView
+ wrapTemplate : wrapTemplate,
+ ExpandableView : ExpandableView,
+ DraggableViewMixin : DraggableViewMixin,
+ SelectableViewMixin : SelectableViewMixin,
+ ListItemView : ListItemView
};
});
diff -r bdc4017c2e7e9ecb5dfa3d36798f535402ec80aa -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f static/scripts/mvc/collection/collection-model.js
--- a/static/scripts/mvc/collection/collection-model.js
+++ b/static/scripts/mvc/collection/collection-model.js
@@ -1,29 +1,57 @@
define([
- "mvc/dataset/hda-model",
+ "mvc/dataset/dataset-model",
"mvc/base-mvc",
"utils/localization"
-], function( HDA_MODEL, BASE_MVC, _l ){
+], function( DATASET, BASE_MVC, _l ){
//==============================================================================
-/** @class Backbone model for Dataset collection elements.
- * DC Elements contain a sub-model named 'object'. This class moves that
- * 'object' from the JSON in the attributes list to a full, instantiated
- * sub-model found in this.object. This is done on intialization and
- * everytime the 'change:object' event is fired.
- *
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
+/*
+Notes:
+
+Terminology:
+ DatasetCollection/DC : a container of datasets or nested DatasetCollections
+ Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection
+ HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history
+
+
+This all seems too complex unfortunately:
+
+- Terminology collision between DatasetCollections (DCs) and Backbone Collections.
+- In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*
+ either a dataset or a nested DC. This would make the hierarchy much taller. I've
+ decided to merge the contained JSON with the DC element json - making the 'has a'
+ relation into an 'is a' relation. This seems simpler to me and allowed a lot of
+ DRY in both models and views, but may make tracking or tracing within these models
+ more difficult (since DatasetCollectionElements are now *also* DatasetAssociations
+ or DatasetCollections (nested)). This also violates the rule of thumb about
+ favoring aggregation over inheritance.
+- Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.
+ These each should a) be usable on their own, b) be usable in the context of
+ nesting within a collection model (at least in the case of ListPaired), and
+ c) be usable within the context of other container models (like History or
+ LibraryFolder, etc.). I've tried to separate/extract classes in order to
+ handle those three situations, but it's proven difficult to do in a simple,
+ readable manner.
+- Ideally, histories and libraries would inherit from the same server models as
+ dataset collections do since they are (in essence) dataset collections themselves -
+ making the whole nested structure simpler. This would be a large, error-prone
+ refactoring and migration.
+
+Many of the classes and heirarchy are meant as extension points so, while the
+relations and flow may be difficult to understand initially, they'll allow us to
+handle the growth or flux dataset collection in the future (w/o actually implementing
+any YAGNI).
+
+*/
+//_________________________________________________________________________________________________ ELEMENTS
+/** @class mixin for Dataset collection elements.
+ * When collection elements are passed from the API, the underlying element is
+ * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).
+ * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues
+ * effectively changing a DCE from a container to a subclass.
*/
-var DatasetCollectionElement = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend(
-/** @lends DatasetCollectionElement.prototype */{
+var DatasetCollectionElementMixin = {
- //TODO:?? this model may be unneccessary - it reflects the api structure, but...
- // if we munge the element with the element.object at parse, we can flatten the entire hierarchy
-
- /** logger used to record this.log messages, commonly set to console */
- // comment this out to suppress log output
- //logger : console,
-
+ /** default attributes used by elements in a dataset collection */
defaults : {
model_class : 'DatasetCollectionElement',
element_identifier : null,
@@ -31,137 +59,52 @@
element_type : null
},
- /** Set up.
- * @see Backbone.Collection#initialize
- */
- initialize : function( model, options ){
- this.info( this + '.initialize:', model, options );
- options = options || {};
- //this._setUpListeners();
-
- this.object = this._createObjectModel();
- this.on( 'change:object', function(){
- //this.log( 'change:object' );
-//TODO: prob. better to update the sub-model instead of re-creating it
- this.object = this._createObjectModel();
- });
+ /** merge the attributes of the sub-object 'object' into this model */
+ _mergeObject : function( attributes ){
+ _.extend( attributes, attributes.object );
+ delete attributes.object;
+ return attributes;
},
- _createObjectModel : function(){
- //this.log( '_createObjectModel', this.get( 'object' ), this.object );
- //TODO: same patterns as HDCA _createElementsModel - refactor to BASE_MVC.hasSubModel?
- if( _.isUndefined( this.object ) ){ this.object = null; }
- if( !this.get( 'object' ) ){ return this.object; }
-
- var object = this.get( 'object' ),
- ObjectClass = this._getObjectClass();
- this.unset( 'object', { silent: true });
- this.object = new ObjectClass( object );
-
- return this.object;
+ /** override to merge this.object into this */
+ constructor : function( attributes, options ){
+ this.debug( '\t DatasetCollectionElement.constructor:', attributes, options );
+ attributes = this._mergeObject( attributes );
+ Backbone.Model.apply( this, arguments );
},
- _getObjectClass : function(){
- this.debug( 'DCE, element_type:', this.get( 'element_type' ) );
- switch( this.get( 'element_type' ) ){
- case 'dataset_collection':
- return DatasetCollection;
- case 'hda':
- return HDA_MODEL.HistoryDatasetAssociation;
- }
- throw new TypeError( 'Unknown element_type: ' + this.get( 'element_type' ) );
- },
+ /** when the model is fetched, merge this.object into this */
+ parse : function( response, options ){
+ var attributes = response;
+ attributes = this._mergeObject( attributes );
+ return attributes;
+ }
+};
- toJSON : function(){
- var json = Backbone.Model.prototype.toJSON.call( this );
- if( this.object ){
- json.object = this.object.toJSON();
- }
- return json;
- },
+//TODO: unused?
+/** Concrete class of Generic DatasetCollectionElement */
+var DatasetCollectionElement = Backbone.Model
+ .extend( BASE_MVC.LoggableMixin )
+ .extend( DatasetCollectionElementMixin );
- hasDetails : function(){
- return ( this.object !== null
- && this.object.hasDetails() );
- },
-
- /** String representation. */
- toString : function(){
- var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );
- return ([ 'DatasetCollectionElement(', objStr, ')' ].join( '' ));
- }
-});
-
-
+
//==============================================================================
-/** @class Backbone model for
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
-var HDADCE = DatasetCollectionElement.extend(
-/** @lends DatasetCollectionElement.prototype */{
-
- _getObjectClass : function(){
- return HDA_MODEL.HistoryDatasetAssociation;
- },
-
- /** String representation. */
- toString : function(){
- var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );
- return ([ 'HDADCE(', objStr, ')' ].join( '' ));
- }
-});
-
-
-//==============================================================================
-/** @class Backbone model for
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
-var DCDCE = DatasetCollectionElement.extend(
-/** @lends DatasetCollectionElement.prototype */{
-
- _getObjectClass : function(){
- return DatasetCollection;
- },
-
- getVisibleContents : function(){
- return this.object? this.object.getVisibleContents(): [];
- },
-
- /** String representation. */
- toString : function(){
- var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );
- return ([ 'DCDCE(', objStr, ')' ].join( '' ));
- }
-});
-
-
-//==============================================================================
-/** @class Backbone collection for DCEs.
- * NOTE: used *only* in second level of list:paired collections (a
- * collection that contains collections)
- *
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
+/** @class Base/Abstract Backbone collection for Generic DCEs. */
var DCECollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend(
-/** @lends DatasetCollectionElementCollection.prototype */{
+/** @lends DCECollection.prototype */{
model: DatasetCollectionElement,
// comment this out to suppress log output
/** logger used to record this.log messages, commonly set to console */
//logger : console,
+//TODO: unused?
/** Set up.
* @see Backbone.Collection#initialize
*/
- initialize : function( models, options ){
+ initialize : function( attributes, options ){
+ this.debug( this + '(DCECollection).initialize:', attributes, options );
options = options || {};
- this.info( this + '.initialize:', models, options );
//this._setUpListeners();
},
@@ -173,69 +116,98 @@
//==============================================================================
-/** @class Backbone collection for
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
+/** @class Backbone model for a dataset collection element that is a dataset (HDA).
*/
-var HDADCECollection = DCECollection.extend(
-/** @lends DatasetCollectionElementCollection.prototype */{
- model: HDADCE,
+var DatasetDCE = DATASET.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,
+/** @lends DatasetDCE.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ defaults : _.extend( {}, DATASET.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ),
+
+ // because all objects have constructors (as this hashmap would even if this next line wasn't present)
+ // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
+ // - re-apply manually it now
+ /** call the mixin constructor */
+ constructor : function( attributes, options ){
+ this.debug( '\t DatasetDCE.constructor:', attributes, options );
+ //DATASET.DatasetAssociation.prototype.constructor.call( this, attributes, options );
+ DatasetCollectionElementMixin.constructor.call( this, attributes, options );
+ },
+
+//TODO: unused?
+ /** set up */
+ initialize : function( attributes, options ){
+ this.debug( this + '(DatasetDCE).initialize:', attributes, options );
+ DATASET.DatasetAssociation.prototype.initialize.call( this, attributes, options );
+ },
/** String representation. */
toString : function(){
- return ([ 'HDADCECollection(', this.length, ')' ].join( '' ));
+ var objStr = this.get( 'element_identifier' );
+ return ([ 'DatasetDCE(', objStr, ')' ].join( '' ));
+ }
+}));
+
+
+//==============================================================================
+/** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).
+ */
+var DatasetDCECollection = DCECollection.extend(
+/** @lends DatasetDCECollection.prototype */{
+ model: DatasetDCE,
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+//TODO: unused?
+ /** */
+ initialize : function( attributes, options ){
+ this.debug( this + '(DatasetDCECollection).initialize:', attributes, options );
+ DCECollection.prototype.initialize.call( this, attributes, options );
+ },
+
+ /** String representation. */
+ toString : function(){
+ return ([ 'DatasetDCECollection(', this.length, ')' ].join( '' ));
}
});
-//==============================================================================
-/** @class Backbone collection for
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
+//_________________________________________________________________________________________________ COLLECTIONS
+/** @class Backbone model for Dataset Collections.
+ * The DC API returns an array of JSON objects under the attribute elements.
+ * This model:
+ * - removes that array/attribute ('elements') from the model,
+ * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),
+ * - passes that json onto the bbone collection
+ * - caches the bbone collection in this.elements
*/
-var DCDCECollection = DCECollection.extend(
-/** @lends DatasetCollectionElementCollection.prototype */{
- model: DCDCE,
+var DatasetCollection = Backbone.Model
+ .extend( BASE_MVC.LoggableMixin )
+ .extend( BASE_MVC.SearchableModelMixin )
+.extend(/** @lends DatasetCollection.prototype */{
- /** String representation. */
- toString : function(){
- return ([ 'DCDCECollection(', this.length, ')' ].join( '' ));
- }
-});
-
-
-//==============================================================================
-/** @class Backbone model for Dataset Collections.
- * DCs contain a bbone collection named 'elements' using the class found in
- * this.collectionClass (gen. DatasetCollectionElementCollection). DCs move
- * that 'object' from the JSON in the attributes list to a full, instantiated
- * collection found in this.elements. This is done on intialization and
- * everytime the 'change:elements' event is fired.
- *
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
-var DatasetCollection = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend(
-/** @lends ListDatasetCollection.prototype */{
-
- //logger : console,
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
/** default attributes for a model */
defaults : {
- collection_type : 'list'
+ /* 'list', 'paired', or 'list:paired' */
+ collection_type : null,
+ //??
+ deleted : false
},
+ /** Which class to use for elements */
collectionClass : DCECollection,
/** */
initialize : function( model, options ){
- this.info( 'DatasetCollection.initialize:', model, options );
+ this.debug( this + '(DatasetCollection).initialize:', model, options, this );
//historyContent.HistoryContent.prototype.initialize.call( this, attrs, options );
this.elements = this._createElementsModel();
-//TODO:?? no way to use parse here?
this.on( 'change:elements', function(){
this.log( 'change:elements' );
//TODO: prob. better to update the collection instead of re-creating it
@@ -245,15 +217,17 @@
/** move elements model attribute to full collection */
_createElementsModel : function(){
- this.log( '_createElementsModel', this.get( 'elements' ), this.elements );
+ this.debug( this + '._createElementsModel', this.collectionClass, this.get( 'elements' ), this.elements );
//TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?
var elements = this.get( 'elements' ) || [];
- this.info( 'elements:', elements );
this.unset( 'elements', { silent: true });
this.elements = new this.collectionClass( elements );
+ //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );
return this.elements;
},
+ // ........................................................................ common queries
+ /** pass the elements back within the model json when this is serialized */
toJSON : function(){
var json = Backbone.Model.prototype.toJSON.call( this );
if( this.elements ){
@@ -262,17 +236,43 @@
return json;
},
+ /** is the collection done with updates and ready to be used? (finished running, etc.) */
+ inReadyState : function(){
+//TODO: state currenly unimplemented for collections
+ return true;
+ },
+
+ //TODO:?? the following are the same interface as DatasetAssociation - can we combine?
+ /** Does the DC contain any elements yet? Is a fetch() required? */
hasDetails : function(){
//TODO: this is incorrect for (accidentally) empty collections
this.debug( 'hasDetails:', this.elements.length );
return this.elements.length !== 0;
},
+ /** Given the filters, what models in this.elements would be returned? */
getVisibleContents : function( filters ){
- //TODO: filters unused for now
+ // filters unused for now
return this.elements;
},
+ // ........................................................................ ajax
+ /** save this dataset, _Mark_ing it as deleted (just a flag) */
+ 'delete' : function( options ){
+ if( this.get( 'deleted' ) ){ return jQuery.when(); }
+ return this.save( { deleted: true }, options );
+ },
+ /** save this dataset, _Mark_ing it as undeleted */
+ undelete : function( options ){
+ if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }
+ return this.save( { deleted: false }, options );
+ },
+
+ // ........................................................................ searchable
+ searchAttributes : [
+ 'name'
+ ],
+
// ........................................................................ misc
/** String representation */
toString : function(){
@@ -283,10 +283,21 @@
//==============================================================================
+/** Model for a DatasetCollection containing datasets (non-nested).
+ */
var ListDatasetCollection = DatasetCollection.extend(
/** @lends ListDatasetCollection.prototype */{
- collectionClass : HDADCECollection,
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ collectionClass : DatasetDCECollection,
+
+//TODO: unused?
+ initialize : function( attrs, options ){
+ this.debug( this + '(ListDatasetCollection).initialize:', attrs, options );
+ DatasetCollection.prototype.initialize.call( this, attrs, options );
+ },
/** String representation. */
toString : function(){
@@ -296,8 +307,20 @@
//==============================================================================
+/** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).
+ */
var PairDatasetCollection = ListDatasetCollection.extend(
-/** @lends ListDatasetCollection.prototype */{
+/** @lends PairDatasetCollection.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+//TODO: unused?
+ /** */
+ initialize : function( attrs, options ){
+ this.debug( this + '(PairDatasetCollection).initialize:', attrs, options );
+ ListDatasetCollection.prototype.initialize.call( this, attrs, options );
+ },
/** String representation. */
toString : function(){
@@ -306,14 +329,129 @@
});
+//_________________________________________________________________________________________________ NESTED COLLECTIONS
+// this is where things get weird, man. Weird.
+//TODO: it might be possible to compact all the following...I think.
//==============================================================================
+/** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection
+ * (a nested collection). Currently only list:paired.
+ */
+var NestedDCDCE = DatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,
+/** @lends NestedDCDCE.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ // because all objects have constructors (as this hashmap would even if this next line wasn't present)
+ // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model
+ // - re-apply manually it now
+ /** call the mixin constructor */
+ constructor : function( attributes, options ){
+ this.debug( '\t NestedDCDCE.constructor:', attributes, options );
+ DatasetCollectionElementMixin.constructor.call( this, attributes, options );
+ },
+
+ /** String representation. */
+ toString : function(){
+ var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );
+ return ([ 'NestedDCDCE(', objStr, ')' ].join( '' ));
+ }
+}));
+
+
+//==============================================================================
+/** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).
+ */
+var NestedDCDCECollection = DCECollection.extend(
+/** @lends NestedDCDCECollection.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ model: NestedDCDCE,
+
+//TODO: unused?
+ /** */
+ initialize : function( attrs, options ){
+ this.debug( this + '(NestedDCDCECollection).initialize:', attrs, options );
+ DCECollection.prototype.initialize.call( this, attrs, options );
+ },
+
+ /** String representation. */
+ toString : function(){
+ return ([ 'NestedDCDCECollection(', this.length, ')' ].join( '' ));
+ }
+});
+
+
+//==============================================================================
+/** @class Backbone model for a paired dataset collection within a list:paired dataset collection.
+ */
+var NestedPairDCDCE = PairDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,
+/** @lends NestedPairDCDCE.prototype */{
+//TODO:?? possibly rename to NestedDatasetCollection?
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ /** */
+ constructor : function( attributes, options ){
+ this.debug( '\t NestedPairDCDCE.constructor:', attributes, options );
+ //DatasetCollection.constructor.call( this, attributes, options );
+ DatasetCollectionElementMixin.constructor.call( this, attributes, options );
+ },
+
+ /** String representation. */
+ toString : function(){
+ var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );
+ return ([ 'NestedPairDCDCE(', objStr, ')' ].join( '' ));
+ }
+}));
+
+
+//==============================================================================
+/** @class Backbone collection for a backbone collection containing paired dataset collections.
+ */
+var NestedPairDCDCECollection = NestedDCDCECollection.extend(
+/** @lends PairDCDCECollection.prototype */{
+
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
+
+ model: NestedPairDCDCE,
+
+//TODO: unused?
+ /** */
+ initialize : function( attrs, options ){
+ this.debug( this + '(NestedPairDCDCECollection).initialize:', attrs, options );
+ NestedDCDCECollection.prototype.initialize.call( this, attrs, options );
+ },
+
+ /** String representation. */
+ toString : function(){
+ return ([ 'NestedPairDCDCECollection(', this.length, ')' ].join( '' ));
+ }
+});
+
+
+//==============================================================================
+/** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).
+ */
var ListPairedDatasetCollection = DatasetCollection.extend(
-/** @lends ListDatasetCollection.prototype */{
+/** @lends ListPairedDatasetCollection.prototype */{
- collectionClass : DCDCECollection,
+ /** logger used to record this.log messages, commonly set to console */
+ //logger : console,
// list:paired is the only collection that itself contains collections
- //collectionClass : DatasetCollectionCollection,
+ collectionClass : NestedPairDCDCECollection,
+
+//TODO: unused?
+ /** */
+ initialize : function( attributes, options ){
+ this.debug( this + '(ListPairedDatasetCollection).initialize:', attributes, options );
+ DatasetCollection.prototype.initialize.call( this, attributes, options );
+ },
/** String representation. */
toString : function(){
@@ -324,7 +462,6 @@
//==============================================================================
return {
- //DatasetCollection : DatasetCollection,
ListDatasetCollection : ListDatasetCollection,
PairDatasetCollection : PairDatasetCollection,
ListPairedDatasetCollection : ListPairedDatasetCollection
diff -r bdc4017c2e7e9ecb5dfa3d36798f535402ec80aa -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f static/scripts/mvc/collection/collection-panel.js
--- a/static/scripts/mvc/collection/collection-panel.js
+++ b/static/scripts/mvc/collection/collection-panel.js
@@ -21,7 +21,6 @@
//MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)
/** logger used to record this.log messages, commonly set to console */
- // comment this out to suppress log output
//logger : console,
tagName : 'div',
@@ -30,7 +29,8 @@
/** (in ms) that jquery effects will use */
fxSpeed : 'fast',
- DCEViewClass : DC_BASE.DCEBaseView,
+ DatasetDCEViewClass : DC_BASE.DatasetDCEBaseView,
+ NestedDCEViewClass : DC_BASE.NestedDCEBaseView,
// ......................................................................... SET UP
/** Set up the view, set up storage, bind listeners to HistoryContents events
@@ -47,8 +47,6 @@
this.hasUser = attributes.hasUser;
this.panelStack = [];
this.parentName = attributes.parentName;
-
- window.collectionPanel = this;
},
/** create any event listeners for the panel
@@ -194,10 +192,8 @@
//this.debug( 'content json:', JSON.stringify( content, null, ' ' ) );
var contentView = null,
ContentClass = this._getContentClass( content );
- //this.debug( 'content.object json:', JSON.stringify( content.object, null, ' ' ) );
this.debug( 'ContentClass:', ContentClass );
- //this.debug( 'content:', content );
- this.debug( 'content.object:', content.object );
+ this.debug( 'content:', content );
contentView = new ContentClass({
model : content,
linkTarget : this.linkTarget,
@@ -213,6 +209,7 @@
/** */
_getContentClass : function( content ){
this.debug( this + '._getContentClass:', content );
+ this.debug( 'DCEViewClass:', this.DCEViewClass );
switch( content.get( 'element_type' ) ){
case 'hda':
return this.DCEViewClass;
@@ -336,7 +333,9 @@
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection. */
var ListCollectionPanel = CollectionPanel.extend({
- DCEViewClass : DC_BASE.HDADCEBaseView,
+
+ DCEViewClass : DC_BASE.DatasetDCEBaseView,
+
// ........................................................................ misc
/** string rep */
toString : function(){
@@ -348,6 +347,7 @@
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection. */
var PairCollectionPanel = ListCollectionPanel.extend({
+
// ........................................................................ misc
/** string rep */
toString : function(){
@@ -359,7 +359,9 @@
// =============================================================================
/** @class non-editable, read-only View/Controller for a dataset collection. */
var ListOfPairsCollectionPanel = CollectionPanel.extend({
- DCEViewClass : DC_BASE.DCDCEBaseView,
+
+ DCEViewClass : DC_BASE.NestedDCDCEBaseView,
+
// ........................................................................ misc
/** string rep */
toString : function(){
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